\end{figure}
-\section{Implicit solvation\index{implicit solvation}\index{Generalized Born methods}}
-\label{sec:gbsa}
-Implicit solvent models provide an efficient way of representing
-the electrostatic effects of solvent molecules, while saving a
-large piece of the computations involved in an accurate, aqueous
-description of the surrounding water in molecular dynamics simulations.
-Implicit solvation models offer several advantages compared with
-explicit solvation, including eliminating the need for the equilibration of water
-around the solute, and the absence of viscosity, which allows the protein
-to more quickly explore conformational space.
-
-Implicit solvent calculations in {\gromacs} can be done using the
-generalized Born-formalism, and the Still~\cite{Still97}, HCT~\cite{Truhlar96},
-and OBC~\cite{Case04} models are available for calculating the Born radii.
-
-Here, the free energy $G_{\mathrm{solv}}$ of solvation is the sum of three terms,
-a solvent-solvent cavity term ($G_{\mathrm{cav}}$), a solute-solvent van der
-Waals term ($G_{\mathrm{vdw}}$), and finally a solvent-solute electrostatics
-polarization term ($G_{\mathrm{pol}}$).
-
-The sum of $G_{\mathrm{cav}}$ and $G_{\mathrm{vdw}}$ corresponds to the (non-polar)
-free energy of solvation for a molecule from which all charges
-have been removed, and is commonly called $G_{\mathrm{np}}$,
-calculated from the total solvent accessible surface area
-multiplied with a surface tension.
-The total expression for the solvation free energy then becomes:
-
-\beq
-G_{\mathrm{solv}} = G_{\mathrm{np}} + G_{\mathrm{pol}}
-\label{eqn:gb_solv}
-\eeq
-
-Under the generalized Born model, $G_{\mathrm{pol}}$ is calculated from the generalized Born equation~\cite{Still97}:
-
-\beq
-G_{\mathrm{pol}} = \left(1-\frac{1}{\epsilon}\right) \sum_{i=1}^n \sum_{j>i}^n \frac {q_i q_j}{\sqrt{r^2_{ij} + b_i b_j \exp\left(\frac{-r^2_{ij}}{4 b_i b_j}\right)}}
-\label{eqn:gb_still}
-\eeq
-
-In {\gromacs}, we have introduced the substitution~\cite{Larsson10}:
-
-\beq
-c_i=\frac{1}{\sqrt{b_i}}
-\label{eqn:gb_subst}
-\eeq
-
-which makes it possible to introduce a cheap transformation to a new
-variable $x$ when evaluating each interaction, such that:
-
-\beq
-x=\frac{r_{ij}}{\sqrt{b_i b_j }} = r_{ij} c_i c_j
-\label{eqn:gb_subst2}
-\eeq
-
-In the end, the full re-formulation of~\ref{eqn:gb_still} becomes:
-
-\beq
-G_{\mathrm{pol}} = \left(1-\frac{1}{\epsilon}\right) \sum_{i=1}^n \sum_{j>i}^n \frac{q_i q_j}{\sqrt{b_i b_j}} ~\xi (x) = \left(1-\frac{1}{\epsilon}\right) \sum_{i=1}^n q_i c_i \sum_{j>i}^n q_j c_j~\xi (x)
-\label{eqn:gb_final}
-\eeq
-
-The non-polar part ($G_{\mathrm{np}}$) of Equation~\ref{eqn:gb_solv} is calculated
-directly from the Born radius of each atom using a simple ACE type
-approximation by Schaefer {\em et al.}~\cite{Karplus98}, including a
-simple loop over all atoms.
-This requires only one extra solvation parameter, independent of atom type,
-but differing slightly between the three Born radii models.
-
% LocalWords: GROningen MAchine BIOSON Groningen GROMACS Berendsen der Spoel
% LocalWords: Drunen Comp Phys Comm ROck NS FFT pbc EM ifthenelse gmxlite ff
% LocalWords: octahedra triclinic Ewald PME PPPM trjconv xy solvated
\subsection{CHARMM\index{CHARMM force field}}
\label{subsec:charmmff}
-{\gromacs} supports the CHARMM force field for proteins~\cite{mackerell04, mackerell98}, lipids~\cite{feller00} and nucleic acids~\cite{foloppe00,Mac2000}. The protein parameters (and to some extent the lipid and nucleic acid parameters) were thoroughly tested -- both by comparing potential energies between the port and the standard parameter set in the CHARMM molecular simulation package, as well by how the protein force field behaves together with {\gromacs}-specific techniques such as virtual sites (enabling long time steps) and a fast implicit solvent recently implemented~\cite{Larsson10} -- and the details and results are presented in the paper by Bjelkmar et al.~\cite{Bjelkmar10}. The nucleic acid parameters, as well as the ones for HEME, were converted and tested by Michel Cuendet.
+{\gromacs} supports the CHARMM force field for proteins~\cite{mackerell04, mackerell98}, lipids~\cite{feller00} and nucleic acids~\cite{foloppe00,Mac2000}. The protein parameters (and to some extent the lipid and nucleic acid parameters) were thoroughly tested -- both by comparing potential energies between the port and the standard parameter set in the CHARMM molecular simulation package, as well by how the protein force field behaves together with {\gromacs}-specific techniques such as virtual sites (enabling long time steps) recently implemented~\cite{Larsson10} -- and the details and results are presented in the paper by Bjelkmar et al.~\cite{Bjelkmar10}. The nucleic acid parameters, as well as the ones for HEME, were converted and tested by Michel Cuendet.
When selecting the CHARMM force field in {\tt \normindex{pdb2gmx}} the default option is to use \normindex{CMAP} (for torsional correction map). To exclude CMAP, use {\tt -nocmap}. The basic form of the CMAP term implemented in {\gromacs} is a function of the $\phi$ and $\psi$ backbone torsion angles. This term is defined in the {\tt .rtp} file by a {\tt [ cmap ]} statement at the end of each residue supporting CMAP. The following five atom names define the two torsional angles. Atoms 1-4 define $\phi$, and atoms 2-5 define $\psi$. The corresponding atom types are then matched to the correct CMAP type in the {\tt cmap.itp} file that contains the correction maps.
energy monitor group exclusions (see \secref{groupconcept}).
-\section{Implicit solvation parameters\index{implicit solvation parameters}}
-Starting with {\gromacs} 4.5, implicit solvent is supported. A section in the
-topology has been introduced to list those parameters:
-
-{\small
-\begin{verbatim}
-[ implicit_genborn_params ]
-; Atomtype sar st pi gbr hct
-NH1 0.155 1 1.028 0.17063 0.79 ; N
-N 0.155 1 1 0.155 0.79 ; Proline backbone N
-H 0.1 1 1 0.115 0.85 ; H
-CT1 0.180 1 1.276 0.190 0.72 ; C
-\end{verbatim}}
-
-In this example the atom type is listed first, followed by five
-numbers, and a comment (following a semicolon).
-
-Values in columns 1-3 are not currently used. They pertain to more
-elaborate surface area algorithms, the one from Qiu {\em et al.}~\cite{Still97} in
-particular. Column 4 contains the atomic van der Waals radii, which are used
-in computing the Born radii. The dielectric offset is specified in
-the {\tt *.mdp} file, and gets subtracted from the input van der Waals radii for the different
-Born radii methods, as described by Onufriev {\em et al.}~\cite{Case04}. Column 5 is the
-scale factor for the HCT and OBC models. The values are taken from the Tinker implementation of
-the HCT pairwise scaling method~\cite{Truhlar96}. This method has been modified such that the
-scaling factors have been adjusted to minimize differences between analytical surface areas and
-GB using the HCT algorithm. The scaling is further modified in that it is not applied pairwise
-as proposed by Hawkins {\em et al.}~\cite{Truhlar96}, but on a per-atom (rather than a per-pair)
-basis.
-
-
\section{Constraint algorithms\index{constraint algorithms}}
\label{sec:constraints}
Constraints are defined in the {\tt [~constraints~]} section.
#include "ffnonbonded.itp"
#include "ffbonded.itp"
-#include "gbsa.itp"
\end{verbatim}}
The two {\tt \#define} statements set up the conditions so that
switched potential yes yes
switched forces yes yes
non-periodic systems yes Z + walls
-implicit solvent yes no
free energy perturbed non-bondeds yes yes
energy group contributions yes only on CPU
energy group exclusions yes no
CASSCF method.
-Implicit solvent
-^^^^^^^^^^^^^^^^
-
-.. mdp:: implicit-solvent
-
- .. mdp-value:: no
-
- No implicit solvent
-
- .. mdp-value:: GBSA
-
- Do a simulation with implicit solvent using the Generalized Born
- formalism. Three different methods for calculating the Born
- radii are available, Still, HCT and OBC. These are specified
- with the :mdp:`gb-algorithm` field. The non-polar solvation is
- specified with the :mdp:`sa-algorithm` field.
-
-.. mdp:: gb-algorithm
-
- .. mdp-value:: Still
-
- Use the Still method to calculate the Born radii
-
- .. mdp-value:: HCT
-
- Use the Hawkins-Cramer-Truhlar method to calculate the Born
- radii
-
- .. mdp-value:: OBC
-
- Use the Onufriev-Bashford-Case method to calculate the Born
- radii
-
-.. mdp:: nstgbradii
-
- (1) \[steps\]
- Frequency to (re)-calculate the Born radii. For most practial
- purposes, setting a value larger than 1 violates energy
- conservation and leads to unstable trajectories.
-
-.. mdp:: rgbradii
-
- (1.0) \[nm\]
- Cut-off for the calculation of the Born radii. Currently must be
- equal to rlist
-
-.. mdp:: gb-epsilon-solvent
-
- (80)
- Dielectric constant for the implicit solvent
-
-.. mdp:: gb-saltconc
-
- (0) \[M\]
- Salt concentration for implicit solvent models, currently not used
-
-.. mdp:: gb-obc-alpha
-.. mdp:: gb-obc-beta
-.. mdp:: gb-obc-gamma
-
- Scale factors for the OBC model. Default values of 1, 0.78 and 4.85
- respectively are for OBC(II). Values for OBC(I) are 0.8, 0 and 2.91
- respectively
-
-.. mdp:: gb-dielectric-offset
-
- (0.009) \[nm\]
- Distance for the di-electric offset when calculating the Born
- radii. This is the offset between the center of each atom the
- center of the polarization energy for the corresponding atom
-
-.. mdp:: sa-algorithm
-
- .. mdp-value:: Ace-approximation
-
- Use an Ace-type approximation
-
- .. mdp-value:: None
-
- No non-polar solvation calculation done. For GBSA only the polar
- part gets calculated
-
-.. mdp:: sa-surface-tension
-
- \[kJ mol-1 nm-2\]
- Default value for surface tension with SA algorithms. The default
- value is -1; Note that if this default value is not changed it will
- be overridden by :ref:`gmx grompp` using values that are specific
- for the choice of radii algorithm (0.0049 kcal/mol/Angstrom^2 for
- Still, 0.0054 kcal/mol/Angstrom2 for HCT/OBC) Setting it to 0 will
- while using an sa-algorithm other than None means no non-polar
- calculations are done.
-
-
Computational Electrophysiology
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Use these options to switch on and control ion/water position exchanges in "Computational
Removed features
^^^^^^^^^^^^^^^^
-This feature has been removed from |Gromacs|, but so that old
+These features have been removed from |Gromacs|, but so that old
:ref:`mdp` and :ref:`tpr` files cannot be mistakenly misused, we still
parse this option. :ref:`gmx grompp` and :ref:`gmx mdrun` will issue a
fatal error if this is set.
(no)
+.. mdp:: implicit-solvent
+
+ (no)
+
.. _reference manual: gmx-manual-parent-dir_
* Neighbor search
* Launch GPU operations
* Communication of coordinates
-* Born radii
* Force
* Waiting + Communication of force
* Particle mesh Ewald
to a breakdown in the model physics, even if the starting configuration of
the system is reasonable.
-If using implicit solvation, starting your equilibration with a smaller time
+When using no explict solvent, starting your equilibration with a smaller time
step than your production run can help energy equipartition more stably.
There are several common situations in which instability frequently arises,
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/forcerec.h"
-#include "gromacs/mdlib/genborn.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/mdrun.h"
mdAlgorithmsSetupAtomData(cr, ir, top_global, top_local, fr,
nullptr, mdAtoms, vsite, nullptr);
- if (ir->implicit_solvent)
- {
- make_local_gb(cr, fr->born, ir->gb_algorithm);
- }
-
auto mdatoms = mdAtoms->mdatoms();
if (!thisRankHasDuty(cr, DUTY_PME))
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
tpxv_PullExternalPotential, /**< Added pull type external potential */
tpxv_GenericParamsForElectricField, /**< Introduced KeyValueTree and moved electric field parameters */
tpxv_AcceleratedWeightHistogram, /**< sampling with accelerated weight histogram method (AWH) */
+ tpxv_RemoveImplicitSolvation, /**< removed support for implicit solvation */
tpxv_Count /**< the total number of tpxv versions */
};
} t_ftupd;
/*
+ * TODO The following three lines make little sense, please clarify if
+ * you've had to work out how ftupd works.
+ *
* The entries should be ordered in:
* 1. ascending function type number
* 2. ascending file version number
+ *
+ * Because we support reading of old .tpr file versions (even when
+ * mdrun can no longer run the simulation), we need to be able to read
+ * obsolete t_interaction_function types. Any data read from such
+ * fields is discarded. Their names have _NOLONGERUSED appended to
+ * them to make things clear.
*/
static const t_ftupd ftupd[] = {
{ 34, F_FENEBONDS },
{ tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
{ 43, F_TABDIHS },
{ 65, F_CMAP },
- { 60, F_GB12 },
- { 61, F_GB13 },
- { 61, F_GB14 },
- { 72, F_GBPOL },
- { 72, F_NPSOLVATION },
+ { 60, F_GB12_NOLONGERUSED },
+ { 61, F_GB13_NOLONGERUSED },
+ { 61, F_GB14_NOLONGERUSED },
+ { 72, F_GBPOL_NOLONGERUSED },
+ { 72, F_NPSOLVATION_NOLONGERUSED },
{ 41, F_LJC14_Q },
{ 41, F_LJC_PAIRS_NB },
{ 32, F_BHAM_LR_NOLONGERUSED },
}
gmx_fio_do_real(fio, ir->tabext);
- gmx_fio_do_int(fio, ir->gb_algorithm);
- gmx_fio_do_int(fio, ir->nstgbradii);
- gmx_fio_do_real(fio, ir->rgbradii);
- gmx_fio_do_real(fio, ir->gb_saltconc);
- gmx_fio_do_int(fio, ir->implicit_solvent);
- if (file_version >= 55)
+ // This permits reading a .tpr file that used implicit solvent,
+ // and later permitting mdrun to refuse to run it.
+ if (bRead)
{
- gmx_fio_do_real(fio, ir->gb_epsilon_solvent);
- gmx_fio_do_real(fio, ir->gb_obc_alpha);
- gmx_fio_do_real(fio, ir->gb_obc_beta);
- gmx_fio_do_real(fio, ir->gb_obc_gamma);
- if (file_version >= 60)
+ if (file_version < tpxv_RemoveImplicitSolvation)
{
- gmx_fio_do_real(fio, ir->gb_dielectric_offset);
- gmx_fio_do_int(fio, ir->sa_algorithm);
+ gmx_fio_do_int(fio, idum);
+ gmx_fio_do_int(fio, idum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_int(fio, idum);
+ ir->implicit_solvent = (idum > 0);
}
else
{
- ir->gb_dielectric_offset = 0.009;
- ir->sa_algorithm = esaAPPROX;
+ ir->implicit_solvent = false;
}
- gmx_fio_do_real(fio, ir->sa_surface_tension);
-
- /* Override sa_surface_tension if it is not changed in the mpd-file */
- if (ir->sa_surface_tension < 0)
+ if (file_version >= 55 && file_version < tpxv_RemoveImplicitSolvation)
{
- if (ir->gb_algorithm == egbSTILL)
- {
- ir->sa_surface_tension = 0.0049 * 100 * CAL2JOULE;
- }
- else if (ir->gb_algorithm == egbHCT || ir->gb_algorithm == egbOBC)
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ if (file_version >= 60)
{
- ir->sa_surface_tension = 0.0054 * 100 * CAL2JOULE;
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_int(fio, idum);
}
+ gmx_fio_do_real(fio, rdum);
}
-
- }
- else
- {
- /* Better use sensible values than insane (0.0) ones... */
- ir->gb_epsilon_solvent = 80;
- ir->gb_obc_alpha = 1.0;
- ir->gb_obc_beta = 0.8;
- ir->gb_obc_gamma = 4.85;
- ir->sa_surface_tension = 2.092;
}
-
if (file_version >= 81)
{
gmx_fio_do_real(fio, ir->fourier_spacing);
gmx_fio_do_int(fio, iparams->vsiten.n);
gmx_fio_do_real(fio, iparams->vsiten.a);
break;
- case F_GB12:
- case F_GB13:
- case F_GB14:
- /* We got rid of some parameters in version 68 */
- if (bRead && file_version < 68)
+ case F_GB12_NOLONGERUSED:
+ case F_GB13_NOLONGERUSED:
+ case F_GB14_NOLONGERUSED:
+ // Implicit solvent parameters can still be read, but never used
+ if (bRead)
{
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
+ if (file_version < 68)
+ {
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ }
+ if (file_version < tpxv_RemoveImplicitSolvation)
+ {
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ gmx_fio_do_real(fio, rdum);
+ }
}
- gmx_fio_do_real(fio, iparams->gb.sar);
- gmx_fio_do_real(fio, iparams->gb.st);
- gmx_fio_do_real(fio, iparams->gb.pi);
- gmx_fio_do_real(fio, iparams->gb.gbr);
- gmx_fio_do_real(fio, iparams->gb.bmlt);
break;
case F_CMAP:
gmx_fio_do_int(fio, iparams->cmap.cmapA);
j = atomtypes->nr;
if (bRead)
{
- snew(atomtypes->radius, j);
- snew(atomtypes->vol, j);
- snew(atomtypes->surftens, j);
snew(atomtypes->atomnumber, j);
- snew(atomtypes->gb_radius, j);
- snew(atomtypes->S_hct, j);
}
- gmx_fio_ndo_real(fio, atomtypes->radius, j);
- gmx_fio_ndo_real(fio, atomtypes->vol, j);
- gmx_fio_ndo_real(fio, atomtypes->surftens, j);
+ if (bRead && file_version < tpxv_RemoveImplicitSolvation)
+ {
+ std::vector<real> dummy(atomtypes->nr, 0);
+ gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
+ gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
+ gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
+ }
if (file_version >= 40)
{
gmx_fio_ndo_int(fio, atomtypes->atomnumber, j);
}
- if (file_version >= 60)
+ if (bRead && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
{
- gmx_fio_ndo_real(fio, atomtypes->gb_radius, j);
- gmx_fio_ndo_real(fio, atomtypes->S_hct, j);
+ std::vector<real> dummy(atomtypes->nr, 0);
+ gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
+ gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
FscalC[i] = -qq[i]*tabscale*FF*rC;
break;
- case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
- gmx_fatal(FARGS, "Free energy and GB not implemented.\n");
- break;
-
case GMX_NBKERNEL_ELEC_EWALD:
if (bConvertEwaldToCoulomb)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
felec = -qq*FF*tabscale*rinv;
break;
- case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
- /* GB */
- gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
- break;
-
case GMX_NBKERNEL_ELEC_EWALD:
ewrt = rsq*rinv*ewtabscale;
ewitab = ewrt;
/* potentials */
real * energygrp_elec;
real * energygrp_vdw;
- real * energygrp_polarization;
}
nb_kernel_data_t;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
- 'GeneralizedBorn' : ['rinv','r'],
'CubicSplineTable' : ['rinv','r','table'],
'Ewald' : ['rinv','rinvsq','r'],
}
'Coulomb' : 'Coul',
'Ewald' : 'Ew',
'ReactionField' : 'RF',
- 'GeneralizedBorn' : 'GB',
'CubicSplineTable' : 'CSTab',
'LennardJones' : 'LJ',
'Buckingham' : 'Bham',
return 0
# No need for LJ-only water optimization, or water optimization with implicit solvent.
- if('Water' in KernelGeom[0] and (KernelElec=='None' or 'GeneralizedBorn' in KernelElec)):
+ if('Water' in KernelGeom[0] and KernelElec=='None'):
return 0
# Non-matching table settings are pointless
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_128_fma_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_128_fma_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_128_fma_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_pd(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_pd();
- vgbsum = _mm_setzero_pd();
- vvdwsum = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- vfeps = _mm_frcz_pd(rt);
-#else
- vfeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- twovfeps = _mm_add_pd(vfeps,vfeps);
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(vfeps,_mm_macc_pd(H,vfeps,G),F);
- VV = _mm_macc_pd(vfeps,Fp,Y);
- vvdw6 = _mm_mul_pd(c6_00,VV);
- FF = _mm_macc_pd(vfeps,_mm_macc_pd(twovfeps,H,G),Fp);
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(vfeps,_mm_macc_pd(H,vfeps,G),F);
- VV = _mm_macc_pd(vfeps,Fp,Y);
- vvdw12 = _mm_mul_pd(c12_00,VV);
- FF = _mm_macc_pd(vfeps,_mm_macc_pd(twovfeps,H,G),Fp);
- fvdw12 = _mm_mul_pd(c12_00,FF);
- vvdw = _mm_add_pd(vvdw12,vvdw6);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_pd(velecsum,velec);
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 95 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- vfeps = _mm_frcz_pd(rt);
-#else
- vfeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- twovfeps = _mm_add_pd(vfeps,vfeps);
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(vfeps,_mm_macc_pd(H,vfeps,G),F);
- VV = _mm_macc_pd(vfeps,Fp,Y);
- vvdw6 = _mm_mul_pd(c6_00,VV);
- FF = _mm_macc_pd(vfeps,_mm_macc_pd(twovfeps,H,G),Fp);
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(vfeps,_mm_macc_pd(H,vfeps,G),F);
- VV = _mm_macc_pd(vfeps,Fp,Y);
- vvdw12 = _mm_mul_pd(c12_00,VV);
- FF = _mm_macc_pd(vfeps,_mm_macc_pd(twovfeps,H,G),Fp);
- fvdw12 = _mm_mul_pd(c12_00,FF);
- vvdw = _mm_add_pd(vvdw12,vvdw6);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_unpacklo_pd(velec,_mm_setzero_pd());
- velecsum = _mm_add_pd(velecsum,velec);
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdw = _mm_unpacklo_pd(vvdw,_mm_setzero_pd());
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 95 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*95);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_128_fma_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_128_fma_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_pd(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- vfeps = _mm_frcz_pd(rt);
-#else
- vfeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- twovfeps = _mm_add_pd(vfeps,vfeps);
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(vfeps,_mm_macc_pd(H,vfeps,G),F);
- FF = _mm_macc_pd(vfeps,_mm_macc_pd(twovfeps,H,G),Fp);
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(vfeps,_mm_macc_pd(H,vfeps,G),F);
- FF = _mm_macc_pd(vfeps,_mm_macc_pd(twovfeps,H,G),Fp);
- fvdw12 = _mm_mul_pd(c12_00,FF);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 85 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- vfeps = _mm_frcz_pd(rt);
-#else
- vfeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- twovfeps = _mm_add_pd(vfeps,vfeps);
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(vfeps,_mm_macc_pd(H,vfeps,G),F);
- FF = _mm_macc_pd(vfeps,_mm_macc_pd(twovfeps,H,G),Fp);
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + _mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(vfeps,_mm_macc_pd(H,vfeps,G),F);
- FF = _mm_macc_pd(vfeps,_mm_macc_pd(twovfeps,H,G),Fp);
- fvdw12 = _mm_mul_pd(c12_00,FF);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 85 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*85);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_128_fma_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_128_fma_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_128_fma_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_pd();
- vgbsum = _mm_setzero_pd();
- vvdwsum = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_pd(c6_00,rinvsix);
- vvdw12 = _mm_mul_pd(c12_00,_mm_mul_pd(rinvsix,rinvsix));
- vvdw = _mm_msub_pd( vvdw12,one_twelfth, _mm_mul_pd(vvdw6,one_sixth) );
- fvdw = _mm_mul_pd(_mm_sub_pd(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_pd(velecsum,velec);
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 74 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_pd(c6_00,rinvsix);
- vvdw12 = _mm_mul_pd(c12_00,_mm_mul_pd(rinvsix,rinvsix));
- vvdw = _mm_msub_pd( vvdw12,one_twelfth, _mm_mul_pd(vvdw6,one_sixth) );
- fvdw = _mm_mul_pd(_mm_sub_pd(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_unpacklo_pd(velec,_mm_setzero_pd());
- velecsum = _mm_add_pd(velecsum,velec);
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdw = _mm_unpacklo_pd(vvdw,_mm_setzero_pd());
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 74 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*74);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_128_fma_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_128_fma_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_pd(_mm_msub_pd(c12_00,rinvsix,c6_00),_mm_mul_pd(rinvsix,rinvsq00));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 67 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_pd(_mm_msub_pd(c12_00,rinvsix,c6_00),_mm_mul_pd(rinvsix,rinvsq00));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 67 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*67);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_128_fma_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_128_fma_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_128_fma_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_128_fma_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
-
- /* Reset potential sums */
- velecsum = _mm_setzero_pd();
- vgbsum = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_pd(velecsum,velec);
- vgbsum = _mm_add_pd(vgbsum,vgb);
-
- fscal = felec;
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 61 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_unpacklo_pd(velec,_mm_setzero_pd());
- velecsum = _mm_add_pd(velecsum,velec);
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- vgbsum = _mm_add_pd(vgbsum,vgb);
-
- fscal = felec;
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 61 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 9 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*9 + inneriter*61);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_128_fma_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_128_fma_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
-
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- fscal = felec;
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 59 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r00,vgb));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv00,fgb),rinv00);
-
- fscal = felec;
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Update vectorial force */
- fix0 = _mm_macc_pd(dx00,fscal,fix0);
- fiy0 = _mm_macc_pd(dy00,fscal,fiy0);
- fiz0 = _mm_macc_pd(dz00,fscal,fiz0);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,
- _mm_mul_pd(dx00,fscal),
- _mm_mul_pd(dy00,fscal),
- _mm_mul_pd(dz00,fscal));
-
- /* Inner loop uses 59 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*7 + inneriter*59);
-}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_t nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_128_fma_double;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_128_fma_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_double;
nb_kernel_info_t
{ nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "None", "None", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "Ewald", "None", "LJEwald", "None", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_double", "avx_128_fma_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
};
int
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
__m128d velec,felec,velecsum,facel,crf,krf,krf2;
real *charge;
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- /* #endif */
/* #if KERNEL_VDW != 'None' */
int nvdwtype;
__m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
__m128d one_sixth = _mm_set1_pd(1.0/6.0);
__m128d one_twelfth = _mm_set1_pd(1.0/12.0);
/* #endif */
- /* #if 'Table' in KERNEL_ELEC or 'GeneralizedBorn' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
+ /* #if 'Table' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
__m128i vfitab;
__m128i ifour = _mm_set1_epi32(4);
__m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
/* #endif */
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
- /* #endif */
-
/* #if 'Water' in GEOMETRY_I */
/* Setup water-specific parameters */
inr = nlist->iinr[0];
/* #for I in PARTICLES_ELEC_I */
iq{I} = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+{I}));
/* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isai{I} = _mm_load1_pd(invsqrta+inr+{I});
- /* #endif */
/* #endfor */
/* #for I in PARTICLES_VDW_I */
vdwioffset{I} = 2*nvdwtype*vdwtype[inr+{I}];
/* #if KERNEL_ELEC != 'None' */
velecsum = _mm_setzero_pd();
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- vgbsum = _mm_setzero_pd();
- /* #endif */
/* #if KERNEL_VDW != 'None' */
vvdwsum = _mm_setzero_pd();
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_setzero_pd();
- /* #endif */
/* #for ROUND in ['Loop','Epilogue'] */
/* #else */
jq{J} = _mm_load_sd(charge+jnrA+{J});
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if ROUND =='Loop' */
- isaj{J} = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+{J},invsqrta+jnrB+{J});
- /* #else */
- isaj{J} = _mm_load_sd(invsqrta+jnrA+{J});
- /* #endif */
- /* #endif */
/* #endfor */
/* #for J in PARTICLES_VDW_J */
vdwjidx{J}A = 2*vdwtype[jnrA+{J}];
/* #define INNERFLOPS INNERFLOPS+3 */
/* #endif */
- /* #elif KERNEL_ELEC=='GeneralizedBorn' */
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai{I},isaj{J});
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq{I}{J},_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
- /* #define INNERFLOPS INNERFLOPS+5 */
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r{I}{J},gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_pd(rt);
-#else
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- /* #if ROUND == 'Loop' */
- F = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- /* #else */
- F = _mm_setzero_pd();
- /* #endif */
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,0) +2);
- /* #if ROUND == 'Loop' */
- H = _mm_load_pd( gbtab + _mm_extract_epi32(gbitab,1) +2);
- /* #else */
- H = _mm_setzero_pd();
- /* #endif */
- GMX_MM_TRANSPOSE2_PD(G,H);
- Fp = _mm_macc_pd(gbeps,_mm_macc_pd(gbeps,H,G),F);
- VV = _mm_macc_pd(gbeps,Fp,Y);
- vgb = _mm_mul_pd(gbqqfactor,VV);
- /* #define INNERFLOPS INNERFLOPS+10 */
-
- /* #if 'Force' in KERNEL_VF */
- twogbeps = _mm_add_pd(gbeps,gbeps);
- FF = _mm_macc_pd(_mm_macc_pd(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_macc_pd(fgb,r{I}{J},vgb));
- /* #if ROUND == 'Epilogue' */
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- /* #endif */
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- /* #if ROUND == 'Loop' */
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj{J},isaj{J})));
- /* #else */
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj{J},isaj{J})));
- /* #endif */
- /* #define INNERFLOPS INNERFLOPS+13 */
- /* #endif */
- velec = _mm_mul_pd(qq{I}{J},rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #if 'Force' in KERNEL_VF */
- felec = _mm_mul_pd(_mm_msub_pd(velec,rinv{I}{J},fgb),rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+3 */
- /* #endif */
-
/* #elif KERNEL_ELEC=='Ewald' */
/* EWALD ELECTROSTATICS */
/* #endif */
velecsum = _mm_add_pd(velecsum,velec);
/* #define INNERFLOPS INNERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
- vgb = _mm_and_pd(vgb,cutoff_mask);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
- /* #if ROUND == 'Epilogue' */
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- /* #endif */
- vgbsum = _mm_add_pd(vgbsum,vgb);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
/* #endif */
/* #if 'vdw' in INTERACTION_FLAGS[I][J] */
/* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- /* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #endif */
/* #if KERNEL_VDW != 'None' */
gmx_mm_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai{I},isai{I}));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
- /* #endif */
/* Increment number of inner iterations */
inneriter += j_index_end - j_index_start;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
- 'GeneralizedBorn' : ['rinv','r'],
'CubicSplineTable' : ['rinv','r','table'],
'Ewald' : ['rinv','rinvsq','r'],
}
'Coulomb' : 'Coul',
'Ewald' : 'Ew',
'ReactionField' : 'RF',
- 'GeneralizedBorn' : 'GB',
'CubicSplineTable' : 'CSTab',
'LennardJones' : 'LJ',
'Buckingham' : 'Bham',
return 0
# No need for LJ-only water optimization, or water optimization with implicit solvent.
- if('Water' in KernelGeom[0] and (KernelElec=='None' or 'GeneralizedBorn' in KernelElec)):
+ if('Water' in KernelGeom[0] and KernelElec=='None'):
return 0
# Non-matching table settings are pointless
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_128_fma_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_128_fma_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_128_fma_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX_128, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,twogbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,twovfeps,vftabscale,Y,F,G,H,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_ps(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_ps();
- vgbsum = _mm_setzero_ps();
- vvdwsum = _mm_setzero_ps();
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- vfeps = _mm_frcz_ps(rt);
-#else
- vfeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- twovfeps = _mm_add_ps(vfeps,vfeps);
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(vfeps,_mm_macc_ps(H,vfeps,G),F);
- VV = _mm_macc_ps(vfeps,Fp,Y);
- vvdw6 = _mm_mul_ps(c6_00,VV);
- FF = _mm_macc_ps(vfeps,_mm_macc_ps(twovfeps,H,G),Fp);
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(vfeps,_mm_macc_ps(H,vfeps,G),F);
- VV = _mm_macc_ps(vfeps,Fp,Y);
- vvdw12 = _mm_mul_ps(c12_00,VV);
- FF = _mm_macc_ps(vfeps,_mm_macc_ps(twovfeps,H,G),Fp);
- fvdw12 = _mm_mul_ps(c12_00,FF);
- vvdw = _mm_add_ps(vvdw12,vvdw6);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_ps(velecsum,velec);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 95 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- vfeps = _mm_frcz_ps(rt);
-#else
- vfeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- twovfeps = _mm_add_ps(vfeps,vfeps);
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(vfeps,_mm_macc_ps(H,vfeps,G),F);
- VV = _mm_macc_ps(vfeps,Fp,Y);
- vvdw6 = _mm_mul_ps(c6_00,VV);
- FF = _mm_macc_ps(vfeps,_mm_macc_ps(twovfeps,H,G),Fp);
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(vfeps,_mm_macc_ps(H,vfeps,G),F);
- VV = _mm_macc_ps(vfeps,Fp,Y);
- vvdw12 = _mm_mul_ps(c12_00,VV);
- FF = _mm_macc_ps(vfeps,_mm_macc_ps(twovfeps,H,G),Fp);
- fvdw12 = _mm_mul_ps(c12_00,FF);
- vvdw = _mm_add_ps(vvdw12,vvdw6);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_andnot_ps(dummy_mask,velec);
- velecsum = _mm_add_ps(velecsum,velec);
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdw = _mm_andnot_ps(dummy_mask,vvdw);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 96 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*96);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_128_fma_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_128_fma_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX_128, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,twogbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,twovfeps,vftabscale,Y,F,G,H,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_ps(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- vfeps = _mm_frcz_ps(rt);
-#else
- vfeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- twovfeps = _mm_add_ps(vfeps,vfeps);
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(vfeps,_mm_macc_ps(H,vfeps,G),F);
- FF = _mm_macc_ps(vfeps,_mm_macc_ps(twovfeps,H,G),Fp);
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(vfeps,_mm_macc_ps(H,vfeps,G),F);
- FF = _mm_macc_ps(vfeps,_mm_macc_ps(twovfeps,H,G),Fp);
- fvdw12 = _mm_mul_ps(c12_00,FF);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 85 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- vfeps = _mm_frcz_ps(rt);
-#else
- vfeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- twovfeps = _mm_add_ps(vfeps,vfeps);
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(vfeps,_mm_macc_ps(H,vfeps,G),F);
- FF = _mm_macc_ps(vfeps,_mm_macc_ps(twovfeps,H,G),Fp);
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + _mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(vfeps,_mm_macc_ps(H,vfeps,G),F);
- FF = _mm_macc_ps(vfeps,_mm_macc_ps(twovfeps,H,G),Fp);
- fvdw12 = _mm_mul_ps(c12_00,FF);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 86 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*86);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_128_fma_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_128_fma_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_128_fma_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX_128, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,twogbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,twovfeps,vftabscale,Y,F,G,H,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_ps();
- vgbsum = _mm_setzero_ps();
- vvdwsum = _mm_setzero_ps();
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_ps(c6_00,rinvsix);
- vvdw12 = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
- vvdw = _mm_msub_ps(vvdw12,one_twelfth,_mm_mul_ps(vvdw6,one_sixth));
- fvdw = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_ps(velecsum,velec);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 74 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_ps(c6_00,rinvsix);
- vvdw12 = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
- vvdw = _mm_msub_ps(vvdw12,one_twelfth,_mm_mul_ps(vvdw6,one_sixth));
- fvdw = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_andnot_ps(dummy_mask,velec);
- velecsum = _mm_add_ps(velecsum,velec);
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdw = _mm_andnot_ps(dummy_mask,vvdw);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 75 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*75);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_128_fma_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_128_fma_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX_128, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,twogbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,twovfeps,vftabscale,Y,F,G,H,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_ps(_mm_msub_ps(c12_00,rinvsix,c6_00),_mm_mul_ps(rinvsix,rinvsq00));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 67 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_ps(_mm_msub_ps(c12_00,rinvsix,c6_00),_mm_mul_ps(rinvsix,rinvsq00));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 68 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*68);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_128_fma_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_128_fma_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_128_fma_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_128_fma_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX_128, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,twogbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,twovfeps,vftabscale,Y,F,G,H,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
-
- /* Reset potential sums */
- velecsum = _mm_setzero_ps();
- vgbsum = _mm_setzero_ps();
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_ps(velecsum,velec);
- vgbsum = _mm_add_ps(vgbsum,vgb);
-
- fscal = felec;
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 61 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_andnot_ps(dummy_mask,velec);
- velecsum = _mm_add_ps(velecsum,velec);
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm_add_ps(vgbsum,vgb);
-
- fscal = felec;
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 62 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 9 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*9 + inneriter*62);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_128_fma_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_128_fma_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX_128, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,twogbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,twovfeps,vftabscale,Y,F,G,H,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
-
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- fscal = felec;
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 59 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx128fma_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r00,vgb));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv00,fgb),rinv00);
-
- fscal = felec;
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Update vectorial force */
- fix0 = _mm_macc_ps(dx00,fscal,fix0);
- fiy0 = _mm_macc_ps(dy00,fscal,fiy0);
- fiz0 = _mm_macc_ps(dz00,fscal,fiz0);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm_mul_ps(dx00,fscal),
- _mm_mul_ps(dy00,fscal),
- _mm_mul_ps(dz00,fscal));
-
- /* Inner loop uses 60 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*7 + inneriter*60);
-}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_t nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_128_fma_single;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_128_fma_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_single;
nb_kernel_info_t
{ nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "None", "None", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "Ewald", "None", "LJEwald", "None", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_128_fma_single", "avx_128_fma_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
};
int
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
__m128 velec,felec,velecsum,facel,crf,krf,krf2;
real *charge;
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,twogbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- /* #endif */
/* #if KERNEL_VDW != 'None' */
int nvdwtype;
__m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
__m128 one_sixth = _mm_set1_ps(1.0/6.0);
__m128 one_twelfth = _mm_set1_ps(1.0/12.0);
/* #endif */
- /* #if 'Table' in KERNEL_ELEC or 'GeneralizedBorn' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
+ /* #if 'Table' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
__m128i vfitab;
__m128i ifour = _mm_set1_epi32(4);
__m128 rt,vfeps,twovfeps,vftabscale,Y,F,G,H,Fp,VV,FF;
/* #endif */
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
- /* #endif */
-
/* #if 'Water' in GEOMETRY_I */
/* Setup water-specific parameters */
inr = nlist->iinr[0];
/* #for I in PARTICLES_ELEC_I */
iq{I} = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+{I}));
/* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isai{I} = _mm_load1_ps(invsqrta+inr+{I});
- /* #endif */
/* #endfor */
/* #for I in PARTICLES_VDW_I */
vdwioffset{I} = 2*nvdwtype*vdwtype[inr+{I}];
/* #if KERNEL_ELEC != 'None' */
velecsum = _mm_setzero_ps();
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- vgbsum = _mm_setzero_ps();
- /* #endif */
/* #if KERNEL_VDW != 'None' */
vvdwsum = _mm_setzero_ps();
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_setzero_ps();
- /* #endif */
/* #for ROUND in ['Loop','Epilogue'] */
/* #for J in PARTICLES_ELEC_J */
jq{J} = gmx_mm_load_4real_swizzle_ps(charge+jnrA+{J},charge+jnrB+{J},
charge+jnrC+{J},charge+jnrD+{J});
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isaj{J} = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+{J},invsqrta+jnrB+{J},
- invsqrta+jnrC+{J},invsqrta+jnrD+{J});
- /* #endif */
/* #endfor */
/* #for J in PARTICLES_VDW_J */
vdwjidx{J}A = 2*vdwtype[jnrA+{J}];
/* #define INNERFLOPS INNERFLOPS+3 */
/* #endif */
- /* #elif KERNEL_ELEC=='GeneralizedBorn' */
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai{I},isaj{J});
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq{I}{J},_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
- /* #define INNERFLOPS INNERFLOPS+5 */
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r{I}{J},gbscale);
- gbitab = _mm_cvttps_epi32(rt);
-#ifdef __XOP__
- gbeps = _mm_frcz_ps(rt);
-#else
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
-#endif
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + _mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Fp = _mm_macc_ps(gbeps,_mm_macc_ps(gbeps,H,G),F);
- VV = _mm_macc_ps(gbeps,Fp,Y);
- vgb = _mm_mul_ps(gbqqfactor,VV);
- /* #define INNERFLOPS INNERFLOPS+10 */
-
- /* #if 'Force' in KERNEL_VF */
- twogbeps = _mm_add_ps(gbeps,gbeps);
- FF = _mm_macc_ps(_mm_macc_ps(twogbeps,H,G),gbeps,Fp);
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_macc_ps(fgb,r{I}{J},vgb));
- /* #if ROUND == 'Epilogue' */
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- /* #endif */
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* #if ROUND == 'Loop' */
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- /* #else */
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- /* #endif */
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj{J},isaj{J})));
- /* #define INNERFLOPS INNERFLOPS+13 */
- /* #endif */
- velec = _mm_mul_ps(qq{I}{J},rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #if 'Force' in KERNEL_VF */
- felec = _mm_mul_ps(_mm_msub_ps(velec,rinv{I}{J},fgb),rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+3 */
- /* #endif */
-
/* #elif KERNEL_ELEC=='Ewald' */
/* EWALD ELECTROSTATICS */
/* #endif */
velecsum = _mm_add_ps(velecsum,velec);
/* #define INNERFLOPS INNERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
- vgb = _mm_and_ps(vgb,cutoff_mask);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
- /* #if ROUND == 'Epilogue' */
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- /* #endif */
- vgbsum = _mm_add_ps(vgbsum,vgb);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
/* #endif */
/* #if 'vdw' in INTERACTION_FLAGS[I][J] */
/* ## Note special check for TIP4P-TIP4P. Since we are cutting of all hydrogen interactions we also cut the LJ-only O-O interaction */
gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- /* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #endif */
/* #if KERNEL_VDW != 'None' */
gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai{I},isai{I}));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
- /* #endif */
/* Increment number of inner iterations */
inneriter += j_index_end - j_index_start;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
- 'GeneralizedBorn' : ['rinv','r'],
'CubicSplineTable' : ['rinv','r','table'],
'Ewald' : ['rinv','rinvsq','r'],
}
'Coulomb' : 'Coul',
'Ewald' : 'Ew',
'ReactionField' : 'RF',
- 'GeneralizedBorn' : 'GB',
'CubicSplineTable' : 'CSTab',
'LennardJones' : 'LJ',
'Buckingham' : 'Bham',
return 0
# No need for LJ-only water optimization, or water optimization with implicit solvent.
- if('Water' in KernelGeom[0] and (KernelElec=='None' or 'GeneralizedBorn' in KernelElec)):
+ if('Water' in KernelGeom[0] and KernelElec=='None'):
return 0
# Non-matching table settings are pointless
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_256_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_256_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_256_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_256_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m256d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m256d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m256d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256d minushalf = _mm256_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m256d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m256d one_sixth = _mm256_set1_pd(1.0/6.0);
- __m256d one_twelfth = _mm256_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m256d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256d dummy_mask,cutoff_mask;
- __m128 tmpmask0,tmpmask1;
- __m256d signbit = _mm256_castsi256_pd( _mm256_set1_epi32(0x80000000) );
- __m256d one = _mm256_set1_pd(1.0);
- __m256d two = _mm256_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm256_set1_pd(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_pd();
- fiy0 = _mm256_setzero_pd();
- fiz0 = _mm256_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_pd(facel,_mm256_set1_pd(charge[inr+0]));
- isai0 = _mm256_set1_pd(invsqrta[inr+0]);
- vdwioffsetptr0 = vdwparam+2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm256_setzero_pd();
- vgbsum = _mm256_setzero_pd();
- vvdwsum = _mm256_setzero_pd();
- dvdasum = _mm256_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
- gmx_mm256_load_4pair_swizzle_pd(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm256_mul_pd(r00,vftabscale);
- vfitab = _mm256_cvttpd_epi32(rt);
- vfeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(vfeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(vfeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(vfeps,Fp));
- vvdw6 = _mm256_mul_pd(c6_00,VV);
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(vfeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fvdw6 = _mm256_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(vfeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(vfeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(vfeps,Fp));
- vvdw12 = _mm256_mul_pd(c12_00,VV);
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(vfeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fvdw12 = _mm256_mul_pd(c12_00,FF);
- vvdw = _mm256_add_pd(vvdw12,vvdw6);
- fvdw = _mm256_xor_pd(signbit,_mm256_mul_pd(_mm256_add_pd(fvdw6,fvdw12),_mm256_mul_pd(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm256_add_pd(velecsum,velec);
- vgbsum = _mm256_add_pd(vgbsum,vgb);
- vvdwsum = _mm256_add_pd(vvdwsum,vvdw);
-
- fscal = _mm256_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 91 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_pd(mask,val) to clear dummy entries.
- */
- tmpmask0 = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
-
- tmpmask1 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(3,3,2,2));
- tmpmask0 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(1,1,0,0));
- dummy_mask = _mm256_castps_pd(gmx_mm256_set_m128(tmpmask1,tmpmask0));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
- r00 = _mm256_andnot_pd(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
- gmx_mm256_load_4pair_swizzle_pd(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm256_mul_pd(r00,vftabscale);
- vfitab = _mm256_cvttpd_epi32(rt);
- vfeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdatmp = _mm256_andnot_pd(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(vfeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(vfeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(vfeps,Fp));
- vvdw6 = _mm256_mul_pd(c6_00,VV);
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(vfeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fvdw6 = _mm256_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(vfeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(vfeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(vfeps,Fp));
- vvdw12 = _mm256_mul_pd(c12_00,VV);
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(vfeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fvdw12 = _mm256_mul_pd(c12_00,FF);
- vvdw = _mm256_add_pd(vvdw12,vvdw6);
- fvdw = _mm256_xor_pd(signbit,_mm256_mul_pd(_mm256_add_pd(fvdw6,fvdw12),_mm256_mul_pd(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm256_andnot_pd(dummy_mask,velec);
- velecsum = _mm256_add_pd(velecsum,velec);
- vgb = _mm256_andnot_pd(dummy_mask,vgb);
- vgbsum = _mm256_add_pd(vgbsum,vgb);
- vvdw = _mm256_andnot_pd(dummy_mask,vvdw);
- vvdwsum = _mm256_add_pd(vvdwsum,vvdw);
-
- fscal = _mm256_add_pd(felec,fvdw);
-
- fscal = _mm256_andnot_pd(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 92 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm256_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm256_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm256_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm256_mul_pd(dvdasum, _mm256_mul_pd(isai0,isai0));
- gmx_mm256_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*92);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_256_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_256_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m256d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m256d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m256d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256d minushalf = _mm256_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m256d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m256d one_sixth = _mm256_set1_pd(1.0/6.0);
- __m256d one_twelfth = _mm256_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m256d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256d dummy_mask,cutoff_mask;
- __m128 tmpmask0,tmpmask1;
- __m256d signbit = _mm256_castsi256_pd( _mm256_set1_epi32(0x80000000) );
- __m256d one = _mm256_set1_pd(1.0);
- __m256d two = _mm256_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm256_set1_pd(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_pd();
- fiy0 = _mm256_setzero_pd();
- fiz0 = _mm256_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_pd(facel,_mm256_set1_pd(charge[inr+0]));
- isai0 = _mm256_set1_pd(invsqrta[inr+0]);
- vdwioffsetptr0 = vdwparam+2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm256_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
- gmx_mm256_load_4pair_swizzle_pd(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm256_mul_pd(r00,vftabscale);
- vfitab = _mm256_cvttpd_epi32(rt);
- vfeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(vfeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(vfeps,_mm256_add_pd(G,Heps)));
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(vfeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fvdw6 = _mm256_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(vfeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(vfeps,_mm256_add_pd(G,Heps)));
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(vfeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fvdw12 = _mm256_mul_pd(c12_00,FF);
- fvdw = _mm256_xor_pd(signbit,_mm256_mul_pd(_mm256_add_pd(fvdw6,fvdw12),_mm256_mul_pd(vftabscale,rinv00)));
-
- fscal = _mm256_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 81 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_pd(mask,val) to clear dummy entries.
- */
- tmpmask0 = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
-
- tmpmask1 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(3,3,2,2));
- tmpmask0 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(1,1,0,0));
- dummy_mask = _mm256_castps_pd(gmx_mm256_set_m128(tmpmask1,tmpmask0));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
- r00 = _mm256_andnot_pd(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
- gmx_mm256_load_4pair_swizzle_pd(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm256_mul_pd(r00,vftabscale);
- vfitab = _mm256_cvttpd_epi32(rt);
- vfeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdatmp = _mm256_andnot_pd(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(vfeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(vfeps,_mm256_add_pd(G,Heps)));
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(vfeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fvdw6 = _mm256_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,0) );
- F = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,1) );
- G = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,2) );
- H = _mm256_load_pd( vftab + _mm_extract_epi32(vfitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(vfeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(vfeps,_mm256_add_pd(G,Heps)));
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(vfeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fvdw12 = _mm256_mul_pd(c12_00,FF);
- fvdw = _mm256_xor_pd(signbit,_mm256_mul_pd(_mm256_add_pd(fvdw6,fvdw12),_mm256_mul_pd(vftabscale,rinv00)));
-
- fscal = _mm256_add_pd(felec,fvdw);
-
- fscal = _mm256_andnot_pd(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 82 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm256_mul_pd(dvdasum, _mm256_mul_pd(isai0,isai0));
- gmx_mm256_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*82);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_256_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_256_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_256_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_256_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m256d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m256d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m256d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256d minushalf = _mm256_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m256d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m256d one_sixth = _mm256_set1_pd(1.0/6.0);
- __m256d one_twelfth = _mm256_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m256d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256d dummy_mask,cutoff_mask;
- __m128 tmpmask0,tmpmask1;
- __m256d signbit = _mm256_castsi256_pd( _mm256_set1_epi32(0x80000000) );
- __m256d one = _mm256_set1_pd(1.0);
- __m256d two = _mm256_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_pd();
- fiy0 = _mm256_setzero_pd();
- fiz0 = _mm256_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_pd(facel,_mm256_set1_pd(charge[inr+0]));
- isai0 = _mm256_set1_pd(invsqrta[inr+0]);
- vdwioffsetptr0 = vdwparam+2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm256_setzero_pd();
- vgbsum = _mm256_setzero_pd();
- vvdwsum = _mm256_setzero_pd();
- dvdasum = _mm256_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- rinvsq00 = _mm256_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
- gmx_mm256_load_4pair_swizzle_pd(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm256_mul_pd(_mm256_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm256_mul_pd(c6_00,rinvsix);
- vvdw12 = _mm256_mul_pd(c12_00,_mm256_mul_pd(rinvsix,rinvsix));
- vvdw = _mm256_sub_pd( _mm256_mul_pd(vvdw12,one_twelfth) , _mm256_mul_pd(vvdw6,one_sixth) );
- fvdw = _mm256_mul_pd(_mm256_sub_pd(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm256_add_pd(velecsum,velec);
- vgbsum = _mm256_add_pd(vgbsum,vgb);
- vvdwsum = _mm256_add_pd(vvdwsum,vvdw);
-
- fscal = _mm256_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 70 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_pd(mask,val) to clear dummy entries.
- */
- tmpmask0 = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
-
- tmpmask1 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(3,3,2,2));
- tmpmask0 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(1,1,0,0));
- dummy_mask = _mm256_castps_pd(gmx_mm256_set_m128(tmpmask1,tmpmask0));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- rinvsq00 = _mm256_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
- r00 = _mm256_andnot_pd(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
- gmx_mm256_load_4pair_swizzle_pd(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdatmp = _mm256_andnot_pd(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm256_mul_pd(_mm256_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm256_mul_pd(c6_00,rinvsix);
- vvdw12 = _mm256_mul_pd(c12_00,_mm256_mul_pd(rinvsix,rinvsix));
- vvdw = _mm256_sub_pd( _mm256_mul_pd(vvdw12,one_twelfth) , _mm256_mul_pd(vvdw6,one_sixth) );
- fvdw = _mm256_mul_pd(_mm256_sub_pd(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm256_andnot_pd(dummy_mask,velec);
- velecsum = _mm256_add_pd(velecsum,velec);
- vgb = _mm256_andnot_pd(dummy_mask,vgb);
- vgbsum = _mm256_add_pd(vgbsum,vgb);
- vvdw = _mm256_andnot_pd(dummy_mask,vvdw);
- vvdwsum = _mm256_add_pd(vvdwsum,vvdw);
-
- fscal = _mm256_add_pd(felec,fvdw);
-
- fscal = _mm256_andnot_pd(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 71 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm256_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm256_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm256_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm256_mul_pd(dvdasum, _mm256_mul_pd(isai0,isai0));
- gmx_mm256_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*71);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m256d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m256d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m256d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256d minushalf = _mm256_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m256d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m256d one_sixth = _mm256_set1_pd(1.0/6.0);
- __m256d one_twelfth = _mm256_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m256d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256d dummy_mask,cutoff_mask;
- __m128 tmpmask0,tmpmask1;
- __m256d signbit = _mm256_castsi256_pd( _mm256_set1_epi32(0x80000000) );
- __m256d one = _mm256_set1_pd(1.0);
- __m256d two = _mm256_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_pd();
- fiy0 = _mm256_setzero_pd();
- fiz0 = _mm256_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_pd(facel,_mm256_set1_pd(charge[inr+0]));
- isai0 = _mm256_set1_pd(invsqrta[inr+0]);
- vdwioffsetptr0 = vdwparam+2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm256_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- rinvsq00 = _mm256_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
- gmx_mm256_load_4pair_swizzle_pd(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm256_mul_pd(_mm256_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(c12_00,rinvsix),c6_00),_mm256_mul_pd(rinvsix,rinvsq00));
-
- fscal = _mm256_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 63 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_pd(mask,val) to clear dummy entries.
- */
- tmpmask0 = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
-
- tmpmask1 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(3,3,2,2));
- tmpmask0 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(1,1,0,0));
- dummy_mask = _mm256_castps_pd(gmx_mm256_set_m128(tmpmask1,tmpmask0));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- rinvsq00 = _mm256_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
- r00 = _mm256_andnot_pd(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
- gmx_mm256_load_4pair_swizzle_pd(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdatmp = _mm256_andnot_pd(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm256_mul_pd(_mm256_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(c12_00,rinvsix),c6_00),_mm256_mul_pd(rinvsix,rinvsq00));
-
- fscal = _mm256_add_pd(felec,fvdw);
-
- fscal = _mm256_andnot_pd(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 64 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm256_mul_pd(dvdasum, _mm256_mul_pd(isai0,isai0));
- gmx_mm256_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*64);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_256_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_256_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m256d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m256d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m256d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256d minushalf = _mm256_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m256d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256d dummy_mask,cutoff_mask;
- __m128 tmpmask0,tmpmask1;
- __m256d signbit = _mm256_castsi256_pd( _mm256_set1_epi32(0x80000000) );
- __m256d one = _mm256_set1_pd(1.0);
- __m256d two = _mm256_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_pd();
- fiy0 = _mm256_setzero_pd();
- fiz0 = _mm256_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_pd(facel,_mm256_set1_pd(charge[inr+0]));
- isai0 = _mm256_set1_pd(invsqrta[inr+0]);
-
- /* Reset potential sums */
- velecsum = _mm256_setzero_pd();
- vgbsum = _mm256_setzero_pd();
- dvdasum = _mm256_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm256_add_pd(velecsum,velec);
- vgbsum = _mm256_add_pd(vgbsum,vgb);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 57 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_pd(mask,val) to clear dummy entries.
- */
- tmpmask0 = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
-
- tmpmask1 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(3,3,2,2));
- tmpmask0 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(1,1,0,0));
- dummy_mask = _mm256_castps_pd(gmx_mm256_set_m128(tmpmask1,tmpmask0));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
- r00 = _mm256_andnot_pd(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdatmp = _mm256_andnot_pd(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm256_andnot_pd(dummy_mask,velec);
- velecsum = _mm256_add_pd(velecsum,velec);
- vgb = _mm256_andnot_pd(dummy_mask,vgb);
- vgbsum = _mm256_add_pd(vgbsum,vgb);
-
- fscal = felec;
-
- fscal = _mm256_andnot_pd(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 58 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm256_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm256_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- dvdasum = _mm256_mul_pd(dvdasum, _mm256_mul_pd(isai0,isai0));
- gmx_mm256_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 9 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*9 + inneriter*58);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with AVX, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m256d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m256d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m256d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256d minushalf = _mm256_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m256d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256d dummy_mask,cutoff_mask;
- __m128 tmpmask0,tmpmask1;
- __m256d signbit = _mm256_castsi256_pd( _mm256_set1_epi32(0x80000000) );
- __m256d one = _mm256_set1_pd(1.0);
- __m256d two = _mm256_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_pd();
- fiy0 = _mm256_setzero_pd();
- fiz0 = _mm256_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_pd(facel,_mm256_set1_pd(charge[inr+0]));
- isai0 = _mm256_set1_pd(invsqrta[inr+0]);
-
- dvdasum = _mm256_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 55 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_pd(mask,val) to clear dummy entries.
- */
- tmpmask0 = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
-
- tmpmask1 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(3,3,2,2));
- tmpmask0 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(1,1,0,0));
- dummy_mask = _mm256_castps_pd(gmx_mm256_set_m128(tmpmask1,tmpmask0));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_pd(ix0,jx0);
- dy00 = _mm256_sub_pd(iy0,jy0);
- dz00 = _mm256_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_pd(rsq00,rinv00);
- r00 = _mm256_andnot_pd(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai0,isaj0);
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r00,gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
-
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
- dvdatmp = _mm256_andnot_pd(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
- velec = _mm256_mul_pd(qq00,rinv00);
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- fscal = _mm256_andnot_pd(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_pd(fscal,dx00);
- ty = _mm256_mul_pd(fscal,dy00);
- tz = _mm256_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_pd(fix0,tx);
- fiy0 = _mm256_add_pd(fiy0,ty);
- fiz0 = _mm256_add_pd(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 56 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm256_mul_pd(dvdasum, _mm256_mul_pd(isai0,isai0));
- gmx_mm256_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*7 + inneriter*56);
-}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_t nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_256_double;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_256_double;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_256_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_256_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_256_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_256_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_256_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_double;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_256_double;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_256_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_256_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_256_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_256_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_256_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_256_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_double;
nb_kernel_info_t
{ nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_256_double, "nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_256_double", "avx_256_double", "None", "None", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_256_double", "avx_256_double", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_256_double, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_256_double", "avx_256_double", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_256_double", "avx_256_double", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_256_double, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_256_double", "avx_256_double", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_256_double", "avx_256_double", "Ewald", "None", "LJEwald", "None", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_256_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_256_double", "avx_256_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_256_double", "avx_256_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_256_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_256_double", "avx_256_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_double", "avx_256_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_256_double", "avx_256_double", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_double, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_double", "avx_256_double", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_double", "avx_256_double", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_double, "nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_double", "avx_256_double", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_256_double", "avx_256_double", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_256_double, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_256_double", "avx_256_double", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_256_double", "avx_256_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_256_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_256_double", "avx_256_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_256_double", "avx_256_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_avx_256_double", "avx_256_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_256_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_256_double", "avx_256_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_256_double", "avx_256_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_double", "avx_256_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_double", "avx_256_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_double", "avx_256_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_double", "avx_256_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_double", "avx_256_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
};
int
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
__m256d velec,felec,velecsum,facel,crf,krf,krf2;
real *charge;
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- __m128i gbitab;
- __m256d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256d minushalf = _mm256_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- /* #endif */
/* #if KERNEL_VDW != 'None' */
int nvdwtype;
__m256d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
__m256d one_sixth = _mm256_set1_pd(1.0/6.0);
__m256d one_twelfth = _mm256_set1_pd(1.0/12.0);
/* #endif */
- /* #if 'Table' in KERNEL_ELEC or 'GeneralizedBorn' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
+ /* #if 'Table' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
__m128i vfitab;
__m128i ifour = _mm_set1_epi32(4);
__m256d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
/* #endif */
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
- /* #endif */
-
/* #if 'Water' in GEOMETRY_I */
/* Setup water-specific parameters */
inr = nlist->iinr[0];
/* #for I in PARTICLES_ELEC_I */
iq{I} = _mm256_mul_pd(facel,_mm256_set1_pd(charge[inr+{I}]));
/* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isai{I} = _mm256_set1_pd(invsqrta[inr+{I}]);
- /* #endif */
/* #endfor */
/* #for I in PARTICLES_VDW_I */
vdwioffsetptr{I} = vdwparam+2*nvdwtype*vdwtype[inr+{I}];
/* #if KERNEL_ELEC != 'None' */
velecsum = _mm256_setzero_pd();
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- vgbsum = _mm256_setzero_pd();
- /* #endif */
/* #if KERNEL_VDW != 'None' */
vvdwsum = _mm256_setzero_pd();
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm256_setzero_pd();
- /* #endif */
/* #for ROUND in ['Loop','Epilogue'] */
/* #for J in PARTICLES_ELEC_J */
jq{J} = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+{J},charge+jnrB+{J},
charge+jnrC+{J},charge+jnrD+{J});
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isaj{J} = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+{J},invsqrta+jnrB+{J},
- invsqrta+jnrC+{J},invsqrta+jnrD+{J});
- /* #endif */
/* #endfor */
/* #for J in PARTICLES_VDW_J */
vdwjidx{J}A = 2*vdwtype[jnrA+{J}];
/* #define INNERFLOPS INNERFLOPS+3 */
/* #endif */
- /* #elif KERNEL_ELEC=='GeneralizedBorn' */
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_pd(isai{I},isaj{J});
- gbqqfactor = _mm256_xor_pd(signbit,_mm256_mul_pd(qq{I}{J},_mm256_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_pd(isaprod,gbtabscale);
- /* #define INNERFLOPS INNERFLOPS+5 */
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_pd(r{I}{J},gbscale);
- gbitab = _mm256_cvttpd_epi32(rt);
- gbeps = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
- F = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
- G = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
- H = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
- GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
- Heps = _mm256_mul_pd(gbeps,H);
- Fp = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
- VV = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
- vgb = _mm256_mul_pd(gbqqfactor,VV);
- /* #define INNERFLOPS INNERFLOPS+10 */
-
- /* #if 'Force' in KERNEL_VF */
- FF = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
- fgb = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
- dvdatmp = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r{I}{J})));
- /* #if ROUND == 'Epilogue' */
- dvdatmp = _mm256_andnot_pd(dummy_mask,dvdatmp);
- /* #endif */
- dvdasum = _mm256_add_pd(dvdasum,dvdatmp);
- /* #if ROUND == 'Loop' */
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- /* #else */
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- /* #endif */
- gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
- _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj{J},isaj{J})));
- /* #define INNERFLOPS INNERFLOPS+12 */
- /* #endif */
- velec = _mm256_mul_pd(qq{I}{J},rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #if 'Force' in KERNEL_VF */
- felec = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv{I}{J}),fgb),rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+3 */
- /* #endif */
-
/* #elif KERNEL_ELEC=='Ewald' */
/* EWALD ELECTROSTATICS */
/* #endif */
velecsum = _mm256_add_pd(velecsum,velec);
/* #define INNERFLOPS INNERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
- vgb = _mm256_and_pd(vgb,cutoff_mask);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
- /* #if ROUND == 'Epilogue' */
- vgb = _mm256_andnot_pd(dummy_mask,vgb);
- /* #endif */
- vgbsum = _mm256_add_pd(vgbsum,vgb);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
/* #endif */
/* #if 'vdw' in INTERACTION_FLAGS[I][J] */
/* ## Note special check for TIP4P-TIP4P. Since we are cutting of all hydrogen interactions we also cut the LJ-only O-O interaction */
gmx_mm256_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- gmx_mm256_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- /* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #endif */
/* #if KERNEL_VDW != 'None' */
gmx_mm256_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm256_mul_pd(dvdasum, _mm256_mul_pd(isai{I},isai{I}));
- gmx_mm256_update_1pot_pd(dvdasum,dvda+inr);
- /* #endif */
/* Increment number of inner iterations */
inneriter += j_index_end - j_index_start;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
- 'GeneralizedBorn' : ['rinv','r'],
'CubicSplineTable' : ['rinv','r','table'],
'Ewald' : ['rinv','rinvsq','r'],
}
'Coulomb' : 'Coul',
'Ewald' : 'Ew',
'ReactionField' : 'RF',
- 'GeneralizedBorn' : 'GB',
'CubicSplineTable' : 'CSTab',
'LennardJones' : 'LJ',
'Buckingham' : 'Bham',
return 0
# No need for LJ-only water optimization, or water optimization with implicit solvent.
- if('Water' in KernelGeom[0] and (KernelElec=='None' or 'GeneralizedBorn' in KernelElec)):
+ if('Water' in KernelGeom[0] and KernelElec=='None'):
return 0
# Non-matching table settings are pointless
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_256_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_256_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_256_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_256_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D,E,F,G,H refer to j loop unrolling done with AVX, e.g. for the eight different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrE,jnrF,jnrG,jnrH;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int j_coord_offsetE,j_coord_offsetF,j_coord_offsetG,j_coord_offsetH;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD,*fjptrE,*fjptrF,*fjptrG,*fjptrH;
- real scratch[4*DIM];
- __m256 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D,vdwjidx0E,vdwjidx0F,vdwjidx0G,vdwjidx0H;
- __m256 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m256i gbitab;
- __m128i gbitab_lo,gbitab_hi;
- __m256 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256 minushalf = _mm256_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m256 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m256 one_sixth = _mm256_set1_ps(1.0/6.0);
- __m256 one_twelfth = _mm256_set1_ps(1.0/12.0);
- __m256i vfitab;
- __m128i vfitab_lo,vfitab_hi;
- __m128i ifour = _mm_set1_epi32(4);
- __m256 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256 dummy_mask,cutoff_mask;
- __m256 signbit = _mm256_castsi256_ps( _mm256_set1_epi32(0x80000000) );
- __m256 one = _mm256_set1_ps(1.0);
- __m256 two = _mm256_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm256_set1_ps(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = jnrE = jnrF = jnrG = jnrH = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
- j_coord_offsetE = 0;
- j_coord_offsetF = 0;
- j_coord_offsetG = 0;
- j_coord_offsetH = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_ps();
- fiy0 = _mm256_setzero_ps();
- fiz0 = _mm256_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_ps(facel,_mm256_set1_ps(charge[inr+0]));
- isai0 = _mm256_set1_ps(invsqrta[inr+0]);
- vdwioffsetptr0 = vdwparam+2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm256_setzero_ps();
- vgbsum = _mm256_setzero_ps();
- vvdwsum = _mm256_setzero_ps();
- dvdasum = _mm256_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+7]>=0; jidx+=8)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- jnrE = jjnr[jidx+4];
- jnrF = jjnr[jidx+5];
- jnrG = jjnr[jidx+6];
- jnrH = jjnr[jidx+7];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
- vdwjidx0E = 2*vdwtype[jnrE+0];
- vdwjidx0F = 2*vdwtype[jnrF+0];
- vdwjidx0G = 2*vdwtype[jnrG+0];
- vdwjidx0H = 2*vdwtype[jnrH+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
- gmx_mm256_load_8pair_swizzle_ps(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- vdwioffsetptr0+vdwjidx0E,
- vdwioffsetptr0+vdwjidx0F,
- vdwioffsetptr0+vdwjidx0G,
- vdwioffsetptr0+vdwjidx0H,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm256_mul_ps(r00,vftabscale);
- vfitab = _mm256_cvttps_epi32(rt);
- vfeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- vfitab_lo = _mm256_extractf128_si256(vfitab,0x0);
- vfitab_hi = _mm256_extractf128_si256(vfitab,0x1);
- vfitab_lo = _mm_slli_epi32(vfitab_lo,3);
- vfitab_hi = _mm_slli_epi32(vfitab_hi,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- fjptrE = dvda+jnrE;
- fjptrF = dvda+jnrF;
- fjptrG = dvda+jnrG;
- fjptrH = dvda+jnrH;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,0)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,1)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,2)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,3)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(vfeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(vfeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(vfeps,Fp));
- vvdw6 = _mm256_mul_ps(c6_00,VV);
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(vfeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fvdw6 = _mm256_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab_lo = _mm_add_epi32(vfitab_lo,ifour);
- vfitab_hi = _mm_add_epi32(vfitab_hi,ifour);
- Y = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,0)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,1)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,2)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,3)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(vfeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(vfeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(vfeps,Fp));
- vvdw12 = _mm256_mul_ps(c12_00,VV);
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(vfeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fvdw12 = _mm256_mul_ps(c12_00,FF);
- vvdw = _mm256_add_ps(vvdw12,vvdw6);
- fvdw = _mm256_xor_ps(signbit,_mm256_mul_ps(_mm256_add_ps(fvdw6,fvdw12),_mm256_mul_ps(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm256_add_ps(velecsum,velec);
- vgbsum = _mm256_add_ps(vgbsum,vgb);
- vvdwsum = _mm256_add_ps(vvdwsum,vvdw);
-
- fscal = _mm256_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- fjptrE = f+j_coord_offsetE;
- fjptrF = f+j_coord_offsetF;
- fjptrG = f+j_coord_offsetG;
- fjptrH = f+j_coord_offsetH;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 91 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- jnrlistE = jjnr[jidx+4];
- jnrlistF = jjnr[jidx+5];
- jnrlistG = jjnr[jidx+6];
- jnrlistH = jjnr[jidx+7];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm256_set_m128(gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx+4)),_mm_setzero_si128())),
- gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128())));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- jnrE = (jnrlistE>=0) ? jnrlistE : 0;
- jnrF = (jnrlistF>=0) ? jnrlistF : 0;
- jnrG = (jnrlistG>=0) ? jnrlistG : 0;
- jnrH = (jnrlistH>=0) ? jnrlistH : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
- vdwjidx0E = 2*vdwtype[jnrE+0];
- vdwjidx0F = 2*vdwtype[jnrF+0];
- vdwjidx0G = 2*vdwtype[jnrG+0];
- vdwjidx0H = 2*vdwtype[jnrH+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
- r00 = _mm256_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
- gmx_mm256_load_8pair_swizzle_ps(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- vdwioffsetptr0+vdwjidx0E,
- vdwioffsetptr0+vdwjidx0F,
- vdwioffsetptr0+vdwjidx0G,
- vdwioffsetptr0+vdwjidx0H,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm256_mul_ps(r00,vftabscale);
- vfitab = _mm256_cvttps_epi32(rt);
- vfeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- vfitab_lo = _mm256_extractf128_si256(vfitab,0x0);
- vfitab_hi = _mm256_extractf128_si256(vfitab,0x1);
- vfitab_lo = _mm_slli_epi32(vfitab_lo,3);
- vfitab_hi = _mm_slli_epi32(vfitab_hi,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdatmp = _mm256_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- fjptrE = (jnrlistE>=0) ? dvda+jnrE : scratch;
- fjptrF = (jnrlistF>=0) ? dvda+jnrF : scratch;
- fjptrG = (jnrlistG>=0) ? dvda+jnrG : scratch;
- fjptrH = (jnrlistH>=0) ? dvda+jnrH : scratch;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,0)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,1)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,2)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,3)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(vfeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(vfeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(vfeps,Fp));
- vvdw6 = _mm256_mul_ps(c6_00,VV);
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(vfeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fvdw6 = _mm256_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab_lo = _mm_add_epi32(vfitab_lo,ifour);
- vfitab_hi = _mm_add_epi32(vfitab_hi,ifour);
- Y = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,0)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,1)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,2)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,3)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(vfeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(vfeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(vfeps,Fp));
- vvdw12 = _mm256_mul_ps(c12_00,VV);
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(vfeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fvdw12 = _mm256_mul_ps(c12_00,FF);
- vvdw = _mm256_add_ps(vvdw12,vvdw6);
- fvdw = _mm256_xor_ps(signbit,_mm256_mul_ps(_mm256_add_ps(fvdw6,fvdw12),_mm256_mul_ps(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm256_andnot_ps(dummy_mask,velec);
- velecsum = _mm256_add_ps(velecsum,velec);
- vgb = _mm256_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm256_add_ps(vgbsum,vgb);
- vvdw = _mm256_andnot_ps(dummy_mask,vvdw);
- vvdwsum = _mm256_add_ps(vvdwsum,vvdw);
-
- fscal = _mm256_add_ps(felec,fvdw);
-
- fscal = _mm256_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- fjptrE = (jnrlistE>=0) ? f+j_coord_offsetE : scratch;
- fjptrF = (jnrlistF>=0) ? f+j_coord_offsetF : scratch;
- fjptrG = (jnrlistG>=0) ? f+j_coord_offsetG : scratch;
- fjptrH = (jnrlistH>=0) ? f+j_coord_offsetH : scratch;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 92 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm256_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm256_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm256_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm256_mul_ps(dvdasum, _mm256_mul_ps(isai0,isai0));
- gmx_mm256_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*92);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_256_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_256_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D,E,F,G,H refer to j loop unrolling done with AVX, e.g. for the eight different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrE,jnrF,jnrG,jnrH;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int j_coord_offsetE,j_coord_offsetF,j_coord_offsetG,j_coord_offsetH;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD,*fjptrE,*fjptrF,*fjptrG,*fjptrH;
- real scratch[4*DIM];
- __m256 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D,vdwjidx0E,vdwjidx0F,vdwjidx0G,vdwjidx0H;
- __m256 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m256i gbitab;
- __m128i gbitab_lo,gbitab_hi;
- __m256 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256 minushalf = _mm256_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m256 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m256 one_sixth = _mm256_set1_ps(1.0/6.0);
- __m256 one_twelfth = _mm256_set1_ps(1.0/12.0);
- __m256i vfitab;
- __m128i vfitab_lo,vfitab_hi;
- __m128i ifour = _mm_set1_epi32(4);
- __m256 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256 dummy_mask,cutoff_mask;
- __m256 signbit = _mm256_castsi256_ps( _mm256_set1_epi32(0x80000000) );
- __m256 one = _mm256_set1_ps(1.0);
- __m256 two = _mm256_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm256_set1_ps(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = jnrE = jnrF = jnrG = jnrH = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
- j_coord_offsetE = 0;
- j_coord_offsetF = 0;
- j_coord_offsetG = 0;
- j_coord_offsetH = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_ps();
- fiy0 = _mm256_setzero_ps();
- fiz0 = _mm256_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_ps(facel,_mm256_set1_ps(charge[inr+0]));
- isai0 = _mm256_set1_ps(invsqrta[inr+0]);
- vdwioffsetptr0 = vdwparam+2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm256_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+7]>=0; jidx+=8)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- jnrE = jjnr[jidx+4];
- jnrF = jjnr[jidx+5];
- jnrG = jjnr[jidx+6];
- jnrH = jjnr[jidx+7];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
- vdwjidx0E = 2*vdwtype[jnrE+0];
- vdwjidx0F = 2*vdwtype[jnrF+0];
- vdwjidx0G = 2*vdwtype[jnrG+0];
- vdwjidx0H = 2*vdwtype[jnrH+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
- gmx_mm256_load_8pair_swizzle_ps(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- vdwioffsetptr0+vdwjidx0E,
- vdwioffsetptr0+vdwjidx0F,
- vdwioffsetptr0+vdwjidx0G,
- vdwioffsetptr0+vdwjidx0H,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm256_mul_ps(r00,vftabscale);
- vfitab = _mm256_cvttps_epi32(rt);
- vfeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- vfitab_lo = _mm256_extractf128_si256(vfitab,0x0);
- vfitab_hi = _mm256_extractf128_si256(vfitab,0x1);
- vfitab_lo = _mm_slli_epi32(vfitab_lo,3);
- vfitab_hi = _mm_slli_epi32(vfitab_hi,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- fjptrE = dvda+jnrE;
- fjptrF = dvda+jnrF;
- fjptrG = dvda+jnrG;
- fjptrH = dvda+jnrH;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,0)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,1)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,2)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,3)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(vfeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(vfeps,_mm256_add_ps(G,Heps)));
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(vfeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fvdw6 = _mm256_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab_lo = _mm_add_epi32(vfitab_lo,ifour);
- vfitab_hi = _mm_add_epi32(vfitab_hi,ifour);
- Y = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,0)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,1)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,2)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,3)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(vfeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(vfeps,_mm256_add_ps(G,Heps)));
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(vfeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fvdw12 = _mm256_mul_ps(c12_00,FF);
- fvdw = _mm256_xor_ps(signbit,_mm256_mul_ps(_mm256_add_ps(fvdw6,fvdw12),_mm256_mul_ps(vftabscale,rinv00)));
-
- fscal = _mm256_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- fjptrE = f+j_coord_offsetE;
- fjptrF = f+j_coord_offsetF;
- fjptrG = f+j_coord_offsetG;
- fjptrH = f+j_coord_offsetH;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 81 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- jnrlistE = jjnr[jidx+4];
- jnrlistF = jjnr[jidx+5];
- jnrlistG = jjnr[jidx+6];
- jnrlistH = jjnr[jidx+7];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm256_set_m128(gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx+4)),_mm_setzero_si128())),
- gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128())));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- jnrE = (jnrlistE>=0) ? jnrlistE : 0;
- jnrF = (jnrlistF>=0) ? jnrlistF : 0;
- jnrG = (jnrlistG>=0) ? jnrlistG : 0;
- jnrH = (jnrlistH>=0) ? jnrlistH : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
- vdwjidx0E = 2*vdwtype[jnrE+0];
- vdwjidx0F = 2*vdwtype[jnrF+0];
- vdwjidx0G = 2*vdwtype[jnrG+0];
- vdwjidx0H = 2*vdwtype[jnrH+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
- r00 = _mm256_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
- gmx_mm256_load_8pair_swizzle_ps(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- vdwioffsetptr0+vdwjidx0E,
- vdwioffsetptr0+vdwjidx0F,
- vdwioffsetptr0+vdwjidx0G,
- vdwioffsetptr0+vdwjidx0H,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm256_mul_ps(r00,vftabscale);
- vfitab = _mm256_cvttps_epi32(rt);
- vfeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- vfitab_lo = _mm256_extractf128_si256(vfitab,0x0);
- vfitab_hi = _mm256_extractf128_si256(vfitab,0x1);
- vfitab_lo = _mm_slli_epi32(vfitab_lo,3);
- vfitab_hi = _mm_slli_epi32(vfitab_hi,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdatmp = _mm256_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- fjptrE = (jnrlistE>=0) ? dvda+jnrE : scratch;
- fjptrF = (jnrlistF>=0) ? dvda+jnrF : scratch;
- fjptrG = (jnrlistG>=0) ? dvda+jnrG : scratch;
- fjptrH = (jnrlistH>=0) ? dvda+jnrH : scratch;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,0)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,1)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,2)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,3)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(vfeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(vfeps,_mm256_add_ps(G,Heps)));
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(vfeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fvdw6 = _mm256_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab_lo = _mm_add_epi32(vfitab_lo,ifour);
- vfitab_hi = _mm_add_epi32(vfitab_hi,ifour);
- Y = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,0)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,1)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,2)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(vftab + _mm_extract_epi32(vfitab_hi,3)),
- _mm_load_ps(vftab + _mm_extract_epi32(vfitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(vfeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(vfeps,_mm256_add_ps(G,Heps)));
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(vfeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fvdw12 = _mm256_mul_ps(c12_00,FF);
- fvdw = _mm256_xor_ps(signbit,_mm256_mul_ps(_mm256_add_ps(fvdw6,fvdw12),_mm256_mul_ps(vftabscale,rinv00)));
-
- fscal = _mm256_add_ps(felec,fvdw);
-
- fscal = _mm256_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- fjptrE = (jnrlistE>=0) ? f+j_coord_offsetE : scratch;
- fjptrF = (jnrlistF>=0) ? f+j_coord_offsetF : scratch;
- fjptrG = (jnrlistG>=0) ? f+j_coord_offsetG : scratch;
- fjptrH = (jnrlistH>=0) ? f+j_coord_offsetH : scratch;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 82 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm256_mul_ps(dvdasum, _mm256_mul_ps(isai0,isai0));
- gmx_mm256_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*82);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_256_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_256_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_256_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_256_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D,E,F,G,H refer to j loop unrolling done with AVX, e.g. for the eight different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrE,jnrF,jnrG,jnrH;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int j_coord_offsetE,j_coord_offsetF,j_coord_offsetG,j_coord_offsetH;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD,*fjptrE,*fjptrF,*fjptrG,*fjptrH;
- real scratch[4*DIM];
- __m256 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D,vdwjidx0E,vdwjidx0F,vdwjidx0G,vdwjidx0H;
- __m256 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m256i gbitab;
- __m128i gbitab_lo,gbitab_hi;
- __m256 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256 minushalf = _mm256_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m256 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m256 one_sixth = _mm256_set1_ps(1.0/6.0);
- __m256 one_twelfth = _mm256_set1_ps(1.0/12.0);
- __m256i vfitab;
- __m128i vfitab_lo,vfitab_hi;
- __m128i ifour = _mm_set1_epi32(4);
- __m256 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256 dummy_mask,cutoff_mask;
- __m256 signbit = _mm256_castsi256_ps( _mm256_set1_epi32(0x80000000) );
- __m256 one = _mm256_set1_ps(1.0);
- __m256 two = _mm256_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = jnrE = jnrF = jnrG = jnrH = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
- j_coord_offsetE = 0;
- j_coord_offsetF = 0;
- j_coord_offsetG = 0;
- j_coord_offsetH = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_ps();
- fiy0 = _mm256_setzero_ps();
- fiz0 = _mm256_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_ps(facel,_mm256_set1_ps(charge[inr+0]));
- isai0 = _mm256_set1_ps(invsqrta[inr+0]);
- vdwioffsetptr0 = vdwparam+2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm256_setzero_ps();
- vgbsum = _mm256_setzero_ps();
- vvdwsum = _mm256_setzero_ps();
- dvdasum = _mm256_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+7]>=0; jidx+=8)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- jnrE = jjnr[jidx+4];
- jnrF = jjnr[jidx+5];
- jnrG = jjnr[jidx+6];
- jnrH = jjnr[jidx+7];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- rinvsq00 = _mm256_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
- vdwjidx0E = 2*vdwtype[jnrE+0];
- vdwjidx0F = 2*vdwtype[jnrF+0];
- vdwjidx0G = 2*vdwtype[jnrG+0];
- vdwjidx0H = 2*vdwtype[jnrH+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
- gmx_mm256_load_8pair_swizzle_ps(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- vdwioffsetptr0+vdwjidx0E,
- vdwioffsetptr0+vdwjidx0F,
- vdwioffsetptr0+vdwjidx0G,
- vdwioffsetptr0+vdwjidx0H,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- fjptrE = dvda+jnrE;
- fjptrF = dvda+jnrF;
- fjptrG = dvda+jnrG;
- fjptrH = dvda+jnrH;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm256_mul_ps(_mm256_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm256_mul_ps(c6_00,rinvsix);
- vvdw12 = _mm256_mul_ps(c12_00,_mm256_mul_ps(rinvsix,rinvsix));
- vvdw = _mm256_sub_ps( _mm256_mul_ps(vvdw12,one_twelfth) , _mm256_mul_ps(vvdw6,one_sixth) );
- fvdw = _mm256_mul_ps(_mm256_sub_ps(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm256_add_ps(velecsum,velec);
- vgbsum = _mm256_add_ps(vgbsum,vgb);
- vvdwsum = _mm256_add_ps(vvdwsum,vvdw);
-
- fscal = _mm256_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- fjptrE = f+j_coord_offsetE;
- fjptrF = f+j_coord_offsetF;
- fjptrG = f+j_coord_offsetG;
- fjptrH = f+j_coord_offsetH;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 70 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- jnrlistE = jjnr[jidx+4];
- jnrlistF = jjnr[jidx+5];
- jnrlistG = jjnr[jidx+6];
- jnrlistH = jjnr[jidx+7];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm256_set_m128(gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx+4)),_mm_setzero_si128())),
- gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128())));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- jnrE = (jnrlistE>=0) ? jnrlistE : 0;
- jnrF = (jnrlistF>=0) ? jnrlistF : 0;
- jnrG = (jnrlistG>=0) ? jnrlistG : 0;
- jnrH = (jnrlistH>=0) ? jnrlistH : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- rinvsq00 = _mm256_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
- vdwjidx0E = 2*vdwtype[jnrE+0];
- vdwjidx0F = 2*vdwtype[jnrF+0];
- vdwjidx0G = 2*vdwtype[jnrG+0];
- vdwjidx0H = 2*vdwtype[jnrH+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
- r00 = _mm256_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
- gmx_mm256_load_8pair_swizzle_ps(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- vdwioffsetptr0+vdwjidx0E,
- vdwioffsetptr0+vdwjidx0F,
- vdwioffsetptr0+vdwjidx0G,
- vdwioffsetptr0+vdwjidx0H,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdatmp = _mm256_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- fjptrE = (jnrlistE>=0) ? dvda+jnrE : scratch;
- fjptrF = (jnrlistF>=0) ? dvda+jnrF : scratch;
- fjptrG = (jnrlistG>=0) ? dvda+jnrG : scratch;
- fjptrH = (jnrlistH>=0) ? dvda+jnrH : scratch;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm256_mul_ps(_mm256_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm256_mul_ps(c6_00,rinvsix);
- vvdw12 = _mm256_mul_ps(c12_00,_mm256_mul_ps(rinvsix,rinvsix));
- vvdw = _mm256_sub_ps( _mm256_mul_ps(vvdw12,one_twelfth) , _mm256_mul_ps(vvdw6,one_sixth) );
- fvdw = _mm256_mul_ps(_mm256_sub_ps(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm256_andnot_ps(dummy_mask,velec);
- velecsum = _mm256_add_ps(velecsum,velec);
- vgb = _mm256_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm256_add_ps(vgbsum,vgb);
- vvdw = _mm256_andnot_ps(dummy_mask,vvdw);
- vvdwsum = _mm256_add_ps(vvdwsum,vvdw);
-
- fscal = _mm256_add_ps(felec,fvdw);
-
- fscal = _mm256_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- fjptrE = (jnrlistE>=0) ? f+j_coord_offsetE : scratch;
- fjptrF = (jnrlistF>=0) ? f+j_coord_offsetF : scratch;
- fjptrG = (jnrlistG>=0) ? f+j_coord_offsetG : scratch;
- fjptrH = (jnrlistH>=0) ? f+j_coord_offsetH : scratch;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 71 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm256_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm256_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm256_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm256_mul_ps(dvdasum, _mm256_mul_ps(isai0,isai0));
- gmx_mm256_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*71);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D,E,F,G,H refer to j loop unrolling done with AVX, e.g. for the eight different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrE,jnrF,jnrG,jnrH;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int j_coord_offsetE,j_coord_offsetF,j_coord_offsetG,j_coord_offsetH;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD,*fjptrE,*fjptrF,*fjptrG,*fjptrH;
- real scratch[4*DIM];
- __m256 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D,vdwjidx0E,vdwjidx0F,vdwjidx0G,vdwjidx0H;
- __m256 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m256i gbitab;
- __m128i gbitab_lo,gbitab_hi;
- __m256 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256 minushalf = _mm256_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m256 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m256 one_sixth = _mm256_set1_ps(1.0/6.0);
- __m256 one_twelfth = _mm256_set1_ps(1.0/12.0);
- __m256i vfitab;
- __m128i vfitab_lo,vfitab_hi;
- __m128i ifour = _mm_set1_epi32(4);
- __m256 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256 dummy_mask,cutoff_mask;
- __m256 signbit = _mm256_castsi256_ps( _mm256_set1_epi32(0x80000000) );
- __m256 one = _mm256_set1_ps(1.0);
- __m256 two = _mm256_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = jnrE = jnrF = jnrG = jnrH = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
- j_coord_offsetE = 0;
- j_coord_offsetF = 0;
- j_coord_offsetG = 0;
- j_coord_offsetH = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_ps();
- fiy0 = _mm256_setzero_ps();
- fiz0 = _mm256_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_ps(facel,_mm256_set1_ps(charge[inr+0]));
- isai0 = _mm256_set1_ps(invsqrta[inr+0]);
- vdwioffsetptr0 = vdwparam+2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm256_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+7]>=0; jidx+=8)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- jnrE = jjnr[jidx+4];
- jnrF = jjnr[jidx+5];
- jnrG = jjnr[jidx+6];
- jnrH = jjnr[jidx+7];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- rinvsq00 = _mm256_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
- vdwjidx0E = 2*vdwtype[jnrE+0];
- vdwjidx0F = 2*vdwtype[jnrF+0];
- vdwjidx0G = 2*vdwtype[jnrG+0];
- vdwjidx0H = 2*vdwtype[jnrH+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
- gmx_mm256_load_8pair_swizzle_ps(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- vdwioffsetptr0+vdwjidx0E,
- vdwioffsetptr0+vdwjidx0F,
- vdwioffsetptr0+vdwjidx0G,
- vdwioffsetptr0+vdwjidx0H,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- fjptrE = dvda+jnrE;
- fjptrF = dvda+jnrF;
- fjptrG = dvda+jnrG;
- fjptrH = dvda+jnrH;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm256_mul_ps(_mm256_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(c12_00,rinvsix),c6_00),_mm256_mul_ps(rinvsix,rinvsq00));
-
- fscal = _mm256_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- fjptrE = f+j_coord_offsetE;
- fjptrF = f+j_coord_offsetF;
- fjptrG = f+j_coord_offsetG;
- fjptrH = f+j_coord_offsetH;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 63 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- jnrlistE = jjnr[jidx+4];
- jnrlistF = jjnr[jidx+5];
- jnrlistG = jjnr[jidx+6];
- jnrlistH = jjnr[jidx+7];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm256_set_m128(gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx+4)),_mm_setzero_si128())),
- gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128())));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- jnrE = (jnrlistE>=0) ? jnrlistE : 0;
- jnrF = (jnrlistF>=0) ? jnrlistF : 0;
- jnrG = (jnrlistG>=0) ? jnrlistG : 0;
- jnrH = (jnrlistH>=0) ? jnrlistH : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- rinvsq00 = _mm256_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
- vdwjidx0E = 2*vdwtype[jnrE+0];
- vdwjidx0F = 2*vdwtype[jnrF+0];
- vdwjidx0G = 2*vdwtype[jnrG+0];
- vdwjidx0H = 2*vdwtype[jnrH+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
- r00 = _mm256_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
- gmx_mm256_load_8pair_swizzle_ps(vdwioffsetptr0+vdwjidx0A,
- vdwioffsetptr0+vdwjidx0B,
- vdwioffsetptr0+vdwjidx0C,
- vdwioffsetptr0+vdwjidx0D,
- vdwioffsetptr0+vdwjidx0E,
- vdwioffsetptr0+vdwjidx0F,
- vdwioffsetptr0+vdwjidx0G,
- vdwioffsetptr0+vdwjidx0H,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdatmp = _mm256_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- fjptrE = (jnrlistE>=0) ? dvda+jnrE : scratch;
- fjptrF = (jnrlistF>=0) ? dvda+jnrF : scratch;
- fjptrG = (jnrlistG>=0) ? dvda+jnrG : scratch;
- fjptrH = (jnrlistH>=0) ? dvda+jnrH : scratch;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm256_mul_ps(_mm256_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(c12_00,rinvsix),c6_00),_mm256_mul_ps(rinvsix,rinvsq00));
-
- fscal = _mm256_add_ps(felec,fvdw);
-
- fscal = _mm256_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- fjptrE = (jnrlistE>=0) ? f+j_coord_offsetE : scratch;
- fjptrF = (jnrlistF>=0) ? f+j_coord_offsetF : scratch;
- fjptrG = (jnrlistG>=0) ? f+j_coord_offsetG : scratch;
- fjptrH = (jnrlistH>=0) ? f+j_coord_offsetH : scratch;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 64 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm256_mul_ps(dvdasum, _mm256_mul_ps(isai0,isai0));
- gmx_mm256_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*64);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS avx_256_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_avx_256_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D,E,F,G,H refer to j loop unrolling done with AVX, e.g. for the eight different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrE,jnrF,jnrG,jnrH;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int j_coord_offsetE,j_coord_offsetF,j_coord_offsetG,j_coord_offsetH;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD,*fjptrE,*fjptrF,*fjptrG,*fjptrH;
- real scratch[4*DIM];
- __m256 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D,vdwjidx0E,vdwjidx0F,vdwjidx0G,vdwjidx0H;
- __m256 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m256i gbitab;
- __m128i gbitab_lo,gbitab_hi;
- __m256 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256 minushalf = _mm256_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m256i vfitab;
- __m128i vfitab_lo,vfitab_hi;
- __m128i ifour = _mm_set1_epi32(4);
- __m256 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256 dummy_mask,cutoff_mask;
- __m256 signbit = _mm256_castsi256_ps( _mm256_set1_epi32(0x80000000) );
- __m256 one = _mm256_set1_ps(1.0);
- __m256 two = _mm256_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = jnrE = jnrF = jnrG = jnrH = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
- j_coord_offsetE = 0;
- j_coord_offsetF = 0;
- j_coord_offsetG = 0;
- j_coord_offsetH = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_ps();
- fiy0 = _mm256_setzero_ps();
- fiz0 = _mm256_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_ps(facel,_mm256_set1_ps(charge[inr+0]));
- isai0 = _mm256_set1_ps(invsqrta[inr+0]);
-
- /* Reset potential sums */
- velecsum = _mm256_setzero_ps();
- vgbsum = _mm256_setzero_ps();
- dvdasum = _mm256_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+7]>=0; jidx+=8)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- jnrE = jjnr[jidx+4];
- jnrF = jjnr[jidx+5];
- jnrG = jjnr[jidx+6];
- jnrH = jjnr[jidx+7];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- fjptrE = dvda+jnrE;
- fjptrF = dvda+jnrF;
- fjptrG = dvda+jnrG;
- fjptrH = dvda+jnrH;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm256_add_ps(velecsum,velec);
- vgbsum = _mm256_add_ps(vgbsum,vgb);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- fjptrE = f+j_coord_offsetE;
- fjptrF = f+j_coord_offsetF;
- fjptrG = f+j_coord_offsetG;
- fjptrH = f+j_coord_offsetH;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 57 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- jnrlistE = jjnr[jidx+4];
- jnrlistF = jjnr[jidx+5];
- jnrlistG = jjnr[jidx+6];
- jnrlistH = jjnr[jidx+7];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm256_set_m128(gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx+4)),_mm_setzero_si128())),
- gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128())));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- jnrE = (jnrlistE>=0) ? jnrlistE : 0;
- jnrF = (jnrlistF>=0) ? jnrlistF : 0;
- jnrG = (jnrlistG>=0) ? jnrlistG : 0;
- jnrH = (jnrlistH>=0) ? jnrlistH : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
- r00 = _mm256_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdatmp = _mm256_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- fjptrE = (jnrlistE>=0) ? dvda+jnrE : scratch;
- fjptrF = (jnrlistF>=0) ? dvda+jnrF : scratch;
- fjptrG = (jnrlistG>=0) ? dvda+jnrG : scratch;
- fjptrH = (jnrlistH>=0) ? dvda+jnrH : scratch;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm256_andnot_ps(dummy_mask,velec);
- velecsum = _mm256_add_ps(velecsum,velec);
- vgb = _mm256_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm256_add_ps(vgbsum,vgb);
-
- fscal = felec;
-
- fscal = _mm256_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- fjptrE = (jnrlistE>=0) ? f+j_coord_offsetE : scratch;
- fjptrF = (jnrlistF>=0) ? f+j_coord_offsetF : scratch;
- fjptrG = (jnrlistG>=0) ? f+j_coord_offsetG : scratch;
- fjptrH = (jnrlistH>=0) ? f+j_coord_offsetH : scratch;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 58 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm256_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm256_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- dvdasum = _mm256_mul_ps(dvdasum, _mm256_mul_ps(isai0,isai0));
- gmx_mm256_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 9 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*9 + inneriter*58);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D,E,F,G,H refer to j loop unrolling done with AVX, e.g. for the eight different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrE,jnrF,jnrG,jnrH;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int jnrlistE,jnrlistF,jnrlistG,jnrlistH;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int j_coord_offsetE,j_coord_offsetF,j_coord_offsetG,j_coord_offsetH;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD,*fjptrE,*fjptrF,*fjptrG,*fjptrH;
- real scratch[4*DIM];
- __m256 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- real * vdwioffsetptr0;
- __m256 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D,vdwjidx0E,vdwjidx0F,vdwjidx0G,vdwjidx0H;
- __m256 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m256 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m256 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m256i gbitab;
- __m128i gbitab_lo,gbitab_hi;
- __m256 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256 minushalf = _mm256_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m256i vfitab;
- __m128i vfitab_lo,vfitab_hi;
- __m128i ifour = _mm_set1_epi32(4);
- __m256 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m256 dummy_mask,cutoff_mask;
- __m256 signbit = _mm256_castsi256_ps( _mm256_set1_epi32(0x80000000) );
- __m256 one = _mm256_set1_ps(1.0);
- __m256 two = _mm256_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm256_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = jnrE = jnrF = jnrG = jnrH = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
- j_coord_offsetE = 0;
- j_coord_offsetF = 0;
- j_coord_offsetG = 0;
- j_coord_offsetH = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm256_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm256_setzero_ps();
- fiy0 = _mm256_setzero_ps();
- fiz0 = _mm256_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm256_mul_ps(facel,_mm256_set1_ps(charge[inr+0]));
- isai0 = _mm256_set1_ps(invsqrta[inr+0]);
-
- dvdasum = _mm256_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+7]>=0; jidx+=8)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- jnrE = jjnr[jidx+4];
- jnrF = jjnr[jidx+5];
- jnrG = jjnr[jidx+6];
- jnrH = jjnr[jidx+7];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- fjptrE = dvda+jnrE;
- fjptrF = dvda+jnrF;
- fjptrG = dvda+jnrG;
- fjptrH = dvda+jnrH;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- fjptrE = f+j_coord_offsetE;
- fjptrF = f+j_coord_offsetF;
- fjptrG = f+j_coord_offsetG;
- fjptrH = f+j_coord_offsetH;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 55 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- jnrlistE = jjnr[jidx+4];
- jnrlistF = jjnr[jidx+5];
- jnrlistG = jjnr[jidx+6];
- jnrlistH = jjnr[jidx+7];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm256_set_m128(gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx+4)),_mm_setzero_si128())),
- gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128())));
-
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- jnrE = (jnrlistE>=0) ? jnrlistE : 0;
- jnrF = (jnrlistF>=0) ? jnrlistF : 0;
- jnrG = (jnrlistG>=0) ? jnrlistG : 0;
- jnrH = (jnrlistH>=0) ? jnrlistH : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
- j_coord_offsetE = DIM*jnrE;
- j_coord_offsetF = DIM*jnrF;
- j_coord_offsetG = DIM*jnrG;
- j_coord_offsetH = DIM*jnrH;
-
- /* load j atom coordinates */
- gmx_mm256_load_1rvec_8ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- x+j_coord_offsetE,x+j_coord_offsetF,
- x+j_coord_offsetG,x+j_coord_offsetH,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm256_sub_ps(ix0,jx0);
- dy00 = _mm256_sub_ps(iy0,jy0);
- dz00 = _mm256_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm256_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = avx256_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm256_load_8real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0,
- charge+jnrE+0,charge+jnrF+0,
- charge+jnrG+0,charge+jnrH+0);
- isaj0 = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0,
- invsqrta+jnrE+0,invsqrta+jnrF+0,
- invsqrta+jnrG+0,invsqrta+jnrH+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm256_mul_ps(rsq00,rinv00);
- r00 = _mm256_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm256_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai0,isaj0);
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq00,_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r00,gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
-
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r00)));
- dvdatmp = _mm256_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- fjptrE = (jnrlistE>=0) ? dvda+jnrE : scratch;
- fjptrF = (jnrlistF>=0) ? dvda+jnrF : scratch;
- fjptrG = (jnrlistG>=0) ? dvda+jnrG : scratch;
- fjptrH = (jnrlistH>=0) ? dvda+jnrH : scratch;
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj0,isaj0)));
- velec = _mm256_mul_ps(qq00,rinv00);
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- fscal = _mm256_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm256_mul_ps(fscal,dx00);
- ty = _mm256_mul_ps(fscal,dy00);
- tz = _mm256_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm256_add_ps(fix0,tx);
- fiy0 = _mm256_add_ps(fiy0,ty);
- fiz0 = _mm256_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- fjptrE = (jnrlistE>=0) ? f+j_coord_offsetE : scratch;
- fjptrF = (jnrlistF>=0) ? f+j_coord_offsetF : scratch;
- fjptrG = (jnrlistG>=0) ? f+j_coord_offsetG : scratch;
- fjptrH = (jnrlistH>=0) ? f+j_coord_offsetH : scratch;
- gmx_mm256_decrement_1rvec_8ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,tx,ty,tz);
-
- /* Inner loop uses 56 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm256_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm256_mul_ps(dvdasum, _mm256_mul_ps(isai0,isai0));
- gmx_mm256_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*7 + inneriter*56);
-}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_t nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_256_single;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_256_single;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_256_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_256_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_256_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_256_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_256_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_single;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_256_single;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_256_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_256_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_256_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_256_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_256_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_256_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_single;
nb_kernel_info_t
{ nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_256_single, "nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_avx_256_single", "avx_256_single", "None", "None", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_avx_256_single", "avx_256_single", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_256_single, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_avx_256_single", "avx_256_single", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_avx_256_single", "avx_256_single", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_256_single, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_avx_256_single", "avx_256_single", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_avx_256_single", "avx_256_single", "Ewald", "None", "LJEwald", "None", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_256_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_avx_256_single", "avx_256_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_avx_256_single", "avx_256_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_256_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_avx_256_single", "avx_256_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_avx_256_single", "avx_256_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_avx_256_single", "avx_256_single", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_single, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_avx_256_single", "avx_256_single", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_single", "avx_256_single", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_single, "nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_single", "avx_256_single", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_avx_256_single", "avx_256_single", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_256_single, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_avx_256_single", "avx_256_single", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_avx_256_single", "avx_256_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_256_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_avx_256_single", "avx_256_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_avx_256_single", "avx_256_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_avx_256_single", "avx_256_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_256_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_avx_256_single", "avx_256_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_avx_256_single", "avx_256_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_single", "avx_256_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_avx_256_single", "avx_256_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_avx_256_single", "avx_256_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_avx_256_single", "avx_256_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_avx_256_single", "avx_256_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
};
int
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
__m256 velec,felec,velecsum,facel,crf,krf,krf2;
real *charge;
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- __m256i gbitab;
- __m128i gbitab_lo,gbitab_hi;
- __m256 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m256 minushalf = _mm256_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- /* #endif */
/* #if KERNEL_VDW != 'None' */
int nvdwtype;
__m256 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
__m256 one_sixth = _mm256_set1_ps(1.0/6.0);
__m256 one_twelfth = _mm256_set1_ps(1.0/12.0);
/* #endif */
- /* #if 'Table' in KERNEL_ELEC or 'GeneralizedBorn' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
+ /* #if 'Table' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
__m256i vfitab;
__m128i vfitab_lo,vfitab_hi;
__m128i ifour = _mm_set1_epi32(4);
/* #endif */
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm256_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm256_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
- /* #endif */
-
/* #if 'Water' in GEOMETRY_I */
/* Setup water-specific parameters */
inr = nlist->iinr[0];
/* #for I in PARTICLES_ELEC_I */
iq{I} = _mm256_mul_ps(facel,_mm256_set1_ps(charge[inr+{I}]));
/* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isai{I} = _mm256_set1_ps(invsqrta[inr+{I}]);
- /* #endif */
/* #endfor */
/* #for I in PARTICLES_VDW_I */
vdwioffsetptr{I} = vdwparam+2*nvdwtype*vdwtype[inr+{I}];
/* #if KERNEL_ELEC != 'None' */
velecsum = _mm256_setzero_ps();
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- vgbsum = _mm256_setzero_ps();
- /* #endif */
/* #if KERNEL_VDW != 'None' */
vvdwsum = _mm256_setzero_ps();
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm256_setzero_ps();
- /* #endif */
/* #for ROUND in ['Loop','Epilogue'] */
charge+jnrC+{J},charge+jnrD+{J},
charge+jnrE+{J},charge+jnrF+{J},
charge+jnrG+{J},charge+jnrH+{J});
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isaj{J} = gmx_mm256_load_8real_swizzle_ps(invsqrta+jnrA+{J},invsqrta+jnrB+{J},
- invsqrta+jnrC+{J},invsqrta+jnrD+{J},
- invsqrta+jnrE+{J},invsqrta+jnrF+{J},
- invsqrta+jnrG+{J},invsqrta+jnrH+{J});
- /* #endif */
/* #endfor */
/* #for J in PARTICLES_VDW_J */
vdwjidx{J}A = 2*vdwtype[jnrA+{J}];
/* #define INNERFLOPS INNERFLOPS+3 */
/* #endif */
- /* #elif KERNEL_ELEC=='GeneralizedBorn' */
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm256_mul_ps(isai{I},isaj{J});
- gbqqfactor = _mm256_xor_ps(signbit,_mm256_mul_ps(qq{I}{J},_mm256_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm256_mul_ps(isaprod,gbtabscale);
- /* #define INNERFLOPS INNERFLOPS+5 */
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm256_mul_ps(r{I}{J},gbscale);
- gbitab = _mm256_cvttps_epi32(rt);
- gbeps = _mm256_sub_ps(rt,_mm256_round_ps(rt, _MM_FROUND_FLOOR));
- /* AVX1 does not support 256-bit integer operations, so now we go to 128-bit mode... */
- gbitab_lo = _mm256_extractf128_si256(gbitab,0x0);
- gbitab_hi = _mm256_extractf128_si256(gbitab,0x1);
- gbitab_lo = _mm_slli_epi32(gbitab_lo,2);
- gbitab_hi = _mm_slli_epi32(gbitab_hi,2);
- Y = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,0)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,0)));
- F = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,1)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,1)));
- G = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,2)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,2)));
- H = gmx_mm256_set_m128(_mm_load_ps(gbtab + _mm_extract_epi32(gbitab_hi,3)),
- _mm_load_ps(gbtab + _mm_extract_epi32(gbitab_lo,3)));
- GMX_MM256_HALFTRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm256_mul_ps(gbeps,H);
- Fp = _mm256_add_ps(F,_mm256_mul_ps(gbeps,_mm256_add_ps(G,Heps)));
- VV = _mm256_add_ps(Y,_mm256_mul_ps(gbeps,Fp));
- vgb = _mm256_mul_ps(gbqqfactor,VV);
- /* #define INNERFLOPS INNERFLOPS+10 */
-
- /* #if 'Force' in KERNEL_VF */
- FF = _mm256_add_ps(Fp,_mm256_mul_ps(gbeps,_mm256_add_ps(G,_mm256_add_ps(Heps,Heps))));
- fgb = _mm256_mul_ps(gbqqfactor,_mm256_mul_ps(FF,gbscale));
- dvdatmp = _mm256_mul_ps(minushalf,_mm256_add_ps(vgb,_mm256_mul_ps(fgb,r{I}{J})));
- /* #if ROUND == 'Epilogue' */
- dvdatmp = _mm256_andnot_ps(dummy_mask,dvdatmp);
- /* #endif */
- dvdasum = _mm256_add_ps(dvdasum,dvdatmp);
- /* #if ROUND == 'Loop' */
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- fjptrE = dvda+jnrE;
- fjptrF = dvda+jnrF;
- fjptrG = dvda+jnrG;
- fjptrH = dvda+jnrH;
- /* #else */
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- fjptrE = (jnrlistE>=0) ? dvda+jnrE : scratch;
- fjptrF = (jnrlistF>=0) ? dvda+jnrF : scratch;
- fjptrG = (jnrlistG>=0) ? dvda+jnrG : scratch;
- fjptrH = (jnrlistH>=0) ? dvda+jnrH : scratch;
- /* #endif */
- gmx_mm256_increment_8real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,fjptrE,fjptrF,fjptrG,fjptrH,
- _mm256_mul_ps(dvdatmp,_mm256_mul_ps(isaj{J},isaj{J})));
- /* #define INNERFLOPS INNERFLOPS+12 */
- /* #endif */
- velec = _mm256_mul_ps(qq{I}{J},rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #if 'Force' in KERNEL_VF */
- felec = _mm256_mul_ps(_mm256_sub_ps(_mm256_mul_ps(velec,rinv{I}{J}),fgb),rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+3 */
- /* #endif */
-
/* #elif KERNEL_ELEC=='Ewald' */
/* EWALD ELECTROSTATICS */
/* #endif */
velecsum = _mm256_add_ps(velecsum,velec);
/* #define INNERFLOPS INNERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
- vgb = _mm256_and_ps(vgb,cutoff_mask);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
- /* #if ROUND == 'Epilogue' */
- vgb = _mm256_andnot_ps(dummy_mask,vgb);
- /* #endif */
- vgbsum = _mm256_add_ps(vgbsum,vgb);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
/* #endif */
/* #if 'vdw' in INTERACTION_FLAGS[I][J] */
/* ## Note special check for TIP4P-TIP4P. Since we are cutting of all hydrogen interactions we also cut the LJ-only O-O interaction */
gmx_mm256_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- gmx_mm256_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- /* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #endif */
/* #if KERNEL_VDW != 'None' */
gmx_mm256_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm256_mul_ps(dvdasum, _mm256_mul_ps(isai{I},isai{I}));
- gmx_mm256_update_1pot_ps(dvdasum,dvda+inr);
- /* #endif */
/* Increment number of inner iterations */
inneriter += j_index_end - j_index_start;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
- 'GeneralizedBorn' : ['rinv','r'],
'CubicSplineTable' : ['rinv','r','table'],
'Ewald' : ['rinv','rinvsq','r'],
}
'Coulomb' : 'Coul',
'Ewald' : 'Ew',
'ReactionField' : 'RF',
- 'GeneralizedBorn' : 'GB',
'CubicSplineTable' : 'CSTab',
'LennardJones' : 'LJ',
'Buckingham' : 'Bham',
return 0
# No need for LJ-only water optimization, or water optimization with implicit solvent.
- if('Water' in KernelGeom[0] and (KernelElec=='None' or 'GeneralizedBorn' in KernelElec)):
+ if('Water' in KernelGeom[0] and KernelElec=='None'):
return 0
# Non-matching table settings are pointless
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS c kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: Buckingham
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- int i_shift_offset,i_coord_offset,j_coord_offset;
- int j_index_start,j_index_end;
- int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
- real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real *shiftvec,*fshift,*x,*f;
- int vdwioffset0;
- real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0;
- real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
- real velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- int gbitab;
- real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- int vfitab;
- real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
- real *vftab;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = fr->ic->epsfac;
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = fr->gbtab->scale;
- gbtab = fr->gbtab->data;
- gbinvepsdiff = (1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
- shX = shiftvec[i_shift_offset+XX];
- shY = shiftvec[i_shift_offset+YY];
- shZ = shiftvec[i_shift_offset+ZZ];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- ix0 = shX + x[i_coord_offset+DIM*0+XX];
- iy0 = shY + x[i_coord_offset+DIM*0+YY];
- iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
-
- fix0 = 0.0;
- fiy0 = 0.0;
- fiz0 = 0.0;
-
- /* Load parameters for i particles */
- iq0 = facel*charge[inr+0];
- isai0 = invsqrta[inr+0];
- vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = 0.0;
- vgbsum = 0.0;
- vvdwsum = 0.0;
- dvdasum = 0.0;
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end; jidx++)
- {
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[jidx];
- j_coord_offset = DIM*jnr;
-
- /* load j atom coordinates */
- jx0 = x[j_coord_offset+DIM*0+XX];
- jy0 = x[j_coord_offset+DIM*0+YY];
- jz0 = x[j_coord_offset+DIM*0+ZZ];
-
- /* Calculate displacement vector */
- dx00 = ix0 - jx0;
- dy00 = iy0 - jy0;
- dz00 = iz0 - jz0;
-
- /* Calculate squared distance and things based on it */
- rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
-
- rinv00 = 1.0/sqrt(rsq00);
-
- rinvsq00 = rinv00*rinv00;
-
- /* Load parameters for j particles */
- jq0 = charge[jnr+0];
- isaj0 = invsqrta[jnr+0];
- vdwjidx0 = 3*vdwtype[jnr+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = rsq00*rinv00;
-
- qq00 = iq0*jq0;
- c6_00 = vdwparam[vdwioffset0+vdwjidx0];
- cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
- cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = isai0*isaj0;
- gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
- gbscale = isaprod*gbtabscale;
- dvdaj = dvda[jnr+0];
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = r00*gbscale;
- gbitab = rt;
- gbeps = rt-gbitab;
- gbitab = 4*gbitab;
-
- Y = gbtab[gbitab];
- F = gbtab[gbitab+1];
- Geps = gbeps*gbtab[gbitab+2];
- Heps2 = gbeps*gbeps*gbtab[gbitab+3];
- Fp = F+Geps+Heps2;
- VV = Y+gbeps*Fp;
- vgb = gbqqfactor*VV;
-
- FF = Fp+Geps+2.0*Heps2;
- fgb = gbqqfactor*FF*gbscale;
- dvdatmp = -0.5*(vgb+fgb*r00);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
- velec = qq00*rinv00;
- felec = (velec*rinv00-fgb)*rinv00;
-
- /* BUCKINGHAM DISPERSION/REPULSION */
- rinvsix = rinvsq00*rinvsq00*rinvsq00;
- vvdw6 = c6_00*rinvsix;
- br = cexp2_00*r00;
- vvdwexp = cexp1_00*exp(-br);
- vvdw = vvdwexp - vvdw6*(1.0/6.0);
- fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
-
- /* Update potential sums from outer loop */
- velecsum += velec;
- vgbsum += vgb;
- vvdwsum += vvdw;
-
- fscal = felec+fvdw;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx00;
- ty = fscal*dy00;
- tz = fscal*dz00;
-
- /* Update vectorial force */
- fix0 += tx;
- fiy0 += ty;
- fiz0 += tz;
- f[j_coord_offset+DIM*0+XX] -= tx;
- f[j_coord_offset+DIM*0+YY] -= ty;
- f[j_coord_offset+DIM*0+ZZ] -= tz;
-
- /* Inner loop uses 97 flops */
- }
- /* End of innermost loop */
-
- tx = ty = tz = 0;
- f[i_coord_offset+DIM*0+XX] += fix0;
- f[i_coord_offset+DIM*0+YY] += fiy0;
- f[i_coord_offset+DIM*0+ZZ] += fiz0;
- tx += fix0;
- ty += fiy0;
- tz += fiz0;
- fshift[i_shift_offset+XX] += tx;
- fshift[i_shift_offset+YY] += ty;
- fshift[i_shift_offset+ZZ] += tz;
-
- ggid = gid[iidx];
- /* Update potential energies */
- kernel_data->energygrp_elec[ggid] += velecsum;
- kernel_data->energygrp_polarization[ggid] += vgbsum;
- kernel_data->energygrp_vdw[ggid] += vvdwsum;
- dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 16 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*16 + inneriter*97);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: Buckingham
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- int i_shift_offset,i_coord_offset,j_coord_offset;
- int j_index_start,j_index_end;
- int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
- real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real *shiftvec,*fshift,*x,*f;
- int vdwioffset0;
- real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0;
- real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
- real velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- int gbitab;
- real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- int vfitab;
- real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
- real *vftab;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = fr->ic->epsfac;
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = fr->gbtab->scale;
- gbtab = fr->gbtab->data;
- gbinvepsdiff = (1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
- shX = shiftvec[i_shift_offset+XX];
- shY = shiftvec[i_shift_offset+YY];
- shZ = shiftvec[i_shift_offset+ZZ];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- ix0 = shX + x[i_coord_offset+DIM*0+XX];
- iy0 = shY + x[i_coord_offset+DIM*0+YY];
- iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
-
- fix0 = 0.0;
- fiy0 = 0.0;
- fiz0 = 0.0;
-
- /* Load parameters for i particles */
- iq0 = facel*charge[inr+0];
- isai0 = invsqrta[inr+0];
- vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
-
- dvdasum = 0.0;
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end; jidx++)
- {
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[jidx];
- j_coord_offset = DIM*jnr;
-
- /* load j atom coordinates */
- jx0 = x[j_coord_offset+DIM*0+XX];
- jy0 = x[j_coord_offset+DIM*0+YY];
- jz0 = x[j_coord_offset+DIM*0+ZZ];
-
- /* Calculate displacement vector */
- dx00 = ix0 - jx0;
- dy00 = iy0 - jy0;
- dz00 = iz0 - jz0;
-
- /* Calculate squared distance and things based on it */
- rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
-
- rinv00 = 1.0/sqrt(rsq00);
-
- rinvsq00 = rinv00*rinv00;
-
- /* Load parameters for j particles */
- jq0 = charge[jnr+0];
- isaj0 = invsqrta[jnr+0];
- vdwjidx0 = 3*vdwtype[jnr+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = rsq00*rinv00;
-
- qq00 = iq0*jq0;
- c6_00 = vdwparam[vdwioffset0+vdwjidx0];
- cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
- cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = isai0*isaj0;
- gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
- gbscale = isaprod*gbtabscale;
- dvdaj = dvda[jnr+0];
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = r00*gbscale;
- gbitab = rt;
- gbeps = rt-gbitab;
- gbitab = 4*gbitab;
-
- Y = gbtab[gbitab];
- F = gbtab[gbitab+1];
- Geps = gbeps*gbtab[gbitab+2];
- Heps2 = gbeps*gbeps*gbtab[gbitab+3];
- Fp = F+Geps+Heps2;
- VV = Y+gbeps*Fp;
- vgb = gbqqfactor*VV;
-
- FF = Fp+Geps+2.0*Heps2;
- fgb = gbqqfactor*FF*gbscale;
- dvdatmp = -0.5*(vgb+fgb*r00);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
- velec = qq00*rinv00;
- felec = (velec*rinv00-fgb)*rinv00;
-
- /* BUCKINGHAM DISPERSION/REPULSION */
- rinvsix = rinvsq00*rinvsq00*rinvsq00;
- vvdw6 = c6_00*rinvsix;
- br = cexp2_00*r00;
- vvdwexp = cexp1_00*exp(-br);
- fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
-
- fscal = felec+fvdw;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx00;
- ty = fscal*dy00;
- tz = fscal*dz00;
-
- /* Update vectorial force */
- fix0 += tx;
- fiy0 += ty;
- fiz0 += tz;
- f[j_coord_offset+DIM*0+XX] -= tx;
- f[j_coord_offset+DIM*0+YY] -= ty;
- f[j_coord_offset+DIM*0+ZZ] -= tz;
-
- /* Inner loop uses 92 flops */
- }
- /* End of innermost loop */
-
- tx = ty = tz = 0;
- f[i_coord_offset+DIM*0+XX] += fix0;
- f[i_coord_offset+DIM*0+YY] += fiy0;
- f[i_coord_offset+DIM*0+ZZ] += fiz0;
- tx += fix0;
- ty += fiy0;
- tz += fiz0;
- fshift[i_shift_offset+XX] += tx;
- fshift[i_shift_offset+YY] += ty;
- fshift[i_shift_offset+ZZ] += tz;
-
- dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 13 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*92);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS c kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- int i_shift_offset,i_coord_offset,j_coord_offset;
- int j_index_start,j_index_end;
- int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
- real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real *shiftvec,*fshift,*x,*f;
- int vdwioffset0;
- real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0;
- real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
- real velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- int gbitab;
- real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- int vfitab;
- real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
- real *vftab;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = fr->ic->epsfac;
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = kernel_data->table_vdw->scale;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = fr->gbtab->scale;
- gbtab = fr->gbtab->data;
- gbinvepsdiff = (1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
- shX = shiftvec[i_shift_offset+XX];
- shY = shiftvec[i_shift_offset+YY];
- shZ = shiftvec[i_shift_offset+ZZ];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- ix0 = shX + x[i_coord_offset+DIM*0+XX];
- iy0 = shY + x[i_coord_offset+DIM*0+YY];
- iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
-
- fix0 = 0.0;
- fiy0 = 0.0;
- fiz0 = 0.0;
-
- /* Load parameters for i particles */
- iq0 = facel*charge[inr+0];
- isai0 = invsqrta[inr+0];
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = 0.0;
- vgbsum = 0.0;
- vvdwsum = 0.0;
- dvdasum = 0.0;
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end; jidx++)
- {
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[jidx];
- j_coord_offset = DIM*jnr;
-
- /* load j atom coordinates */
- jx0 = x[j_coord_offset+DIM*0+XX];
- jy0 = x[j_coord_offset+DIM*0+YY];
- jz0 = x[j_coord_offset+DIM*0+ZZ];
-
- /* Calculate displacement vector */
- dx00 = ix0 - jx0;
- dy00 = iy0 - jy0;
- dz00 = iz0 - jz0;
-
- /* Calculate squared distance and things based on it */
- rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
-
- rinv00 = 1.0/sqrt(rsq00);
-
- /* Load parameters for j particles */
- jq0 = charge[jnr+0];
- isaj0 = invsqrta[jnr+0];
- vdwjidx0 = 2*vdwtype[jnr+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = rsq00*rinv00;
-
- qq00 = iq0*jq0;
- c6_00 = vdwparam[vdwioffset0+vdwjidx0];
- c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = r00*vftabscale;
- vfitab = rt;
- vfeps = rt-vfitab;
- vfitab = 2*4*vfitab;
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = isai0*isaj0;
- gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
- gbscale = isaprod*gbtabscale;
- dvdaj = dvda[jnr+0];
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = r00*gbscale;
- gbitab = rt;
- gbeps = rt-gbitab;
- gbitab = 4*gbitab;
-
- Y = gbtab[gbitab];
- F = gbtab[gbitab+1];
- Geps = gbeps*gbtab[gbitab+2];
- Heps2 = gbeps*gbeps*gbtab[gbitab+3];
- Fp = F+Geps+Heps2;
- VV = Y+gbeps*Fp;
- vgb = gbqqfactor*VV;
-
- FF = Fp+Geps+2.0*Heps2;
- fgb = gbqqfactor*FF*gbscale;
- dvdatmp = -0.5*(vgb+fgb*r00);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
- velec = qq00*rinv00;
- felec = (velec*rinv00-fgb)*rinv00;
-
- /* CUBIC SPLINE TABLE DISPERSION */
- vfitab += 0;
- Y = vftab[vfitab];
- F = vftab[vfitab+1];
- Geps = vfeps*vftab[vfitab+2];
- Heps2 = vfeps*vfeps*vftab[vfitab+3];
- Fp = F+Geps+Heps2;
- VV = Y+vfeps*Fp;
- vvdw6 = c6_00*VV;
- FF = Fp+Geps+2.0*Heps2;
- fvdw6 = c6_00*FF;
-
- /* CUBIC SPLINE TABLE REPULSION */
- Y = vftab[vfitab+4];
- F = vftab[vfitab+5];
- Geps = vfeps*vftab[vfitab+6];
- Heps2 = vfeps*vfeps*vftab[vfitab+7];
- Fp = F+Geps+Heps2;
- VV = Y+vfeps*Fp;
- vvdw12 = c12_00*VV;
- FF = Fp+Geps+2.0*Heps2;
- fvdw12 = c12_00*FF;
- vvdw = vvdw12+vvdw6;
- fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
-
- /* Update potential sums from outer loop */
- velecsum += velec;
- vgbsum += vgb;
- vvdwsum += vvdw;
-
- fscal = felec+fvdw;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx00;
- ty = fscal*dy00;
- tz = fscal*dz00;
-
- /* Update vectorial force */
- fix0 += tx;
- fiy0 += ty;
- fiz0 += tz;
- f[j_coord_offset+DIM*0+XX] -= tx;
- f[j_coord_offset+DIM*0+YY] -= ty;
- f[j_coord_offset+DIM*0+ZZ] -= tz;
-
- /* Inner loop uses 91 flops */
- }
- /* End of innermost loop */
-
- tx = ty = tz = 0;
- f[i_coord_offset+DIM*0+XX] += fix0;
- f[i_coord_offset+DIM*0+YY] += fiy0;
- f[i_coord_offset+DIM*0+ZZ] += fiz0;
- tx += fix0;
- ty += fiy0;
- tz += fiz0;
- fshift[i_shift_offset+XX] += tx;
- fshift[i_shift_offset+YY] += ty;
- fshift[i_shift_offset+ZZ] += tz;
-
- ggid = gid[iidx];
- /* Update potential energies */
- kernel_data->energygrp_elec[ggid] += velecsum;
- kernel_data->energygrp_polarization[ggid] += vgbsum;
- kernel_data->energygrp_vdw[ggid] += vvdwsum;
- dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 16 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*16 + inneriter*91);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- int i_shift_offset,i_coord_offset,j_coord_offset;
- int j_index_start,j_index_end;
- int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
- real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real *shiftvec,*fshift,*x,*f;
- int vdwioffset0;
- real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0;
- real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
- real velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- int gbitab;
- real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- int vfitab;
- real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
- real *vftab;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = fr->ic->epsfac;
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = kernel_data->table_vdw->scale;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = fr->gbtab->scale;
- gbtab = fr->gbtab->data;
- gbinvepsdiff = (1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
- shX = shiftvec[i_shift_offset+XX];
- shY = shiftvec[i_shift_offset+YY];
- shZ = shiftvec[i_shift_offset+ZZ];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- ix0 = shX + x[i_coord_offset+DIM*0+XX];
- iy0 = shY + x[i_coord_offset+DIM*0+YY];
- iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
-
- fix0 = 0.0;
- fiy0 = 0.0;
- fiz0 = 0.0;
-
- /* Load parameters for i particles */
- iq0 = facel*charge[inr+0];
- isai0 = invsqrta[inr+0];
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = 0.0;
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end; jidx++)
- {
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[jidx];
- j_coord_offset = DIM*jnr;
-
- /* load j atom coordinates */
- jx0 = x[j_coord_offset+DIM*0+XX];
- jy0 = x[j_coord_offset+DIM*0+YY];
- jz0 = x[j_coord_offset+DIM*0+ZZ];
-
- /* Calculate displacement vector */
- dx00 = ix0 - jx0;
- dy00 = iy0 - jy0;
- dz00 = iz0 - jz0;
-
- /* Calculate squared distance and things based on it */
- rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
-
- rinv00 = 1.0/sqrt(rsq00);
-
- /* Load parameters for j particles */
- jq0 = charge[jnr+0];
- isaj0 = invsqrta[jnr+0];
- vdwjidx0 = 2*vdwtype[jnr+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = rsq00*rinv00;
-
- qq00 = iq0*jq0;
- c6_00 = vdwparam[vdwioffset0+vdwjidx0];
- c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = r00*vftabscale;
- vfitab = rt;
- vfeps = rt-vfitab;
- vfitab = 2*4*vfitab;
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = isai0*isaj0;
- gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
- gbscale = isaprod*gbtabscale;
- dvdaj = dvda[jnr+0];
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = r00*gbscale;
- gbitab = rt;
- gbeps = rt-gbitab;
- gbitab = 4*gbitab;
-
- Y = gbtab[gbitab];
- F = gbtab[gbitab+1];
- Geps = gbeps*gbtab[gbitab+2];
- Heps2 = gbeps*gbeps*gbtab[gbitab+3];
- Fp = F+Geps+Heps2;
- VV = Y+gbeps*Fp;
- vgb = gbqqfactor*VV;
-
- FF = Fp+Geps+2.0*Heps2;
- fgb = gbqqfactor*FF*gbscale;
- dvdatmp = -0.5*(vgb+fgb*r00);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
- velec = qq00*rinv00;
- felec = (velec*rinv00-fgb)*rinv00;
-
- /* CUBIC SPLINE TABLE DISPERSION */
- vfitab += 0;
- F = vftab[vfitab+1];
- Geps = vfeps*vftab[vfitab+2];
- Heps2 = vfeps*vfeps*vftab[vfitab+3];
- Fp = F+Geps+Heps2;
- FF = Fp+Geps+2.0*Heps2;
- fvdw6 = c6_00*FF;
-
- /* CUBIC SPLINE TABLE REPULSION */
- F = vftab[vfitab+5];
- Geps = vfeps*vftab[vfitab+6];
- Heps2 = vfeps*vfeps*vftab[vfitab+7];
- Fp = F+Geps+Heps2;
- FF = Fp+Geps+2.0*Heps2;
- fvdw12 = c12_00*FF;
- fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
-
- fscal = felec+fvdw;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx00;
- ty = fscal*dy00;
- tz = fscal*dz00;
-
- /* Update vectorial force */
- fix0 += tx;
- fiy0 += ty;
- fiz0 += tz;
- f[j_coord_offset+DIM*0+XX] -= tx;
- f[j_coord_offset+DIM*0+YY] -= ty;
- f[j_coord_offset+DIM*0+ZZ] -= tz;
-
- /* Inner loop uses 81 flops */
- }
- /* End of innermost loop */
-
- tx = ty = tz = 0;
- f[i_coord_offset+DIM*0+XX] += fix0;
- f[i_coord_offset+DIM*0+YY] += fiy0;
- f[i_coord_offset+DIM*0+ZZ] += fiz0;
- tx += fix0;
- ty += fiy0;
- tz += fiz0;
- fshift[i_shift_offset+XX] += tx;
- fshift[i_shift_offset+YY] += ty;
- fshift[i_shift_offset+ZZ] += tz;
-
- dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 13 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*81);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS c kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_c
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_c
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- int i_shift_offset,i_coord_offset,j_coord_offset;
- int j_index_start,j_index_end;
- int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
- real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real *shiftvec,*fshift,*x,*f;
- int vdwioffset0;
- real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0;
- real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
- real velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- int gbitab;
- real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- int vfitab;
- real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
- real *vftab;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = fr->ic->epsfac;
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = fr->gbtab->scale;
- gbtab = fr->gbtab->data;
- gbinvepsdiff = (1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
- shX = shiftvec[i_shift_offset+XX];
- shY = shiftvec[i_shift_offset+YY];
- shZ = shiftvec[i_shift_offset+ZZ];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- ix0 = shX + x[i_coord_offset+DIM*0+XX];
- iy0 = shY + x[i_coord_offset+DIM*0+YY];
- iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
-
- fix0 = 0.0;
- fiy0 = 0.0;
- fiz0 = 0.0;
-
- /* Load parameters for i particles */
- iq0 = facel*charge[inr+0];
- isai0 = invsqrta[inr+0];
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = 0.0;
- vgbsum = 0.0;
- vvdwsum = 0.0;
- dvdasum = 0.0;
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end; jidx++)
- {
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[jidx];
- j_coord_offset = DIM*jnr;
-
- /* load j atom coordinates */
- jx0 = x[j_coord_offset+DIM*0+XX];
- jy0 = x[j_coord_offset+DIM*0+YY];
- jz0 = x[j_coord_offset+DIM*0+ZZ];
-
- /* Calculate displacement vector */
- dx00 = ix0 - jx0;
- dy00 = iy0 - jy0;
- dz00 = iz0 - jz0;
-
- /* Calculate squared distance and things based on it */
- rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
-
- rinv00 = 1.0/sqrt(rsq00);
-
- rinvsq00 = rinv00*rinv00;
-
- /* Load parameters for j particles */
- jq0 = charge[jnr+0];
- isaj0 = invsqrta[jnr+0];
- vdwjidx0 = 2*vdwtype[jnr+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = rsq00*rinv00;
-
- qq00 = iq0*jq0;
- c6_00 = vdwparam[vdwioffset0+vdwjidx0];
- c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = isai0*isaj0;
- gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
- gbscale = isaprod*gbtabscale;
- dvdaj = dvda[jnr+0];
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = r00*gbscale;
- gbitab = rt;
- gbeps = rt-gbitab;
- gbitab = 4*gbitab;
-
- Y = gbtab[gbitab];
- F = gbtab[gbitab+1];
- Geps = gbeps*gbtab[gbitab+2];
- Heps2 = gbeps*gbeps*gbtab[gbitab+3];
- Fp = F+Geps+Heps2;
- VV = Y+gbeps*Fp;
- vgb = gbqqfactor*VV;
-
- FF = Fp+Geps+2.0*Heps2;
- fgb = gbqqfactor*FF*gbscale;
- dvdatmp = -0.5*(vgb+fgb*r00);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
- velec = qq00*rinv00;
- felec = (velec*rinv00-fgb)*rinv00;
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = rinvsq00*rinvsq00*rinvsq00;
- vvdw6 = c6_00*rinvsix;
- vvdw12 = c12_00*rinvsix*rinvsix;
- vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
- fvdw = (vvdw12-vvdw6)*rinvsq00;
-
- /* Update potential sums from outer loop */
- velecsum += velec;
- vgbsum += vgb;
- vvdwsum += vvdw;
-
- fscal = felec+fvdw;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx00;
- ty = fscal*dy00;
- tz = fscal*dz00;
-
- /* Update vectorial force */
- fix0 += tx;
- fiy0 += ty;
- fiz0 += tz;
- f[j_coord_offset+DIM*0+XX] -= tx;
- f[j_coord_offset+DIM*0+YY] -= ty;
- f[j_coord_offset+DIM*0+ZZ] -= tz;
-
- /* Inner loop uses 71 flops */
- }
- /* End of innermost loop */
-
- tx = ty = tz = 0;
- f[i_coord_offset+DIM*0+XX] += fix0;
- f[i_coord_offset+DIM*0+YY] += fiy0;
- f[i_coord_offset+DIM*0+ZZ] += fiz0;
- tx += fix0;
- ty += fiy0;
- tz += fiz0;
- fshift[i_shift_offset+XX] += tx;
- fshift[i_shift_offset+YY] += ty;
- fshift[i_shift_offset+ZZ] += tz;
-
- ggid = gid[iidx];
- /* Update potential energies */
- kernel_data->energygrp_elec[ggid] += velecsum;
- kernel_data->energygrp_polarization[ggid] += vgbsum;
- kernel_data->energygrp_vdw[ggid] += vvdwsum;
- dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 16 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*16 + inneriter*71);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- int i_shift_offset,i_coord_offset,j_coord_offset;
- int j_index_start,j_index_end;
- int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
- real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real *shiftvec,*fshift,*x,*f;
- int vdwioffset0;
- real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0;
- real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
- real velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- int gbitab;
- real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- int vfitab;
- real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
- real *vftab;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = fr->ic->epsfac;
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = fr->gbtab->scale;
- gbtab = fr->gbtab->data;
- gbinvepsdiff = (1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
- shX = shiftvec[i_shift_offset+XX];
- shY = shiftvec[i_shift_offset+YY];
- shZ = shiftvec[i_shift_offset+ZZ];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- ix0 = shX + x[i_coord_offset+DIM*0+XX];
- iy0 = shY + x[i_coord_offset+DIM*0+YY];
- iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
-
- fix0 = 0.0;
- fiy0 = 0.0;
- fiz0 = 0.0;
-
- /* Load parameters for i particles */
- iq0 = facel*charge[inr+0];
- isai0 = invsqrta[inr+0];
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = 0.0;
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end; jidx++)
- {
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[jidx];
- j_coord_offset = DIM*jnr;
-
- /* load j atom coordinates */
- jx0 = x[j_coord_offset+DIM*0+XX];
- jy0 = x[j_coord_offset+DIM*0+YY];
- jz0 = x[j_coord_offset+DIM*0+ZZ];
-
- /* Calculate displacement vector */
- dx00 = ix0 - jx0;
- dy00 = iy0 - jy0;
- dz00 = iz0 - jz0;
-
- /* Calculate squared distance and things based on it */
- rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
-
- rinv00 = 1.0/sqrt(rsq00);
-
- rinvsq00 = rinv00*rinv00;
-
- /* Load parameters for j particles */
- jq0 = charge[jnr+0];
- isaj0 = invsqrta[jnr+0];
- vdwjidx0 = 2*vdwtype[jnr+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = rsq00*rinv00;
-
- qq00 = iq0*jq0;
- c6_00 = vdwparam[vdwioffset0+vdwjidx0];
- c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = isai0*isaj0;
- gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
- gbscale = isaprod*gbtabscale;
- dvdaj = dvda[jnr+0];
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = r00*gbscale;
- gbitab = rt;
- gbeps = rt-gbitab;
- gbitab = 4*gbitab;
-
- Y = gbtab[gbitab];
- F = gbtab[gbitab+1];
- Geps = gbeps*gbtab[gbitab+2];
- Heps2 = gbeps*gbeps*gbtab[gbitab+3];
- Fp = F+Geps+Heps2;
- VV = Y+gbeps*Fp;
- vgb = gbqqfactor*VV;
-
- FF = Fp+Geps+2.0*Heps2;
- fgb = gbqqfactor*FF*gbscale;
- dvdatmp = -0.5*(vgb+fgb*r00);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
- velec = qq00*rinv00;
- felec = (velec*rinv00-fgb)*rinv00;
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = rinvsq00*rinvsq00*rinvsq00;
- fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
-
- fscal = felec+fvdw;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx00;
- ty = fscal*dy00;
- tz = fscal*dz00;
-
- /* Update vectorial force */
- fix0 += tx;
- fiy0 += ty;
- fiz0 += tz;
- f[j_coord_offset+DIM*0+XX] -= tx;
- f[j_coord_offset+DIM*0+YY] -= ty;
- f[j_coord_offset+DIM*0+ZZ] -= tz;
-
- /* Inner loop uses 64 flops */
- }
- /* End of innermost loop */
-
- tx = ty = tz = 0;
- f[i_coord_offset+DIM*0+XX] += fix0;
- f[i_coord_offset+DIM*0+YY] += fiy0;
- f[i_coord_offset+DIM*0+ZZ] += fiz0;
- tx += fix0;
- ty += fiy0;
- tz += fiz0;
- fshift[i_shift_offset+XX] += tx;
- fshift[i_shift_offset+YY] += ty;
- fshift[i_shift_offset+ZZ] += tz;
-
- dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 13 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*64);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS c kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- int i_shift_offset,i_coord_offset,j_coord_offset;
- int j_index_start,j_index_end;
- int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
- real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real *shiftvec,*fshift,*x,*f;
- int vdwioffset0;
- real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0;
- real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
- real velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- int gbitab;
- real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- real *invsqrta,*dvda,*gbtab;
- int vfitab;
- real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
- real *vftab;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = fr->ic->epsfac;
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = fr->gbtab->scale;
- gbtab = fr->gbtab->data;
- gbinvepsdiff = (1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
- shX = shiftvec[i_shift_offset+XX];
- shY = shiftvec[i_shift_offset+YY];
- shZ = shiftvec[i_shift_offset+ZZ];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- ix0 = shX + x[i_coord_offset+DIM*0+XX];
- iy0 = shY + x[i_coord_offset+DIM*0+YY];
- iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
-
- fix0 = 0.0;
- fiy0 = 0.0;
- fiz0 = 0.0;
-
- /* Load parameters for i particles */
- iq0 = facel*charge[inr+0];
- isai0 = invsqrta[inr+0];
-
- /* Reset potential sums */
- velecsum = 0.0;
- vgbsum = 0.0;
- dvdasum = 0.0;
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end; jidx++)
- {
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[jidx];
- j_coord_offset = DIM*jnr;
-
- /* load j atom coordinates */
- jx0 = x[j_coord_offset+DIM*0+XX];
- jy0 = x[j_coord_offset+DIM*0+YY];
- jz0 = x[j_coord_offset+DIM*0+ZZ];
-
- /* Calculate displacement vector */
- dx00 = ix0 - jx0;
- dy00 = iy0 - jy0;
- dz00 = iz0 - jz0;
-
- /* Calculate squared distance and things based on it */
- rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
-
- rinv00 = 1.0/sqrt(rsq00);
-
- /* Load parameters for j particles */
- jq0 = charge[jnr+0];
- isaj0 = invsqrta[jnr+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = rsq00*rinv00;
-
- qq00 = iq0*jq0;
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = isai0*isaj0;
- gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
- gbscale = isaprod*gbtabscale;
- dvdaj = dvda[jnr+0];
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = r00*gbscale;
- gbitab = rt;
- gbeps = rt-gbitab;
- gbitab = 4*gbitab;
-
- Y = gbtab[gbitab];
- F = gbtab[gbitab+1];
- Geps = gbeps*gbtab[gbitab+2];
- Heps2 = gbeps*gbeps*gbtab[gbitab+3];
- Fp = F+Geps+Heps2;
- VV = Y+gbeps*Fp;
- vgb = gbqqfactor*VV;
-
- FF = Fp+Geps+2.0*Heps2;
- fgb = gbqqfactor*FF*gbscale;
- dvdatmp = -0.5*(vgb+fgb*r00);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
- velec = qq00*rinv00;
- felec = (velec*rinv00-fgb)*rinv00;
-
- /* Update potential sums from outer loop */
- velecsum += velec;
- vgbsum += vgb;
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx00;
- ty = fscal*dy00;
- tz = fscal*dz00;
-
- /* Update vectorial force */
- fix0 += tx;
- fiy0 += ty;
- fiz0 += tz;
- f[j_coord_offset+DIM*0+XX] -= tx;
- f[j_coord_offset+DIM*0+YY] -= ty;
- f[j_coord_offset+DIM*0+ZZ] -= tz;
-
- /* Inner loop uses 58 flops */
- }
- /* End of innermost loop */
-
- tx = ty = tz = 0;
- f[i_coord_offset+DIM*0+XX] += fix0;
- f[i_coord_offset+DIM*0+YY] += fiy0;
- f[i_coord_offset+DIM*0+ZZ] += fiz0;
- tx += fix0;
- ty += fiy0;
- tz += fiz0;
- fshift[i_shift_offset+XX] += tx;
- fshift[i_shift_offset+YY] += ty;
- fshift[i_shift_offset+ZZ] += tz;
-
- ggid = gid[iidx];
- /* Update potential energies */
- kernel_data->energygrp_elec[ggid] += velecsum;
- kernel_data->energygrp_polarization[ggid] += vgbsum;
- dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 15 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*15 + inneriter*58);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- int i_shift_offset,i_coord_offset,j_coord_offset;
- int j_index_start,j_index_end;
- int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
- real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real *shiftvec,*fshift,*x,*f;
- int vdwioffset0;
- real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0;
- real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
- real velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- int gbitab;
- real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- real *invsqrta,*dvda,*gbtab;
- int vfitab;
- real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
- real *vftab;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = fr->ic->epsfac;
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = fr->gbtab->scale;
- gbtab = fr->gbtab->data;
- gbinvepsdiff = (1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
- shX = shiftvec[i_shift_offset+XX];
- shY = shiftvec[i_shift_offset+YY];
- shZ = shiftvec[i_shift_offset+ZZ];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- ix0 = shX + x[i_coord_offset+DIM*0+XX];
- iy0 = shY + x[i_coord_offset+DIM*0+YY];
- iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
-
- fix0 = 0.0;
- fiy0 = 0.0;
- fiz0 = 0.0;
-
- /* Load parameters for i particles */
- iq0 = facel*charge[inr+0];
- isai0 = invsqrta[inr+0];
-
- dvdasum = 0.0;
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end; jidx++)
- {
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[jidx];
- j_coord_offset = DIM*jnr;
-
- /* load j atom coordinates */
- jx0 = x[j_coord_offset+DIM*0+XX];
- jy0 = x[j_coord_offset+DIM*0+YY];
- jz0 = x[j_coord_offset+DIM*0+ZZ];
-
- /* Calculate displacement vector */
- dx00 = ix0 - jx0;
- dy00 = iy0 - jy0;
- dz00 = iz0 - jz0;
-
- /* Calculate squared distance and things based on it */
- rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
-
- rinv00 = 1.0/sqrt(rsq00);
-
- /* Load parameters for j particles */
- jq0 = charge[jnr+0];
- isaj0 = invsqrta[jnr+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = rsq00*rinv00;
-
- qq00 = iq0*jq0;
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = isai0*isaj0;
- gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
- gbscale = isaprod*gbtabscale;
- dvdaj = dvda[jnr+0];
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = r00*gbscale;
- gbitab = rt;
- gbeps = rt-gbitab;
- gbitab = 4*gbitab;
-
- Y = gbtab[gbitab];
- F = gbtab[gbitab+1];
- Geps = gbeps*gbtab[gbitab+2];
- Heps2 = gbeps*gbeps*gbtab[gbitab+3];
- Fp = F+Geps+Heps2;
- VV = Y+gbeps*Fp;
- vgb = gbqqfactor*VV;
-
- FF = Fp+Geps+2.0*Heps2;
- fgb = gbqqfactor*FF*gbscale;
- dvdatmp = -0.5*(vgb+fgb*r00);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
- velec = qq00*rinv00;
- felec = (velec*rinv00-fgb)*rinv00;
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx00;
- ty = fscal*dy00;
- tz = fscal*dz00;
-
- /* Update vectorial force */
- fix0 += tx;
- fiy0 += ty;
- fiz0 += tz;
- f[j_coord_offset+DIM*0+XX] -= tx;
- f[j_coord_offset+DIM*0+YY] -= ty;
- f[j_coord_offset+DIM*0+ZZ] -= tz;
-
- /* Inner loop uses 56 flops */
- }
- /* End of innermost loop */
-
- tx = ty = tz = 0;
- f[i_coord_offset+DIM*0+XX] += fix0;
- f[i_coord_offset+DIM*0+YY] += fiy0;
- f[i_coord_offset+DIM*0+ZZ] += fiz0;
- tx += fix0;
- ty += fiy0;
- tz += fiz0;
- fshift[i_shift_offset+XX] += tx;
- fshift[i_shift_offset+YY] += ty;
- fshift[i_shift_offset+ZZ] += tz;
-
- dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 13 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*56);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team.
- * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "nb_kernel_allvsallgb.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/utility/real.h"
-#include "gromacs/utility/smalloc.h"
-
-typedef struct
-{
- real ** pvdwparam;
- int * jindex;
- int ** exclusion_mask;
-}
-gmx_allvsall_data_t;
-
-static int
-calc_maxoffset(int i, int natoms)
-{
- int maxoffset;
-
- if ((natoms % 2) == 1)
- {
- /* Odd number of atoms, easy */
- maxoffset = natoms/2;
- }
- else if ((natoms % 4) == 0)
- {
- /* Multiple of four is hard */
- if (i < natoms/2)
- {
- if ((i % 2) == 0)
- {
- maxoffset = natoms/2;
- }
- else
- {
- maxoffset = natoms/2-1;
- }
- }
- else
- {
- if ((i % 2) == 1)
- {
- maxoffset = natoms/2;
- }
- else
- {
- maxoffset = natoms/2-1;
- }
- }
- }
- else
- {
- /* natoms/2 = odd */
- if ((i % 2) == 0)
- {
- maxoffset = natoms/2;
- }
- else
- {
- maxoffset = natoms/2-1;
- }
- }
-
- return maxoffset;
-}
-
-
-static void
-setup_exclusions_and_indices(gmx_allvsall_data_t * aadata,
- t_blocka * excl,
- int natoms)
-{
- int i, j, k;
- int nj0, nj1;
- int max_offset;
- int max_excl_offset;
- int iexcl;
-
- /* This routine can appear to be a bit complex, but it is mostly book-keeping.
- * To enable the fast all-vs-all kernel we need to be able to stream through all coordinates
- * whether they should interact or not.
- *
- * To avoid looping over the exclusions, we create a simple mask that is 1 if the interaction
- * should be present, otherwise 0. Since exclusions typically only occur when i & j are close,
- * we create a jindex array with three elements per i atom: the starting point, the point to
- * which we need to check exclusions, and the end point.
- * This way we only have to allocate a short exclusion mask per i atom.
- */
-
- /* Allocate memory for our modified jindex array */
- snew(aadata->jindex, 3*natoms);
-
- /* Pointer to lists with exclusion masks */
- snew(aadata->exclusion_mask, natoms);
-
- for (i = 0; i < natoms; i++)
- {
- /* Start */
- aadata->jindex[3*i] = i+1;
- max_offset = calc_maxoffset(i, natoms);
-
- /* Exclusions */
- nj0 = excl->index[i];
- nj1 = excl->index[i+1];
-
- /* first check the max range */
- max_excl_offset = -1;
-
- for (j = nj0; j < nj1; j++)
- {
- iexcl = excl->a[j];
-
- k = iexcl - i;
-
- if (k+natoms <= max_offset)
- {
- k += natoms;
- }
-
- max_excl_offset = (k > max_excl_offset) ? k : max_excl_offset;
- }
-
- max_excl_offset = (max_offset < max_excl_offset) ? max_offset : max_excl_offset;
-
- aadata->jindex[3*i+1] = i+1+max_excl_offset;
-
- snew(aadata->exclusion_mask[i], max_excl_offset);
- /* Include everything by default */
- for (j = 0; j < max_excl_offset; j++)
- {
- /* Use all-ones to mark interactions that should be present, compatible with SSE */
- aadata->exclusion_mask[i][j] = 0xFFFFFFFF;
- }
-
- /* Go through exclusions again */
- for (j = nj0; j < nj1; j++)
- {
- iexcl = excl->a[j];
-
- k = iexcl - i;
-
- if (k+natoms <= max_offset)
- {
- k += natoms;
- }
-
- if (k > 0 && k <= max_excl_offset)
- {
- /* Excluded, kill it! */
- aadata->exclusion_mask[i][k-1] = 0;
- }
- }
-
- /* End */
- aadata->jindex[3*i+2] = i+1+max_offset;
- }
-}
-
-
-static void
-setup_aadata(gmx_allvsall_data_t ** p_aadata,
- t_blocka * excl,
- int natoms,
- int * type,
- int ntype,
- real * pvdwparam)
-{
- int i, j, idx;
- gmx_allvsall_data_t *aadata;
- real *p;
-
- snew(aadata, 1);
- *p_aadata = aadata;
-
- /* Generate vdw params */
- snew(aadata->pvdwparam, ntype);
-
- for (i = 0; i < ntype; i++)
- {
- snew(aadata->pvdwparam[i], 2*natoms);
- p = aadata->pvdwparam[i];
-
- /* Lets keep it simple and use multiple steps - first create temp. c6/c12 arrays */
- for (j = 0; j < natoms; j++)
- {
- idx = i*ntype+type[j];
- p[2*j] = pvdwparam[2*idx];
- p[2*j+1] = pvdwparam[2*idx+1];
- }
- }
-
- setup_exclusions_and_indices(aadata, excl, natoms);
-}
-
-
-
-void
-nb_kernel_allvsallgb(t_nblist gmx_unused * nlist,
- rvec * xx,
- rvec * ff,
- struct t_forcerec * fr,
- t_mdatoms * mdatoms,
- nb_kernel_data_t * kernel_data,
- t_nrnb * nrnb)
-{
- gmx_allvsall_data_t *aadata;
- int natoms;
- int ni0, ni1;
- int nj0, nj1, nj2;
- int i, j, k;
- real * charge;
- int * type;
- real facel;
- real * pvdw;
- int ggid;
- int * mask;
- real * GBtab;
- real gbfactor;
- real * invsqrta;
- real * dvda;
- real vgbtot, dvdasum;
- int nnn, n0;
-
- real ix, iy, iz, iq;
- real fix, fiy, fiz;
- real jx, jy, jz, qq;
- real dx, dy, dz;
- real tx, ty, tz;
- real rsq, rinv, rinvsq, rinvsix;
- real vcoul, vctot;
- real c6, c12, Vvdw6, Vvdw12, Vvdwtot;
- real fscal, dvdatmp, fijC, vgb;
- real Y, F, Fp, Geps, Heps2, VV, FF, eps, eps2, r, rt;
- real dvdaj, gbscale, isaprod, isai, isaj, gbtabscale;
- real * f;
- real * x;
- t_blocka * excl;
- real * Vvdw;
- real * Vc;
- real * vpol;
-
- x = xx[0];
- f = ff[0];
- charge = mdatoms->chargeA;
- type = mdatoms->typeA;
- gbfactor = ((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
- facel = fr->ic->epsfac;
- GBtab = fr->gbtab->data;
- gbtabscale = fr->gbtab->scale;
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- vpol = kernel_data->energygrp_polarization;
-
- natoms = mdatoms->nr;
- ni0 = 0;
- ni1 = mdatoms->homenr;
-
- aadata = reinterpret_cast<gmx_allvsall_data_t *>(fr->AllvsAll_work);
- excl = kernel_data->exclusions;
-
- Vc = kernel_data->energygrp_elec;
- Vvdw = kernel_data->energygrp_vdw;
-
- if (aadata == NULL)
- {
- setup_aadata(&aadata, excl, natoms, type, fr->ntype, fr->nbfp);
- fr->AllvsAll_work = aadata;
- }
-
- for (i = ni0; i < ni1; i++)
- {
- /* We assume shifts are NOT used for all-vs-all interactions */
-
- /* Load i atom data */
- ix = x[3*i];
- iy = x[3*i+1];
- iz = x[3*i+2];
- iq = facel*charge[i];
-
- isai = invsqrta[i];
-
- pvdw = aadata->pvdwparam[type[i]];
-
- /* Zero the potential energy for this list */
- Vvdwtot = 0.0;
- vctot = 0.0;
- vgbtot = 0.0;
- dvdasum = 0.0;
-
- /* Clear i atom forces */
- fix = 0.0;
- fiy = 0.0;
- fiz = 0.0;
-
- /* Load limits for loop over neighbors */
- nj0 = aadata->jindex[3*i];
- nj1 = aadata->jindex[3*i+1];
- nj2 = aadata->jindex[3*i+2];
-
- mask = aadata->exclusion_mask[i];
-
- /* Prologue part, including exclusion mask */
- for (j = nj0; j < nj1; j++, mask++)
- {
- if (*mask != 0)
- {
- k = j%natoms;
-
- /* load j atom coordinates */
- jx = x[3*k];
- jy = x[3*k+1];
- jz = x[3*k+2];
-
- /* Calculate distance */
- dx = ix - jx;
- dy = iy - jy;
- dz = iz - jz;
- rsq = dx*dx+dy*dy+dz*dz;
-
- /* Calculate 1/r and 1/r2 */
- rinv = 1.0/sqrt(rsq);
-
- /* Load parameters for j atom */
- isaj = invsqrta[k];
- isaprod = isai*isaj;
- qq = iq*charge[k];
- vcoul = qq*rinv;
- fscal = vcoul*rinv;
- qq = isaprod*(-qq)*gbfactor;
- gbscale = isaprod*gbtabscale;
- c6 = pvdw[2*k];
- c12 = pvdw[2*k+1];
- rinvsq = rinv*rinv;
-
- /* Tabulated Generalized-Born interaction */
- dvdaj = dvda[k];
- r = rsq*rinv;
-
- /* Calculate table index */
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vgb = qq*VV;
- fijC = qq*FF*gbscale;
- dvdatmp = -0.5*(vgb+fijC*r);
- dvdasum = dvdasum + dvdatmp;
- dvda[k] = dvdaj+dvdatmp*isaj*isaj;
- vctot = vctot + vcoul;
- vgbtot = vgbtot + vgb;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq-(fijC-fscal)*rinv;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx;
- ty = fscal*dy;
- tz = fscal*dz;
-
- /* Increment i atom force */
- fix = fix + tx;
- fiy = fiy + ty;
- fiz = fiz + tz;
-
- /* Decrement j atom force */
- f[3*k] = f[3*k] - tx;
- f[3*k+1] = f[3*k+1] - ty;
- f[3*k+2] = f[3*k+2] - tz;
- }
- /* Inner loop uses 38 flops/iteration */
- }
-
- /* Main part, no exclusions */
- for (j = nj1; j < nj2; j++)
- {
- k = j%natoms;
-
- /* load j atom coordinates */
- jx = x[3*k];
- jy = x[3*k+1];
- jz = x[3*k+2];
-
- /* Calculate distance */
- dx = ix - jx;
- dy = iy - jy;
- dz = iz - jz;
- rsq = dx*dx+dy*dy+dz*dz;
-
- /* Calculate 1/r and 1/r2 */
- rinv = 1.0/sqrt(rsq);
-
- /* Load parameters for j atom */
- isaj = invsqrta[k];
- isaprod = isai*isaj;
- qq = iq*charge[k];
- vcoul = qq*rinv;
- fscal = vcoul*rinv;
- qq = isaprod*(-qq)*gbfactor;
- gbscale = isaprod*gbtabscale;
- c6 = pvdw[2*k];
- c12 = pvdw[2*k+1];
- rinvsq = rinv*rinv;
-
- /* Tabulated Generalized-Born interaction */
- dvdaj = dvda[k];
- r = rsq*rinv;
-
- /* Calculate table index */
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vgb = qq*VV;
- fijC = qq*FF*gbscale;
- dvdatmp = -0.5*(vgb+fijC*r);
- dvdasum = dvdasum + dvdatmp;
- dvda[k] = dvdaj+dvdatmp*isaj*isaj;
- vctot = vctot + vcoul;
- vgbtot = vgbtot + vgb;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq-(fijC-fscal)*rinv;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx;
- ty = fscal*dy;
- tz = fscal*dz;
-
- /* Increment i atom force */
- fix = fix + tx;
- fiy = fiy + ty;
- fiz = fiz + tz;
-
- /* Decrement j atom force */
- f[3*k] = f[3*k] - tx;
- f[3*k+1] = f[3*k+1] - ty;
- f[3*k+2] = f[3*k+2] - tz;
-
- /* Inner loop uses 38 flops/iteration */
- }
-
- f[3*i] += fix;
- f[3*i+1] += fiy;
- f[3*i+2] += fiz;
-
- /* Add potential energies to the group for this list */
- ggid = 0;
-
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
- vpol[ggid] = vpol[ggid] + vgbtot;
- dvda[i] = dvda[i] + dvdasum*isai*isai;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
- /* 12 flops per outer iteration
- * 19 flops per inner iteration
- */
- inc_nrnb(nrnb, eNR_NBKERNEL_ELEC_VDW_VF, (ni1-ni0)*12 + ((ni1-ni0)*natoms/2)*19);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2014,2015,2017,2018, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef _NB_KERNEL_ALLVSALLGB_H
-#define _NB_KERNEL_ALLVSALLGB_H
-
-#include "config.h"
-
-#include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/gmxlib/nonbonded/nb_kernel.h"
-#include "gromacs/math/vectypes.h"
-#include "gromacs/mdtypes/mdatom.h"
-#include "gromacs/mdtypes/nblist.h"
-
-void
-nb_kernel_allvsallgb(t_nblist * nlist,
- rvec * x,
- rvec * f,
- struct t_forcerec * fr,
- t_mdatoms * mdatoms,
- nb_kernel_data_t * kernel_data,
- t_nrnb * nrnb);
-
-#endif
nb_kernel_t nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_F_c;
nb_kernel_t nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_VF_c;
nb_kernel_t nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4W4_F_c;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_c;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_c;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_c;
nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_F_c;
nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_VF_c;
nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomP1P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3W3_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4P1_F_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c;
-nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4W4_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomP1P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3W3_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4P1_F_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c;
-nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4W4_F_c;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c;
-nb_kernel_t nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c;
-nb_kernel_t nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_c;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_c;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_c;
nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW4P1_F_c;
nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW4W4_VF_c;
nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4W4_F_c;
nb_kernel_info_t
{ nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_F_c, "nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_F_c", "c", "None", "None", "Buckingham", "PotentialShift", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_VF_c, "nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_VF_c", "c", "None", "None", "Buckingham", "PotentialSwitch", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_F_c, "nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_F_c", "c", "None", "None", "Buckingham", "PotentialSwitch", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Water4", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_c, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_c", "c", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_c, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_c", "c", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_c, "nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_c", "c", "Ewald", "None", "LJEwald", "None", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_F_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_F_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "Water4Particle", "", "Force" },
{ nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_VF_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_VF_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "Water4Water4", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_F_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_F_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_c", "c", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c", "c", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_c", "c", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c", "c", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_c", "c", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c", "c", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_c", "c", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c", "c", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_c", "c", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c", "c", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_c", "c", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwBham_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwBham_GeomP1P1_F_c", "c", "Coulomb", "None", "Buckingham", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwBham_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW3P1_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwBham_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW3W3_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwBham_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW4P1_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwBham_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW4W4_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwBham_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwBham_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwBham_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwBham_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwBham_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_c", "c", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c", "c", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c", "c", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c", "c", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c", "c", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c", "c", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c, "nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c", "c", "GeneralizedBorn", "None", "Buckingham", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c, "nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c", "c", "GeneralizedBorn", "None", "Buckingham", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwBham_GeomW4P1_VF_c, "nb_kernel_ElecRF_VdwBham_GeomW4P1_VF_c", "c", "ReactionField", "None", "Buckingham", "None", "Water4Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwBham_GeomW4P1_F_c, "nb_kernel_ElecRF_VdwBham_GeomW4P1_F_c", "c", "ReactionField", "None", "Buckingham", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecRF_VdwBham_GeomW4W4_VF_c, "nb_kernel_ElecRF_VdwBham_GeomW4W4_VF_c", "c", "ReactionField", "None", "Buckingham", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecRF_VdwBham_GeomW4W4_F_c, "nb_kernel_ElecRF_VdwBham_GeomW4W4_F_c", "c", "ReactionField", "None", "Buckingham", "None", "Water4Water4", "", "Force" }
+ { nb_kernel_ElecRF_VdwBham_GeomW4W4_F_c, "nb_kernel_ElecRF_VdwBham_GeomW4W4_F_c", "c", "ReactionField", "None", "Buckingham", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_c", "c", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c", "c", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_c", "c", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c", "c", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_c", "c", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c", "c", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_c", "c", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c", "c", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_c", "c", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c", "c", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_c", "c", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwBham_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwBham_GeomP1P1_F_c", "c", "Coulomb", "None", "Buckingham", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW3P1_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW3W3_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW4P1_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW4W4_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Water4", "", "Force" }
};
int
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real velec,felec,velecsum,facel,crf,krf,krf2;
real *charge;
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- int gbitab;
- real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- real *invsqrta,*dvda,*gbtab;
- /* #endif */
/* #if KERNEL_VDW != 'None' */
int nvdwtype;
real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
int *vdwtype;
real *vdwparam;
/* #endif */
- /* #if 'Table' in KERNEL_ELEC or 'GeneralizedBorn' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
+ /* #if 'Table' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
int vfitab;
real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
real *vftab;
/* #endif */
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = fr->gbtab->scale;
- gbtab = fr->gbtab->data;
- gbinvepsdiff = (1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
- /* #endif */
-
/* #if 'Water' in GEOMETRY_I */
/* Setup water-specific parameters */
inr = nlist->iinr[0];
/* #for I in PARTICLES_ELEC_I */
iq{I} = facel*charge[inr+{I}];
/* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isai{I} = invsqrta[inr+{I}];
- /* #endif */
/* #endfor */
/* #for I in PARTICLES_VDW_I */
vdwioffset{I} = {NVDWPARAM}*nvdwtype*vdwtype[inr+{I}];
/* #if KERNEL_ELEC != 'None' */
velecsum = 0.0;
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- vgbsum = 0.0;
- /* #endif */
/* #if KERNEL_VDW != 'None' */
vvdwsum = 0.0;
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = 0.0;
- /* #endif */
/* Start inner kernel loop */
for(jidx=j_index_start; jidx<j_index_end; jidx++)
/* Load parameters for j particles */
/* #for J in PARTICLES_ELEC_J */
jq{J} = charge[jnr+{J}];
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isaj{J} = invsqrta[jnr+{J}];
- /* #endif */
/* #endfor */
/* #for J in PARTICLES_VDW_J */
vdwjidx{J} = {NVDWPARAM}*vdwtype[jnr+{J}];
/* #define INNERFLOPS INNERFLOPS+3 */
/* #endif */
- /* #elif KERNEL_ELEC=='GeneralizedBorn' */
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = isai{I}*isaj{J};
- gbqqfactor = isaprod*(-qq{I}{J})*gbinvepsdiff;
- gbscale = isaprod*gbtabscale;
- dvdaj = dvda[jnr+{J}];
- /* #define INNERFLOPS INNERFLOPS+5 */
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = r{I}{J}*gbscale;
- gbitab = rt;
- gbeps = rt-gbitab;
- gbitab = 4*gbitab;
-
- Y = gbtab[gbitab];
- F = gbtab[gbitab+1];
- Geps = gbeps*gbtab[gbitab+2];
- Heps2 = gbeps*gbeps*gbtab[gbitab+3];
- Fp = F+Geps+Heps2;
- VV = Y+gbeps*Fp;
- vgb = gbqqfactor*VV;
- /* #define INNERFLOPS INNERFLOPS+10 */
-
- /* #if 'Force' in KERNEL_VF */
- FF = Fp+Geps+2.0*Heps2;
- fgb = gbqqfactor*FF*gbscale;
- dvdatmp = -0.5*(vgb+fgb*r{I}{J});
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj{J}*isaj{J};
- /* #define INNERFLOPS INNERFLOPS+13 */
- /* #endif */
- velec = qq{I}{J}*rinv{I}{J};
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #if 'Force' in KERNEL_VF */
- felec = (velec*rinv{I}{J}-fgb)*rinv{I}{J};
- /* #define INNERFLOPS INNERFLOPS+3 */
- /* #endif */
-
/* #elif KERNEL_ELEC=='Ewald' */
/* EWALD ELECTROSTATICS */
/* #if 'electrostatics' in INTERACTION_FLAGS[I][J] */
velecsum += velec;
/* #define INNERFLOPS INNERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- vgbsum += vgb;
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
/* #endif */
/* #if 'vdw' in INTERACTION_FLAGS[I][J] */
vvdwsum += vvdw;
kernel_data->energygrp_elec[ggid] += velecsum;
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- kernel_data->energygrp_polarization[ggid] += vgbsum;
- /* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #endif */
/* #if KERNEL_VDW != 'None' */
kernel_data->energygrp_vdw[ggid] += vvdwsum;
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvda[inr] = dvda[inr] + dvdasum*isai{I}*isai{I};
- /* #endif */
/* Increment number of inner iterations */
inneriter += j_index_end - j_index_start;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
- 'GeneralizedBorn' : ['rinv','r'],
'CubicSplineTable' : ['rinv','r','table'],
'Ewald' : ['rinv','rinvsq','r'],
}
'Coulomb' : 'Coul',
'Ewald' : 'Ew',
'ReactionField' : 'RF',
- 'GeneralizedBorn' : 'GB',
'CubicSplineTable' : 'CSTab',
'LennardJones' : 'LJ',
'Buckingham' : 'Bham',
return 0
# No need for LJ-only water optimization, or water optimization with implicit solvent.
- if('Water' in KernelGeom[0] and (KernelElec=='None' or 'GeneralizedBorn' in KernelElec)):
+ if('Water' in KernelGeom[0] and KernelElec=='None'):
return 0
# Non-matching table settings are pointless
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_sparc64_hpc_ace_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with double precision SIMD, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- _fjsp_v2r8 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- _fjsp_v2r8 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- _fjsp_v2r8 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- _fjsp_v2r8 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- _fjsp_v2r8 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- _fjsp_v2r8 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- _fjsp_v2r8 minushalf = gmx_fjsp_set1_v2r8(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- _fjsp_v2r8 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- _fjsp_v2r8 one_sixth = gmx_fjsp_set1_v2r8(1.0/6.0);
- _fjsp_v2r8 one_twelfth = gmx_fjsp_set1_v2r8(1.0/12.0);
- _fjsp_v2r8 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- _fjsp_v2r8 itab_tmp;
- _fjsp_v2r8 dummy_mask,cutoff_mask;
- _fjsp_v2r8 one = gmx_fjsp_set1_v2r8(1.0);
- _fjsp_v2r8 two = gmx_fjsp_set1_v2r8(2.0);
- union { _fjsp_v2r8 simd; long long int i[2]; } vfconv,gbconv,ewconv;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = gmx_fjsp_set1_v2r8(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = gmx_fjsp_set1_v2r8(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = gmx_fjsp_set1_v2r8(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = gmx_fjsp_set1_v2r8((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_fjsp_load_shift_and_1rvec_broadcast_v2r8(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _fjsp_setzero_v2r8();
- fiy0 = _fjsp_setzero_v2r8();
- fiz0 = _fjsp_setzero_v2r8();
-
- /* Load parameters for i particles */
- iq0 = _fjsp_mul_v2r8(facel,gmx_fjsp_load1_v2r8(charge+inr+0));
- isai0 = gmx_fjsp_load1_v2r8(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _fjsp_setzero_v2r8();
- vgbsum = _fjsp_setzero_v2r8();
- vvdwsum = _fjsp_setzero_v2r8();
- dvdasum = _fjsp_setzero_v2r8();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_2ptr_swizzle_v2r8(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_fjsp_load_2real_swizzle_v2r8(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_fjsp_load_2real_swizzle_v2r8(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
- gmx_fjsp_load_2pair_swizzle_v2r8(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _fjsp_mul_v2r8(r00,vftabscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- vfeps = _fjsp_sub_v2r8(rt, _fjsp_xtod_v2r8(itab_tmp));
- twovfeps = _fjsp_add_v2r8(vfeps,vfeps);
- _fjsp_store_v2r8(&vfconv.simd,itab_tmp);
-
- vfconv.i[0] *= 8;
- vfconv.i[1] *= 8;
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] );
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] +2);
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_2real_swizzle_v2r8(dvda+jnrA,dvda+jnrB,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _fjsp_load_v2r8( vftab + vfconv.i[0] );
- F = _fjsp_load_v2r8( vftab + vfconv.i[1] );
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( vftab + vfconv.i[0] + 2 );
- H = _fjsp_load_v2r8( vftab + vfconv.i[1] + 2 );
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(H,vfeps,G),F);
- VV = _fjsp_madd_v2r8(vfeps,Fp,Y);
- vvdw6 = _fjsp_mul_v2r8(c6_00,VV);
- FF = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(twovfeps,H,G),Fp);
- fvdw6 = _fjsp_mul_v2r8(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- Y = _fjsp_load_v2r8( vftab + vfconv.i[0] + 4 );
- F = _fjsp_load_v2r8( vftab + vfconv.i[1] + 4 );
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( vftab + vfconv.i[0] + 6 );
- H = _fjsp_load_v2r8( vftab + vfconv.i[1] + 6 );
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(H,vfeps,G),F);
- VV = _fjsp_madd_v2r8(vfeps,Fp,Y);
- vvdw12 = _fjsp_mul_v2r8(c12_00,VV);
- FF = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(twovfeps,H,G),Fp);
- fvdw12 = _fjsp_mul_v2r8(c12_00,FF);
- vvdw = _fjsp_add_v2r8(vvdw12,vvdw6);
- fvdw = _fjsp_neg_v2r8(_fjsp_mul_v2r8(_fjsp_add_v2r8(fvdw6,fvdw12),_fjsp_mul_v2r8(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _fjsp_add_v2r8(velecsum,velec);
- vgbsum = _fjsp_add_v2r8(vgbsum,vgb);
- vvdwsum = _fjsp_add_v2r8(vvdwsum,vvdw);
-
- fscal = _fjsp_add_v2r8(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_2ptr_swizzle_v2r8(f+j_coord_offsetA,f+j_coord_offsetB,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 95 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_1ptr_swizzle_v2r8(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),charge+jnrA+0);
- isaj0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
- gmx_fjsp_load_2pair_swizzle_v2r8(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _fjsp_mul_v2r8(r00,vftabscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- vfeps = _fjsp_sub_v2r8(rt, _fjsp_xtod_v2r8(itab_tmp));
- twovfeps = _fjsp_add_v2r8(vfeps,vfeps);
- _fjsp_store_v2r8(&vfconv.simd,itab_tmp);
-
- vfconv.i[0] *= 8;
- vfconv.i[1] *= 8;
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_1real_v2r8(dvda+jnrA,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _fjsp_load_v2r8( vftab + vfconv.i[0] );
- F = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( vftab + vfconv.i[0] + 2 );
- H = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(H,vfeps,G),F);
- VV = _fjsp_madd_v2r8(vfeps,Fp,Y);
- vvdw6 = _fjsp_mul_v2r8(c6_00,VV);
- FF = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(twovfeps,H,G),Fp);
- fvdw6 = _fjsp_mul_v2r8(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- Y = _fjsp_load_v2r8( vftab + vfconv.i[0] + 4 );
- F = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( vftab + vfconv.i[0] + 6 );
- H = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(H,vfeps,G),F);
- VV = _fjsp_madd_v2r8(vfeps,Fp,Y);
- vvdw12 = _fjsp_mul_v2r8(c12_00,VV);
- FF = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(twovfeps,H,G),Fp);
- fvdw12 = _fjsp_mul_v2r8(c12_00,FF);
- vvdw = _fjsp_add_v2r8(vvdw12,vvdw6);
- fvdw = _fjsp_neg_v2r8(_fjsp_mul_v2r8(_fjsp_add_v2r8(fvdw6,fvdw12),_fjsp_mul_v2r8(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _fjsp_unpacklo_v2r8(velec,_fjsp_setzero_v2r8());
- velecsum = _fjsp_add_v2r8(velecsum,velec);
- vgb = _fjsp_unpacklo_v2r8(vgb,_fjsp_setzero_v2r8());
- vgbsum = _fjsp_add_v2r8(vgbsum,vgb);
- vvdw = _fjsp_unpacklo_v2r8(vvdw,_fjsp_setzero_v2r8());
- vvdwsum = _fjsp_add_v2r8(vvdwsum,vvdw);
-
- fscal = _fjsp_add_v2r8(felec,fvdw);
-
- fscal = _fjsp_unpacklo_v2r8(fscal,_fjsp_setzero_v2r8());
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_1ptr_swizzle_v2r8(f+j_coord_offsetA,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 95 flops */
- }
-
- /* End of innermost loop */
-
- gmx_fjsp_update_iforce_1atom_swizzle_v2r8(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_fjsp_update_1pot_v2r8(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_fjsp_update_1pot_v2r8(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_fjsp_update_1pot_v2r8(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _fjsp_mul_v2r8(dvdasum, _fjsp_mul_v2r8(isai0,isai0));
- gmx_fjsp_update_1pot_v2r8(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*95);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with double precision SIMD, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- _fjsp_v2r8 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- _fjsp_v2r8 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- _fjsp_v2r8 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- _fjsp_v2r8 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- _fjsp_v2r8 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- _fjsp_v2r8 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- _fjsp_v2r8 minushalf = gmx_fjsp_set1_v2r8(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- _fjsp_v2r8 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- _fjsp_v2r8 one_sixth = gmx_fjsp_set1_v2r8(1.0/6.0);
- _fjsp_v2r8 one_twelfth = gmx_fjsp_set1_v2r8(1.0/12.0);
- _fjsp_v2r8 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- _fjsp_v2r8 itab_tmp;
- _fjsp_v2r8 dummy_mask,cutoff_mask;
- _fjsp_v2r8 one = gmx_fjsp_set1_v2r8(1.0);
- _fjsp_v2r8 two = gmx_fjsp_set1_v2r8(2.0);
- union { _fjsp_v2r8 simd; long long int i[2]; } vfconv,gbconv,ewconv;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = gmx_fjsp_set1_v2r8(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = gmx_fjsp_set1_v2r8(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = gmx_fjsp_set1_v2r8(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = gmx_fjsp_set1_v2r8((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_fjsp_load_shift_and_1rvec_broadcast_v2r8(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _fjsp_setzero_v2r8();
- fiy0 = _fjsp_setzero_v2r8();
- fiz0 = _fjsp_setzero_v2r8();
-
- /* Load parameters for i particles */
- iq0 = _fjsp_mul_v2r8(facel,gmx_fjsp_load1_v2r8(charge+inr+0));
- isai0 = gmx_fjsp_load1_v2r8(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _fjsp_setzero_v2r8();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_2ptr_swizzle_v2r8(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_fjsp_load_2real_swizzle_v2r8(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_fjsp_load_2real_swizzle_v2r8(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
- gmx_fjsp_load_2pair_swizzle_v2r8(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _fjsp_mul_v2r8(r00,vftabscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- vfeps = _fjsp_sub_v2r8(rt, _fjsp_xtod_v2r8(itab_tmp));
- twovfeps = _fjsp_add_v2r8(vfeps,vfeps);
- _fjsp_store_v2r8(&vfconv.simd,itab_tmp);
-
- vfconv.i[0] *= 8;
- vfconv.i[1] *= 8;
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] );
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] +2);
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_2real_swizzle_v2r8(dvda+jnrA,dvda+jnrB,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _fjsp_load_v2r8( vftab + vfconv.i[0] );
- F = _fjsp_load_v2r8( vftab + vfconv.i[1] );
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( vftab + vfconv.i[0] + 2 );
- H = _fjsp_load_v2r8( vftab + vfconv.i[1] + 2 );
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(H,vfeps,G),F);
- FF = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(twovfeps,H,G),Fp);
- fvdw6 = _fjsp_mul_v2r8(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- Y = _fjsp_load_v2r8( vftab + vfconv.i[0] + 4 );
- F = _fjsp_load_v2r8( vftab + vfconv.i[1] + 4 );
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( vftab + vfconv.i[0] + 6 );
- H = _fjsp_load_v2r8( vftab + vfconv.i[1] + 6 );
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(H,vfeps,G),F);
- FF = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(twovfeps,H,G),Fp);
- fvdw12 = _fjsp_mul_v2r8(c12_00,FF);
- fvdw = _fjsp_neg_v2r8(_fjsp_mul_v2r8(_fjsp_add_v2r8(fvdw6,fvdw12),_fjsp_mul_v2r8(vftabscale,rinv00)));
-
- fscal = _fjsp_add_v2r8(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_2ptr_swizzle_v2r8(f+j_coord_offsetA,f+j_coord_offsetB,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 85 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_1ptr_swizzle_v2r8(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),charge+jnrA+0);
- isaj0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
- gmx_fjsp_load_2pair_swizzle_v2r8(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _fjsp_mul_v2r8(r00,vftabscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- vfeps = _fjsp_sub_v2r8(rt, _fjsp_xtod_v2r8(itab_tmp));
- twovfeps = _fjsp_add_v2r8(vfeps,vfeps);
- _fjsp_store_v2r8(&vfconv.simd,itab_tmp);
-
- vfconv.i[0] *= 8;
- vfconv.i[1] *= 8;
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_1real_v2r8(dvda+jnrA,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _fjsp_load_v2r8( vftab + vfconv.i[0] );
- F = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( vftab + vfconv.i[0] + 2 );
- H = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(H,vfeps,G),F);
- FF = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(twovfeps,H,G),Fp);
- fvdw6 = _fjsp_mul_v2r8(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- Y = _fjsp_load_v2r8( vftab + vfconv.i[0] + 4 );
- F = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( vftab + vfconv.i[0] + 6 );
- H = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(H,vfeps,G),F);
- FF = _fjsp_madd_v2r8(vfeps,_fjsp_madd_v2r8(twovfeps,H,G),Fp);
- fvdw12 = _fjsp_mul_v2r8(c12_00,FF);
- fvdw = _fjsp_neg_v2r8(_fjsp_mul_v2r8(_fjsp_add_v2r8(fvdw6,fvdw12),_fjsp_mul_v2r8(vftabscale,rinv00)));
-
- fscal = _fjsp_add_v2r8(felec,fvdw);
-
- fscal = _fjsp_unpacklo_v2r8(fscal,_fjsp_setzero_v2r8());
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_1ptr_swizzle_v2r8(f+j_coord_offsetA,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 85 flops */
- }
-
- /* End of innermost loop */
-
- gmx_fjsp_update_iforce_1atom_swizzle_v2r8(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _fjsp_mul_v2r8(dvdasum, _fjsp_mul_v2r8(isai0,isai0));
- gmx_fjsp_update_1pot_v2r8(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*85);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_sparc64_hpc_ace_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with double precision SIMD, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- _fjsp_v2r8 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- _fjsp_v2r8 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- _fjsp_v2r8 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- _fjsp_v2r8 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- _fjsp_v2r8 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- _fjsp_v2r8 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- _fjsp_v2r8 minushalf = gmx_fjsp_set1_v2r8(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- _fjsp_v2r8 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- _fjsp_v2r8 one_sixth = gmx_fjsp_set1_v2r8(1.0/6.0);
- _fjsp_v2r8 one_twelfth = gmx_fjsp_set1_v2r8(1.0/12.0);
- _fjsp_v2r8 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- _fjsp_v2r8 itab_tmp;
- _fjsp_v2r8 dummy_mask,cutoff_mask;
- _fjsp_v2r8 one = gmx_fjsp_set1_v2r8(1.0);
- _fjsp_v2r8 two = gmx_fjsp_set1_v2r8(2.0);
- union { _fjsp_v2r8 simd; long long int i[2]; } vfconv,gbconv,ewconv;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = gmx_fjsp_set1_v2r8(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = gmx_fjsp_set1_v2r8(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = gmx_fjsp_set1_v2r8((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_fjsp_load_shift_and_1rvec_broadcast_v2r8(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _fjsp_setzero_v2r8();
- fiy0 = _fjsp_setzero_v2r8();
- fiz0 = _fjsp_setzero_v2r8();
-
- /* Load parameters for i particles */
- iq0 = _fjsp_mul_v2r8(facel,gmx_fjsp_load1_v2r8(charge+inr+0));
- isai0 = gmx_fjsp_load1_v2r8(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _fjsp_setzero_v2r8();
- vgbsum = _fjsp_setzero_v2r8();
- vvdwsum = _fjsp_setzero_v2r8();
- dvdasum = _fjsp_setzero_v2r8();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_2ptr_swizzle_v2r8(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- rinvsq00 = _fjsp_mul_v2r8(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_fjsp_load_2real_swizzle_v2r8(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_fjsp_load_2real_swizzle_v2r8(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
- gmx_fjsp_load_2pair_swizzle_v2r8(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] );
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] +2);
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_2real_swizzle_v2r8(dvda+jnrA,dvda+jnrB,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _fjsp_mul_v2r8(_fjsp_mul_v2r8(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _fjsp_mul_v2r8(c6_00,rinvsix);
- vvdw12 = _fjsp_mul_v2r8(c12_00,_fjsp_mul_v2r8(rinvsix,rinvsix));
- vvdw = _fjsp_msub_v2r8( vvdw12,one_twelfth, _fjsp_mul_v2r8(vvdw6,one_sixth) );
- fvdw = _fjsp_mul_v2r8(_fjsp_sub_v2r8(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _fjsp_add_v2r8(velecsum,velec);
- vgbsum = _fjsp_add_v2r8(vgbsum,vgb);
- vvdwsum = _fjsp_add_v2r8(vvdwsum,vvdw);
-
- fscal = _fjsp_add_v2r8(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_2ptr_swizzle_v2r8(f+j_coord_offsetA,f+j_coord_offsetB,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 74 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_1ptr_swizzle_v2r8(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- rinvsq00 = _fjsp_mul_v2r8(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),charge+jnrA+0);
- isaj0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
- gmx_fjsp_load_2pair_swizzle_v2r8(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_1real_v2r8(dvda+jnrA,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _fjsp_mul_v2r8(_fjsp_mul_v2r8(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _fjsp_mul_v2r8(c6_00,rinvsix);
- vvdw12 = _fjsp_mul_v2r8(c12_00,_fjsp_mul_v2r8(rinvsix,rinvsix));
- vvdw = _fjsp_msub_v2r8( vvdw12,one_twelfth, _fjsp_mul_v2r8(vvdw6,one_sixth) );
- fvdw = _fjsp_mul_v2r8(_fjsp_sub_v2r8(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _fjsp_unpacklo_v2r8(velec,_fjsp_setzero_v2r8());
- velecsum = _fjsp_add_v2r8(velecsum,velec);
- vgb = _fjsp_unpacklo_v2r8(vgb,_fjsp_setzero_v2r8());
- vgbsum = _fjsp_add_v2r8(vgbsum,vgb);
- vvdw = _fjsp_unpacklo_v2r8(vvdw,_fjsp_setzero_v2r8());
- vvdwsum = _fjsp_add_v2r8(vvdwsum,vvdw);
-
- fscal = _fjsp_add_v2r8(felec,fvdw);
-
- fscal = _fjsp_unpacklo_v2r8(fscal,_fjsp_setzero_v2r8());
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_1ptr_swizzle_v2r8(f+j_coord_offsetA,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 74 flops */
- }
-
- /* End of innermost loop */
-
- gmx_fjsp_update_iforce_1atom_swizzle_v2r8(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_fjsp_update_1pot_v2r8(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_fjsp_update_1pot_v2r8(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_fjsp_update_1pot_v2r8(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _fjsp_mul_v2r8(dvdasum, _fjsp_mul_v2r8(isai0,isai0));
- gmx_fjsp_update_1pot_v2r8(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*74);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with double precision SIMD, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- _fjsp_v2r8 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- _fjsp_v2r8 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- _fjsp_v2r8 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- _fjsp_v2r8 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- _fjsp_v2r8 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- _fjsp_v2r8 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- _fjsp_v2r8 minushalf = gmx_fjsp_set1_v2r8(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- _fjsp_v2r8 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- _fjsp_v2r8 one_sixth = gmx_fjsp_set1_v2r8(1.0/6.0);
- _fjsp_v2r8 one_twelfth = gmx_fjsp_set1_v2r8(1.0/12.0);
- _fjsp_v2r8 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- _fjsp_v2r8 itab_tmp;
- _fjsp_v2r8 dummy_mask,cutoff_mask;
- _fjsp_v2r8 one = gmx_fjsp_set1_v2r8(1.0);
- _fjsp_v2r8 two = gmx_fjsp_set1_v2r8(2.0);
- union { _fjsp_v2r8 simd; long long int i[2]; } vfconv,gbconv,ewconv;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = gmx_fjsp_set1_v2r8(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = gmx_fjsp_set1_v2r8(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = gmx_fjsp_set1_v2r8((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_fjsp_load_shift_and_1rvec_broadcast_v2r8(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _fjsp_setzero_v2r8();
- fiy0 = _fjsp_setzero_v2r8();
- fiz0 = _fjsp_setzero_v2r8();
-
- /* Load parameters for i particles */
- iq0 = _fjsp_mul_v2r8(facel,gmx_fjsp_load1_v2r8(charge+inr+0));
- isai0 = gmx_fjsp_load1_v2r8(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _fjsp_setzero_v2r8();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_2ptr_swizzle_v2r8(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- rinvsq00 = _fjsp_mul_v2r8(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_fjsp_load_2real_swizzle_v2r8(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_fjsp_load_2real_swizzle_v2r8(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
- gmx_fjsp_load_2pair_swizzle_v2r8(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] );
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] +2);
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_2real_swizzle_v2r8(dvda+jnrA,dvda+jnrB,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _fjsp_mul_v2r8(_fjsp_mul_v2r8(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _fjsp_mul_v2r8(_fjsp_msub_v2r8(c12_00,rinvsix,c6_00),_fjsp_mul_v2r8(rinvsix,rinvsq00));
-
- fscal = _fjsp_add_v2r8(felec,fvdw);
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_2ptr_swizzle_v2r8(f+j_coord_offsetA,f+j_coord_offsetB,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 67 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_1ptr_swizzle_v2r8(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- rinvsq00 = _fjsp_mul_v2r8(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),charge+jnrA+0);
- isaj0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
- gmx_fjsp_load_2pair_swizzle_v2r8(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_1real_v2r8(dvda+jnrA,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _fjsp_mul_v2r8(_fjsp_mul_v2r8(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _fjsp_mul_v2r8(_fjsp_msub_v2r8(c12_00,rinvsix,c6_00),_fjsp_mul_v2r8(rinvsix,rinvsq00));
-
- fscal = _fjsp_add_v2r8(felec,fvdw);
-
- fscal = _fjsp_unpacklo_v2r8(fscal,_fjsp_setzero_v2r8());
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_1ptr_swizzle_v2r8(f+j_coord_offsetA,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 67 flops */
- }
-
- /* End of innermost loop */
-
- gmx_fjsp_update_iforce_1atom_swizzle_v2r8(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _fjsp_mul_v2r8(dvdasum, _fjsp_mul_v2r8(isai0,isai0));
- gmx_fjsp_update_1pot_v2r8(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*67);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sparc64_hpc_ace_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_sparc64_hpc_ace_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with double precision SIMD, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- _fjsp_v2r8 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- _fjsp_v2r8 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- _fjsp_v2r8 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- _fjsp_v2r8 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- _fjsp_v2r8 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- _fjsp_v2r8 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- _fjsp_v2r8 minushalf = gmx_fjsp_set1_v2r8(-0.5);
- real *invsqrta,*dvda,*gbtab;
- _fjsp_v2r8 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- _fjsp_v2r8 itab_tmp;
- _fjsp_v2r8 dummy_mask,cutoff_mask;
- _fjsp_v2r8 one = gmx_fjsp_set1_v2r8(1.0);
- _fjsp_v2r8 two = gmx_fjsp_set1_v2r8(2.0);
- union { _fjsp_v2r8 simd; long long int i[2]; } vfconv,gbconv,ewconv;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = gmx_fjsp_set1_v2r8(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = gmx_fjsp_set1_v2r8(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = gmx_fjsp_set1_v2r8((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_fjsp_load_shift_and_1rvec_broadcast_v2r8(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _fjsp_setzero_v2r8();
- fiy0 = _fjsp_setzero_v2r8();
- fiz0 = _fjsp_setzero_v2r8();
-
- /* Load parameters for i particles */
- iq0 = _fjsp_mul_v2r8(facel,gmx_fjsp_load1_v2r8(charge+inr+0));
- isai0 = gmx_fjsp_load1_v2r8(invsqrta+inr+0);
-
- /* Reset potential sums */
- velecsum = _fjsp_setzero_v2r8();
- vgbsum = _fjsp_setzero_v2r8();
- dvdasum = _fjsp_setzero_v2r8();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_2ptr_swizzle_v2r8(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_fjsp_load_2real_swizzle_v2r8(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_fjsp_load_2real_swizzle_v2r8(invsqrta+jnrA+0,invsqrta+jnrB+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] );
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] +2);
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_2real_swizzle_v2r8(dvda+jnrA,dvda+jnrB,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _fjsp_add_v2r8(velecsum,velec);
- vgbsum = _fjsp_add_v2r8(vgbsum,vgb);
-
- fscal = felec;
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_2ptr_swizzle_v2r8(f+j_coord_offsetA,f+j_coord_offsetB,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 61 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_1ptr_swizzle_v2r8(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),charge+jnrA+0);
- isaj0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),invsqrta+jnrA+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_1real_v2r8(dvda+jnrA,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _fjsp_unpacklo_v2r8(velec,_fjsp_setzero_v2r8());
- velecsum = _fjsp_add_v2r8(velecsum,velec);
- vgb = _fjsp_unpacklo_v2r8(vgb,_fjsp_setzero_v2r8());
- vgbsum = _fjsp_add_v2r8(vgbsum,vgb);
-
- fscal = felec;
-
- fscal = _fjsp_unpacklo_v2r8(fscal,_fjsp_setzero_v2r8());
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_1ptr_swizzle_v2r8(f+j_coord_offsetA,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 61 flops */
- }
-
- /* End of innermost loop */
-
- gmx_fjsp_update_iforce_1atom_swizzle_v2r8(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_fjsp_update_1pot_v2r8(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_fjsp_update_1pot_v2r8(vgbsum,kernel_data->energygrp_polarization+ggid);
- dvdasum = _fjsp_mul_v2r8(dvdasum, _fjsp_mul_v2r8(isai0,isai0));
- gmx_fjsp_update_1pot_v2r8(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 9 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*9 + inneriter*61);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with double precision SIMD, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- _fjsp_v2r8 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- _fjsp_v2r8 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- _fjsp_v2r8 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- _fjsp_v2r8 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- _fjsp_v2r8 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- _fjsp_v2r8 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- _fjsp_v2r8 minushalf = gmx_fjsp_set1_v2r8(-0.5);
- real *invsqrta,*dvda,*gbtab;
- _fjsp_v2r8 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
- real *vftab;
- _fjsp_v2r8 itab_tmp;
- _fjsp_v2r8 dummy_mask,cutoff_mask;
- _fjsp_v2r8 one = gmx_fjsp_set1_v2r8(1.0);
- _fjsp_v2r8 two = gmx_fjsp_set1_v2r8(2.0);
- union { _fjsp_v2r8 simd; long long int i[2]; } vfconv,gbconv,ewconv;
-
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = gmx_fjsp_set1_v2r8(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = gmx_fjsp_set1_v2r8(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = gmx_fjsp_set1_v2r8((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_fjsp_load_shift_and_1rvec_broadcast_v2r8(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _fjsp_setzero_v2r8();
- fiy0 = _fjsp_setzero_v2r8();
- fiz0 = _fjsp_setzero_v2r8();
-
- /* Load parameters for i particles */
- iq0 = _fjsp_mul_v2r8(facel,gmx_fjsp_load1_v2r8(charge+inr+0));
- isai0 = gmx_fjsp_load1_v2r8(invsqrta+inr+0);
-
- dvdasum = _fjsp_setzero_v2r8();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_2ptr_swizzle_v2r8(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_fjsp_load_2real_swizzle_v2r8(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_fjsp_load_2real_swizzle_v2r8(invsqrta+jnrA+0,invsqrta+jnrB+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] );
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] +2);
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_2real_swizzle_v2r8(dvda+jnrA,dvda+jnrB,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- fscal = felec;
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_2ptr_swizzle_v2r8(f+j_coord_offsetA,f+j_coord_offsetB,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 59 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_fjsp_load_1rvec_1ptr_swizzle_v2r8(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _fjsp_sub_v2r8(ix0,jx0);
- dy00 = _fjsp_sub_v2r8(iy0,jy0);
- dz00 = _fjsp_sub_v2r8(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_fjsp_calc_rsq_v2r8(dx00,dy00,dz00);
-
- rinv00 = gmx_fjsp_invsqrt_v2r8(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),charge+jnrA+0);
- isaj0 = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),invsqrta+jnrA+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _fjsp_mul_v2r8(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _fjsp_mul_v2r8(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai0,isaj0);
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq00,_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r00,gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- F = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- H = _fjsp_setzero_v2r8();
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
-
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r00,vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- gmx_fjsp_increment_1real_v2r8(dvda+jnrA,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj0,isaj0)));
- velec = _fjsp_mul_v2r8(qq00,rinv00);
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv00,fgb),rinv00);
-
- fscal = felec;
-
- fscal = _fjsp_unpacklo_v2r8(fscal,_fjsp_setzero_v2r8());
-
- /* Update vectorial force */
- fix0 = _fjsp_madd_v2r8(dx00,fscal,fix0);
- fiy0 = _fjsp_madd_v2r8(dy00,fscal,fiy0);
- fiz0 = _fjsp_madd_v2r8(dz00,fscal,fiz0);
-
- gmx_fjsp_decrement_fma_1rvec_1ptr_swizzle_v2r8(f+j_coord_offsetA,fscal,dx00,dy00,dz00);
-
- /* Inner loop uses 59 flops */
- }
-
- /* End of innermost loop */
-
- gmx_fjsp_update_iforce_1atom_swizzle_v2r8(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _fjsp_mul_v2r8(dvdasum, _fjsp_mul_v2r8(isai0,isai0));
- gmx_fjsp_update_1pot_v2r8(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*7 + inneriter*59);
-}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_t nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double;
nb_kernel_info_t
{ nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "None", "None", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Ewald", "None", "LJEwald", "None", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sparc64_hpc_ace_double", "sparc64_hpc_ace_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
};
int
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
_fjsp_v2r8 velec,felec,velecsum,facel,crf,krf,krf2;
real *charge;
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- _fjsp_v2r8 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,twogbeps,dvdatmp;
- _fjsp_v2r8 minushalf = gmx_fjsp_set1_v2r8(-0.5);
- real *invsqrta,*dvda,*gbtab;
- /* #endif */
/* #if KERNEL_VDW != 'None' */
int nvdwtype;
_fjsp_v2r8 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
_fjsp_v2r8 one_sixth = gmx_fjsp_set1_v2r8(1.0/6.0);
_fjsp_v2r8 one_twelfth = gmx_fjsp_set1_v2r8(1.0/12.0);
/* #endif */
- /* #if 'Table' in KERNEL_ELEC or 'GeneralizedBorn' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
+ /* #if 'Table' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
_fjsp_v2r8 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF,twovfeps;
real *vftab;
/* #endif */
/* #endif */
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = gmx_fjsp_set1_v2r8(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = gmx_fjsp_set1_v2r8((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
- /* #endif */
-
/* #if 'Water' in GEOMETRY_I */
/* Setup water-specific parameters */
inr = nlist->iinr[0];
/* #for I in PARTICLES_ELEC_I */
iq{I} = _fjsp_mul_v2r8(facel,gmx_fjsp_load1_v2r8(charge+inr+{I}));
/* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isai{I} = gmx_fjsp_load1_v2r8(invsqrta+inr+{I});
- /* #endif */
/* #endfor */
/* #for I in PARTICLES_VDW_I */
vdwioffset{I} = 2*nvdwtype*vdwtype[inr+{I}];
/* #if KERNEL_ELEC != 'None' */
velecsum = _fjsp_setzero_v2r8();
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- vgbsum = _fjsp_setzero_v2r8();
- /* #endif */
/* #if KERNEL_VDW != 'None' */
vvdwsum = _fjsp_setzero_v2r8();
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _fjsp_setzero_v2r8();
- /* #endif */
/* #for ROUND in ['Loop','Epilogue'] */
/* #else */
jq{J} = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),charge+jnrA+{J});
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if ROUND =='Loop' */
- isaj{J} = gmx_fjsp_load_2real_swizzle_v2r8(invsqrta+jnrA+{J},invsqrta+jnrB+{J});
- /* #else */
- isaj{J} = _fjsp_loadl_v2r8(_fjsp_setzero_v2r8(),invsqrta+jnrA+{J});
- /* #endif */
- /* #endif */
/* #endfor */
/* #for J in PARTICLES_VDW_J */
vdwjidx{J}A = 2*vdwtype[jnrA+{J}];
/* #define INNERFLOPS INNERFLOPS+3 */
/* #endif */
- /* #elif KERNEL_ELEC=='GeneralizedBorn' */
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _fjsp_mul_v2r8(isai{I},isaj{J});
- gbqqfactor = _fjsp_neg_v2r8(_fjsp_mul_v2r8(qq{I}{J},_fjsp_mul_v2r8(isaprod,gbinvepsdiff)));
- gbscale = _fjsp_mul_v2r8(isaprod,gbtabscale);
- /* #define INNERFLOPS INNERFLOPS+5 */
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _fjsp_mul_v2r8(r{I}{J},gbscale);
- itab_tmp = _fjsp_dtox_v2r8(rt);
- gbeps = _fjsp_sub_v2r8(rt,_fjsp_xtod_v2r8(itab_tmp));
- _fjsp_store_v2r8(&gbconv.simd,itab_tmp);
-
- Y = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] );
- /* #if ROUND == 'Loop' */
- F = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] );
- /* #else */
- F = _fjsp_setzero_v2r8();
- /* #endif */
- GMX_FJSP_TRANSPOSE2_V2R8(Y,F);
- G = _fjsp_load_v2r8( gbtab + 4*gbconv.i[0] +2);
- /* #if ROUND == 'Loop' */
- H = _fjsp_load_v2r8( gbtab + 4*gbconv.i[1] +2);
- /* #else */
- H = _fjsp_setzero_v2r8();
- /* #endif */
- GMX_FJSP_TRANSPOSE2_V2R8(G,H);
- Fp = _fjsp_madd_v2r8(gbeps,_fjsp_madd_v2r8(gbeps,H,G),F);
- VV = _fjsp_madd_v2r8(gbeps,Fp,Y);
- vgb = _fjsp_mul_v2r8(gbqqfactor,VV);
- /* #define INNERFLOPS INNERFLOPS+10 */
-
- /* #if 'Force' in KERNEL_VF */
- twogbeps = _fjsp_add_v2r8(gbeps,gbeps);
- FF = _fjsp_madd_v2r8(_fjsp_madd_v2r8(twogbeps,H,G),gbeps,Fp);
- fgb = _fjsp_mul_v2r8(gbqqfactor,_fjsp_mul_v2r8(FF,gbscale));
- dvdatmp = _fjsp_mul_v2r8(minushalf,_fjsp_madd_v2r8(fgb,r{I}{J},vgb));
- dvdasum = _fjsp_add_v2r8(dvdasum,dvdatmp);
- /* #if ROUND == 'Loop' */
- gmx_fjsp_increment_2real_swizzle_v2r8(dvda+jnrA,dvda+jnrB,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj{J},isaj{J})));
- /* #else */
- gmx_fjsp_increment_1real_v2r8(dvda+jnrA,_fjsp_mul_v2r8(dvdatmp,_fjsp_mul_v2r8(isaj{J},isaj{J})));
- /* #endif */
- /* #define INNERFLOPS INNERFLOPS+13 */
- /* #endif */
- velec = _fjsp_mul_v2r8(qq{I}{J},rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #if 'Force' in KERNEL_VF */
- felec = _fjsp_mul_v2r8(_fjsp_msub_v2r8(velec,rinv{I}{J},fgb),rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+3 */
- /* #endif */
-
/* #elif KERNEL_ELEC=='Ewald' */
/* EWALD ELECTROSTATICS */
/* #endif */
velecsum = _fjsp_add_v2r8(velecsum,velec);
/* #define INNERFLOPS INNERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
- vgb = _fjsp_and_v2r8(vgb,cutoff_mask);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
- /* #if ROUND == 'Epilogue' */
- vgb = _fjsp_unpacklo_v2r8(vgb,_fjsp_setzero_v2r8());
- /* #endif */
- vgbsum = _fjsp_add_v2r8(vgbsum,vgb);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
/* #endif */
/* #if 'vdw' in INTERACTION_FLAGS[I][J] */
/* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
gmx_fjsp_update_1pot_v2r8(velecsum,kernel_data->energygrp_elec+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- gmx_fjsp_update_1pot_v2r8(vgbsum,kernel_data->energygrp_polarization+ggid);
- /* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #endif */
/* #if KERNEL_VDW != 'None' */
gmx_fjsp_update_1pot_v2r8(vvdwsum,kernel_data->energygrp_vdw+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _fjsp_mul_v2r8(dvdasum, _fjsp_mul_v2r8(isai{I},isai{I}));
- gmx_fjsp_update_1pot_v2r8(dvdasum,dvda+inr);
- /* #endif */
/* Increment number of inner iterations */
inneriter += j_index_end - j_index_start;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
- 'GeneralizedBorn' : ['rinv','r'],
'CubicSplineTable' : ['rinv','r','table'],
'Ewald' : ['rinv','rinvsq','r'],
}
'Coulomb' : 'Coul',
'Ewald' : 'Ew',
'ReactionField' : 'RF',
- 'GeneralizedBorn' : 'GB',
'CubicSplineTable' : 'CSTab',
'LennardJones' : 'LJ',
'Buckingham' : 'Bham',
return 0
# No need for LJ-only water optimization, or water optimization with implicit solvent.
- if('Water' in KernelGeom[0] and (KernelElec=='None' or 'GeneralizedBorn' in KernelElec)):
+ if('Water' in KernelGeom[0] and KernelElec=='None'):
return 0
# Non-matching table settings are pointless
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse2_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse2_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse2_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse2_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_pd(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_pd();
- vgbsum = _mm_setzero_pd();
- vvdwsum = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
- vfeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(vfitab));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(vfeps,Fp));
- vvdw6 = _mm_mul_pd(c6_00,VV);
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(vfeps,Fp));
- vvdw12 = _mm_mul_pd(c12_00,VV);
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw12 = _mm_mul_pd(c12_00,FF);
- vvdw = _mm_add_pd(vvdw12,vvdw6);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_pd(velecsum,velec);
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 92 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
- vfeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(vfitab));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(vfeps,Fp));
- vvdw6 = _mm_mul_pd(c6_00,VV);
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(vfeps,Fp));
- vvdw12 = _mm_mul_pd(c12_00,VV);
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw12 = _mm_mul_pd(c12_00,FF);
- vvdw = _mm_add_pd(vvdw12,vvdw6);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_unpacklo_pd(velec,_mm_setzero_pd());
- velecsum = _mm_add_pd(velecsum,velec);
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdw = _mm_unpacklo_pd(vvdw,_mm_setzero_pd());
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 92 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*92);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse2_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse2_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_pd(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
- vfeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(vfitab));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw12 = _mm_mul_pd(c12_00,FF);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 82 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
- vfeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(vfitab));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw12 = _mm_mul_pd(c12_00,FF);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 82 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*82);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse2_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse2_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_pd();
- vgbsum = _mm_setzero_pd();
- vvdwsum = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_pd(c6_00,rinvsix);
- vvdw12 = _mm_mul_pd(c12_00,_mm_mul_pd(rinvsix,rinvsix));
- vvdw = _mm_sub_pd( _mm_mul_pd(vvdw12,one_twelfth) , _mm_mul_pd(vvdw6,one_sixth) );
- fvdw = _mm_mul_pd(_mm_sub_pd(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_pd(velecsum,velec);
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 71 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_pd(c6_00,rinvsix);
- vvdw12 = _mm_mul_pd(c12_00,_mm_mul_pd(rinvsix,rinvsix));
- vvdw = _mm_sub_pd( _mm_mul_pd(vvdw12,one_twelfth) , _mm_mul_pd(vvdw6,one_sixth) );
- fvdw = _mm_mul_pd(_mm_sub_pd(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_unpacklo_pd(velec,_mm_setzero_pd());
- velecsum = _mm_add_pd(velecsum,velec);
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdw = _mm_unpacklo_pd(vvdw,_mm_setzero_pd());
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 71 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*71);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(c12_00,rinvsix),c6_00),_mm_mul_pd(rinvsix,rinvsq00));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 64 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(c12_00,rinvsix),c6_00),_mm_mul_pd(rinvsix,rinvsq00));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 64 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*64);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse2_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse2_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse2_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse2_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
-
- /* Reset potential sums */
- velecsum = _mm_setzero_pd();
- vgbsum = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_pd(velecsum,velec);
- vgbsum = _mm_add_pd(vgbsum,vgb);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 58 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_unpacklo_pd(velec,_mm_setzero_pd());
- velecsum = _mm_add_pd(velecsum,velec);
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- vgbsum = _mm_add_pd(vgbsum,vgb);
-
- fscal = felec;
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 58 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 9 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*9 + inneriter*58);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse2_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse2_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
-
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 56 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 56 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*7 + inneriter*56);
-}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_t nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse2_double;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse2_double;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse2_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse2_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse2_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse2_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse2_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_double;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse2_double;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse2_double;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse2_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse2_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse2_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse2_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse2_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse2_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_double;
nb_kernel_info_t
{ nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse2_double, "nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse2_double", "sse2_double", "None", "None", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse2_double, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse2_double", "sse2_double", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse2_double, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse2_double", "sse2_double", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse2_double, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse2_double", "sse2_double", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse2_double, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse2_double", "sse2_double", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse2_double, "nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse2_double", "sse2_double", "Ewald", "None", "LJEwald", "None", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse2_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse2_double", "sse2_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse2_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse2_double", "sse2_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse2_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse2_double", "sse2_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_double", "sse2_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_double, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_double", "sse2_double", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_double, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_double", "sse2_double", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse2_double, "nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse2_double", "sse2_double", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse2_double, "nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse2_double", "sse2_double", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse2_double, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse2_double", "sse2_double", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse2_double, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse2_double", "sse2_double", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse2_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse2_double", "sse2_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse2_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse2_double", "sse2_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse2_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse2_double", "sse2_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_sse2_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_sse2_double", "sse2_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse2_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse2_double", "sse2_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse2_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse2_double", "sse2_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_double", "sse2_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_double", "sse2_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_double", "sse2_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_double", "sse2_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_double", "sse2_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
};
int
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
__m128d velec,felec,velecsum,facel,crf,krf,krf2;
real *charge;
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- /* #endif */
/* #if KERNEL_VDW != 'None' */
int nvdwtype;
__m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
__m128d one_sixth = _mm_set1_pd(1.0/6.0);
__m128d one_twelfth = _mm_set1_pd(1.0/12.0);
/* #endif */
- /* #if 'Table' in KERNEL_ELEC or 'GeneralizedBorn' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
+ /* #if 'Table' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
__m128i vfitab;
__m128i ifour = _mm_set1_epi32(4);
__m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
/* #endif */
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
- /* #endif */
-
/* #if 'Water' in GEOMETRY_I */
/* Setup water-specific parameters */
inr = nlist->iinr[0];
/* #for I in PARTICLES_ELEC_I */
iq{I} = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+{I}));
/* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isai{I} = _mm_load1_pd(invsqrta+inr+{I});
- /* #endif */
/* #endfor */
/* #for I in PARTICLES_VDW_I */
vdwioffset{I} = 2*nvdwtype*vdwtype[inr+{I}];
/* #if KERNEL_ELEC != 'None' */
velecsum = _mm_setzero_pd();
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- vgbsum = _mm_setzero_pd();
- /* #endif */
/* #if KERNEL_VDW != 'None' */
vvdwsum = _mm_setzero_pd();
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_setzero_pd();
- /* #endif */
/* #for ROUND in ['Loop','Epilogue'] */
/* #else */
jq{J} = _mm_load_sd(charge+jnrA+{J});
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if ROUND =='Loop' */
- isaj{J} = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+{J},invsqrta+jnrB+{J});
- /* #else */
- isaj{J} = _mm_load_sd(invsqrta+jnrA+{J});
- /* #endif */
- /* #endif */
/* #endfor */
/* #for J in PARTICLES_VDW_J */
vdwjidx{J}A = 2*vdwtype[jnrA+{J}];
/* #define INNERFLOPS INNERFLOPS+3 */
/* #endif */
- /* #elif KERNEL_ELEC=='GeneralizedBorn' */
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai{I},isaj{J});
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq{I}{J},_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
- /* #define INNERFLOPS INNERFLOPS+5 */
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r{I}{J},gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_cvtepi32_pd(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- /* #if ROUND == 'Loop' */
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- /* #else */
- F = _mm_setzero_pd();
- /* #endif */
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- /* #if ROUND == 'Loop' */
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- /* #else */
- H = _mm_setzero_pd();
- /* #endif */
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
- /* #define INNERFLOPS INNERFLOPS+10 */
-
- /* #if 'Force' in KERNEL_VF */
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r{I}{J})));
- /* #if ROUND == 'Epilogue' */
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- /* #endif */
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- /* #if ROUND == 'Loop' */
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj{J},isaj{J})));
- /* #else */
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj{J},isaj{J})));
- /* #endif */
- /* #define INNERFLOPS INNERFLOPS+13 */
- /* #endif */
- velec = _mm_mul_pd(qq{I}{J},rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #if 'Force' in KERNEL_VF */
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv{I}{J}),fgb),rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+3 */
- /* #endif */
-
/* #elif KERNEL_ELEC=='Ewald' */
/* EWALD ELECTROSTATICS */
/* #endif */
velecsum = _mm_add_pd(velecsum,velec);
/* #define INNERFLOPS INNERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
- vgb = _mm_and_pd(vgb,cutoff_mask);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
- /* #if ROUND == 'Epilogue' */
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- /* #endif */
- vgbsum = _mm_add_pd(vgbsum,vgb);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
/* #endif */
/* #if 'vdw' in INTERACTION_FLAGS[I][J] */
/* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- /* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #endif */
/* #if KERNEL_VDW != 'None' */
gmx_mm_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai{I},isai{I}));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
- /* #endif */
/* Increment number of inner iterations */
inneriter += j_index_end - j_index_start;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
- 'GeneralizedBorn' : ['rinv','r'],
'CubicSplineTable' : ['rinv','r','table'],
'Ewald' : ['rinv','rinvsq','r'],
}
'Coulomb' : 'Coul',
'Ewald' : 'Ew',
'ReactionField' : 'RF',
- 'GeneralizedBorn' : 'GB',
'CubicSplineTable' : 'CSTab',
'LennardJones' : 'LJ',
'Buckingham' : 'Bham',
return 0
# No need for LJ-only water optimization, or water optimization with implicit solvent.
- if('Water' in KernelGeom[0] and (KernelElec=='None' or 'GeneralizedBorn' in KernelElec)):
+ if('Water' in KernelGeom[0] and KernelElec=='None'):
return 0
# Non-matching table settings are pointless
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse2_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse2_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse2_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse2_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_ps(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_ps();
- vgbsum = _mm_setzero_ps();
- vvdwsum = _mm_setzero_ps();
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
- vfeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(vfitab));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(vfeps,Fp));
- vvdw6 = _mm_mul_ps(c6_00,VV);
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(vfeps,Fp));
- vvdw12 = _mm_mul_ps(c12_00,VV);
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw12 = _mm_mul_ps(c12_00,FF);
- vvdw = _mm_add_ps(vvdw12,vvdw6);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_ps(velecsum,velec);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 92 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
- vfeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(vfitab));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(vfeps,Fp));
- vvdw6 = _mm_mul_ps(c6_00,VV);
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(vfeps,Fp));
- vvdw12 = _mm_mul_ps(c12_00,VV);
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw12 = _mm_mul_ps(c12_00,FF);
- vvdw = _mm_add_ps(vvdw12,vvdw6);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_andnot_ps(dummy_mask,velec);
- velecsum = _mm_add_ps(velecsum,velec);
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdw = _mm_andnot_ps(dummy_mask,vvdw);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 93 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*93);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse2_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse2_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_ps(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
- vfeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(vfitab));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw12 = _mm_mul_ps(c12_00,FF);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 82 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
- vfeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(vfitab));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw12 = _mm_mul_ps(c12_00,FF);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 83 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*83);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse2_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse2_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_ps();
- vgbsum = _mm_setzero_ps();
- vvdwsum = _mm_setzero_ps();
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_ps(c6_00,rinvsix);
- vvdw12 = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
- vvdw = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
- fvdw = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_ps(velecsum,velec);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 71 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_ps(c6_00,rinvsix);
- vvdw12 = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
- vvdw = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
- fvdw = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_andnot_ps(dummy_mask,velec);
- velecsum = _mm_add_ps(velecsum,velec);
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdw = _mm_andnot_ps(dummy_mask,vvdw);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 72 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*72);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 64 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 65 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*65);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse2_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse2_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse2_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse2_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
-
- /* Reset potential sums */
- velecsum = _mm_setzero_ps();
- vgbsum = _mm_setzero_ps();
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_ps(velecsum,velec);
- vgbsum = _mm_add_ps(vgbsum,vgb);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 58 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_andnot_ps(dummy_mask,velec);
- velecsum = _mm_add_ps(velecsum,velec);
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm_add_ps(vgbsum,vgb);
-
- fscal = felec;
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 59 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 9 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*9 + inneriter*59);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse2_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse2_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
-
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 56 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse2_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 57 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*7 + inneriter*57);
-}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_t nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse2_single;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse2_single;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse2_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse2_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse2_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse2_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse2_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_single;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse2_single;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse2_single;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse2_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse2_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse2_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse2_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse2_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse2_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_single;
nb_kernel_info_t
{ nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse2_single, "nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse2_single", "sse2_single", "None", "None", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse2_single, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse2_single", "sse2_single", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse2_single, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse2_single", "sse2_single", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse2_single, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse2_single", "sse2_single", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse2_single, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse2_single", "sse2_single", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse2_single, "nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse2_single", "sse2_single", "Ewald", "None", "LJEwald", "None", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse2_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse2_single", "sse2_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse2_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse2_single", "sse2_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse2_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse2_single", "sse2_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse2_single", "sse2_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_single, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_single", "sse2_single", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_single, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_single", "sse2_single", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse2_single, "nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse2_single", "sse2_single", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse2_single, "nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse2_single", "sse2_single", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse2_single, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse2_single", "sse2_single", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse2_single, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse2_single", "sse2_single", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse2_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse2_single", "sse2_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse2_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse2_single", "sse2_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse2_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse2_single", "sse2_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_sse2_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_sse2_single", "sse2_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse2_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse2_single", "sse2_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse2_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse2_single", "sse2_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_single", "sse2_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse2_single", "sse2_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse2_single", "sse2_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse2_single", "sse2_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse2_single", "sse2_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
};
int
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
__m128 velec,felec,velecsum,facel,crf,krf,krf2;
real *charge;
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- /* #endif */
/* #if KERNEL_VDW != 'None' */
int nvdwtype;
__m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
__m128 one_sixth = _mm_set1_ps(1.0/6.0);
__m128 one_twelfth = _mm_set1_ps(1.0/12.0);
/* #endif */
- /* #if 'Table' in KERNEL_ELEC or 'GeneralizedBorn' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
+ /* #if 'Table' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
__m128i vfitab;
__m128i ifour = _mm_set1_epi32(4);
__m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
/* #endif */
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
- /* #endif */
-
/* #if 'Water' in GEOMETRY_I */
/* Setup water-specific parameters */
inr = nlist->iinr[0];
/* #for I in PARTICLES_ELEC_I */
iq{I} = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+{I}));
/* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isai{I} = _mm_load1_ps(invsqrta+inr+{I});
- /* #endif */
/* #endfor */
/* #for I in PARTICLES_VDW_I */
vdwioffset{I} = 2*nvdwtype*vdwtype[inr+{I}];
/* #if KERNEL_ELEC != 'None' */
velecsum = _mm_setzero_ps();
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- vgbsum = _mm_setzero_ps();
- /* #endif */
/* #if KERNEL_VDW != 'None' */
vvdwsum = _mm_setzero_ps();
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_setzero_ps();
- /* #endif */
/* #for ROUND in ['Loop','Epilogue'] */
/* #for J in PARTICLES_ELEC_J */
jq{J} = gmx_mm_load_4real_swizzle_ps(charge+jnrA+{J},charge+jnrB+{J},
charge+jnrC+{J},charge+jnrD+{J});
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isaj{J} = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+{J},invsqrta+jnrB+{J},
- invsqrta+jnrC+{J},invsqrta+jnrD+{J});
- /* #endif */
/* #endfor */
/* #for J in PARTICLES_VDW_J */
vdwjidx{J}A = 2*vdwtype[jnrA+{J}];
/* #define INNERFLOPS INNERFLOPS+3 */
/* #endif */
- /* #elif KERNEL_ELEC=='GeneralizedBorn' */
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai{I},isaj{J});
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq{I}{J},_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
- /* #define INNERFLOPS INNERFLOPS+5 */
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r{I}{J},gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
- /* #define INNERFLOPS INNERFLOPS+10 */
-
- /* #if 'Force' in KERNEL_VF */
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r{I}{J})));
- /* #if ROUND == 'Epilogue' */
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- /* #endif */
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* #if ROUND == 'Loop' */
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- /* #else */
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- /* #endif */
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj{J},isaj{J})));
- /* #define INNERFLOPS INNERFLOPS+13 */
- /* #endif */
- velec = _mm_mul_ps(qq{I}{J},rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #if 'Force' in KERNEL_VF */
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv{I}{J}),fgb),rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+3 */
- /* #endif */
-
/* #elif KERNEL_ELEC=='Ewald' */
/* EWALD ELECTROSTATICS */
/* #endif */
velecsum = _mm_add_ps(velecsum,velec);
/* #define INNERFLOPS INNERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
- vgb = _mm_and_ps(vgb,cutoff_mask);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
- /* #if ROUND == 'Epilogue' */
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- /* #endif */
- vgbsum = _mm_add_ps(vgbsum,vgb);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
/* #endif */
/* #if 'vdw' in INTERACTION_FLAGS[I][J] */
/* ## Note special check for TIP4P-TIP4P. Since we are cutting of all hydrogen interactions we also cut the LJ-only O-O interaction */
gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- /* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #endif */
/* #if KERNEL_VDW != 'None' */
gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai{I},isai{I}));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
- /* #endif */
/* Increment number of inner iterations */
inneriter += j_index_end - j_index_start;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
- 'GeneralizedBorn' : ['rinv','r'],
'CubicSplineTable' : ['rinv','r','table'],
'Ewald' : ['rinv','rinvsq','r'],
}
'Coulomb' : 'Coul',
'Ewald' : 'Ew',
'ReactionField' : 'RF',
- 'GeneralizedBorn' : 'GB',
'CubicSplineTable' : 'CSTab',
'LennardJones' : 'LJ',
'Buckingham' : 'Bham',
return 0
# No need for LJ-only water optimization, or water optimization with implicit solvent.
- if('Water' in KernelGeom[0] and (KernelElec=='None' or 'GeneralizedBorn' in KernelElec)):
+ if('Water' in KernelGeom[0] and KernelElec=='None'):
return 0
# Non-matching table settings are pointless
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse4_1_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse4_1_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse4_1_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse4_1_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_pd(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_pd();
- vgbsum = _mm_setzero_pd();
- vvdwsum = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
- vfeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(vfeps,Fp));
- vvdw6 = _mm_mul_pd(c6_00,VV);
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(vfeps,Fp));
- vvdw12 = _mm_mul_pd(c12_00,VV);
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw12 = _mm_mul_pd(c12_00,FF);
- vvdw = _mm_add_pd(vvdw12,vvdw6);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_pd(velecsum,velec);
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 92 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
- vfeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(vfeps,Fp));
- vvdw6 = _mm_mul_pd(c6_00,VV);
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(vfeps,Fp));
- vvdw12 = _mm_mul_pd(c12_00,VV);
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw12 = _mm_mul_pd(c12_00,FF);
- vvdw = _mm_add_pd(vvdw12,vvdw6);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_unpacklo_pd(velec,_mm_setzero_pd());
- velecsum = _mm_add_pd(velecsum,velec);
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdw = _mm_unpacklo_pd(vvdw,_mm_setzero_pd());
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 92 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*92);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse4_1_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse4_1_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_pd(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
- vfeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw12 = _mm_mul_pd(c12_00,FF);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 82 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_pd(r00,vftabscale);
- vfitab = _mm_cvttpd_epi32(rt);
- vfeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw6 = _mm_mul_pd(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( vftab + gmx_mm_extract_epi32(vfitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(vfeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(vfeps,_mm_add_pd(G,Heps)));
- FF = _mm_add_pd(Fp,_mm_mul_pd(vfeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fvdw12 = _mm_mul_pd(c12_00,FF);
- fvdw = _mm_xor_pd(signbit,_mm_mul_pd(_mm_add_pd(fvdw6,fvdw12),_mm_mul_pd(vftabscale,rinv00)));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 82 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*82);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse4_1_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse4_1_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_pd();
- vgbsum = _mm_setzero_pd();
- vvdwsum = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_pd(c6_00,rinvsix);
- vvdw12 = _mm_mul_pd(c12_00,_mm_mul_pd(rinvsix,rinvsix));
- vvdw = _mm_sub_pd( _mm_mul_pd(vvdw12,one_twelfth) , _mm_mul_pd(vvdw6,one_sixth) );
- fvdw = _mm_mul_pd(_mm_sub_pd(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_pd(velecsum,velec);
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 71 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_pd(c6_00,rinvsix);
- vvdw12 = _mm_mul_pd(c12_00,_mm_mul_pd(rinvsix,rinvsix));
- vvdw = _mm_sub_pd( _mm_mul_pd(vvdw12,one_twelfth) , _mm_mul_pd(vvdw6,one_sixth) );
- fvdw = _mm_mul_pd(_mm_sub_pd(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_unpacklo_pd(velec,_mm_setzero_pd());
- velecsum = _mm_add_pd(velecsum,velec);
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- vgbsum = _mm_add_pd(vgbsum,vgb);
- vvdw = _mm_unpacklo_pd(vvdw,_mm_setzero_pd());
- vvdwsum = _mm_add_pd(vvdwsum,vvdw);
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 71 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*71);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128d one_sixth = _mm_set1_pd(1.0/6.0);
- __m128d one_twelfth = _mm_set1_pd(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_2pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(c12_00,rinvsix),c6_00),_mm_mul_pd(rinvsix,rinvsq00));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 64 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- rinvsq00 = _mm_mul_pd(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
- gmx_mm_load_1pair_swizzle_pd(vdwparam+vdwioffset0+vdwjidx0A,&c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_pd(_mm_mul_pd(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(c12_00,rinvsix),c6_00),_mm_mul_pd(rinvsix,rinvsq00));
-
- fscal = _mm_add_pd(felec,fvdw);
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 64 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*64);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse4_1_double kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse4_1_double.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse4_1_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse4_1_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
-
- /* Reset potential sums */
- velecsum = _mm_setzero_pd();
- vgbsum = _mm_setzero_pd();
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_pd(velecsum,velec);
- vgbsum = _mm_add_pd(vgbsum,vgb);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 58 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_unpacklo_pd(velec,_mm_setzero_pd());
- velecsum = _mm_add_pd(velecsum,velec);
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- vgbsum = _mm_add_pd(vgbsum,vgb);
-
- fscal = felec;
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 58 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 9 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*9 + inneriter*58);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse4_1_double
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse4_1_double
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B refer to j loop unrolling done with SSE double precision, e.g. for the two different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB;
- int j_coord_offsetA,j_coord_offsetB;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- __m128d tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128d ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B;
- __m128d jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128d dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128d velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128d dummy_mask,cutoff_mask;
- __m128d signbit = gmx_mm_castsi128_pd( _mm_set_epi32(0x80000000,0x00000000,0x80000000,0x00000000) );
- __m128d one = _mm_set1_pd(1.0);
- __m128d two = _mm_set1_pd(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_pd(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_pd();
- fiy0 = _mm_setzero_pd();
- fiz0 = _mm_setzero_pd();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+0));
- isai0 = _mm_load1_pd(invsqrta+inr+0);
-
- dvdasum = _mm_setzero_pd();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end-1; jidx+=2)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_2ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_2real_swizzle_pd(charge+jnrA+0,charge+jnrB+0);
- isaj0 = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_2ptr_swizzle_pd(f+j_coord_offsetA,f+j_coord_offsetB,tx,ty,tz);
-
- /* Inner loop uses 56 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- jnrA = jjnr[jidx];
- j_coord_offsetA = DIM*jnrA;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_1ptr_swizzle_pd(x+j_coord_offsetA,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_pd(ix0,jx0);
- dy00 = _mm_sub_pd(iy0,jy0);
- dz00 = _mm_sub_pd(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_pd(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_d(rsq00);
-
- /* Load parameters for j particles */
- jq0 = _mm_load_sd(charge+jnrA+0);
- isaj0 = _mm_load_sd(invsqrta+jnrA+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_pd(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_pd(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai0,isaj0);
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq00,_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r00,gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- H = _mm_setzero_pd();
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
-
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r00)));
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj0,isaj0)));
- velec = _mm_mul_pd(qq00,rinv00);
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- fscal = _mm_unpacklo_pd(fscal,_mm_setzero_pd());
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_pd(fscal,dx00);
- ty = _mm_mul_pd(fscal,dy00);
- tz = _mm_mul_pd(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_pd(fix0,tx);
- fiy0 = _mm_add_pd(fiy0,ty);
- fiz0 = _mm_add_pd(fiz0,tz);
-
- gmx_mm_decrement_1rvec_1ptr_swizzle_pd(f+j_coord_offsetA,tx,ty,tz);
-
- /* Inner loop uses 56 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai0,isai0));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*7 + inneriter*56);
-}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_t nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse4_1_double;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse4_1_double;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse4_1_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse4_1_double;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse4_1_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse4_1_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse4_1_double;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse4_1_double;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse4_1_double;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse4_1_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse4_1_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse4_1_double;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse4_1_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse4_1_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse4_1_double;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_double;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_double;
nb_kernel_info_t
{ nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse4_1_double", "sse4_1_double", "None", "None", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse4_1_double", "sse4_1_double", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse4_1_double", "sse4_1_double", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "Ewald", "None", "LJEwald", "None", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse4_1_double", "sse4_1_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse4_1_double", "sse4_1_double", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_double", "sse4_1_double", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_double", "sse4_1_double", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse4_1_double", "sse4_1_double", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse4_1_double", "sse4_1_double", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse4_1_double", "sse4_1_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse4_1_double", "sse4_1_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_double", "sse4_1_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_double", "sse4_1_double", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_double, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_double", "sse4_1_double", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
};
int
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
__m128d velec,felec,velecsum,facel,crf,krf,krf2;
real *charge;
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- __m128i gbitab;
- __m128d vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
- __m128d minushalf = _mm_set1_pd(-0.5);
- real *invsqrta,*dvda,*gbtab;
- /* #endif */
/* #if KERNEL_VDW != 'None' */
int nvdwtype;
__m128d rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
__m128d one_sixth = _mm_set1_pd(1.0/6.0);
__m128d one_twelfth = _mm_set1_pd(1.0/12.0);
/* #endif */
- /* #if 'Table' in KERNEL_ELEC or 'GeneralizedBorn' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
+ /* #if 'Table' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
__m128i vfitab;
__m128i ifour = _mm_set1_epi32(4);
__m128d rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
/* #endif */
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_pd(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_pd((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
- /* #endif */
-
/* #if 'Water' in GEOMETRY_I */
/* Setup water-specific parameters */
inr = nlist->iinr[0];
/* #for I in PARTICLES_ELEC_I */
iq{I} = _mm_mul_pd(facel,_mm_load1_pd(charge+inr+{I}));
/* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isai{I} = _mm_load1_pd(invsqrta+inr+{I});
- /* #endif */
/* #endfor */
/* #for I in PARTICLES_VDW_I */
vdwioffset{I} = 2*nvdwtype*vdwtype[inr+{I}];
/* #if KERNEL_ELEC != 'None' */
velecsum = _mm_setzero_pd();
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- vgbsum = _mm_setzero_pd();
- /* #endif */
/* #if KERNEL_VDW != 'None' */
vvdwsum = _mm_setzero_pd();
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_setzero_pd();
- /* #endif */
/* #for ROUND in ['Loop','Epilogue'] */
/* #else */
jq{J} = _mm_load_sd(charge+jnrA+{J});
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if ROUND =='Loop' */
- isaj{J} = gmx_mm_load_2real_swizzle_pd(invsqrta+jnrA+{J},invsqrta+jnrB+{J});
- /* #else */
- isaj{J} = _mm_load_sd(invsqrta+jnrA+{J});
- /* #endif */
- /* #endif */
/* #endfor */
/* #for J in PARTICLES_VDW_J */
vdwjidx{J}A = 2*vdwtype[jnrA+{J}];
/* #define INNERFLOPS INNERFLOPS+3 */
/* #endif */
- /* #elif KERNEL_ELEC=='GeneralizedBorn' */
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_pd(isai{I},isaj{J});
- gbqqfactor = _mm_xor_pd(signbit,_mm_mul_pd(qq{I}{J},_mm_mul_pd(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_pd(isaprod,gbtabscale);
- /* #define INNERFLOPS INNERFLOPS+5 */
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_pd(r{I}{J},gbscale);
- gbitab = _mm_cvttpd_epi32(rt);
- gbeps = _mm_sub_pd(rt,_mm_round_pd(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
-
- Y = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- /* #if ROUND == 'Loop' */
- F = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- /* #else */
- F = _mm_setzero_pd();
- /* #endif */
- GMX_MM_TRANSPOSE2_PD(Y,F);
- G = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,0) +2);
- /* #if ROUND == 'Loop' */
- H = _mm_load_pd( gbtab + gmx_mm_extract_epi32(gbitab,1) +2);
- /* #else */
- H = _mm_setzero_pd();
- /* #endif */
- GMX_MM_TRANSPOSE2_PD(G,H);
- Heps = _mm_mul_pd(gbeps,H);
- Fp = _mm_add_pd(F,_mm_mul_pd(gbeps,_mm_add_pd(G,Heps)));
- VV = _mm_add_pd(Y,_mm_mul_pd(gbeps,Fp));
- vgb = _mm_mul_pd(gbqqfactor,VV);
- /* #define INNERFLOPS INNERFLOPS+10 */
-
- /* #if 'Force' in KERNEL_VF */
- FF = _mm_add_pd(Fp,_mm_mul_pd(gbeps,_mm_add_pd(G,_mm_add_pd(Heps,Heps))));
- fgb = _mm_mul_pd(gbqqfactor,_mm_mul_pd(FF,gbscale));
- dvdatmp = _mm_mul_pd(minushalf,_mm_add_pd(vgb,_mm_mul_pd(fgb,r{I}{J})));
- /* #if ROUND == 'Epilogue' */
- dvdatmp = _mm_unpacklo_pd(dvdatmp,_mm_setzero_pd());
- /* #endif */
- dvdasum = _mm_add_pd(dvdasum,dvdatmp);
- /* #if ROUND == 'Loop' */
- gmx_mm_increment_2real_swizzle_pd(dvda+jnrA,dvda+jnrB,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj{J},isaj{J})));
- /* #else */
- gmx_mm_increment_1real_pd(dvda+jnrA,_mm_mul_pd(dvdatmp,_mm_mul_pd(isaj{J},isaj{J})));
- /* #endif */
- /* #define INNERFLOPS INNERFLOPS+13 */
- /* #endif */
- velec = _mm_mul_pd(qq{I}{J},rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #if 'Force' in KERNEL_VF */
- felec = _mm_mul_pd(_mm_sub_pd(_mm_mul_pd(velec,rinv{I}{J}),fgb),rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+3 */
- /* #endif */
-
/* #elif KERNEL_ELEC=='Ewald' */
/* EWALD ELECTROSTATICS */
/* #endif */
velecsum = _mm_add_pd(velecsum,velec);
/* #define INNERFLOPS INNERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
- vgb = _mm_and_pd(vgb,cutoff_mask);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
- /* #if ROUND == 'Epilogue' */
- vgb = _mm_unpacklo_pd(vgb,_mm_setzero_pd());
- /* #endif */
- vgbsum = _mm_add_pd(vgbsum,vgb);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
/* #endif */
/* #if 'vdw' in INTERACTION_FLAGS[I][J] */
/* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
gmx_mm_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- gmx_mm_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
- /* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #endif */
/* #if KERNEL_VDW != 'None' */
gmx_mm_update_1pot_pd(vvdwsum,kernel_data->energygrp_vdw+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_mul_pd(dvdasum, _mm_mul_pd(isai{I},isai{I}));
- gmx_mm_update_1pot_pd(dvdasum,dvda+inr);
- /* #endif */
/* Increment number of inner iterations */
inneriter += j_index_end - j_index_start;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'None' : [],
'Coulomb' : ['rinv','rinvsq'],
'ReactionField' : ['rinv','rinvsq'],
- 'GeneralizedBorn' : ['rinv','r'],
'CubicSplineTable' : ['rinv','r','table'],
'Ewald' : ['rinv','rinvsq','r'],
}
'Coulomb' : 'Coul',
'Ewald' : 'Ew',
'ReactionField' : 'RF',
- 'GeneralizedBorn' : 'GB',
'CubicSplineTable' : 'CSTab',
'LennardJones' : 'LJ',
'Buckingham' : 'Bham',
return 0
# No need for LJ-only water optimization, or water optimization with implicit solvent.
- if('Water' in KernelGeom[0] and (KernelElec=='None' or 'GeneralizedBorn' in KernelElec)):
+ if('Water' in KernelGeom[0] and KernelElec=='None'):
return 0
# Non-matching table settings are pointless
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse4_1_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse4_1_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse4_1_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse4_1_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_ps(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_ps();
- vgbsum = _mm_setzero_ps();
- vvdwsum = _mm_setzero_ps();
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
- vfeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(vfeps,Fp));
- vvdw6 = _mm_mul_ps(c6_00,VV);
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(vfeps,Fp));
- vvdw12 = _mm_mul_ps(c12_00,VV);
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw12 = _mm_mul_ps(c12_00,FF);
- vvdw = _mm_add_ps(vvdw12,vvdw6);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_ps(velecsum,velec);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 92 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
- vfeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(vfeps,Fp));
- vvdw6 = _mm_mul_ps(c6_00,VV);
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(vfeps,Fp));
- vvdw12 = _mm_mul_ps(c12_00,VV);
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw12 = _mm_mul_ps(c12_00,FF);
- vvdw = _mm_add_ps(vvdw12,vvdw6);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_andnot_ps(dummy_mask,velec);
- velecsum = _mm_add_ps(velecsum,velec);
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdw = _mm_andnot_ps(dummy_mask,vvdw);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 93 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*93);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse4_1_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: CubicSplineTable
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse4_1_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- vftab = kernel_data->table_vdw->data;
- vftabscale = _mm_set1_ps(kernel_data->table_vdw->scale);
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
- vfeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw12 = _mm_mul_ps(c12_00,FF);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 82 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* Calculate table index by multiplying r with table scale and truncate to integer */
- rt = _mm_mul_ps(r00,vftabscale);
- vfitab = _mm_cvttps_epi32(rt);
- vfeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- vfitab = _mm_slli_epi32(vfitab,3);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* CUBIC SPLINE TABLE DISPERSION */
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw6 = _mm_mul_ps(c6_00,FF);
-
- /* CUBIC SPLINE TABLE REPULSION */
- vfitab = _mm_add_epi32(vfitab,ifour);
- Y = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,0) );
- F = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,1) );
- G = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,2) );
- H = _mm_load_ps( vftab + gmx_mm_extract_epi32(vfitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(vfeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(vfeps,_mm_add_ps(G,Heps)));
- FF = _mm_add_ps(Fp,_mm_mul_ps(vfeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fvdw12 = _mm_mul_ps(c12_00,FF);
- fvdw = _mm_xor_ps(signbit,_mm_mul_ps(_mm_add_ps(fvdw6,fvdw12),_mm_mul_ps(vftabscale,rinv00)));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 83 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*83);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse4_1_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse4_1_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- /* Reset potential sums */
- velecsum = _mm_setzero_ps();
- vgbsum = _mm_setzero_ps();
- vvdwsum = _mm_setzero_ps();
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_ps(c6_00,rinvsix);
- vvdw12 = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
- vvdw = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
- fvdw = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_ps(velecsum,velec);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 71 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- vvdw6 = _mm_mul_ps(c6_00,rinvsix);
- vvdw12 = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
- vvdw = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
- fvdw = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_andnot_ps(dummy_mask,velec);
- velecsum = _mm_add_ps(velecsum,velec);
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm_add_ps(vgbsum,vgb);
- vvdw = _mm_andnot_ps(dummy_mask,vvdw);
- vvdwsum = _mm_add_ps(vvdwsum,vvdw);
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 72 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 10 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*72);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: LennardJones
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- int nvdwtype;
- __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
- int *vdwtype;
- real *vdwparam;
- __m128 one_sixth = _mm_set1_ps(1.0/6.0);
- __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
- nvdwtype = fr->ntype;
- vdwparam = fr->nbfp;
- vdwtype = mdatoms->typeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
- vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
-
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 64 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- rinvsq00 = _mm_mul_ps(rinv00,rinv00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
- vdwjidx0A = 2*vdwtype[jnrA+0];
- vdwjidx0B = 2*vdwtype[jnrB+0];
- vdwjidx0C = 2*vdwtype[jnrC+0];
- vdwjidx0D = 2*vdwtype[jnrD+0];
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
- gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
- vdwparam+vdwioffset0+vdwjidx0B,
- vdwparam+vdwioffset0+vdwjidx0C,
- vdwparam+vdwioffset0+vdwjidx0D,
- &c6_00,&c12_00);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* LENNARD-JONES DISPERSION/REPULSION */
-
- rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
- fvdw = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
-
- fscal = _mm_add_ps(felec,fvdw);
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 65 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*65);
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the GROMACS sse4_1_single kernel generator.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "../nb_kernel.h"
-#include "gromacs/gmxlib/nrnb.h"
-
-#include "kernelutil_x86_sse4_1_single.h"
-
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse4_1_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: PotentialAndForce
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse4_1_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
-
- /* Reset potential sums */
- velecsum = _mm_setzero_ps();
- vgbsum = _mm_setzero_ps();
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velecsum = _mm_add_ps(velecsum,velec);
- vgbsum = _mm_add_ps(vgbsum,vgb);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 58 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- /* Update potential sum for this i atom from the interaction with this j atom. */
- velec = _mm_andnot_ps(dummy_mask,velec);
- velecsum = _mm_add_ps(velecsum,velec);
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- vgbsum = _mm_add_ps(vgbsum,vgb);
-
- fscal = felec;
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 59 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- ggid = gid[iidx];
- /* Update potential energies */
- gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 9 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*9 + inneriter*59);
-}
-/*
- * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse4_1_single
- * Electrostatics interaction: GeneralizedBorn
- * VdW interaction: None
- * Geometry: Particle-Particle
- * Calculate force/pot: Force
- */
-void
-nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse4_1_single
- (t_nblist * gmx_restrict nlist,
- rvec * gmx_restrict xx,
- rvec * gmx_restrict ff,
- struct t_forcerec * gmx_restrict fr,
- t_mdatoms * gmx_restrict mdatoms,
- nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
- t_nrnb * gmx_restrict nrnb)
-{
- /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
- * just 0 for non-waters.
- * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
- * jnr indices corresponding to data put in the four positions in the SIMD register.
- */
- int i_shift_offset,i_coord_offset,outeriter,inneriter;
- int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
- int jnrA,jnrB,jnrC,jnrD;
- int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
- int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
- int *iinr,*jindex,*jjnr,*shiftidx,*gid;
- real rcutoff_scalar;
- real *shiftvec,*fshift,*x,*f;
- real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
- real scratch[4*DIM];
- __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
- int vdwioffset0;
- __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
- int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
- __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
- __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
- __m128 velec,felec,velecsum,facel,crf,krf,krf2;
- real *charge;
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- __m128i vfitab;
- __m128i ifour = _mm_set1_epi32(4);
- __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
- real *vftab;
- __m128 dummy_mask,cutoff_mask;
- __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
- __m128 one = _mm_set1_ps(1.0);
- __m128 two = _mm_set1_ps(2.0);
- x = xx[0];
- f = ff[0];
-
- nri = nlist->nri;
- iinr = nlist->iinr;
- jindex = nlist->jindex;
- jjnr = nlist->jjnr;
- shiftidx = nlist->shift;
- gid = nlist->gid;
- shiftvec = fr->shift_vec[0];
- fshift = fr->fshift[0];
- facel = _mm_set1_ps(fr->ic->epsfac);
- charge = mdatoms->chargeA;
-
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
-
- /* Avoid stupid compiler warnings */
- jnrA = jnrB = jnrC = jnrD = 0;
- j_coord_offsetA = 0;
- j_coord_offsetB = 0;
- j_coord_offsetC = 0;
- j_coord_offsetD = 0;
-
- outeriter = 0;
- inneriter = 0;
-
- for(iidx=0;iidx<4*DIM;iidx++)
- {
- scratch[iidx] = 0.0;
- }
-
- /* Start outer loop over neighborlists */
- for(iidx=0; iidx<nri; iidx++)
- {
- /* Load shift vector for this list */
- i_shift_offset = DIM*shiftidx[iidx];
-
- /* Load limits for loop over neighbors */
- j_index_start = jindex[iidx];
- j_index_end = jindex[iidx+1];
-
- /* Get outer coordinate index */
- inr = iinr[iidx];
- i_coord_offset = DIM*inr;
-
- /* Load i particle coords and add shift vector */
- gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
-
- fix0 = _mm_setzero_ps();
- fiy0 = _mm_setzero_ps();
- fiz0 = _mm_setzero_ps();
-
- /* Load parameters for i particles */
- iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
- isai0 = _mm_load1_ps(invsqrta+inr+0);
-
- dvdasum = _mm_setzero_ps();
-
- /* Start inner kernel loop */
- for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrA = jjnr[jidx];
- jnrB = jjnr[jidx+1];
- jnrC = jjnr[jidx+2];
- jnrD = jjnr[jidx+3];
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = f+j_coord_offsetA;
- fjptrB = f+j_coord_offsetB;
- fjptrC = f+j_coord_offsetC;
- fjptrD = f+j_coord_offsetD;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 56 flops */
- }
-
- if(jidx<j_index_end)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnrlistA = jjnr[jidx];
- jnrlistB = jjnr[jidx+1];
- jnrlistC = jjnr[jidx+2];
- jnrlistD = jjnr[jidx+3];
- /* Sign of each element will be negative for non-real atoms.
- * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
- * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
- */
- dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
- jnrA = (jnrlistA>=0) ? jnrlistA : 0;
- jnrB = (jnrlistB>=0) ? jnrlistB : 0;
- jnrC = (jnrlistC>=0) ? jnrlistC : 0;
- jnrD = (jnrlistD>=0) ? jnrlistD : 0;
- j_coord_offsetA = DIM*jnrA;
- j_coord_offsetB = DIM*jnrB;
- j_coord_offsetC = DIM*jnrC;
- j_coord_offsetD = DIM*jnrD;
-
- /* load j atom coordinates */
- gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
- x+j_coord_offsetC,x+j_coord_offsetD,
- &jx0,&jy0,&jz0);
-
- /* Calculate displacement vector */
- dx00 = _mm_sub_ps(ix0,jx0);
- dy00 = _mm_sub_ps(iy0,jy0);
- dz00 = _mm_sub_ps(iz0,jz0);
-
- /* Calculate squared distance and things based on it */
- rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
-
- rinv00 = sse41_invsqrt_f(rsq00);
-
- /* Load parameters for j particles */
- jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
- charge+jnrC+0,charge+jnrD+0);
- isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
- invsqrta+jnrC+0,invsqrta+jnrD+0);
-
- /**************************
- * CALCULATE INTERACTIONS *
- **************************/
-
- r00 = _mm_mul_ps(rsq00,rinv00);
- r00 = _mm_andnot_ps(dummy_mask,r00);
-
- /* Compute parameters for interactions between i and j atoms */
- qq00 = _mm_mul_ps(iq0,jq0);
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai0,isaj0);
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r00,gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
-
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
- velec = _mm_mul_ps(qq00,rinv00);
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
-
- fscal = felec;
-
- fscal = _mm_andnot_ps(dummy_mask,fscal);
-
- /* Calculate temporary vectorial force */
- tx = _mm_mul_ps(fscal,dx00);
- ty = _mm_mul_ps(fscal,dy00);
- tz = _mm_mul_ps(fscal,dz00);
-
- /* Update vectorial force */
- fix0 = _mm_add_ps(fix0,tx);
- fiy0 = _mm_add_ps(fiy0,ty);
- fiz0 = _mm_add_ps(fiz0,tz);
-
- fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
- fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
- fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
- fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
- gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
-
- /* Inner loop uses 57 flops */
- }
-
- /* End of innermost loop */
-
- gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
- f+i_coord_offset,fshift+i_shift_offset);
-
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
-
- /* Increment number of inner iterations */
- inneriter += j_index_end - j_index_start;
-
- /* Outer loop uses 7 flops */
- }
-
- /* Increment number of outer iterations */
- outeriter += nri;
-
- /* Update outer/inner flops */
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*7 + inneriter*57);
-}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_t nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse4_1_single;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse4_1_single;
nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse4_1_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse4_1_single;
nb_kernel_t nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse4_1_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse4_1_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse4_1_single;
nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse4_1_single;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse4_1_single;
-nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse4_1_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse4_1_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse4_1_single;
nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse4_1_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse4_1_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse4_1_single;
nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_single;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_single;
nb_kernel_info_t
{ nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_sse4_1_single", "sse4_1_single", "None", "None", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_sse4_1_single", "sse4_1_single", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecEw_VdwLJEw_GeomP1P1_F_sse4_1_single", "sse4_1_single", "Ewald", "None", "LJEwald", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecEw_VdwLJEw_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "Ewald", "None", "LJEwald", "None", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_sse4_1_single", "sse4_1_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "PotentialAndForce" },
{ nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_sse4_1_single", "sse4_1_single", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_sse4_1_single", "sse4_1_single", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_single", "sse4_1_single", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecGB_VdwNone_GeomP1P1_F_sse4_1_single", "sse4_1_single", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "Force" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
- { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_sse4_1_single", "sse4_1_single", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_sse4_1_single", "sse4_1_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
{ nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_sse4_1_single", "sse4_1_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
{ nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
- { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_single", "sse4_1_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_sse4_1_single", "sse4_1_single", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_single, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_sse4_1_single", "sse4_1_single", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" }
};
int
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
__m128 velec,felec,velecsum,facel,crf,krf,krf2;
real *charge;
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- __m128i gbitab;
- __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
- __m128 minushalf = _mm_set1_ps(-0.5);
- real *invsqrta,*dvda,*gbtab;
- /* #endif */
/* #if KERNEL_VDW != 'None' */
int nvdwtype;
__m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
__m128 one_sixth = _mm_set1_ps(1.0/6.0);
__m128 one_twelfth = _mm_set1_ps(1.0/12.0);
/* #endif */
- /* #if 'Table' in KERNEL_ELEC or 'GeneralizedBorn' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
+ /* #if 'Table' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
__m128i vfitab;
__m128i ifour = _mm_set1_epi32(4);
__m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
/* #endif */
/* #endif */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- invsqrta = fr->invsqrta;
- dvda = fr->dvda;
- gbtabscale = _mm_set1_ps(fr->gbtab->scale);
- gbtab = fr->gbtab->data;
- gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
- /* #endif */
-
/* #if 'Water' in GEOMETRY_I */
/* Setup water-specific parameters */
inr = nlist->iinr[0];
/* #for I in PARTICLES_ELEC_I */
iq{I} = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+{I}));
/* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isai{I} = _mm_load1_ps(invsqrta+inr+{I});
- /* #endif */
/* #endfor */
/* #for I in PARTICLES_VDW_I */
vdwioffset{I} = 2*nvdwtype*vdwtype[inr+{I}];
/* #if KERNEL_ELEC != 'None' */
velecsum = _mm_setzero_ps();
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- vgbsum = _mm_setzero_ps();
- /* #endif */
/* #if KERNEL_VDW != 'None' */
vvdwsum = _mm_setzero_ps();
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_setzero_ps();
- /* #endif */
/* #for ROUND in ['Loop','Epilogue'] */
/* #for J in PARTICLES_ELEC_J */
jq{J} = gmx_mm_load_4real_swizzle_ps(charge+jnrA+{J},charge+jnrB+{J},
charge+jnrC+{J},charge+jnrD+{J});
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- isaj{J} = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+{J},invsqrta+jnrB+{J},
- invsqrta+jnrC+{J},invsqrta+jnrD+{J});
- /* #endif */
/* #endfor */
/* #for J in PARTICLES_VDW_J */
vdwjidx{J}A = 2*vdwtype[jnrA+{J}];
/* #define INNERFLOPS INNERFLOPS+3 */
/* #endif */
- /* #elif KERNEL_ELEC=='GeneralizedBorn' */
-
- /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
- isaprod = _mm_mul_ps(isai{I},isaj{J});
- gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq{I}{J},_mm_mul_ps(isaprod,gbinvepsdiff)));
- gbscale = _mm_mul_ps(isaprod,gbtabscale);
- /* #define INNERFLOPS INNERFLOPS+5 */
-
- /* Calculate generalized born table index - this is a separate table from the normal one,
- * but we use the same procedure by multiplying r with scale and truncating to integer.
- */
- rt = _mm_mul_ps(r{I}{J},gbscale);
- gbitab = _mm_cvttps_epi32(rt);
- gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
- gbitab = _mm_slli_epi32(gbitab,2);
- Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
- F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
- G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
- H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
- _MM_TRANSPOSE4_PS(Y,F,G,H);
- Heps = _mm_mul_ps(gbeps,H);
- Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
- VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
- vgb = _mm_mul_ps(gbqqfactor,VV);
- /* #define INNERFLOPS INNERFLOPS+10 */
-
- /* #if 'Force' in KERNEL_VF */
- FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
- fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
- dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r{I}{J})));
- /* #if ROUND == 'Epilogue' */
- dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
- /* #endif */
- dvdasum = _mm_add_ps(dvdasum,dvdatmp);
- /* #if ROUND == 'Loop' */
- fjptrA = dvda+jnrA;
- fjptrB = dvda+jnrB;
- fjptrC = dvda+jnrC;
- fjptrD = dvda+jnrD;
- /* #else */
- /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
- fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
- fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
- fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
- fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
- /* #endif */
- gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj{J},isaj{J})));
- /* #define INNERFLOPS INNERFLOPS+13 */
- /* #endif */
- velec = _mm_mul_ps(qq{I}{J},rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #if 'Force' in KERNEL_VF */
- felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv{I}{J}),fgb),rinv{I}{J});
- /* #define INNERFLOPS INNERFLOPS+3 */
- /* #endif */
-
/* #elif KERNEL_ELEC=='Ewald' */
/* EWALD ELECTROSTATICS */
/* #endif */
velecsum = _mm_add_ps(velecsum,velec);
/* #define INNERFLOPS INNERFLOPS+1 */
- /* #if KERNEL_ELEC=='GeneralizedBorn' */
- /* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
- vgb = _mm_and_ps(vgb,cutoff_mask);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
- /* #if ROUND == 'Epilogue' */
- vgb = _mm_andnot_ps(dummy_mask,vgb);
- /* #endif */
- vgbsum = _mm_add_ps(vgbsum,vgb);
- /* #define INNERFLOPS INNERFLOPS+1 */
- /* #endif */
/* #endif */
/* #if 'vdw' in INTERACTION_FLAGS[I][J] */
/* ## Note special check for TIP4P-TIP4P. Since we are cutting of all hydrogen interactions we also cut the LJ-only O-O interaction */
gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC */
- gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
- /* #define OUTERFLOPS OUTERFLOPS+1 */
- /* #endif */
/* #if KERNEL_VDW != 'None' */
gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
/* #define OUTERFLOPS OUTERFLOPS+1 */
/* #endif */
/* #endif */
- /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
- dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai{I},isai{I}));
- gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
- /* #endif */
/* Increment number of inner iterations */
inneriter += j_index_end - j_index_start;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
kernel_data.energygrp_elec = grppener->ener[egCOULSR];
kernel_data.energygrp_vdw = grppener->ener[fr->bBHAM ? egBHAMSR : egLJSR];
- kernel_data.energygrp_polarization = grppener->ener[egGB];
nlist = nblists->nlist_sr;
f = f_shortrange;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{ "NB Generic charge grp kernel", 1 },
{ "NB Free energy kernel", 1 },
{ "NB All-vs-all", 1 },
- { "NB All-vs-all, GB", 1 },
{ "Pair Search distance check", 9 }, /* nbnxn pair dist. check */
/* nbnxn kernel flops are based on inner-loops without exclusion checks.
{ "NxN LJ add LJ Ewald [F]", 36 }, /* extra cost for LJ Ewald */
{ "NxN LJ add LJ Ewald [V&F]", 33 },
{ "1,4 nonbonded interactions", 90 },
- { "Born radii (Still)", 47 },
- { "Born radii (HCT/OBC)", 183 },
- { "Born force chain rule", 15 },
- { "All-vs-All Still radii", 1 },
- { "All-vs-All HCT/OBC radii", 1 },
- { "All-vs-All Born chain rule", 1 },
{ "Calc Weights", 36 },
{ "Spread Q", 6 },
{ "Spread Q Bspline", 2 },
{ "Virtual Site 4fd", 110 },
{ "Virtual Site 4fdn", 254 },
{ "Virtual Site N", 15 },
- { "Mixed Generalized Born stuff", 10 },
{ "CMAP", 1700 }, // Estimate!
{ "Urey-Bradley", 183 },
{ "Cross-Bond-Bond", 163 },
const char *myline = "-----------------------------------------------------------------------------";
*nbfs = 0.0;
- for (i = 0; (i < eNR_NBKERNEL_ALLVSALLGB); i++)
+ for (i = 0; (i < eNR_NBKERNEL_TOTAL_NR); i++)
{
if (std::strstr(nbdata[i].name, "W3-W3") != nullptr)
{
{
add_nrnb(av, av, &(nrnb[i]));
/* Cost due to forces */
- for (j = 0; (j < eNR_NBKERNEL_ALLVSALLGB); j++)
+ for (j = 0; (j < eNR_NBKERNEL_TOTAL_NR); j++)
{
ftot[i] += nrnb[i].n[j]*cost_nrnb(j);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
eNR_NBKERNEL_GENERIC_CG,
eNR_NBKERNEL_FREE_ENERGY, /* Add other generic kernels _before_ the free energy one */
- eNR_NBKERNEL_ALLVSALL,
- eNR_NBKERNEL_ALLVSALLGB,
+ eNR_NBKERNEL_TOTAL_NR,
+ eNR_NBKERNEL_ALLVSALL = eNR_NBKERNEL_TOTAL_NR, // Reuse the symbolic constant that indicates the last kernel
eNR_NBNXN_DIST2,
eNR_NBNXN_LJ_RF, eNR_NBNXN_LJ_RF_E,
eNR_NBNXN_ADD_LJ_PSW, eNR_NBNXN_ADD_LJ_PSW_E,
eNR_NBNXN_ADD_LJ_EWALD, eNR_NBNXN_ADD_LJ_EWALD_E,
eNR_NB14,
- eNR_BORN_RADII_STILL, eNR_BORN_RADII_HCT_OBC,
- eNR_BORN_CHAINRULE,
- eNR_BORN_AVA_RADII_STILL, eNR_BORN_AVA_RADII_HCT_OBC,
- eNR_BORN_AVA_CHAINRULE,
eNR_WEIGHTS, eNR_SPREAD, eNR_SPREADBSP,
eNR_GATHERF, eNR_GATHERFBSP, eNR_FFT,
eNR_CONV, eNR_SOLVEPME, eNR_NS, eNR_RESETX,
eNR_SHAKE_RIJ, eNR_CONSTR_VIR, eNR_SETTLE,
eNR_VSITE2, eNR_VSITE3, eNR_VSITE3FD,
eNR_VSITE3FAD, eNR_VSITE3OUT, eNR_VSITE4FD,
- eNR_VSITE4FDN, eNR_VSITEN, eNR_GB,
+ eNR_VSITE4FDN, eNR_VSITEN,
eNR_CMAP, eNR_UREY_BRADLEY, eNR_CROSS_BOND_BOND,
eNR_CROSS_BOND_ANGLE,
eNRNB
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
newparam->cmap.cmapA = static_cast<int>(old[0]);
newparam->cmap.cmapB = static_cast<int>(old[1]);
break;
- case F_GB12:
- case F_GB13:
- case F_GB14:
- newparam->gb.sar = old[0];
- newparam->gb.st = old[1];
- newparam->gb.pi = old[2];
- newparam->gb.gbr = old[3];
- newparam->gb.bmlt = old[4];
+ case F_GB12_NOLONGERUSED:
+ case F_GB13_NOLONGERUSED:
+ case F_GB14_NOLONGERUSED:
break;
default:
gmx_fatal(FARGS, "unknown function type %d in %s line %d",
{
if (ffparams->functype[type] == ftype)
{
- if (F_GB13 == ftype)
+ if (memcmp(&newparam, &ffparams->iparams[type], (size_t)sizeof(newparam)) == 0)
{
- /* Occasionally, the way the 1-3 reference distance is
- * computed can lead to non-binary-identical results, but I
- * don't know why. */
- if ((gmx_within_tol(newparam.gb.sar, ffparams->iparams[type].gb.sar, 1e-6)) &&
- (gmx_within_tol(newparam.gb.st, ffparams->iparams[type].gb.st, 1e-6)) &&
- (gmx_within_tol(newparam.gb.pi, ffparams->iparams[type].gb.pi, 1e-6)) &&
- (gmx_within_tol(newparam.gb.gbr, ffparams->iparams[type].gb.gbr, 1e-6)) &&
- (gmx_within_tol(newparam.gb.bmlt, ffparams->iparams[type].gb.bmlt, 1e-6)))
- {
- return type;
- }
- }
- else
- {
- if (memcmp(&newparam, &ffparams->iparams[type], (size_t)sizeof(newparam)) == 0)
- {
- return type;
- }
+ return type;
}
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
char ***atomname; /* Names of the atomtypes */
t_param *nb; /* Nonbonded force default params */
int *bondatomtype; /* The bond_atomtype for each atomtype */
- real *radius; /* Radius for GBSA stuff */
- real *vol; /* Effective volume for GBSA */
- real *surftens; /* Surface tension with water, for GBSA */
- real *gb_radius; /* Radius for Still model */
- real *S_hct; /* Overlap factor for HCT model */
int *atomnumber; /* Atomic number, used for QM/MM */
} t_gpp_atomtype;
return ga->atomnumber[nt];
}
-real get_atomtype_radius(int nt, gpp_atomtype_t ga)
-{
- if ((nt < 0) || (nt >= ga->nr))
- {
- return NOTSET;
- }
-
- return ga->radius[nt];
-}
-
-real get_atomtype_vol(int nt, gpp_atomtype_t ga)
-{
- if ((nt < 0) || (nt >= ga->nr))
- {
- return NOTSET;
- }
-
- return ga->vol[nt];
-}
-
-real get_atomtype_surftens(int nt, gpp_atomtype_t ga)
-{
- if ((nt < 0) || (nt >= ga->nr))
- {
- return NOTSET;
- }
-
- return ga->surftens[nt];
-}
-
-real get_atomtype_gb_radius(int nt, gpp_atomtype_t ga)
-{
- if ((nt < 0) || (nt >= ga->nr))
- {
- return NOTSET;
- }
-
- return ga->gb_radius[nt];
-}
-
-real get_atomtype_S_hct(int nt, gpp_atomtype_t ga)
-{
- if ((nt < 0) || (nt >= ga->nr))
- {
- return NOTSET;
- }
-
- return ga->S_hct[nt];
-}
-
real get_atomtype_nbparam(int nt, int param, gpp_atomtype_t ga)
{
if ((nt < 0) || (nt >= ga->nr))
ga->atomname = nullptr;
ga->nb = nullptr;
ga->bondatomtype = nullptr;
- ga->radius = nullptr;
- ga->vol = nullptr;
- ga->surftens = nullptr;
ga->atomnumber = nullptr;
- ga->gb_radius = nullptr;
- ga->S_hct = nullptr;
return ga;
}
-int
-set_atomtype_gbparam(gpp_atomtype_t ga, int i,
- real radius, real vol, real surftens,
- real gb_radius, real S_hct)
-{
- if ( (i < 0) || (i >= ga->nr))
- {
- return NOTSET;
- }
-
- ga->radius[i] = radius;
- ga->vol[i] = vol;
- ga->surftens[i] = surftens;
- ga->gb_radius[i] = gb_radius;
- ga->S_hct[i] = S_hct;
-
- return i;
-}
-
-
int set_atomtype(int nt, gpp_atomtype_t ga, t_symtab *tab,
t_atom *a, const char *name, t_param *nb,
- int bondatomtype,
- real radius, real vol, real surftens, int atomnumber,
- real gb_radius, real S_hct)
+ int bondatomtype, int atomnumber)
{
if ((nt < 0) || (nt >= ga->nr))
{
ga->atomname[nt] = put_symtab(tab, name);
ga->nb[nt] = *nb;
ga->bondatomtype[nt] = bondatomtype;
- ga->radius[nt] = radius;
- ga->vol[nt] = vol;
- ga->surftens[nt] = surftens;
ga->atomnumber[nt] = atomnumber;
- ga->gb_radius[nt] = gb_radius;
- ga->S_hct[nt] = S_hct;
return nt;
}
int add_atomtype(gpp_atomtype_t ga, t_symtab *tab,
t_atom *a, const char *name, t_param *nb,
- int bondatomtype,
- real radius, real vol, real surftens, int atomnumber,
- real gb_radius, real S_hct)
+ int bondatomtype, int atomnumber)
{
int i;
srenew(ga->atomname, ga->nr);
srenew(ga->nb, ga->nr);
srenew(ga->bondatomtype, ga->nr);
- srenew(ga->radius, ga->nr);
- srenew(ga->vol, ga->nr);
- srenew(ga->surftens, ga->nr);
srenew(ga->atomnumber, ga->nr);
- srenew(ga->gb_radius, ga->nr);
- srenew(ga->S_hct, ga->nr);
- return set_atomtype(ga->nr-1, ga, tab, a, name, nb, bondatomtype, radius,
- vol, surftens, atomnumber, gb_radius, S_hct);
+ return set_atomtype(ga->nr-1, ga, tab, a, name, nb, bondatomtype, atomnumber);
}
else
{
sfree(ga->atomname);
sfree(ga->nb);
sfree(ga->bondatomtype);
- sfree(ga->radius);
- sfree(ga->vol);
- sfree(ga->gb_radius);
- sfree(ga->S_hct);
- sfree(ga->surftens);
sfree(ga->atomnumber);
ga->nr = 0;
sfree(ga);
bFound = (param[ntype*typelist[i]+j].c[k] == param[ntype*thistype+j].c[k]);
}
- /* Check radius, volume, surftens */
+ /* Check atomnumber */
tli = typelist[i];
bFound = bFound &&
- (get_atomtype_radius(tli, ga) == get_atomtype_radius(thistype, ga)) &&
- (get_atomtype_vol(tli, ga) == get_atomtype_vol(thistype, ga)) &&
- (get_atomtype_surftens(tli, ga) == get_atomtype_surftens(thistype, ga)) &&
- (get_atomtype_atomnumber(tli, ga) == get_atomtype_atomnumber(thistype, ga)) &&
- (get_atomtype_gb_radius(tli, ga) == get_atomtype_gb_radius(thistype, ga)) &&
- (get_atomtype_S_hct(tli, ga) == get_atomtype_S_hct(thistype, ga));
+ (get_atomtype_atomnumber(tli, ga) == get_atomtype_atomnumber(thistype, ga));
}
if (bFound)
{
t_atoms *atoms;
t_param *nbsnew;
int *typelist;
- real *new_radius;
- real *new_vol;
- real *new_surftens;
- real *new_gb_radius;
- real *new_S_hct;
int *new_atomnumber;
char ***new_atomname;
* ones with identical nonbonded interactions, in addition
* to removing unused ones.
*
- * With Generalized-Born electrostatics, or implicit solvent
- * we also check that the atomtype radius, effective_volume
- * and surface tension match.
- *
* With QM/MM we also check that the atom numbers match
*/
}
}
- snew(new_radius, nat);
- snew(new_vol, nat);
- snew(new_surftens, nat);
snew(new_atomnumber, nat);
- snew(new_gb_radius, nat);
- snew(new_S_hct, nat);
snew(new_atomname, nat);
/* We now have a list of unique atomtypes in typelist */
nbsnew[k].c[l] = plist[ftype].param[ntype*mi+mj].c[l];
}
}
- new_radius[i] = get_atomtype_radius(mi, ga);
- new_vol[i] = get_atomtype_vol(mi, ga);
- new_surftens[i] = get_atomtype_surftens(mi, ga);
new_atomnumber[i] = get_atomtype_atomnumber(mi, ga);
- new_gb_radius[i] = get_atomtype_gb_radius(mi, ga);
- new_S_hct[i] = get_atomtype_S_hct(mi, ga);
new_atomname[i] = ga->atomname[mi];
}
plist[ftype].nr = i;
mtop->ffparams.atnr = nat;
- sfree(ga->radius);
- sfree(ga->vol);
- sfree(ga->surftens);
sfree(ga->atomnumber);
- sfree(ga->gb_radius);
- sfree(ga->S_hct);
/* Dangling atomname pointers ? */
sfree(ga->atomname);
- ga->radius = new_radius;
- ga->vol = new_vol;
- ga->surftens = new_surftens;
ga->atomnumber = new_atomnumber;
- ga->gb_radius = new_gb_radius;
- ga->S_hct = new_S_hct;
ga->atomname = new_atomname;
ga->nr = nat;
/* Copy the atomtype data to the topology atomtype list */
ntype = get_atomtype_ntypes(ga);
atomtypes->nr = ntype;
- snew(atomtypes->radius, ntype);
- snew(atomtypes->vol, ntype);
- snew(atomtypes->surftens, ntype);
snew(atomtypes->atomnumber, ntype);
- snew(atomtypes->gb_radius, ntype);
- snew(atomtypes->S_hct, ntype);
for (i = 0; i < ntype; i++)
{
- atomtypes->radius[i] = ga->radius[i];
- atomtypes->vol[i] = ga->vol[i];
- atomtypes->surftens[i] = ga->surftens[i];
atomtypes->atomnumber[i] = ga->atomnumber[i];
- atomtypes->gb_radius[i] = ga->gb_radius[i];
- atomtypes->S_hct[i] = ga->S_hct[i];
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real get_atomtype_massB(int nt, gpp_atomtype_t at);
real get_atomtype_qA(int nt, gpp_atomtype_t at);
real get_atomtype_qB(int nt, gpp_atomtype_t at);
-real get_atomtype_radius(int nt, gpp_atomtype_t at);
-real get_atomtype_vol(int nt, gpp_atomtype_t at);
-real get_atomtype_surftens(int nt, gpp_atomtype_t at);
-real get_atomtype_gb_radius(int nt, gpp_atomtype_t at);
-real get_atomtype_S_hct(int nt, gpp_atomtype_t at);
int get_atomtype_ptype(int nt, gpp_atomtype_t at);
int get_atomtype_batype(int nt, gpp_atomtype_t at);
int get_atomtype_atomnumber(int nt, gpp_atomtype_t at);
int set_atomtype(int nt, gpp_atomtype_t at, struct t_symtab *tab,
t_atom *a, const char *name, t_param *nb,
- int bondatomtype,
- real radius, real vol, real surftens, int atomnumber,
- real gb_radius, real S_hct);
+ int bondatomtype, int atomnumber);
/* Set the values of an existing atom type nt. Returns nt on success or
NOTSET on error. */
-int
-set_atomtype_gbparam(gpp_atomtype_t at, int i,
- real radius, real vol, real surftens,
- real gb_radius, real S_hct);
-
int add_atomtype(gpp_atomtype_t at, struct t_symtab *tab,
t_atom *a, const char *name, t_param *nb,
- int bondatomtype,
- real radius, real vol, real surftens, int atomnumber,
- real gb_radius, real S_hct);
+ int bondatomtype, int atomnumber);
/* Add a complete new atom type to an existing atomtype structure. Returns
the number of the atom type. */
#include "gromacs/mdlib/calc_verletbuf.h"
#include "gromacs/mdlib/compute_io.h"
#include "gromacs/mdlib/constr.h"
-#include "gromacs/mdlib/genborn.h"
#include "gromacs/mdlib/perf_est.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdrunutility/mdmodules.h"
gmx_molblock_t *molblock, *molbs;
int mb, i, nrmols, nmismatch;
char buf[STRLEN];
- gmx_bool bGB = FALSE;
char warn_buf[STRLEN];
init_mtop(sys);
- /* Set gmx_boolean for GB */
- if (ir->implicit_solvent)
- {
- bGB = TRUE;
- }
-
/* TOPOLOGY processing */
sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab),
plist, comb, reppow, fudgeQQ,
atype, &nrmols, &molinfo, intermolecular_interactions,
ir,
- &nmolblock, &molblock, bGB,
+ &nmolblock, &molblock,
wi);
sys->nmolblock = 0;
return count;
}
-static void check_gbsa_params_charged(gmx_mtop_t *sys, gpp_atomtype_t atype)
-{
- int i, nmiss, natoms, mt;
- real q;
- const t_atoms *atoms;
-
- nmiss = 0;
- for (mt = 0; mt < sys->nmoltype; mt++)
- {
- atoms = &sys->moltype[mt].atoms;
- natoms = atoms->nr;
-
- for (i = 0; i < natoms; i++)
- {
- q = atoms->atom[i].q;
- if ((get_atomtype_radius(atoms->atom[i].type, atype) == 0 ||
- get_atomtype_vol(atoms->atom[i].type, atype) == 0 ||
- get_atomtype_surftens(atoms->atom[i].type, atype) == 0 ||
- get_atomtype_gb_radius(atoms->atom[i].type, atype) == 0 ||
- get_atomtype_S_hct(atoms->atom[i].type, atype) == 0) &&
- q != 0)
- {
- fprintf(stderr, "\nGB parameter(s) zero for atom type '%s' while charge is %g\n",
- get_atomtype_name(atoms->atom[i].type, atype), q);
- nmiss++;
- }
- }
- }
-
- if (nmiss > 0)
- {
- gmx_fatal(FARGS, "Can't do GB electrostatics; the implicit_genborn_params section of the forcefield has parameters with value zero for %d atomtypes that occur as charged atoms.", nmiss);
- }
-}
-
-
-static void check_gbsa_params(gpp_atomtype_t atype)
-{
- int nmiss, i;
-
- /* If we are doing GBSA, check that we got the parameters we need
- * This checking is to see if there are GBSA paratmeters for all
- * atoms in the force field. To go around this for testing purposes
- * comment out the nerror++ counter temporarily
- */
- nmiss = 0;
- for (i = 0; i < get_atomtype_ntypes(atype); i++)
- {
- if (get_atomtype_radius(i, atype) < 0 ||
- get_atomtype_vol(i, atype) < 0 ||
- get_atomtype_surftens(i, atype) < 0 ||
- get_atomtype_gb_radius(i, atype) < 0 ||
- get_atomtype_S_hct(i, atype) < 0)
- {
- fprintf(stderr, "\nGB parameter(s) missing or negative for atom type '%s'\n",
- get_atomtype_name(i, atype));
- nmiss++;
- }
- }
-
- if (nmiss > 0)
- {
- gmx_fatal(FARGS, "Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for %d atomtypes or they might be negative.", nmiss);
- }
-
-}
-
static real calc_temp(const gmx_mtop_t *mtop,
const t_inputrec *ir,
rvec *v)
get_atomtype_ntypes(atype);
}
- if (ir->implicit_solvent != eisNO)
+ if (ir->implicit_solvent)
{
- /* Now we have renumbered the atom types, we can check the GBSA params */
- check_gbsa_params(atype);
-
- /* Check that all atoms that have charge and/or LJ-parameters also have
- * sensible GB-parameters
- */
- check_gbsa_params_charged(sys, atype);
+ gmx_fatal(FARGS, "Implicit solvation is no longer supported");
}
/* PELA: Copy the atomtype data to the topology atomtype list */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
atoms->atom[i].qB = alpha;
atoms->atom[i].m = atoms->atom[i].mB = mm;
k = add_atomtype(atype, tab, &(atoms->atom[i]), type, param,
- atoms->atom[i].type, 0, 0, 0, atomnr, 0, 0);
+ atoms->atom[i].type, atomnr);
}
atoms->atom[i].type = k;
atoms->atom[i].typeB = k;
warning_error(wi, warn_buf);
}
- if (ir->implicit_solvent != eisNO)
- {
- warning_error(wi, "Implicit solvent is not (yet) supported with the with Verlet lists.");
- }
-
if (EEL_USER(ir->coulombtype))
{
sprintf(warn_buf, "Coulomb type %s is not supported with the verlet scheme", eel_names[ir->coulombtype]);
warning(wi, warn_buf);
}
- if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
- {
- sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
- warning_note(wi, warn_buf);
- }
-
if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
{
sprintf(warn_buf, "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old format and exchanging epsilon-r and epsilon-rf", ir->epsilon_r);
if (ir->epsilon_r == 0)
{
sprintf(err_buf,
- "It is pointless to use long-range or Generalized Born electrostatics with infinite relative permittivity."
+ "It is pointless to use long-range electrostatics with infinite relative permittivity."
"Since you are effectively turning of electrostatics, a plain cutoff will be much faster.");
- CHECK(EEL_FULL(ir->coulombtype) || ir->implicit_solvent == eisGBSA);
+ CHECK(EEL_FULL(ir->coulombtype));
}
if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
warning_error(wi, warn_buf);
}
- if (ir->sa_algorithm == esaSTILL)
- {
- sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
- CHECK(ir->sa_algorithm == esaSTILL);
- }
-
- if (ir->implicit_solvent == eisGBSA)
- {
- sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
- CHECK(ir->rgbradii != ir->rlist);
-
- if (ir->coulombtype != eelCUT)
- {
- sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
- CHECK(ir->coulombtype != eelCUT);
- }
- if (ir->vdwtype != evdwCUT)
- {
- sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
- CHECK(ir->vdwtype != evdwCUT);
- }
- if (ir->nstgbradii < 1)
- {
- sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
- warning_note(wi, warn_buf);
- ir->nstgbradii = 1;
- }
- if (ir->sa_algorithm == esaNO)
- {
- sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
- warning_note(wi, warn_buf);
- }
- if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
- {
- sprintf(warn_buf, "Value of sa_surface_tension is < 0. Changing it to 2.05016 or 2.25936 kJ/nm^2/mol for Still and HCT/OBC respectively\n");
- warning_note(wi, warn_buf);
-
- if (ir->gb_algorithm == egbSTILL)
- {
- ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
- }
- else
- {
- ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
- }
- }
- if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
- {
- sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
- CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
- }
-
- }
-
if (ir->bQMMM)
{
if (ir->cutoff_scheme != ecutsGROUP)
t_lambda *fep = ir->fepvals;
t_expanded *expand = ir->expandedvals;
+ const char *no_names[] = { "no", nullptr };
+
init_inputrec_strings();
gmx::TextInputFile stream(mdparin);
inp = read_inpfile(&stream, mdparin, &ninp, wi);
REM_TYPE("rlistlong");
REM_TYPE("nstcalclr");
REM_TYPE("pull-print-com2");
+ REM_TYPE("gb-algorithm");
+ REM_TYPE("nstgbradii");
+ REM_TYPE("rgbradii");
+ REM_TYPE("gb-epsilon-solvent");
+ REM_TYPE("gb-saltconc");
+ REM_TYPE("gb-obc-alpha");
+ REM_TYPE("gb-obc-beta");
+ REM_TYPE("gb-obc-gamma");
+ REM_TYPE("gb-dielectric-offset");
+ REM_TYPE("sa-algorithm");
+ REM_TYPE("sa-surface-tension");
/* replace the following commands with the clearer new versions*/
REPL_TYPE("unconstrained-start", "continuation");
EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
- CCTYPE("IMPLICIT SOLVENT ALGORITHM");
- EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
-
- CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
- CTYPE ("Algorithm for calculating Born radii");
- EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
- CTYPE ("Frequency of calculating the Born radii inside rlist");
- ITYPE ("nstgbradii", ir->nstgbradii, 1);
- CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
- CTYPE ("between rlist and rgbradii is updated every nstlist steps");
- RTYPE ("rgbradii", ir->rgbradii, 1.0);
- CTYPE ("Dielectric coefficient of the implicit solvent");
- RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
- CTYPE ("Salt concentration in M for Generalized Born models");
- RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
- CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
- RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
- RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
- RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
- RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
- EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
- CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
- CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
- RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
+ /* Implicit solvation is no longer supported, but we need grompp
+ to be able to refuse old .mdp files that would have built a tpr
+ to run it. Thus, only "no" is accepted. */
+ EETYPE("implicit-solvent", ir->implicit_solvent, no_names);
/* Coupling stuff */
CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
RTYPE("threshold", ir->swap->threshold, 1.0);
}
- /* AdResS is no longer supported, but we need mdrun to be able to refuse to run old AdResS .tpr files */
- EETYPE("adress", ir->bAdress, yesno_names);
+ /* AdResS is no longer supported, but we need grompp to be able to
+ refuse to process old .mdp files that used it. */
+ EETYPE("adress", ir->bAdress, no_names);
/* User defined thingies */
CCTYPE ("User defined thingies");
}
else
{
- if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
+ if (ir->coulombtype == eelCUT && ir->rcoulomb > 0)
{
sprintf(err_buf,
"You are using a plain Coulomb cut-off, which might produce artifacts.\n"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if (sscanf(buf, "%s%lf", name, &m) == 2)
{
a->m = m;
- add_atomtype(at, tab, a, name, nb, 0, 0.0, 0.0, 0.0, 0, 0.0, 0.0 );
+ add_atomtype(at, tab, a, name, nb, 0, 0);
fprintf(stderr, "\rAtomtype %d", ++nratt);
fflush(stderr);
}
EXPECT_DEATH(runTest(joinStrings(inputMdpFile, "\n")), "A parameter is present with both");
}
+TEST_F(GetIrTest, ImplicitSolventNoWorks)
+{
+ const char *inputMdpFile = "implicit-solvent = no";
+ runTest(inputMdpFile);
+}
+
+TEST_F(GetIrTest, ImplicitSolventYesWorks)
+{
+ const char *inputMdpFile = "implicit-solvent = yes";
+ EXPECT_DEATH(runTest(inputMdpFile), "Invalid enum");
+}
+
} // namespace
} // namespace
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
-
-; IMPLICIT SOLVENT ALGORITHM
-implicit-solvent = No
-
-; GENERALIZED BORN ELECTROSTATICS
-; Algorithm for calculating Born radii
-gb-algorithm = Still
-; Frequency of calculating the Born radii inside rlist
-nstgbradii = 1
-; Cutoff for Born radii calculation; the contribution from atoms
-; between rlist and rgbradii is updated every nstlist steps
-rgbradii = 1
-; Dielectric coefficient of the implicit solvent
-gb-epsilon-solvent = 80
-; Salt concentration in M for Generalized Born models
-gb-saltconc = 0
-; Scaling factors used in the OBC GB model. Default values are OBC(II)
-gb-obc-alpha = 1
-gb-obc-beta = 0.8
-gb-obc-gamma = 4.85
-gb-dielectric-offset = 0.009
-sa-algorithm = Ace-approximation
-; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
-; The value -1 will set default value for Still/HCT/OBC GB-models.
-sa-surface-tension = -1
+implicit-solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
-
-; IMPLICIT SOLVENT ALGORITHM
-implicit-solvent = No
-
-; GENERALIZED BORN ELECTROSTATICS
-; Algorithm for calculating Born radii
-gb-algorithm = Still
-; Frequency of calculating the Born radii inside rlist
-nstgbradii = 1
-; Cutoff for Born radii calculation; the contribution from atoms
-; between rlist and rgbradii is updated every nstlist steps
-rgbradii = 1
-; Dielectric coefficient of the implicit solvent
-gb-epsilon-solvent = 80
-; Salt concentration in M for Generalized Born models
-gb-saltconc = 0
-; Scaling factors used in the OBC GB model. Default values are OBC(II)
-gb-obc-alpha = 1
-gb-obc-beta = 0.8
-gb-obc-gamma = 4.85
-gb-dielectric-offset = 0.009
-sa-algorithm = Ace-approximation
-; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
-; The value -1 will set default value for Still/HCT/OBC GB-models.
-sa-surface-tension = -1
+implicit-solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
-
-; IMPLICIT SOLVENT ALGORITHM
-implicit-solvent = No
-
-; GENERALIZED BORN ELECTROSTATICS
-; Algorithm for calculating Born radii
-gb-algorithm = Still
-; Frequency of calculating the Born radii inside rlist
-nstgbradii = 1
-; Cutoff for Born radii calculation; the contribution from atoms
-; between rlist and rgbradii is updated every nstlist steps
-rgbradii = 1
-; Dielectric coefficient of the implicit solvent
-gb-epsilon-solvent = 80
-; Salt concentration in M for Generalized Born models
-gb-saltconc = 0
-; Scaling factors used in the OBC GB model. Default values are OBC(II)
-gb-obc-alpha = 1
-gb-obc-beta = 0.8
-gb-obc-gamma = 4.85
-gb-dielectric-offset = 0.009
-sa-algorithm = Ace-approximation
-; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
-; The value -1 will set default value for Still/HCT/OBC GB-models.
-sa-surface-tension = -1
+implicit-solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Bool Name="Error parsing mdp file">false</Bool>
+ <String Name="OutputMdpFile">
+; VARIOUS PREPROCESSING OPTIONS
+; Preprocessor information: use cpp syntax.
+; e.g.: -I/home/joe/doe -I/home/mary/roe
+include =
+; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
+define =
+
+; RUN CONTROL PARAMETERS
+integrator = md
+; Start time and timestep in ps
+tinit = 0
+dt = 0.001
+nsteps = 0
+; For exact run continuation or redoing part of a run
+init-step = 0
+; Part index is updated automatically on checkpointing (keeps files separate)
+simulation-part = 1
+; mode for center of mass motion removal
+comm-mode = Linear
+; number of steps for center of mass motion removal
+nstcomm = 100
+; group(s) for center of mass motion removal
+comm-grps =
+
+; LANGEVIN DYNAMICS OPTIONS
+; Friction coefficient (amu/ps) and random seed
+bd-fric = 0
+ld-seed = -1
+
+; ENERGY MINIMIZATION OPTIONS
+; Force tolerance and initial step-size
+emtol = 10
+emstep = 0.01
+; Max number of iterations in relax-shells
+niter = 20
+; Step size (ps^2) for minimization of flexible constraints
+fcstep = 0
+; Frequency of steepest descents steps when doing CG
+nstcgsteep = 1000
+nbfgscorr = 10
+
+; TEST PARTICLE INSERTION OPTIONS
+rtpi = 0.05
+
+; OUTPUT CONTROL OPTIONS
+; Output frequency for coords (x), velocities (v) and forces (f)
+nstxout = 0
+nstvout = 0
+nstfout = 0
+; Output frequency for energies to log file and energy file
+nstlog = 1000
+nstcalcenergy = 100
+nstenergy = 1000
+; Output frequency and precision for .xtc file
+nstxout-compressed = 0
+compressed-x-precision = 1000
+; This selects the subset of atoms for the compressed
+; trajectory file. You can select multiple groups. By
+; default, all atoms will be written.
+compressed-x-grps =
+; Selection of energy groups
+energygrps =
+
+; NEIGHBORSEARCHING PARAMETERS
+; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+cutoff-scheme = Verlet
+; nblist update frequency
+nstlist = 10
+; ns algorithm (simple or grid)
+ns-type = Grid
+; Periodic boundary conditions: xyz, no, xy
+pbc = xyz
+periodic-molecules = no
+; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
+; a value of -1 means: use rlist
+verlet-buffer-tolerance = 0.005
+; nblist cut-off
+rlist = 1
+; long-range cut-off for switched potentials
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype = Cut-off
+coulomb-modifier = Potential-shift-Verlet
+rcoulomb-switch = 0
+rcoulomb = 1
+; Relative dielectric constant for the medium and the reaction field
+epsilon-r = 1
+epsilon-rf = 0
+; Method for doing Van der Waals
+vdw-type = Cut-off
+vdw-modifier = Potential-shift-Verlet
+; cut-off lengths
+rvdw-switch = 0
+rvdw = 1
+; Apply long range dispersion corrections for Energy and Pressure
+DispCorr = No
+; Extension of the potential lookup tables beyond the cut-off
+table-extension = 1
+; Separate tables between energy group pairs
+energygrp-table =
+; Spacing for the PME/PPPM FFT grid
+fourierspacing = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used
+fourier-nx = 0
+fourier-ny = 0
+fourier-nz = 0
+; EWALD/PME/PPPM parameters
+pme-order = 4
+ewald-rtol = 1e-05
+ewald-rtol-lj = 0.001
+lj-pme-comb-rule = Geometric
+ewald-geometry = 3d
+epsilon-surface = 0
+implicit-solvent = no
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling
+tcoupl = No
+nsttcouple = -1
+nh-chain-length = 10
+print-nose-hoover-chain-variables = no
+; Groups to couple separately
+tc-grps =
+; Time constant (ps) and reference temperature (K)
+tau-t =
+ref-t =
+; pressure coupling
+pcoupl = No
+pcoupltype = Isotropic
+nstpcouple = -1
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau-p = 1
+compressibility =
+ref-p =
+; Scaling of reference coordinates, No, All or COM
+refcoord-scaling = No
+
+; OPTIONS FOR QMMM calculations
+QMMM = no
+; Groups treated Quantum Mechanically
+QMMM-grps =
+; QM method
+QMmethod =
+; QMMM scheme
+QMMMscheme = normal
+; QM basisset
+QMbasis =
+; QM charge
+QMcharge =
+; QM multiplicity
+QMmult =
+; Surface Hopping
+SH =
+; CAS space options
+CASorbitals =
+CASelectrons =
+SAon =
+SAoff =
+SAsteps =
+; Scale factor for MM charges
+MMChargeScaleFactor = 1
+
+; SIMULATED ANNEALING
+; Type of annealing for each temperature group (no/single/periodic)
+annealing =
+; Number of time points to use for specifying annealing in each group
+annealing-npoints =
+; List of times at the annealing points for each group
+annealing-time =
+; Temp. at each annealing point, for each group.
+annealing-temp =
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen-vel = no
+gen-temp = 300
+gen-seed = -1
+
+; OPTIONS FOR BONDS
+constraints = none
+; Type of constraint algorithm
+constraint-algorithm = Lincs
+; Do not constrain the start configuration
+continuation = no
+; Use successive overrelaxation to reduce the number of shake iterations
+Shake-SOR = no
+; Relative tolerance of shake
+shake-tol = 0.0001
+; Highest order in the expansion of the constraint coupling matrix
+lincs-order = 4
+; Number of iterations in the final step of LINCS. 1 is fine for
+; normal simulations, but use 2 to conserve energy in NVE runs.
+; For energy minimization with constraints it should be 4 to 8.
+lincs-iter = 1
+; Lincs will write a warning to the stderr if in one step a bond
+; rotates over more degrees than
+lincs-warnangle = 30
+; Convert harmonic bonds to morse potentials
+morse = no
+
+; ENERGY GROUP EXCLUSIONS
+; Pairs of energy groups for which all non-bonded interactions are excluded
+energygrp-excl =
+
+; WALLS
+; Number of walls, type, atom types, densities and box-z scale factor for Ewald
+nwall = 0
+wall-type = 9-3
+wall-r-linpot = -1
+wall-atomtype =
+wall-density =
+wall-ewald-zfac = 3
+
+; COM PULLING
+pull = no
+
+; AWH biasing
+awh = no
+
+; ENFORCED ROTATION
+; Enforced rotation: No or Yes
+rotation = no
+
+; Group to display and/or manipulate in interactive MD session
+IMD-group =
+
+; NMR refinement stuff
+; Distance restraints type: No, Simple or Ensemble
+disre = No
+; Force weighting of pairs in one distance restraint: Conservative or Equal
+disre-weighting = Conservative
+; Use sqrt of the time averaged times the instantaneous violation
+disre-mixed = no
+disre-fc = 1000
+disre-tau = 0
+; Output frequency for pair distances to energy file
+nstdisreout = 100
+; Orientation restraints: No or Yes
+orire = no
+; Orientation restraints force constant and tau for time averaging
+orire-fc = 0
+orire-tau = 0
+orire-fitgrp =
+; Output frequency for trace(SD) and S to energy file
+nstorireout = 100
+
+; Free energy variables
+free-energy = no
+couple-moltype =
+couple-lambda0 = vdw-q
+couple-lambda1 = vdw-q
+couple-intramol = no
+init-lambda = -1
+init-lambda-state = -1
+delta-lambda = 0
+nstdhdl = 50
+fep-lambdas =
+mass-lambdas =
+coul-lambdas =
+vdw-lambdas =
+bonded-lambdas =
+restraint-lambdas =
+temperature-lambdas =
+calc-lambda-neighbors = 1
+init-lambda-weights =
+dhdl-print-energy = no
+sc-alpha = 0
+sc-power = 1
+sc-r-power = 6
+sc-sigma = 0.3
+sc-coul = no
+separate-dhdl-file = yes
+dhdl-derivatives = yes
+dh_hist_size = 0
+dh_hist_spacing = 0.1
+
+; Non-equilibrium MD stuff
+acc-grps =
+accelerate =
+freezegrps =
+freezedim =
+cos-acceleration = 0
+deform =
+
+; simulated tempering variables
+simulated-tempering = no
+simulated-tempering-scaling = geometric
+sim-temp-low = 300
+sim-temp-high = 300
+
+; Ion/water position swapping for computational electrophysiology setups
+; Swap positions along direction: no, X, Y, Z
+swapcoords = no
+adress = no
+
+; User defined thingies
+user1-grps =
+user2-grps =
+userint1 = 0
+userint2 = 0
+userint3 = 0
+userint4 = 0
+userreal1 = 0
+userreal2 = 0
+userreal3 = 0
+userreal4 = 0
+; Electric fields
+; Format for electric-field-x, etc. is: four real variables:
+; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),
+; and sigma (ps) width of the pulse. Omega = 0 means static field,
+; sigma = 0 means no pulse, leaving the field to be a cosine function.
+electric-field-x = 0 0 0 0
+electric-field-y = 0 0 0 0
+electric-field-z = 0 0 0 0
+</String>
+</ReferenceData>
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
-
-; IMPLICIT SOLVENT ALGORITHM
-implicit-solvent = No
-
-; GENERALIZED BORN ELECTROSTATICS
-; Algorithm for calculating Born radii
-gb-algorithm = Still
-; Frequency of calculating the Born radii inside rlist
-nstgbradii = 1
-; Cutoff for Born radii calculation; the contribution from atoms
-; between rlist and rgbradii is updated every nstlist steps
-rgbradii = 1
-; Dielectric coefficient of the implicit solvent
-gb-epsilon-solvent = 80
-; Salt concentration in M for Generalized Born models
-gb-saltconc = 0
-; Scaling factors used in the OBC GB model. Default values are OBC(II)
-gb-obc-alpha = 1
-gb-obc-beta = 0.8
-gb-obc-gamma = 4.85
-gb-dielectric-offset = 0.009
-sa-algorithm = Ace-approximation
-; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
-; The value -1 will set default value for Still/HCT/OBC GB-models.
-sa-surface-tension = -1
+implicit-solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
-
-; IMPLICIT SOLVENT ALGORITHM
-implicit-solvent = No
-
-; GENERALIZED BORN ELECTROSTATICS
-; Algorithm for calculating Born radii
-gb-algorithm = Still
-; Frequency of calculating the Born radii inside rlist
-nstgbradii = 1
-; Cutoff for Born radii calculation; the contribution from atoms
-; between rlist and rgbradii is updated every nstlist steps
-rgbradii = 1
-; Dielectric coefficient of the implicit solvent
-gb-epsilon-solvent = 80
-; Salt concentration in M for Generalized Born models
-gb-saltconc = 0
-; Scaling factors used in the OBC GB model. Default values are OBC(II)
-gb-obc-alpha = 1
-gb-obc-beta = 0.8
-gb-obc-gamma = 4.85
-gb-dielectric-offset = 0.009
-sa-algorithm = Ace-approximation
-; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
-; The value -1 will set default value for Still/HCT/OBC GB-models.
-sa-surface-tension = -1
+implicit-solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
-
-; IMPLICIT SOLVENT ALGORITHM
-implicit-solvent = No
-
-; GENERALIZED BORN ELECTROSTATICS
-; Algorithm for calculating Born radii
-gb-algorithm = Still
-; Frequency of calculating the Born radii inside rlist
-nstgbradii = 1
-; Cutoff for Born radii calculation; the contribution from atoms
-; between rlist and rgbradii is updated every nstlist steps
-rgbradii = 1
-; Dielectric coefficient of the implicit solvent
-gb-epsilon-solvent = 80
-; Salt concentration in M for Generalized Born models
-gb-saltconc = 0
-; Scaling factors used in the OBC GB model. Default values are OBC(II)
-gb-obc-alpha = 1
-gb-obc-beta = 0.8
-gb-obc-gamma = 4.85
-gb-dielectric-offset = 0.009
-sa-algorithm = Ace-approximation
-; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
-; The value -1 will set default value for Still/HCT/OBC GB-models.
-sa-surface-tension = -1
+implicit-solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
lj-pme-comb-rule = Geometric
ewald-geometry = 3d
epsilon-surface = 0
-
-; IMPLICIT SOLVENT ALGORITHM
-implicit-solvent = No
-
-; GENERALIZED BORN ELECTROSTATICS
-; Algorithm for calculating Born radii
-gb-algorithm = Still
-; Frequency of calculating the Born radii inside rlist
-nstgbradii = 1
-; Cutoff for Born radii calculation; the contribution from atoms
-; between rlist and rgbradii is updated every nstlist steps
-rgbradii = 1
-; Dielectric coefficient of the implicit solvent
-gb-epsilon-solvent = 80
-; Salt concentration in M for Generalized Born models
-gb-saltconc = 0
-; Scaling factors used in the OBC GB model. Default values are OBC(II)
-gb-obc-alpha = 1
-gb-obc-beta = 0.8
-gb-obc-gamma = 4.85
-gb-dielectric-offset = 0.009
-sa-algorithm = Ace-approximation
-; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
-; The value -1 will set default value for Still/HCT/OBC GB-models.
-sa-surface-tension = -1
+implicit-solvent = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
set_nec(&(necessary[d_angletypes]), d_atomtypes, d_none);
set_nec(&(necessary[d_dihedraltypes]), d_atomtypes, d_none);
set_nec(&(necessary[d_nonbond_params]), d_atomtypes, d_none);
- set_nec(&(necessary[d_implicit_genborn_params]), d_atomtypes, d_none);
- set_nec(&(necessary[d_implicit_surface_params]), d_atomtypes, d_none);
set_nec(&(necessary[d_cmaptypes]), d_atomtypes, d_none);
set_nec(&(necessary[d_moleculetype]), d_atomtypes, d_none);
set_nec(&(necessary[d_atoms]), d_moleculetype, d_none);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxpreprocess/vsite_parm.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
-#include "gromacs/mdlib/genborn.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
}
-static int
-find_gb_bondlength(t_params *plist, int ai, int aj, real *length)
-{
- int i, j, a1, a2;
-
- int found = 0;
- int status;
-
- for (i = 0; i < F_NRE && !found; i++)
- {
- if (IS_CHEMBOND(i))
- {
- for (j = 0; j < plist[i].nr; j++)
- {
- a1 = plist[i].param[j].a[0];
- a2 = plist[i].param[j].a[1];
-
- if ( (a1 == ai && a2 == aj) || (a1 == aj && a2 == ai))
- {
- /* Equilibrium bond distance */
- *length = plist[i].param[j].c[0];
- found = 1;
- }
- }
- }
- }
- status = !found;
-
- return status;
-}
-
-
-static int
-find_gb_anglelength(t_params *plist, int ai, int ak, real *length)
-{
- int i, j, a1, a2, a3;
- real r12, r23, a123;
- int found = 0;
- int status, status1, status2;
-
- r12 = r23 = 0;
-
- for (i = 0; i < F_NRE && !found; i++)
- {
- if (IS_ANGLE(i))
- {
- for (j = 0; j < plist[i].nr; j++)
- {
- a1 = plist[i].param[j].a[0];
- a2 = plist[i].param[j].a[1];
- a3 = plist[i].param[j].a[2];
-
- /* We dont care what the middle atom is, but use it below */
- if ( (a1 == ai && a3 == ak) || (a1 == ak && a3 == ai) )
- {
- /* Equilibrium bond distance */
- a123 = plist[i].param[j].c[0];
- /* Use middle atom to find reference distances r12 and r23 */
- status1 = find_gb_bondlength(plist, a1, a2, &r12);
- status2 = find_gb_bondlength(plist, a2, a3, &r23);
-
- if (status1 == 0 && status2 == 0)
- {
- /* cosine theorem to get r13 */
- *length = std::sqrt(r12*r12+r23*r23-(2*r12*r23*cos(a123/RAD2DEG)));
- found = 1;
- }
- }
- }
- }
- }
- status = !found;
-
- return status;
-}
-
-static int
-generate_gb_exclusion_interactions(t_molinfo *mi, gpp_atomtype_t atype, t_nextnb *nnb)
-{
- int j, n, ai, aj, ti, tj;
- int ftype;
- t_param param;
- t_params * plist;
- t_atoms * at;
- real radiusi, radiusj;
- real gb_radiusi, gb_radiusj;
- real param_c2, param_c4;
- real distance;
-
- plist = mi->plist;
- at = &mi->atoms;
-
- for (n = 1; n <= nnb->nrex; n++)
- {
- switch (n)
- {
- case 1:
- ftype = F_GB12;
- param_c2 = STILL_P2;
- param_c4 = 0.8875;
- break;
- case 2:
- ftype = F_GB13;
- param_c2 = STILL_P3;
- param_c4 = 0.3516;
- break;
- default:
- /* Put all higher-order exclusions into 1,4 list so we dont miss them */
- ftype = F_GB14;
- param_c2 = STILL_P3;
- param_c4 = 0.3516;
- break;
- }
-
- for (ai = 0; ai < nnb->nr; ai++)
- {
- ti = at->atom[ai].type;
- radiusi = get_atomtype_radius(ti, atype);
- gb_radiusi = get_atomtype_gb_radius(ti, atype);
-
- for (j = 0; j < nnb->nrexcl[ai][n]; j++)
- {
- aj = nnb->a[ai][n][j];
-
- /* Only add the interactions once */
- if (aj > ai)
- {
- tj = at->atom[aj].type;
- radiusj = get_atomtype_radius(tj, atype);
- gb_radiusj = get_atomtype_gb_radius(tj, atype);
-
- /* There is an exclusion of type "ftype" between atoms ai and aj */
- param.a[0] = ai;
- param.a[1] = aj;
-
- /* Reference distance, not used for 1-4 interactions */
- switch (ftype)
- {
- case F_GB12:
- if (find_gb_bondlength(plist, ai, aj, &distance) != 0)
- {
- gmx_fatal(FARGS, "Cannot find bond length for atoms %d-%d", ai, aj);
- }
- break;
- case F_GB13:
- if (find_gb_anglelength(plist, ai, aj, &distance) != 0)
- {
- gmx_fatal(FARGS, "Cannot find length for atoms %d-%d involved in angle", ai, aj);
- }
- break;
- default:
- distance = -1;
- break;
- }
- /* Assign GB parameters */
- /* Sum of radii */
- param.c[0] = radiusi+radiusj;
- /* Reference distance distance */
- param.c[1] = distance;
- /* Still parameter */
- param.c[2] = param_c2;
- /* GB radius */
- param.c[3] = gb_radiusi+gb_radiusj;
- /* Parameter */
- param.c[4] = param_c4;
-
- /* Add it to the parameter list */
- add_param_to_list(&plist[ftype], ¶m);
- }
- }
- }
- }
- return 0;
-}
-
-
static void make_atoms_sys(int nmolb, const gmx_molblock_t *molb,
const t_molinfo *molinfo,
t_atoms *atoms)
int *nmolblock,
gmx_molblock_t **molblock,
gmx_bool bFEP,
- gmx_bool bGenborn,
gmx_bool bZero,
gmx_bool usingFullRangeElectrostatics,
warninp_t wi)
*/
case d_implicit_genborn_params:
- push_gb_params(atype, pline, wi);
+ // Skip this line, so old topologies with
+ // GB parameters can be read.
break;
case d_implicit_surface_params:
- gmx_fatal(FARGS, "Implicit surface directive not supported yet.");
+ // Skip this line, so that any topologies
+ // with surface parameters can be read
+ // (even though these were never formally
+ // supported).
break;
case d_cmaptypes:
- /* nnb contains information about first,2nd,3rd bonded neighbors.
- * Use this to generate GB 1-2,1-3,1-4 interactions when necessary.
- */
- if (bGenborn == TRUE)
- {
- generate_gb_exclusion_interactions(mi0, atype, &nnb);
- }
-
done_nnb(&nnb);
if (bCouple)
const t_inputrec *ir,
int *nmolblock,
gmx_molblock_t **molblock,
- gmx_bool bGenborn,
warninp_t wi)
{
/* Tmpfile might contain a long path */
nrmols, molinfo, intermolecular_interactions,
plist, combination_rule, repulsion_power,
opts, fudgeQQ, nmolblock, molblock,
- ir->efep != efepNO, bGenborn, bZero,
+ ir->efep != efepNO, bZero,
EEL_FULL(ir->coulombtype), wi);
if ((*combination_rule != eCOMB_GEOMETRIC) &&
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const t_inputrec *ir,
int *nmolblock,
gmx_molblock_t **molblock,
- gmx_bool bGB,
warninp_t wi);
/* This routine expects sys->molt[m].ilist to be of size F_NRE and ordered. */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
char type[STRLEN], btype[STRLEN], ptype[STRLEN];
double m, q;
double c[MAXFORCEPARAM];
- double radius, vol, surftens, gb_radius, S_hct;
char tmpfield[12][100]; /* Max 12 fields of width 100 */
char errbuf[STRLEN];
t_atom *atom;
}
/* optional fields */
- surftens = -1;
- vol = -1;
- radius = -1;
- gb_radius = -1;
atomnr = -1;
- S_hct = -1;
switch (nb_funct)
{
{
if (have_bonded_type)
{
- nread = sscanf(line, "%s%s%d%lf%lf%s%lf%lf%lf%lf%lf%lf",
- type, btype, &atomnr, &m, &q, ptype, &c[0], &c[1],
- &radius, &vol, &surftens, &gb_radius);
+ nread = sscanf(line, "%s%s%d%lf%lf%s%lf%lf",
+ type, btype, &atomnr, &m, &q, ptype, &c[0], &c[1]);
if (nread < 8)
{
too_few(wi);
else
{
/* have_atomic_number && !have_bonded_type */
- nread = sscanf(line, "%s%d%lf%lf%s%lf%lf%lf%lf%lf%lf",
- type, &atomnr, &m, &q, ptype, &c[0], &c[1],
- &radius, &vol, &surftens, &gb_radius);
+ nread = sscanf(line, "%s%d%lf%lf%s%lf%lf",
+ type, &atomnr, &m, &q, ptype, &c[0], &c[1]);
if (nread < 7)
{
too_few(wi);
if (have_bonded_type)
{
/* !have_atomic_number && have_bonded_type */
- nread = sscanf(line, "%s%s%lf%lf%s%lf%lf%lf%lf%lf%lf",
- type, btype, &m, &q, ptype, &c[0], &c[1],
- &radius, &vol, &surftens, &gb_radius);
+ nread = sscanf(line, "%s%s%lf%lf%s%lf%lf",
+ type, btype, &m, &q, ptype, &c[0], &c[1]);
if (nread < 7)
{
too_few(wi);
else
{
/* !have_atomic_number && !have_bonded_type */
- nread = sscanf(line, "%s%lf%lf%s%lf%lf%lf%lf%lf%lf",
- type, &m, &q, ptype, &c[0], &c[1],
- &radius, &vol, &surftens, &gb_radius);
+ nread = sscanf(line, "%s%lf%lf%s%lf%lf",
+ type, &m, &q, ptype, &c[0], &c[1]);
if (nread < 6)
{
too_few(wi);
{
if (have_bonded_type)
{
- nread = sscanf(line, "%s%s%d%lf%lf%s%lf%lf%lf%lf%lf%lf%lf",
- type, btype, &atomnr, &m, &q, ptype, &c[0], &c[1], &c[2],
- &radius, &vol, &surftens, &gb_radius);
+ nread = sscanf(line, "%s%s%d%lf%lf%s%lf%lf%lf",
+ type, btype, &atomnr, &m, &q, ptype, &c[0], &c[1], &c[2]);
if (nread < 9)
{
too_few(wi);
else
{
/* have_atomic_number && !have_bonded_type */
- nread = sscanf(line, "%s%d%lf%lf%s%lf%lf%lf%lf%lf%lf%lf",
- type, &atomnr, &m, &q, ptype, &c[0], &c[1], &c[2],
- &radius, &vol, &surftens, &gb_radius);
+ nread = sscanf(line, "%s%d%lf%lf%s%lf%lf%lf",
+ type, &atomnr, &m, &q, ptype, &c[0], &c[1], &c[2]);
if (nread < 8)
{
too_few(wi);
if (have_bonded_type)
{
/* !have_atomic_number && have_bonded_type */
- nread = sscanf(line, "%s%s%lf%lf%s%lf%lf%lf%lf%lf%lf%lf",
- type, btype, &m, &q, ptype, &c[0], &c[1], &c[2],
- &radius, &vol, &surftens, &gb_radius);
+ nread = sscanf(line, "%s%s%lf%lf%s%lf%lf%lf",
+ type, btype, &m, &q, ptype, &c[0], &c[1], &c[2]);
if (nread < 8)
{
too_few(wi);
else
{
/* !have_atomic_number && !have_bonded_type */
- nread = sscanf(line, "%s%lf%lf%s%lf%lf%lf%lf%lf%lf%lf",
- type, &m, &q, ptype, &c[0], &c[1], &c[2],
- &radius, &vol, &surftens, &gb_radius);
+ nread = sscanf(line, "%s%lf%lf%s%lf%lf%lf",
+ type, &m, &q, ptype, &c[0], &c[1], &c[2]);
if (nread < 7)
{
too_few(wi);
sprintf(errbuf, "Overriding atomtype %s", type);
warning(wi, errbuf);
if ((nr = set_atomtype(nr, at, symtab, atom, type, param, batype_nr,
- radius, vol, surftens, atomnr, gb_radius, S_hct)) == NOTSET)
+ atomnr)) == NOTSET)
{
sprintf(errbuf, "Replacing atomtype %s failed", type);
warning_error_and_exit(wi, errbuf, FARGS);
}
}
else if ((add_atomtype(at, symtab, atom, type, param,
- batype_nr, radius, vol,
- surftens, atomnr, gb_radius, S_hct)) == NOTSET)
+ batype_nr, atomnr)) == NOTSET)
{
sprintf(errbuf, "Adding atomtype %s failed", type);
warning_error_and_exit(wi, errbuf, FARGS);
}
}
-void
-push_gb_params (gpp_atomtype_t at, char *line,
- warninp_t wi)
-{
- int atype;
- double radius, vol, surftens, gb_radius, S_hct;
- char atypename[STRLEN];
- char errbuf[STRLEN];
-
- if ( (sscanf(line, "%s%lf%lf%lf%lf%lf", atypename, &radius, &vol, &surftens, &gb_radius, &S_hct)) != 6)
- {
- sprintf(errbuf, "Too few gb parameters for type %s\n", atypename);
- warning(wi, errbuf);
- }
-
- /* Search for atomtype */
- atype = get_atomtype_type(atypename, at);
-
- if (atype == NOTSET)
- {
- printf("Couldn't find topology match for atomtype %s\n", atypename);
- abort();
- }
-
- set_atomtype_gbparam(at, atype, radius, vol, surftens, gb_radius, S_hct);
-}
-
void
push_cmaptype(directive d, t_params bt[], int nral, gpp_atomtype_t at,
t_bond_atomtype bat, char *line,
param.c[i] = 0.0;
}
- nr = add_atomtype(at, symtab, &atom, "decoupled", ¶m, -1, 0.0, 0.0, 0.0, 0, 0, 0);
+ nr = add_atomtype(at, symtab, &atom, "decoupled", ¶m, -1, 0);
/* Add space in the non-bonded parameters matrix */
realloc_nb_params(at, nbparam, pair);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
char *plines, int nb_funct,
warninp_t wi);
-void
-push_gb_params(gpp_atomtype_t atype,
- char *line,
- warninp_t wi);
-
void push_atom(struct t_symtab *symtab,
t_block *cgs,
t_atoms *at,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
char buf[12];
sprintf(buf, "%4d", (i+1));
- add_atomtype(atype, &stab, a, buf, param, 0, 0, 0, 0, 0, 0, 0);
+ add_atomtype(atype, &stab, a, buf, param, 0, 0);
}
print_bt(out, d, atype, ftype, fsubtype, plist, TRUE);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
return
(interaction_function[ftype].flags & IF_BOND) &&
- !(ftype == F_CONNBONDS || ftype == F_POSRES || ftype == F_FBPOSRES) &&
- (ftype < F_GB12 || ftype > F_GB14);
+ !(ftype == F_CONNBONDS || ftype == F_POSRES || ftype == F_FBPOSRES);
}
/*! \brief Compute the bonded part of the listed forces, parallelized over threads
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static void bc_atomtypes(const t_commrec *cr, t_atomtypes *atomtypes)
{
- int nr;
-
block_bc(cr, atomtypes->nr);
-
- nr = atomtypes->nr;
-
- snew_bc(cr, atomtypes->radius, nr);
- snew_bc(cr, atomtypes->vol, nr);
- snew_bc(cr, atomtypes->surftens, nr);
- snew_bc(cr, atomtypes->gb_radius, nr);
- snew_bc(cr, atomtypes->S_hct, nr);
-
- nblock_bc(cr, nr, atomtypes->radius);
- nblock_bc(cr, nr, atomtypes->vol);
- nblock_bc(cr, nr, atomtypes->surftens);
- nblock_bc(cr, nr, atomtypes->gb_radius);
- nblock_bc(cr, nr, atomtypes->S_hct);
}
/*! \brief Broadcasts ir and mtop from the master to all nodes in
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/forcerec-threading.h"
-#include "gromacs/mdlib/genborn.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/qmmm.h"
gmx::ForceWithVirial *forceWithVirial,
gmx_enerdata_t *enerd,
t_fcdata *fcd,
- gmx_localtop_t *top,
- gmx_genborn_t *born,
- gmx_bool bBornRadii,
matrix box,
t_lambda *fepvals,
real *lambda,
enerd->dvdl_lin[efptVDW] += dvdl_walls;
}
- /* If doing GB, reset dvda and calculate the Born radii */
- if (ir->implicit_solvent)
- {
- wallcycle_sub_start(wcycle, ewcsNONBONDED);
-
- for (i = 0; i < born->nr; i++)
- {
- fr->dvda[i] = 0;
- }
-
- if (bBornRadii)
- {
- calc_gb_rad(cr, fr, ir, top, x, fr->gblist, born, md, nrnb);
- }
-
- wallcycle_sub_stop(wcycle, ewcsNONBONDED);
- }
-
where();
/* We only do non-bonded calculation with group scheme here, the verlet
* calls are done from do_force_cutsVERLET(). */
where();
}
- /* If we are doing GB, calculate bonded forces and apply corrections
- * to the solvation forces */
- /* MRS: Eventually, many need to include free energy contribution here! */
- if (ir->implicit_solvent)
- {
- wallcycle_sub_start(wcycle, ewcsLISTED);
- calc_gb_forces(cr, md, born, top, x, forceForUseWithShiftForces, fr, idef,
- ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
- wallcycle_sub_stop(wcycle, ewcsLISTED);
- }
-
#if GMX_MPI
if (TAKETIME)
{
epot[F_LJ] = sum_v(grpp->nener, grpp->ener[egLJSR]);
epot[F_LJ14] = sum_v(grpp->nener, grpp->ener[egLJ14]);
epot[F_COUL14] = sum_v(grpp->nener, grpp->ener[egCOUL14]);
- /* We have already added 1-2,1-3, and 1-4 terms to F_GBPOL */
- epot[F_GBPOL] += sum_v(grpp->nener, grpp->ener[egGB]);
/* lattice part of LR doesnt belong to any group
* and has been added earlier
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_forcerec *fr,
gmx_vsite_t *vsite, rvec mu_tot,
double t, struct gmx_edsam *ed,
- gmx_bool bBornRadii,
int flags,
DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion);
gmx::ForceWithVirial *forceWithVirial,
gmx_enerdata_t *enerd,
t_fcdata *fcd,
- gmx_localtop_t *top,
- gmx_genborn_t *born,
- gmx_bool bBornRadii,
matrix box,
t_lambda *fepvals,
real *lambda,
ir->vdwtype == evdwCUT &&
ir->coulombtype == eelCUT &&
ir->efep == efepNO &&
- (ir->implicit_solvent == eisNO ||
- (ir->implicit_solvent == eisGBSA && (ir->gb_algorithm == egbSTILL ||
- ir->gb_algorithm == egbHCT ||
- ir->gb_algorithm == egbOBC))) &&
getenv("GMX_NO_ALLVSALL") == nullptr
);
gmx_bool bNoSolvOpt,
real print_force)
{
- int i, m, negp_pp, negptable, egi, egj;
+ int m, negp_pp, negptable, egi, egj;
real rtab;
char *env;
double dbl;
/* Check if we can/should do all-vs-all kernels */
fr->bAllvsAll = can_use_allvsall(ir, FALSE, nullptr, nullptr);
fr->AllvsAll_work = nullptr;
- fr->AllvsAll_workgb = nullptr;
/* All-vs-all kernels have not been implemented in 4.6 and later.
* See Redmine #1249. */
fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->ePBC);
}
}
- fr->bGB = (ir->implicit_solvent == eisGBSA);
fr->rc_scaling = ir->refcoord_scaling;
copy_rvec(ir->posres_com, fr->posres_com);
switch (ic->eeltype)
{
case eelCUT:
- fr->nbkernel_elec_interaction = (fr->bGB) ? GMX_NBKERNEL_ELEC_GENERALIZEDBORN : GMX_NBKERNEL_ELEC_COULOMB;
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_COULOMB;
break;
case eelRF:
set_avcsixtwelve(fp, fr, mtop);
}
- fr->gb_epsilon_solvent = ir->gb_epsilon_solvent;
-
- /* Copy the GBSA data (radius, volume and surftens for each
- * atomtype) from the topology atomtype section to forcerec.
- */
- snew(fr->atype_radius, fr->ntype);
- snew(fr->atype_vol, fr->ntype);
- snew(fr->atype_surftens, fr->ntype);
- snew(fr->atype_gb_radius, fr->ntype);
- snew(fr->atype_S_hct, fr->ntype);
-
- if (mtop->atomtypes.nr > 0)
- {
- for (i = 0; i < fr->ntype; i++)
- {
- fr->atype_radius[i] = mtop->atomtypes.radius[i];
- }
- for (i = 0; i < fr->ntype; i++)
- {
- fr->atype_vol[i] = mtop->atomtypes.vol[i];
- }
- for (i = 0; i < fr->ntype; i++)
- {
- fr->atype_surftens[i] = mtop->atomtypes.surftens[i];
- }
- for (i = 0; i < fr->ntype; i++)
- {
- fr->atype_gb_radius[i] = mtop->atomtypes.gb_radius[i];
- }
- for (i = 0; i < fr->ntype; i++)
- {
- fr->atype_S_hct[i] = mtop->atomtypes.S_hct[i];
- }
- }
-
- /* Generate the GB table if needed */
- if (fr->bGB)
+ if (ir->implicit_solvent)
{
- GMX_LOG(mdlog.info).asParagraph().
- appendText("The support for implicit solvent is deprecated, and may be removed "
- "in a future version.");
-#if GMX_DOUBLE
- fr->gbtabscale = 2000;
-#else
- fr->gbtabscale = 500;
-#endif
-
- fr->gbtabr = 100;
- fr->gbtab = make_gb_table(fr);
-
- init_gb(&fr->born, fr, ir, mtop, ir->gb_algorithm);
-
- /* Copy local gb data (for dd, this is done in dd_partition_system) */
- if (!DOMAINDECOMP(cr))
- {
- make_local_gb(cr, fr->born, ir->gb_algorithm);
- }
+ gmx_fatal(FARGS, "Implict solvation is no longer supported.");
}
/* Construct tables for the group scheme. A little unnecessary to
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_MDLIB_FORCEREC_H
#include "gromacs/mdlib/force_flags.h"
-#include "gromacs/mdlib/genborn.h"
#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdtypes/forcerec.h"
struct t_commrec;
struct t_fcdata;
struct t_filenm;
+struct t_inputrec;
namespace gmx
{
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#include "gmxpre.h"
-
-#include "genborn.h"
-
-#include <string.h>
-
-#include <cmath>
-
-#include <algorithm>
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/gmxlib/network.h"
-#include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/math/functions.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/genborn_allvsall.h"
-#include "gromacs/mdtypes/commrec.h"
-#include "gromacs/mdtypes/inputrec.h"
-#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/nblist.h"
-#include "gromacs/pbcutil/ishift.h"
-#include "gromacs/pbcutil/mshift.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/utility/smalloc.h"
-
-
-typedef struct {
- int shift;
- int naj;
- int *aj;
- int aj_nalloc;
-} gbtmpnbl_t;
-
-typedef struct gbtmpnbls {
- int nlist;
- gbtmpnbl_t *list;
- int list_nalloc;
-} t_gbtmpnbls;
-
-/* This function is exactly the same as the one in listed-forces/bonded.cpp. The reason
- * it is copied here is that the bonded gb-interactions are evaluated
- * not in calc_bonds, but rather in calc_gb_forces
- */
-static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
-{
- if (pbc)
- {
- return pbc_dx_aiuc(pbc, xi, xj, dx);
- }
- else
- {
- rvec_sub(xi, xj, dx);
- return CENTRAL;
- }
-}
-
-static int init_gb_nblist(int natoms, t_nblist *nl)
-{
- nl->maxnri = natoms*4;
- nl->maxnrj = 0;
- nl->nri = 0;
- nl->nrj = 0;
- nl->iinr = nullptr;
- nl->gid = nullptr;
- nl->shift = nullptr;
- nl->jindex = nullptr;
- nl->jjnr = nullptr;
- /*nl->nltype = nltype;*/
-
- srenew(nl->iinr, nl->maxnri);
- srenew(nl->gid, nl->maxnri);
- srenew(nl->shift, nl->maxnri);
- srenew(nl->jindex, nl->maxnri+1);
-
- nl->jindex[0] = 0;
-
- return 0;
-}
-
-
-static int init_gb_still(const t_atomtypes *atype, t_idef *idef, t_atoms *atoms,
- gmx_genborn_t *born, int natoms)
-{
-
- int i, j, m, ia, ib;
- real r, ri, rj, ri2, rj2, r3, r4, ratio, term, h, doffset;
-
- real *vsol;
- real *gp;
-
- snew(vsol, natoms);
- snew(gp, natoms);
- snew(born->gpol_still_work, natoms+3);
-
- doffset = born->gb_doffset;
-
- for (i = 0; i < natoms; i++)
- {
- born->gpol_globalindex[i] = born->vsolv_globalindex[i] =
- born->gb_radius_globalindex[i] = 0;
- }
-
- /* Compute atomic solvation volumes for Still method */
- for (i = 0; i < natoms; i++)
- {
- ri = atype->gb_radius[atoms->atom[i].type];
- born->gb_radius_globalindex[i] = ri;
- r3 = ri*ri*ri;
- born->vsolv_globalindex[i] = (4*M_PI/3)*r3;
- }
-
- for (j = 0; j < idef->il[F_GB12].nr; j += 3)
- {
- m = idef->il[F_GB12].iatoms[j];
- ia = idef->il[F_GB12].iatoms[j+1];
- ib = idef->il[F_GB12].iatoms[j+2];
-
- r = 1.01*idef->iparams[m].gb.st;
-
- ri = atype->gb_radius[atoms->atom[ia].type];
- rj = atype->gb_radius[atoms->atom[ib].type];
-
- ri2 = ri*ri;
- rj2 = rj*rj;
-
- ratio = (rj2-ri2-r*r)/(2*ri*r);
- h = ri*(1+ratio);
- term = (M_PI/3.0)*h*h*(3.0*ri-h);
-
- born->vsolv_globalindex[ia] -= term;
-
- ratio = (ri2-rj2-r*r)/(2*rj*r);
- h = rj*(1+ratio);
- term = (M_PI/3.0)*h*h*(3.0*rj-h);
-
- born->vsolv_globalindex[ib] -= term;
- }
-
- /* Get the self-, 1-2 and 1-3 polarization energies for analytical Still
- method */
- /* Self */
- for (j = 0; j < natoms; j++)
- {
- if (born->use_globalindex[j] == 1)
- {
- born->gpol_globalindex[j] = -0.5*ONE_4PI_EPS0/
- (atype->gb_radius[atoms->atom[j].type]-doffset+STILL_P1);
- }
- }
-
- /* 1-2 */
- for (j = 0; j < idef->il[F_GB12].nr; j += 3)
- {
- m = idef->il[F_GB12].iatoms[j];
- ia = idef->il[F_GB12].iatoms[j+1];
- ib = idef->il[F_GB12].iatoms[j+2];
-
- r = idef->iparams[m].gb.st;
-
- r4 = r*r*r*r;
-
- born->gpol_globalindex[ia] = born->gpol_globalindex[ia]+
- STILL_P2*born->vsolv_globalindex[ib]/r4;
- born->gpol_globalindex[ib] = born->gpol_globalindex[ib]+
- STILL_P2*born->vsolv_globalindex[ia]/r4;
- }
-
- /* 1-3 */
- for (j = 0; j < idef->il[F_GB13].nr; j += 3)
- {
- m = idef->il[F_GB13].iatoms[j];
- ia = idef->il[F_GB13].iatoms[j+1];
- ib = idef->il[F_GB13].iatoms[j+2];
-
- r = idef->iparams[m].gb.st;
- r4 = r*r*r*r;
-
- born->gpol_globalindex[ia] = born->gpol_globalindex[ia]+
- STILL_P3*born->vsolv_globalindex[ib]/r4;
- born->gpol_globalindex[ib] = born->gpol_globalindex[ib]+
- STILL_P3*born->vsolv_globalindex[ia]/r4;
- }
-
- sfree(vsol);
- sfree(gp);
-
- return 0;
-}
-
-/* Initialize all GB datastructs and compute polarization energies */
-int init_gb(gmx_genborn_t **p_born,
- t_forcerec *fr, const t_inputrec *ir,
- const gmx_mtop_t *mtop, int gb_algorithm)
-{
- int i, jj, natoms;
- real rai, sk, doffset;
-
- t_atoms atoms;
- gmx_genborn_t *born;
- gmx_localtop_t *localtop;
-
- natoms = mtop->natoms;
-
- atoms = gmx_mtop_global_atoms(mtop);
- localtop = gmx_mtop_generate_local_top(mtop, ir->efep != efepNO);
-
- snew(born, 1);
- *p_born = born;
-
- born->nr = natoms;
-
- snew(born->drobc, natoms);
- snew(born->bRad, natoms);
-
- /* Allocate memory for the global data arrays */
- snew(born->param_globalindex, natoms+3);
- snew(born->gpol_globalindex, natoms+3);
- snew(born->vsolv_globalindex, natoms+3);
- snew(born->gb_radius_globalindex, natoms+3);
- snew(born->use_globalindex, natoms+3);
-
- snew(fr->invsqrta, natoms);
- snew(fr->dvda, natoms);
-
- fr->dadx = nullptr;
- fr->dadx_rawptr = nullptr;
- fr->nalloc_dadx = 0;
- born->gpol_still_work = nullptr;
- born->gpol_hct_work = nullptr;
-
- /* snew(born->asurf,natoms); */
- /* snew(born->dasurf,natoms); */
-
- /* Initialize the gb neighbourlist */
- snew(fr->gblist, 1);
- init_gb_nblist(natoms, fr->gblist);
-
- /* Do the Vsites exclusions (if any) */
- for (i = 0; i < natoms; i++)
- {
- jj = atoms.atom[i].type;
- if (mtop->atomtypes.gb_radius[atoms.atom[i].type] > 0)
- {
- born->use_globalindex[i] = 1;
- }
- else
- {
- born->use_globalindex[i] = 0;
- }
-
- /* If we have a Vsite, put vs_globalindex[i]=0 */
- if (C6 (fr->nbfp, fr->ntype, jj, jj) == 0 &&
- C12(fr->nbfp, fr->ntype, jj, jj) == 0 &&
- atoms.atom[i].q == 0)
- {
- born->use_globalindex[i] = 0;
- }
- }
-
- /* Copy algorithm parameters from inputrecord to local structure */
- born->obc_alpha = ir->gb_obc_alpha;
- born->obc_beta = ir->gb_obc_beta;
- born->obc_gamma = ir->gb_obc_gamma;
- born->gb_doffset = ir->gb_dielectric_offset;
- born->gb_epsilon_solvent = ir->gb_epsilon_solvent;
- born->epsilon_r = ir->epsilon_r;
-
- doffset = born->gb_doffset;
-
- /* Set the surface tension */
- born->sa_surface_tension = ir->sa_surface_tension;
-
- /* If Still model, initialise the polarisation energies */
- if (gb_algorithm == egbSTILL)
- {
- init_gb_still(&(mtop->atomtypes), &(localtop->idef), &atoms,
- born, natoms);
- }
-
-
- /* If HCT/OBC, precalculate the sk*atype->S_hct factors */
- else if (gb_algorithm == egbHCT || gb_algorithm == egbOBC)
- {
-
- snew(born->gpol_hct_work, natoms+3);
-
- for (i = 0; i < natoms; i++)
- {
- if (born->use_globalindex[i] == 1)
- {
- rai = mtop->atomtypes.gb_radius[atoms.atom[i].type]-doffset;
- sk = rai * mtop->atomtypes.S_hct[atoms.atom[i].type];
- born->param_globalindex[i] = sk;
- born->gb_radius_globalindex[i] = rai;
- }
- else
- {
- born->param_globalindex[i] = 0;
- born->gb_radius_globalindex[i] = 0;
- }
- }
- }
-
- /* Allocate memory for work arrays for temporary use */
- snew(born->work, natoms+4);
- snew(born->count, natoms);
- snew(born->nblist_work, natoms);
-
- /* Domain decomposition specific stuff */
- born->nalloc = 0;
-
- return 0;
-}
-
-
-
-static int
-calc_gb_rad_still(t_commrec *cr, t_forcerec *fr, gmx_localtop_t *top,
- rvec x[], t_nblist *nl,
- gmx_genborn_t *born, t_mdatoms *md)
-{
- int i, k, n, nj0, nj1, ai, aj;
- int shift;
- real shX, shY, shZ;
- real gpi, dr2, idr4, rvdw, ratio, ccf, theta, term, rai, raj;
- real ix1, iy1, iz1, jx1, jy1, jz1, dx11, dy11, dz11;
- real rinv, idr2, idr6, vaj, dccf, cosq, sinq, prod, gpi2;
- real factor;
- real vai, prod_ai, icf4, icf6;
-
- factor = 0.5*ONE_4PI_EPS0;
- n = 0;
-
- for (i = 0; i < born->nr; i++)
- {
- born->gpol_still_work[i] = 0;
- }
-
- for (i = 0; i < nl->nri; i++)
- {
- ai = nl->iinr[i];
-
- nj0 = nl->jindex[i];
- nj1 = nl->jindex[i+1];
-
- /* Load shifts for this list */
- shift = nl->shift[i];
- shX = fr->shift_vec[shift][0];
- shY = fr->shift_vec[shift][1];
- shZ = fr->shift_vec[shift][2];
-
- gpi = 0;
-
- rai = top->atomtypes.gb_radius[md->typeA[ai]];
- vai = born->vsolv[ai];
- prod_ai = STILL_P4*vai;
-
- /* Load atom i coordinates, add shift vectors */
- ix1 = shX + x[ai][0];
- iy1 = shY + x[ai][1];
- iz1 = shZ + x[ai][2];
-
- for (k = nj0; k < nj1 && nl->jjnr[k] >= 0; k++)
- {
- aj = nl->jjnr[k];
- jx1 = x[aj][0];
- jy1 = x[aj][1];
- jz1 = x[aj][2];
-
- dx11 = ix1-jx1;
- dy11 = iy1-jy1;
- dz11 = iz1-jz1;
-
- dr2 = dx11*dx11+dy11*dy11+dz11*dz11;
- rinv = gmx::invsqrt(dr2);
- idr2 = rinv*rinv;
- idr4 = idr2*idr2;
- idr6 = idr4*idr2;
-
- raj = top->atomtypes.gb_radius[md->typeA[aj]];
-
- rvdw = rai + raj;
-
- ratio = dr2 / (rvdw * rvdw);
- vaj = born->vsolv[aj];
-
- if (ratio > STILL_P5INV)
- {
- ccf = 1.0;
- dccf = 0.0;
- }
- else
- {
- theta = ratio*STILL_PIP5;
- cosq = cos(theta);
- term = 0.5*(1.0-cosq);
- ccf = term*term;
- sinq = 1.0 - cosq*cosq;
- dccf = 2.0*term*sinq*gmx::invsqrt(sinq)*theta;
- }
-
- prod = STILL_P4*vaj;
- icf4 = ccf*idr4;
- icf6 = (4*ccf-dccf)*idr6;
- born->gpol_still_work[aj] += prod_ai*icf4;
- gpi = gpi+prod*icf4;
-
- /* Save ai->aj and aj->ai chain rule terms */
- fr->dadx[n++] = prod*icf6;
- fr->dadx[n++] = prod_ai*icf6;
- }
- born->gpol_still_work[ai] += gpi;
- }
-
- /* Parallel summations */
- if (DOMAINDECOMP(cr))
- {
- dd_atom_sum_real(cr->dd, born->gpol_still_work);
- }
-
- /* Calculate the radii */
- for (i = 0; i < fr->natoms_force; i++) /* PELA born->nr */
- {
- if (born->use[i] != 0)
- {
- gpi = born->gpol[i]+born->gpol_still_work[i];
- gpi2 = gpi * gpi;
- born->bRad[i] = factor*gmx::invsqrt(gpi2);
- fr->invsqrta[i] = gmx::invsqrt(born->bRad[i]);
- }
- }
-
- /* Extra communication required for DD */
- if (DOMAINDECOMP(cr))
- {
- dd_atom_spread_real(cr->dd, born->bRad);
- dd_atom_spread_real(cr->dd, fr->invsqrta);
- }
-
- return 0;
-
-}
-
-
-static int
-calc_gb_rad_hct(t_commrec *cr, t_forcerec *fr, gmx_localtop_t *top,
- rvec x[], t_nblist *nl,
- gmx_genborn_t *born, t_mdatoms *md)
-{
- int i, k, n, ai, aj, nj0, nj1;
- int shift;
- real shX, shY, shZ;
- real rai, raj, dr2, dr, sk, sk_ai, sk2, sk2_ai, lij, uij, diff2, tmp, sum_ai;
- real rad, min_rad, rinv, rai_inv;
- real ix1, iy1, iz1, jx1, jy1, jz1, dx11, dy11, dz11;
- real lij2, uij2, lij3, uij3, t1, t2, t3;
- real lij_inv, dlij, sk2_rinv, prod, log_term;
- real doffset, raj_inv, dadx_val;
- real *gb_radius;
-
- doffset = born->gb_doffset;
- gb_radius = born->gb_radius;
-
- for (i = 0; i < born->nr; i++)
- {
- born->gpol_hct_work[i] = 0;
- }
-
- /* Keep the compiler happy */
- n = 0;
-
- for (i = 0; i < nl->nri; i++)
- {
- ai = nl->iinr[i];
-
- nj0 = nl->jindex[i];
- nj1 = nl->jindex[i+1];
-
- /* Load shifts for this list */
- shift = nl->shift[i];
- shX = fr->shift_vec[shift][0];
- shY = fr->shift_vec[shift][1];
- shZ = fr->shift_vec[shift][2];
-
- rai = gb_radius[ai];
- rai_inv = 1.0/rai;
-
- sk_ai = born->param[ai];
- sk2_ai = sk_ai*sk_ai;
-
- /* Load atom i coordinates, add shift vectors */
- ix1 = shX + x[ai][0];
- iy1 = shY + x[ai][1];
- iz1 = shZ + x[ai][2];
-
- sum_ai = 0;
-
- for (k = nj0; k < nj1 && nl->jjnr[k] >= 0; k++)
- {
- aj = nl->jjnr[k];
-
- jx1 = x[aj][0];
- jy1 = x[aj][1];
- jz1 = x[aj][2];
-
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
-
- dr2 = dx11*dx11+dy11*dy11+dz11*dz11;
- rinv = gmx::invsqrt(dr2);
- dr = rinv*dr2;
-
- sk = born->param[aj];
- raj = gb_radius[aj];
-
- /* aj -> ai interaction */
- if (rai < dr+sk)
- {
- lij = 1.0/(dr-sk);
- dlij = 1.0;
-
- if (rai > dr-sk)
- {
- lij = rai_inv;
- dlij = 0.0;
- }
-
- lij2 = lij*lij;
- lij3 = lij2*lij;
-
- uij = 1.0/(dr+sk);
- uij2 = uij*uij;
- uij3 = uij2*uij;
-
- diff2 = uij2-lij2;
-
- lij_inv = gmx::invsqrt(lij2);
- sk2 = sk*sk;
- sk2_rinv = sk2*rinv;
- prod = 0.25*sk2_rinv;
-
- log_term = std::log(uij*lij_inv);
-
- tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term +
- prod*(-diff2);
-
- if (rai < sk-dr)
- {
- tmp = tmp + 2.0 * (rai_inv-lij);
- }
-
- t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
- t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
- t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
-
- dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
- /* fr->dadx[n++] = (dlij*t1+duij*t2+t3)*rinv; */
- /* rb2 is moved to chainrule */
-
- sum_ai += 0.5*tmp;
- }
- else
- {
- dadx_val = 0.0;
- }
- fr->dadx[n++] = dadx_val;
-
-
- /* ai -> aj interaction */
- if (raj < dr + sk_ai)
- {
- lij = 1.0/(dr-sk_ai);
- dlij = 1.0;
- raj_inv = 1.0/raj;
-
- if (raj > dr-sk_ai)
- {
- lij = raj_inv;
- dlij = 0.0;
- }
-
- lij2 = lij * lij;
- lij3 = lij2 * lij;
-
- uij = 1.0/(dr+sk_ai);
- uij2 = uij * uij;
- uij3 = uij2 * uij;
-
- diff2 = uij2-lij2;
-
- lij_inv = gmx::invsqrt(lij2);
- sk2 = sk2_ai; /* sk2_ai = sk_ai * sk_ai in i loop above */
- sk2_rinv = sk2*rinv;
- prod = 0.25 * sk2_rinv;
-
- /* log_term = table_log(uij*lij_inv,born->log_table,
- LOG_TABLE_ACCURACY); */
- log_term = std::log(uij*lij_inv);
-
- tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term +
- prod*(-diff2);
-
- if (raj < sk_ai-dr)
- {
- tmp = tmp + 2.0 * (raj_inv-lij);
- }
-
- /* duij = 1.0 */
- t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
- t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
- t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
-
- dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
- /* fr->dadx[n++] = (dlij*t1+duij*t2+t3)*rinv; */ /* rb2 is moved to chainrule */
-
- born->gpol_hct_work[aj] += 0.5*tmp;
- }
- else
- {
- dadx_val = 0.0;
- }
- fr->dadx[n++] = dadx_val;
- }
-
- born->gpol_hct_work[ai] += sum_ai;
- }
-
- /* Parallel summations */
- if (DOMAINDECOMP(cr))
- {
- dd_atom_sum_real(cr->dd, born->gpol_hct_work);
- }
-
- for (i = 0; i < fr->natoms_force; i++) /* PELA born->nr */
- {
- if (born->use[i] != 0)
- {
- rai = top->atomtypes.gb_radius[md->typeA[i]]-doffset;
- sum_ai = 1.0/rai - born->gpol_hct_work[i];
- min_rad = rai + doffset;
- rad = 1.0/sum_ai;
-
- born->bRad[i] = std::max(rad, min_rad);
- fr->invsqrta[i] = gmx::invsqrt(born->bRad[i]);
- }
- }
-
- /* Extra communication required for DD */
- if (DOMAINDECOMP(cr))
- {
- dd_atom_spread_real(cr->dd, born->bRad);
- dd_atom_spread_real(cr->dd, fr->invsqrta);
- }
-
-
- return 0;
-}
-
-static int
-calc_gb_rad_obc(t_commrec *cr, t_forcerec *fr, gmx_localtop_t *top,
- rvec x[], t_nblist *nl, gmx_genborn_t *born, t_mdatoms *md)
-{
- int i, k, ai, aj, nj0, nj1, n;
- int shift;
- real shX, shY, shZ;
- real rai, raj, dr2, dr, sk, sk2, lij, uij, diff2, tmp, sum_ai;
- real sum_ai2, sum_ai3, tsum, tchain, rinv, rai_inv, lij_inv, rai_inv2;
- real log_term, prod, sk2_rinv, sk_ai, sk2_ai;
- real ix1, iy1, iz1, jx1, jy1, jz1, dx11, dy11, dz11;
- real lij2, uij2, lij3, uij3, dlij, t1, t2, t3;
- real doffset, raj_inv, dadx_val;
- real *gb_radius;
-
- /* Keep the compiler happy */
- n = 0;
-
- doffset = born->gb_doffset;
- gb_radius = born->gb_radius;
-
- for (i = 0; i < born->nr; i++)
- {
- born->gpol_hct_work[i] = 0;
- }
-
- for (i = 0; i < nl->nri; i++)
- {
- ai = nl->iinr[i];
-
- nj0 = nl->jindex[i];
- nj1 = nl->jindex[i+1];
-
- /* Load shifts for this list */
- shift = nl->shift[i];
- shX = fr->shift_vec[shift][0];
- shY = fr->shift_vec[shift][1];
- shZ = fr->shift_vec[shift][2];
-
- rai = gb_radius[ai];
- rai_inv = 1.0/rai;
-
- sk_ai = born->param[ai];
- sk2_ai = sk_ai*sk_ai;
-
- /* Load atom i coordinates, add shift vectors */
- ix1 = shX + x[ai][0];
- iy1 = shY + x[ai][1];
- iz1 = shZ + x[ai][2];
-
- sum_ai = 0;
-
- for (k = nj0; k < nj1 && nl->jjnr[k] >= 0; k++)
- {
- aj = nl->jjnr[k];
-
- jx1 = x[aj][0];
- jy1 = x[aj][1];
- jz1 = x[aj][2];
-
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
-
- dr2 = dx11*dx11+dy11*dy11+dz11*dz11;
- rinv = gmx::invsqrt(dr2);
- dr = dr2*rinv;
-
- /* sk is precalculated in init_gb() */
- sk = born->param[aj];
- raj = gb_radius[aj];
-
- /* aj -> ai interaction */
- if (rai < dr+sk)
- {
- lij = 1.0/(dr-sk);
- dlij = 1.0;
-
- if (rai > dr-sk)
- {
- lij = rai_inv;
- dlij = 0.0;
- }
-
- uij = 1.0/(dr+sk);
- lij2 = lij * lij;
- lij3 = lij2 * lij;
- uij2 = uij * uij;
- uij3 = uij2 * uij;
-
- diff2 = uij2-lij2;
-
- lij_inv = gmx::invsqrt(lij2);
- sk2 = sk*sk;
- sk2_rinv = sk2*rinv;
- prod = 0.25*sk2_rinv;
-
- log_term = std::log(uij*lij_inv);
-
- tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2);
-
- if (rai < sk-dr)
- {
- tmp = tmp + 2.0 * (rai_inv-lij);
- }
-
- /* duij = 1.0; */
- t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
- t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
- t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
-
- dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
-
- sum_ai += 0.5*tmp;
- }
- else
- {
- dadx_val = 0.0;
- }
- fr->dadx[n++] = dadx_val;
-
- /* ai -> aj interaction */
- if (raj < dr + sk_ai)
- {
- lij = 1.0/(dr-sk_ai);
- dlij = 1.0;
- raj_inv = 1.0/raj;
-
- if (raj > dr-sk_ai)
- {
- lij = raj_inv;
- dlij = 0.0;
- }
-
- lij2 = lij * lij;
- lij3 = lij2 * lij;
-
- uij = 1.0/(dr+sk_ai);
- uij2 = uij * uij;
- uij3 = uij2 * uij;
-
- diff2 = uij2-lij2;
-
- lij_inv = gmx::invsqrt(lij2);
- sk2 = sk2_ai; /* sk2_ai = sk_ai * sk_ai in i loop above */
- sk2_rinv = sk2*rinv;
- prod = 0.25 * sk2_rinv;
-
- /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */
- log_term = std::log(uij*lij_inv);
-
- tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2);
-
- if (raj < sk_ai-dr)
- {
- tmp = tmp + 2.0 * (raj_inv-lij);
- }
-
- t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
- t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
- t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
-
- dadx_val = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
-
- born->gpol_hct_work[aj] += 0.5*tmp;
-
- }
- else
- {
- dadx_val = 0.0;
- }
- fr->dadx[n++] = dadx_val;
-
- }
- born->gpol_hct_work[ai] += sum_ai;
-
- }
-
- /* Parallel summations */
- if (DOMAINDECOMP(cr))
- {
- dd_atom_sum_real(cr->dd, born->gpol_hct_work);
- }
-
- for (i = 0; i < fr->natoms_force; i++) /* PELA born->nr */
- {
- if (born->use[i] != 0)
- {
- rai = top->atomtypes.gb_radius[md->typeA[i]];
- rai_inv2 = 1.0/rai;
- rai = rai-doffset;
- rai_inv = 1.0/rai;
- sum_ai = rai * born->gpol_hct_work[i];
- sum_ai2 = sum_ai * sum_ai;
- sum_ai3 = sum_ai2 * sum_ai;
-
- tsum = tanh(born->obc_alpha*sum_ai-born->obc_beta*sum_ai2+born->obc_gamma*sum_ai3);
- born->bRad[i] = rai_inv - tsum*rai_inv2;
- born->bRad[i] = 1.0 / born->bRad[i];
-
- fr->invsqrta[i] = gmx::invsqrt(born->bRad[i]);
-
- tchain = rai * (born->obc_alpha-2*born->obc_beta*sum_ai+3*born->obc_gamma*sum_ai2);
- born->drobc[i] = (1.0-tsum*tsum)*tchain*rai_inv2;
- }
- }
-
- /* Extra (local) communication required for DD */
- if (DOMAINDECOMP(cr))
- {
- dd_atom_spread_real(cr->dd, born->bRad);
- dd_atom_spread_real(cr->dd, fr->invsqrta);
- dd_atom_spread_real(cr->dd, born->drobc);
- }
-
- return 0;
-
-}
-
-
-
-int calc_gb_rad(t_commrec *cr, t_forcerec *fr, t_inputrec *ir, gmx_localtop_t *top,
- rvec x[], t_nblist *nl, gmx_genborn_t *born, t_mdatoms *md, t_nrnb *nrnb)
-{
- int cnt;
- int ndadx;
-
- if (fr->bAllvsAll && fr->dadx == nullptr)
- {
- /* We might need up to 8 atoms of padding before and after,
- * and another 4 units to guarantee SSE alignment.
- */
- fr->nalloc_dadx = 2*(md->homenr+12)*(md->nr/2+1+12);
- snew(fr->dadx_rawptr, fr->nalloc_dadx);
- fr->dadx = (real *) (((size_t) fr->dadx_rawptr + 16) & (~((size_t) 15)));
- }
- else
- {
- /* In the SSE-enabled gb-loops, when writing to dadx, we
- * always write 2*4 elements at a time, even in the case with only
- * 1-3 j particles, where we only really need to write 2*(1-3)
- * elements. This is because we want dadx to be aligned to a 16-
- * byte boundary, and being able to use _mm_store/load_ps
- */
- ndadx = 2 * (nl->nrj + 3*nl->nri);
-
- /* First, reallocate the dadx array, we need 3 extra for SSE */
- if (ndadx + 3 > fr->nalloc_dadx)
- {
- fr->nalloc_dadx = over_alloc_large(ndadx) + 3;
- srenew(fr->dadx_rawptr, fr->nalloc_dadx);
- fr->dadx = (real *) (((size_t) fr->dadx_rawptr + 16) & (~((size_t) 15)));
- }
- }
-
- if (fr->bAllvsAll)
- {
- cnt = md->homenr*(md->nr/2+1);
-
- if (ir->gb_algorithm == egbSTILL)
- {
- genborn_allvsall_calc_still_radii(fr, md, born, top, x[0], &fr->AllvsAll_workgb);
- /* 13 flops in outer loop, 47 flops in inner loop */
- inc_nrnb(nrnb, eNR_BORN_AVA_RADII_STILL, md->homenr*13+cnt*47);
- }
- else if (ir->gb_algorithm == egbHCT || ir->gb_algorithm == egbOBC)
- {
- genborn_allvsall_calc_hct_obc_radii(fr, md, born, ir->gb_algorithm, top, x[0], &fr->AllvsAll_workgb);
- /* 24 flops in outer loop, 183 in inner */
- inc_nrnb(nrnb, eNR_BORN_AVA_RADII_HCT_OBC, md->homenr*24+cnt*183);
- }
- else
- {
- gmx_fatal(FARGS, "Bad gb algorithm for all-vs-all interactions");
- }
- return 0;
- }
-
- /* Switch for determining which algorithm to use for Born radii calculation */
-#if GMX_DOUBLE
-
- switch (ir->gb_algorithm)
- {
- case egbSTILL:
- calc_gb_rad_still(cr, fr, top, x, nl, born, md);
- break;
- case egbHCT:
- calc_gb_rad_hct(cr, fr, top, x, nl, born, md);
- break;
- case egbOBC:
- calc_gb_rad_obc(cr, fr, top, x, nl, born, md);
- break;
-
- default:
- gmx_fatal(FARGS, "Unknown double precision algorithm for Born radii calculation: %d", ir->gb_algorithm);
- }
-
-#else
-
- switch (ir->gb_algorithm)
- {
- case egbSTILL:
- calc_gb_rad_still(cr, fr, top, x, nl, born, md);
- break;
- case egbHCT:
- calc_gb_rad_hct(cr, fr, top, x, nl, born, md);
- break;
- case egbOBC:
- calc_gb_rad_obc(cr, fr, top, x, nl, born, md);
- break;
-
- default:
- gmx_fatal(FARGS, "Unknown algorithm for Born radii calculation: %d", ir->gb_algorithm);
- }
-
-#endif /* Double or single precision */
-
- if (fr->bAllvsAll == FALSE)
- {
- switch (ir->gb_algorithm)
- {
- case egbSTILL:
- /* 17 flops per outer loop iteration, 47 flops per inner loop */
- inc_nrnb(nrnb, eNR_BORN_RADII_STILL, nl->nri*17+nl->nrj*47);
- break;
- case egbHCT:
- case egbOBC:
- /* 61 (assuming 10 for tanh) flops for outer loop iteration, 183 flops per inner loop */
- inc_nrnb(nrnb, eNR_BORN_RADII_HCT_OBC, nl->nri*61+nl->nrj*183);
- break;
-
- default:
- break;
- }
- }
-
- return 0;
-}
-
-
-
-real gb_bonds_tab(rvec x[], rvec f[], rvec fshift[], real *charge, real *p_gbtabscale,
- real *invsqrta, real *dvda, real *GBtab, t_idef *idef, real epsilon_r,
- real gb_epsilon_solvent, real facel, const t_pbc *pbc, const t_graph *graph)
-{
- int i, j, n0, m, nnn, ai, aj;
- int ki;
-
- real isai, isaj;
- real r, rsq11;
- real rinv11, iq;
- real isaprod, qq, gbscale, gbtabscale, Y, F, Geps, Heps2, Fp, VV, FF, rt, eps, eps2;
- real vgb, fgb, fijC, dvdatmp, fscal;
- real vctot;
-
- rvec dx;
- ivec dt;
-
- t_iatom *forceatoms;
-
- /* Scale the electrostatics by gb_epsilon_solvent */
- facel = facel * ((1.0/epsilon_r) - 1.0/gb_epsilon_solvent);
-
- gbtabscale = *p_gbtabscale;
- vctot = 0.0;
-
- for (j = F_GB12; j <= F_GB14; j++)
- {
- forceatoms = idef->il[j].iatoms;
-
- for (i = 0; i < idef->il[j].nr; )
- {
- /* To avoid reading in the interaction type, we just increment i to pass over
- * the types in the forceatoms array, this saves some memory accesses
- */
- i++;
- ai = forceatoms[i++];
- aj = forceatoms[i++];
-
- ki = pbc_rvec_sub(pbc, x[ai], x[aj], dx);
- rsq11 = iprod(dx, dx);
-
- isai = invsqrta[ai];
- iq = (-1)*facel*charge[ai];
-
- rinv11 = gmx::invsqrt(rsq11);
- isaj = invsqrta[aj];
- isaprod = isai*isaj;
- qq = isaprod*iq*charge[aj];
- gbscale = isaprod*gbtabscale;
- r = rsq11*rinv11;
- rt = r*gbscale;
- n0 = static_cast<int>(rt);
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vgb = qq*VV;
- fijC = qq*FF*gbscale;
- dvdatmp = -(vgb+fijC*r)*0.5;
- dvda[aj] = dvda[aj] + dvdatmp*isaj*isaj;
- dvda[ai] = dvda[ai] + dvdatmp*isai*isai;
- vctot = vctot + vgb;
- fgb = -(fijC)*rinv11;
-
- if (graph)
- {
- ivec_sub(SHIFT_IVEC(graph, ai), SHIFT_IVEC(graph, aj), dt);
- ki = IVEC2IS(dt);
- }
-
- for (m = 0; (m < DIM); m++) /* 15 */
- {
- fscal = fgb*dx[m];
- f[ai][m] += fscal;
- f[aj][m] -= fscal;
- fshift[ki][m] += fscal;
- fshift[CENTRAL][m] -= fscal;
- }
- }
- }
-
- return vctot;
-}
-
-static real calc_gb_selfcorrections(t_commrec *cr, int natoms,
- real *charge, gmx_genborn_t *born, real *dvda, double facel)
-{
- int i, ai, at0, at1;
- real rai, e, derb, q, q2, fi, rai_inv, vtot;
-
- if (DOMAINDECOMP(cr))
- {
- at0 = 0;
- at1 = cr->dd->nat_home;
- }
- else
- {
- at0 = 0;
- at1 = natoms;
-
- }
-
- /* Scale the electrostatics by gb_epsilon_solvent */
- facel = facel * ((1.0/born->epsilon_r) - 1.0/born->gb_epsilon_solvent);
-
- vtot = 0.0;
-
- /* Apply self corrections */
- for (i = at0; i < at1; i++)
- {
- ai = i;
-
- if (born->use[ai] == 1)
- {
- rai = born->bRad[ai];
- rai_inv = 1.0/rai;
- q = charge[ai];
- q2 = q*q;
- fi = facel*q2;
- e = fi*rai_inv;
- derb = 0.5*e*rai_inv*rai_inv;
- dvda[ai] += derb*rai;
- vtot -= 0.5*e;
- }
- }
-
- return vtot;
-
-}
-
-static real calc_gb_nonpolar(t_commrec *cr, t_forcerec *fr, int natoms, gmx_genborn_t *born, gmx_localtop_t *top,
- real *dvda, t_mdatoms *md)
-{
- int ai, i, at0, at1;
- real e, es, rai, term, probe, tmp, factor;
- real rbi_inv, rbi_inv2;
-
- if (DOMAINDECOMP(cr))
- {
- at0 = 0;
- at1 = cr->dd->nat_home;
- }
- else
- {
- at0 = 0;
- at1 = natoms;
- }
-
- /* factor is the surface tension */
- factor = born->sa_surface_tension;
-
- es = 0;
- probe = 0.14;
- term = M_PI*4;
-
- for (i = at0; i < at1; i++)
- {
- ai = i;
-
- if (born->use[ai] == 1)
- {
- rai = top->atomtypes.gb_radius[md->typeA[ai]];
- rbi_inv = fr->invsqrta[ai];
- rbi_inv2 = rbi_inv * rbi_inv;
- tmp = (rai*rbi_inv2)*(rai*rbi_inv2);
- tmp = tmp*tmp*tmp;
- e = factor*term*(rai+probe)*(rai+probe)*tmp;
- dvda[ai] = dvda[ai] - 6*e*rbi_inv2;
- es = es + e;
- }
- }
-
- return es;
-}
-
-
-
-static real calc_gb_chainrule(int natoms, t_nblist *nl, real *dadx, real *dvda, rvec x[], rvec t[], rvec fshift[],
- rvec shift_vec[], int gb_algorithm, gmx_genborn_t *born)
-{
- int i, k, n, ai, aj, nj0, nj1, n0, n1;
- int shift;
- real shX, shY, shZ;
- real fgb, rbi, fix1, fiy1, fiz1;
- real ix1, iy1, iz1, jx1, jy1, jz1, dx11, dy11, dz11;
- real tx, ty, tz, rbai, rbaj, fgb_ai;
- real *rb;
-
- n = 0;
- rb = born->work;
-
- n0 = 0;
- n1 = natoms;
-
- if (gb_algorithm == egbSTILL)
- {
- for (i = n0; i < n1; i++)
- {
- rbi = born->bRad[i];
- rb[i] = (2 * rbi * rbi * dvda[i])/ONE_4PI_EPS0;
- }
- }
- else if (gb_algorithm == egbHCT)
- {
- for (i = n0; i < n1; i++)
- {
- rbi = born->bRad[i];
- rb[i] = rbi * rbi * dvda[i];
- }
- }
- else if (gb_algorithm == egbOBC)
- {
- for (i = n0; i < n1; i++)
- {
- rbi = born->bRad[i];
- rb[i] = rbi * rbi * born->drobc[i] * dvda[i];
- }
- }
-
- for (i = 0; i < nl->nri; i++)
- {
- ai = nl->iinr[i];
-
- nj0 = nl->jindex[i];
- nj1 = nl->jindex[i+1];
-
- /* Load shifts for this list */
- shift = nl->shift[i];
- shX = shift_vec[shift][0];
- shY = shift_vec[shift][1];
- shZ = shift_vec[shift][2];
-
- /* Load atom i coordinates, add shift vectors */
- ix1 = shX + x[ai][0];
- iy1 = shY + x[ai][1];
- iz1 = shZ + x[ai][2];
-
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- rbai = rb[ai];
-
- for (k = nj0; k < nj1 && nl->jjnr[k] >= 0; k++)
- {
- aj = nl->jjnr[k];
-
- jx1 = x[aj][0];
- jy1 = x[aj][1];
- jz1 = x[aj][2];
-
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
-
- rbaj = rb[aj];
-
- fgb = rbai*dadx[n++];
- fgb_ai = rbaj*dadx[n++];
-
- /* Total force between ai and aj is the sum of ai->aj and aj->ai */
- fgb = fgb + fgb_ai;
-
- tx = fgb * dx11;
- ty = fgb * dy11;
- tz = fgb * dz11;
-
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Update force on atom aj */
- t[aj][0] = t[aj][0] - tx;
- t[aj][1] = t[aj][1] - ty;
- t[aj][2] = t[aj][2] - tz;
- }
-
- /* Update force and shift forces on atom ai */
- t[ai][0] = t[ai][0] + fix1;
- t[ai][1] = t[ai][1] + fiy1;
- t[ai][2] = t[ai][2] + fiz1;
-
- fshift[shift][0] = fshift[shift][0] + fix1;
- fshift[shift][1] = fshift[shift][1] + fiy1;
- fshift[shift][2] = fshift[shift][2] + fiz1;
-
- }
-
- return 0;
-}
-
-
-void
-calc_gb_forces(t_commrec *cr, t_mdatoms *md, gmx_genborn_t *born, gmx_localtop_t *top,
- rvec x[], rvec f[], t_forcerec *fr, t_idef *idef, int gb_algorithm, int sa_algorithm, t_nrnb *nrnb,
- const t_pbc *pbc, const t_graph *graph, gmx_enerdata_t *enerd)
-{
- int cnt;
-
- /* PBC or not? */
- const t_pbc *pbc_null;
-
- if (fr->bMolPBC)
- {
- pbc_null = pbc;
- }
- else
- {
- pbc_null = nullptr;
- }
-
- if (sa_algorithm == esaAPPROX)
- {
- /* Do a simple ACE type approximation for the non-polar solvation */
- enerd->term[F_NPSOLVATION] += calc_gb_nonpolar(cr, fr, born->nr, born, top, fr->dvda, md);
- }
-
- /* Calculate the bonded GB-interactions using either table or analytical formula */
- enerd->term[F_GBPOL] += gb_bonds_tab(x, f, fr->fshift, md->chargeA, &(fr->gbtabscale),
- fr->invsqrta, fr->dvda, fr->gbtab->data, idef, born->epsilon_r, born->gb_epsilon_solvent, fr->ic->epsfac, pbc_null, graph);
-
- /* Calculate self corrections to the GB energies - currently only A state used! (FIXME) */
- enerd->term[F_GBPOL] += calc_gb_selfcorrections(cr, born->nr, md->chargeA, born, fr->dvda, fr->ic->epsfac);
-
- /* If parallel, sum the derivative of the potential w.r.t the born radii */
- if (DOMAINDECOMP(cr))
- {
- dd_atom_sum_real(cr->dd, fr->dvda);
- dd_atom_spread_real(cr->dd, fr->dvda);
- }
-
- if (fr->bAllvsAll)
- {
- genborn_allvsall_calc_chainrule(fr, md, born, x[0], f[0], gb_algorithm, fr->AllvsAll_workgb);
- cnt = md->homenr*(md->nr/2+1);
- /* 9 flops for outer loop, 15 for inner */
- inc_nrnb(nrnb, eNR_BORN_AVA_CHAINRULE, md->homenr*9+cnt*15);
- return;
- }
-
- calc_gb_chainrule(fr->natoms_force, fr->gblist, fr->dadx, fr->dvda,
- x, f, fr->fshift, fr->shift_vec, gb_algorithm, born);
-
- if (!fr->bAllvsAll)
- {
- /* 9 flops for outer loop, 15 for inner */
- inc_nrnb(nrnb, eNR_BORN_CHAINRULE, fr->gblist->nri*9+fr->gblist->nrj*15);
- }
-}
-
-static void add_j_to_gblist(gbtmpnbl_t *list, int aj)
-{
- if (list->naj >= list->aj_nalloc)
- {
- list->aj_nalloc = over_alloc_large(list->naj+1);
- srenew(list->aj, list->aj_nalloc);
- }
-
- list->aj[list->naj++] = aj;
-}
-
-static gbtmpnbl_t *find_gbtmplist(struct gbtmpnbls *lists, int shift)
-{
- int ind, i;
-
- /* Search the list with the same shift, if there is one */
- ind = 0;
- while (ind < lists->nlist && shift != lists->list[ind].shift)
- {
- ind++;
- }
- if (ind == lists->nlist)
- {
- if (lists->nlist == lists->list_nalloc)
- {
- lists->list_nalloc++;
- srenew(lists->list, lists->list_nalloc);
- for (i = lists->nlist; i < lists->list_nalloc; i++)
- {
- lists->list[i].aj = nullptr;
- lists->list[i].aj_nalloc = 0;
- }
-
- }
-
- lists->list[lists->nlist].shift = shift;
- lists->list[lists->nlist].naj = 0;
- lists->nlist++;
- }
-
- return &lists->list[ind];
-}
-
-static void add_bondeds_to_gblist(t_ilist *il,
- gmx_bool bMolPBC, t_pbc *pbc, t_graph *g, rvec *x,
- struct gbtmpnbls *nls)
-{
- int ind, j, ai, aj, found;
- rvec dx;
- ivec dt;
- gbtmpnbl_t *list;
-
- for (ind = 0; ind < il->nr; ind += 3)
- {
- ai = il->iatoms[ind+1];
- aj = il->iatoms[ind+2];
-
- int shift = CENTRAL;
- if (g != nullptr)
- {
- rvec_sub(x[ai], x[aj], dx);
- ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
- shift = IVEC2IS(dt);
- }
- else if (bMolPBC)
- {
- shift = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
- }
-
- /* Find the list for this shift or create one */
- list = find_gbtmplist(&nls[ai], shift);
-
- found = 0;
-
- /* So that we do not add the same bond twice.
- * This happens with some constraints between 1-3 atoms
- * that are in the bond-list but should not be in the GB nb-list */
- for (j = 0; j < list->naj; j++)
- {
- if (list->aj[j] == aj)
- {
- found = 1;
- }
- }
-
- if (found == 0)
- {
- if (ai == aj)
- {
- gmx_incons("ai == aj");
- }
-
- add_j_to_gblist(list, aj);
- }
- }
-}
-
-
-int make_gb_nblist(t_commrec *cr, int gb_algorithm,
- rvec x[], matrix box,
- t_forcerec *fr, t_idef *idef, t_graph *graph, gmx_genborn_t *born)
-{
- int i, j, k, n, nj0, nj1, ai, shift, s;
- t_nblist *nblist;
- t_pbc pbc;
-
- struct gbtmpnbls *nls;
- gbtmpnbl_t *list = nullptr;
-
- set_pbc(&pbc, fr->ePBC, box);
- nls = born->nblist_work;
-
- for (i = 0; i < born->nr; i++)
- {
- nls[i].nlist = 0;
- }
-
- if (fr->bMolPBC)
- {
- set_pbc_dd(&pbc, fr->ePBC, cr->dd->nc, TRUE, box);
- }
-
- switch (gb_algorithm)
- {
- case egbHCT:
- case egbOBC:
- /* Loop over 1-2, 1-3 and 1-4 interactions */
- for (j = F_GB12; j <= F_GB14; j++)
- {
- add_bondeds_to_gblist(&idef->il[j], fr->bMolPBC, &pbc, graph, x, nls);
- }
- break;
- case egbSTILL:
- /* Loop over 1-4 interactions */
- add_bondeds_to_gblist(&idef->il[F_GB14], fr->bMolPBC, &pbc, graph, x, nls);
- break;
- default:
- gmx_incons("Unknown GB algorithm");
- }
-
- /* Loop over the VDWQQ and VDW nblists to set up the nonbonded part of the GB list */
- for (n = 0; (n < fr->nnblists); n++)
- {
- for (i = 0; (i < eNL_NR); i++)
- {
- nblist = &(fr->nblists[n].nlist_sr[i]);
-
- if (nblist->nri > 0 && (i == eNL_VDWQQ || i == eNL_QQ))
- {
- for (j = 0; j < nblist->nri; j++)
- {
- ai = nblist->iinr[j];
- shift = nblist->shift[j];
-
- /* Find the list for this shift or create one */
- list = find_gbtmplist(&nls[ai], shift);
-
- nj0 = nblist->jindex[j];
- nj1 = nblist->jindex[j+1];
-
- /* Add all the j-atoms in the non-bonded list to the GB list */
- for (k = nj0; k < nj1; k++)
- {
- add_j_to_gblist(list, nblist->jjnr[k]);
- }
- }
- }
- }
- }
-
- /* Zero out some counters */
- fr->gblist->nri = 0;
- fr->gblist->nrj = 0;
-
- fr->gblist->jindex[0] = fr->gblist->nri;
-
- for (i = 0; i < fr->natoms_force; i++)
- {
- for (s = 0; s < nls[i].nlist; s++)
- {
- list = &nls[i].list[s];
-
- /* Only add those atoms that actually have neighbours */
- if (born->use[i] != 0)
- {
- fr->gblist->iinr[fr->gblist->nri] = i;
- fr->gblist->shift[fr->gblist->nri] = list->shift;
- fr->gblist->nri++;
-
- for (k = 0; k < list->naj; k++)
- {
- /* Memory allocation for jjnr */
- if (fr->gblist->nrj >= fr->gblist->maxnrj)
- {
- fr->gblist->maxnrj += over_alloc_large(fr->gblist->maxnrj);
-
- if (debug)
- {
- fprintf(debug, "Increasing GB neighbourlist j size to %d\n", fr->gblist->maxnrj);
- }
-
- srenew(fr->gblist->jjnr, fr->gblist->maxnrj);
- }
-
- /* Put in list */
- if (i == list->aj[k])
- {
- gmx_incons("i == list->aj[k]");
- }
- fr->gblist->jjnr[fr->gblist->nrj++] = list->aj[k];
- }
-
- fr->gblist->jindex[fr->gblist->nri] = fr->gblist->nrj;
- }
- }
- }
-
- return 0;
-}
-
-void make_local_gb(const t_commrec *cr, gmx_genborn_t *born, int gb_algorithm)
-{
- int i, at0, at1;
- gmx_domdec_t *dd = nullptr;
-
- if (DOMAINDECOMP(cr))
- {
- dd = cr->dd;
- at0 = 0;
- at1 = dd->nat_tot;
- }
- else
- {
- /* Single node, just copy pointers and return */
- if (gb_algorithm == egbSTILL)
- {
- born->gpol = born->gpol_globalindex;
- born->vsolv = born->vsolv_globalindex;
- born->gb_radius = born->gb_radius_globalindex;
- }
- else
- {
- born->param = born->param_globalindex;
- born->gb_radius = born->gb_radius_globalindex;
- }
-
- born->use = born->use_globalindex;
-
- return;
- }
-
- /* Reallocation of local arrays if necessary */
- /* fr->natoms_force is equal to dd->nat_tot */
- if (DOMAINDECOMP(cr) && dd->nat_tot > born->nalloc)
- {
- int nalloc;
-
- nalloc = dd->nat_tot;
-
- /* Arrays specific to different gb algorithms */
- if (gb_algorithm == egbSTILL)
- {
- srenew(born->gpol, nalloc+3);
- srenew(born->vsolv, nalloc+3);
- srenew(born->gb_radius, nalloc+3);
- for (i = born->nalloc; (i < nalloc+3); i++)
- {
- born->gpol[i] = 0;
- born->vsolv[i] = 0;
- born->gb_radius[i] = 0;
- }
- }
- else
- {
- srenew(born->param, nalloc+3);
- srenew(born->gb_radius, nalloc+3);
- for (i = born->nalloc; (i < nalloc+3); i++)
- {
- born->param[i] = 0;
- born->gb_radius[i] = 0;
- }
- }
-
- /* All gb-algorithms use the array for vsites exclusions */
- srenew(born->use, nalloc+3);
- for (i = born->nalloc; (i < nalloc+3); i++)
- {
- born->use[i] = 0;
- }
-
- born->nalloc = nalloc;
- }
-
- /* With dd, copy algorithm specific arrays */
- if (gb_algorithm == egbSTILL)
- {
- for (i = at0; i < at1; i++)
- {
- born->gpol[i] = born->gpol_globalindex[dd->gatindex[i]];
- born->vsolv[i] = born->vsolv_globalindex[dd->gatindex[i]];
- born->gb_radius[i] = born->gb_radius_globalindex[dd->gatindex[i]];
- born->use[i] = born->use_globalindex[dd->gatindex[i]];
- }
- }
- else
- {
- for (i = at0; i < at1; i++)
- {
- born->param[i] = born->param_globalindex[dd->gatindex[i]];
- born->gb_radius[i] = born->gb_radius_globalindex[dd->gatindex[i]];
- born->use[i] = born->use_globalindex[dd->gatindex[i]];
- }
- }
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef GMX_MDLIB_GENBORN_H
-#define GMX_MDLIB_GENBORN_H
-
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/vectypes.h"
-
-struct gmx_genborn_t;
-struct gmx_enerdata_t;
-struct gmx_localtop_t;
-struct gmx_mtop_t;
-struct t_commrec;
-struct t_forcerec;
-struct t_graph;
-struct t_idef;
-struct t_inputrec;
-struct t_mdatoms;
-struct t_nblist;
-struct t_nrnb;
-struct t_pbc;
-
-typedef struct
-{
- int nbonds;
- int bond[10];
- real length[10];
-} genborn_bonds_t;
-
-typedef struct gbtmpnbls *gbtmpnbls_t;
-
-/* Struct to hold all the information for GB */
-typedef struct gmx_genborn_t
-{
- int nr; /* number of atoms, length of arrays below */
- int n12; /* number of 1-2 (bond) interactions */
- int n13; /* number of 1-3 (angle) terms */
- int n14; /* number of 1-4 (torsion) terms */
- int nalloc; /* Allocation of local arrays (with DD) */
-
-
- /* Arrays below that end with _globalindex are used for setting up initial values of
- * all gb parameters and values. They all have length natoms, which for DD is the
- * global atom number.
- * Values are then taken from these arrays to local copies, that have names without
- * _globalindex, in the routine make_local_gb(), which is called once for single
- * node runs, and for DD at every call to dd_partition_system
- */
-
- real *gpol; /* Atomic polarisation energies */
- real *gpol_globalindex; /* */
- real *gpol_still_work; /* Work array for Still model */
- real *gpol_hct_work; /* Work array for HCT/OBC models */
- real *bRad; /* Atomic Born radii */
- real *vsolv; /* Atomic solvation volumes */
- real *vsolv_globalindex; /* */
- real *gb_radius; /* Radius info, copied from atomtypes */
- real *gb_radius_globalindex;
-
- int *use; /* Array that till if this atom does GB */
- int *use_globalindex; /* Global array for parallelization */
-
- real es; /* Solvation energy and derivatives */
- real *asurf; /* Atomic surface area */
- rvec *dasurf; /* Surface area derivatives */
- real as; /* Total surface area */
-
- real *drobc; /* Parameters for OBC chain rule calculation */
- real *param; /* Precomputed factor rai*atype->S_hct for HCT/OBC */
- real *param_globalindex; /* */
-
- real *log_table; /* Table for logarithm lookup */
-
- real obc_alpha; /* OBC parameters */
- real obc_beta; /* OBC parameters */
- real obc_gamma; /* OBC parameters */
- real gb_doffset; /* Dielectric offset for Still/HCT/OBC */
- real gb_epsilon_solvent; /* */
- real epsilon_r; /* Used for inner dielectric */
-
- real sa_surface_tension; /* Surface tension for non-polar solvation */
-
- real *work; /* Used for parallel summation and in the chain rule, length natoms */
- real *buf; /* Used for parallel summation and in the chain rule, length natoms */
- int *count; /* Used for setting up the special gb nblist, length natoms */
- gbtmpnbls_t nblist_work; /* Used for setting up the special gb nblist, dim natoms*nblist_work_nalloc */
- int nblist_work_nalloc; /* Length of second dimension of nblist_work */
-}
-gmx_genborn_t;
-/* Still parameters - make sure to edit in genborn_sse.c too if you change these! */
-#define STILL_P1 0.073*0.1 /* length */
-#define STILL_P2 0.921*0.1*CAL2JOULE /* energy*length */
-#define STILL_P3 6.211*0.1*CAL2JOULE /* energy*length */
-#define STILL_P4 15.236*0.1*CAL2JOULE
-#define STILL_P5 1.254
-
-#define STILL_P5INV (1.0/STILL_P5)
-#define STILL_PIP5 (M_PI*STILL_P5)
-
-
-/* Initialise GB stuff */
-int init_gb(struct gmx_genborn_t **p_born,
- struct t_forcerec *fr, const struct t_inputrec *ir,
- const gmx_mtop_t *mtop, int gb_algorithm);
-
-
-/* Born radii calculations, both with and without SSE acceleration */
-int calc_gb_rad(struct t_commrec *cr, struct t_forcerec *fr, struct t_inputrec *ir, gmx_localtop_t *top, rvec x[], t_nblist *nl, struct gmx_genborn_t *born, t_mdatoms *md, t_nrnb *nrnb);
-
-
-
-/* Bonded GB interactions */
-real gb_bonds_tab(rvec x[], rvec f[], rvec fshift[], real *charge, real *p_gbtabscale,
- real *invsqrta, real *dvda, real *GBtab, t_idef *idef, real epsilon_r,
- real gb_epsilon_solvent, real facel, const struct t_pbc *pbc,
- const struct t_graph *graph);
-
-
-
-
-/* Functions for calculating adjustments due to ie chain rule terms */
-void
-calc_gb_forces(struct t_commrec *cr, t_mdatoms *md, struct gmx_genborn_t *born, gmx_localtop_t *top,
- rvec x[], rvec f[], struct t_forcerec *fr, t_idef *idef, int gb_algorithm, int sa_algorithm, t_nrnb *nrnb,
- const struct t_pbc *pbc, const struct t_graph *graph, struct gmx_enerdata_t *enerd);
-
-
-int
-make_gb_nblist(struct t_commrec *cr, int gb_algorithm,
- rvec x[], matrix box,
- struct t_forcerec *fr, t_idef *idef, struct t_graph *graph, struct gmx_genborn_t *born);
-
-void
-make_local_gb(const struct t_commrec *cr, struct gmx_genborn_t *born, int gb_algorithm);
-
-#endif
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team.
- * Copyright (c) 2010,2014,2015,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "genborn_allvsall.h"
-
-#include <cmath>
-
-#include <algorithm>
-
-#include "gromacs/gmxlib/network.h"
-#include "gromacs/math/functions.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/genborn.h"
-#include "gromacs/mdtypes/forcerec.h"
-#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/mdatom.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/utility/smalloc.h"
-
-
-typedef struct
-{
- int * jindex_gb;
- int ** exclusion_mask_gb;
-}
-gmx_allvsallgb2_data_t;
-
-static int
-calc_maxoffset(int i, int natoms)
-{
- int maxoffset;
-
- if ((natoms % 2) == 1)
- {
- /* Odd number of atoms, easy */
- maxoffset = natoms/2;
- }
- else if ((natoms % 4) == 0)
- {
- /* Multiple of four is hard */
- if (i < natoms/2)
- {
- if ((i % 2) == 0)
- {
- maxoffset = natoms/2;
- }
- else
- {
- maxoffset = natoms/2-1;
- }
- }
- else
- {
- if ((i % 2) == 1)
- {
- maxoffset = natoms/2;
- }
- else
- {
- maxoffset = natoms/2-1;
- }
- }
- }
- else
- {
- /* natoms/2 = odd */
- if ((i % 2) == 0)
- {
- maxoffset = natoms/2;
- }
- else
- {
- maxoffset = natoms/2-1;
- }
- }
-
- return maxoffset;
-}
-
-static void
-setup_gb_exclusions_and_indices(gmx_allvsallgb2_data_t * aadata,
- t_ilist * ilist,
- int natoms,
- gmx_bool bInclude12,
- gmx_bool bInclude13,
- gmx_bool bInclude14)
-{
- int i, j, k;
- int a1, a2;
- int max_offset;
- int max_excl_offset;
-
- /* This routine can appear to be a bit complex, but it is mostly book-keeping.
- * To enable the fast all-vs-all kernel we need to be able to stream through all coordinates
- * whether they should interact or not.
- *
- * To avoid looping over the exclusions, we create a simple mask that is 1 if the interaction
- * should be present, otherwise 0. Since exclusions typically only occur when i & j are close,
- * we create a jindex array with three elements per i atom: the starting point, the point to
- * which we need to check exclusions, and the end point.
- * This way we only have to allocate a short exclusion mask per i atom.
- */
-
- /* Allocate memory for jindex arrays */
- snew(aadata->jindex_gb, 3*natoms);
-
- /* Pointer to lists with exclusion masks */
- snew(aadata->exclusion_mask_gb, natoms);
-
- for (i = 0; i < natoms; i++)
- {
- /* Start */
- aadata->jindex_gb[3*i] = i+1;
- max_offset = calc_maxoffset(i, natoms);
-
- /* first check the max range of atoms to EXCLUDE */
- max_excl_offset = 0;
- if (!bInclude12)
- {
- for (j = 0; j < ilist[F_GB12].nr; j += 3)
- {
- a1 = ilist[F_GB12].iatoms[j+1];
- a2 = ilist[F_GB12].iatoms[j+2];
-
- if (a1 == i)
- {
- k = a2-a1;
- }
- else if (a2 == i)
- {
- k = a1+natoms-a2;
- }
- else
- {
- continue;
- }
- if (k > 0 && k <= max_offset)
- {
- max_excl_offset = std::max(k, max_excl_offset);
- }
- }
- }
- if (!bInclude13)
- {
- for (j = 0; j < ilist[F_GB13].nr; j += 3)
- {
- a1 = ilist[F_GB13].iatoms[j+1];
- a2 = ilist[F_GB13].iatoms[j+2];
-
-
- if (a1 == i)
- {
- k = a2-a1;
- }
- else if (a2 == i)
- {
- k = a1+natoms-a2;
- }
- else
- {
- continue;
- }
- if (k > 0 && k <= max_offset)
- {
- max_excl_offset = std::max(k, max_excl_offset);
- }
- }
- }
- if (!bInclude14)
- {
- for (j = 0; j < ilist[F_GB14].nr; j += 3)
- {
- a1 = ilist[F_GB14].iatoms[j+1];
- a2 = ilist[F_GB14].iatoms[j+2];
-
-
- if (a1 == i)
- {
- k = a2-a1;
- }
- else if (a2 == i)
- {
- k = a1+natoms-a2;
- }
- else
- {
- continue;
- }
- if (k > 0 && k <= max_offset)
- {
- max_excl_offset = std::max(k, max_excl_offset);
- }
- }
- }
- max_excl_offset = std::min(max_offset, max_excl_offset);
-
- aadata->jindex_gb[3*i+1] = i+1+max_excl_offset;
-
- snew(aadata->exclusion_mask_gb[i], max_excl_offset);
-
- /* Include everything by default */
- for (j = 0; j < max_excl_offset; j++)
- {
- /* Use all-ones to mark interactions that should be present, compatible with SSE */
- aadata->exclusion_mask_gb[i][j] = 0xFFFFFFFF;
- }
- /* Go through exclusions again */
- if (!bInclude12)
- {
- for (j = 0; j < ilist[F_GB12].nr; j += 3)
- {
- a1 = ilist[F_GB12].iatoms[j+1];
- a2 = ilist[F_GB12].iatoms[j+2];
-
- if (a1 == i)
- {
- k = a2-a1;
- }
- else if (a2 == i)
- {
- k = a1+natoms-a2;
- }
- else
- {
- continue;
- }
- if (k > 0 && k <= max_offset)
- {
- aadata->exclusion_mask_gb[i][k-1] = 0;
- }
- }
- }
- if (!bInclude13)
- {
- for (j = 0; j < ilist[F_GB13].nr; j += 3)
- {
- a1 = ilist[F_GB13].iatoms[j+1];
- a2 = ilist[F_GB13].iatoms[j+2];
-
- if (a1 == i)
- {
- k = a2-a1;
- }
- else if (a2 == i)
- {
- k = a1+natoms-a2;
- }
- else
- {
- continue;
- }
- if (k > 0 && k <= max_offset)
- {
- aadata->exclusion_mask_gb[i][k-1] = 0;
- }
- }
- }
- if (!bInclude14)
- {
- for (j = 0; j < ilist[F_GB14].nr; j += 3)
- {
- a1 = ilist[F_GB14].iatoms[j+1];
- a2 = ilist[F_GB14].iatoms[j+2];
-
- if (a1 == i)
- {
- k = a2-a1;
- }
- else if (a2 == i)
- {
- k = a1+natoms-a2;
- }
- else
- {
- continue;
- }
- if (k > 0 && k <= max_offset)
- {
- aadata->exclusion_mask_gb[i][k-1] = 0;
- }
- }
- }
-
- /* End */
-
- /* End */
- aadata->jindex_gb[3*i+2] = i+1+max_offset;
- }
-}
-
-
-static void
-genborn_allvsall_setup(gmx_allvsallgb2_data_t ** p_aadata,
- t_ilist * ilist,
- int natoms,
- gmx_bool bInclude12,
- gmx_bool bInclude13,
- gmx_bool bInclude14)
-{
- gmx_allvsallgb2_data_t *aadata;
-
- snew(aadata, 1);
- *p_aadata = aadata;
-
- setup_gb_exclusions_and_indices(aadata, ilist, natoms, bInclude12, bInclude13, bInclude14);
-}
-
-
-
-int
-genborn_allvsall_calc_still_radii(t_forcerec * fr,
- t_mdatoms * mdatoms,
- gmx_genborn_t * born,
- gmx_localtop_t * top,
- real * x,
- void * work)
-{
- gmx_allvsallgb2_data_t *aadata;
- int natoms;
- int ni0, ni1;
- int nj0, nj1, nj2;
- int i, j, k, n;
- int * mask;
-
- real ix, iy, iz;
- real jx, jy, jz;
- real dx, dy, dz;
- real rsq, rinv;
- real gpi, rai, vai;
- real prod_ai;
- real irsq, idr4, idr6;
- real raj, rvdw, ratio;
- real vaj, ccf, dccf, theta, cosq;
- real term, prod, icf4, icf6, gpi2, factor, sinq;
-
- natoms = mdatoms->nr;
- ni0 = 0;
- ni1 = mdatoms->homenr;
- factor = 0.5*ONE_4PI_EPS0;
- n = 0;
-
- aadata = *((gmx_allvsallgb2_data_t **)work);
-
- if (aadata == nullptr)
- {
- genborn_allvsall_setup(&aadata, top->idef.il, mdatoms->nr,
- FALSE, FALSE, TRUE);
- *((gmx_allvsallgb2_data_t **)work) = aadata;
- }
-
-
- for (i = 0; i < born->nr; i++)
- {
- born->gpol_still_work[i] = 0;
- }
-
-
- for (i = ni0; i < ni1; i++)
- {
- /* We assume shifts are NOT used for all-vs-all interactions */
-
- /* Load i atom data */
- ix = x[3*i];
- iy = x[3*i+1];
- iz = x[3*i+2];
-
- gpi = 0.0;
-
- rai = top->atomtypes.gb_radius[mdatoms->typeA[i]];
- vai = born->vsolv[i];
- prod_ai = STILL_P4*vai;
-
- /* Load limits for loop over neighbors */
- nj0 = aadata->jindex_gb[3*i];
- nj1 = aadata->jindex_gb[3*i+1];
- nj2 = aadata->jindex_gb[3*i+2];
-
- mask = aadata->exclusion_mask_gb[i];
-
- /* Prologue part, including exclusion mask */
- for (j = nj0; j < nj1; j++, mask++)
- {
- if (*mask != 0)
- {
- k = j%natoms;
-
- /* load j atom coordinates */
- jx = x[3*k];
- jy = x[3*k+1];
- jz = x[3*k+2];
-
- /* Calculate distance */
- dx = ix - jx;
- dy = iy - jy;
- dz = iz - jz;
- rsq = dx*dx+dy*dy+dz*dz;
-
- /* Calculate 1/r and 1/r2 */
- rinv = gmx::invsqrt(rsq);
- irsq = rinv*rinv;
- idr4 = irsq*irsq;
- idr6 = idr4*irsq;
-
- raj = top->atomtypes.gb_radius[mdatoms->typeA[k]];
-
- rvdw = rai + raj;
-
- ratio = rsq / (rvdw * rvdw);
- vaj = born->vsolv[k];
-
-
- if (ratio > STILL_P5INV)
- {
- ccf = 1.0;
- dccf = 0.0;
- }
- else
- {
- theta = ratio*STILL_PIP5;
- cosq = cos(theta);
- term = 0.5*(1.0-cosq);
- ccf = term*term;
- sinq = 1.0 - cosq*cosq;
- dccf = 2.0*term*sinq*gmx::invsqrt(sinq)*theta;
- }
-
- prod = STILL_P4*vaj;
- icf4 = ccf*idr4;
- icf6 = (4*ccf-dccf)*idr6;
-
- born->gpol_still_work[k] += prod_ai*icf4;
- gpi = gpi+prod*icf4;
-
- /* Save ai->aj and aj->ai chain rule terms */
- fr->dadx[n++] = prod*icf6;
- fr->dadx[n++] = prod_ai*icf6;
-
- /* 27 flops, plus one cos(x) - estimate at 20 flops => 47 */
-
- }
- }
-
- /* Main part, no exclusions */
- for (j = nj1; j < nj2; j++)
- {
- k = j%natoms;
-
- /* load j atom coordinates */
- jx = x[3*k];
- jy = x[3*k+1];
- jz = x[3*k+2];
-
- /* Calculate distance */
- dx = ix - jx;
- dy = iy - jy;
- dz = iz - jz;
- rsq = dx*dx+dy*dy+dz*dz;
-
- /* Calculate 1/r and 1/r2 */
- rinv = gmx::invsqrt(rsq);
- irsq = rinv*rinv;
- idr4 = irsq*irsq;
- idr6 = idr4*irsq;
-
- raj = top->atomtypes.gb_radius[mdatoms->typeA[k]];
-
- rvdw = rai + raj;
-
- ratio = rsq / (rvdw * rvdw);
- vaj = born->vsolv[k];
-
- if (ratio > STILL_P5INV)
- {
- ccf = 1.0;
- dccf = 0.0;
- }
- else
- {
- theta = ratio*STILL_PIP5;
- cosq = cos(theta);
- term = 0.5*(1.0-cosq);
- ccf = term*term;
- sinq = 1.0 - cosq*cosq;
- dccf = 2.0*term*sinq*gmx::invsqrt(sinq)*theta;
- }
-
- prod = STILL_P4*vaj;
- icf4 = ccf*idr4;
- icf6 = (4*ccf-dccf)*idr6;
-
- born->gpol_still_work[k] += prod_ai*icf4;
- gpi = gpi+prod*icf4;
-
- /* Save ai->aj and aj->ai chain rule terms */
- fr->dadx[n++] = prod*icf6;
- fr->dadx[n++] = prod_ai*icf6;
- }
- born->gpol_still_work[i] += gpi;
- }
-
- /* Parallel summations would go here if ever implemented with DD */
-
- /* Calculate the radii */
- for (i = 0; i < natoms; i++)
- {
- if (born->use[i] != 0)
- {
- gpi = born->gpol[i]+born->gpol_still_work[i];
- gpi2 = gpi * gpi;
- born->bRad[i] = factor*gmx::invsqrt(gpi2);
- fr->invsqrta[i] = gmx::invsqrt(born->bRad[i]);
- }
- }
-
- return 0;
-}
-
-
-
-int
-genborn_allvsall_calc_hct_obc_radii(t_forcerec * fr,
- t_mdatoms * mdatoms,
- gmx_genborn_t * born,
- int gb_algorithm,
- gmx_localtop_t * top,
- real * x,
- void * work)
-{
- gmx_allvsallgb2_data_t *aadata;
- int natoms;
- int ni0, ni1;
- int nj0, nj1, nj2;
- int i, j, k, n;
- int * mask;
-
- real ix, iy, iz;
- real jx, jy, jz;
- real dx, dy, dz;
- real rsq, rinv;
- real prod, raj;
- real rai, doffset, rai_inv, rai_inv2, sk_ai, sk2_ai, sum_ai;
- real dr, sk, lij, dlij, lij2, lij3, uij2, uij3, diff2, uij, log_term;
- real lij_inv, sk2, sk2_rinv, tmp, t1, t2, t3, raj_inv, sum_ai2, sum_ai3, tsum;
- real tchain;
- real dadxi, dadxj;
- real rad, min_rad;
-
- natoms = mdatoms->nr;
- ni0 = 0;
- ni1 = mdatoms->homenr;
-
- n = 0;
- doffset = born->gb_doffset;
-
- aadata = *((gmx_allvsallgb2_data_t **)work);
-
- if (aadata == nullptr)
- {
- genborn_allvsall_setup(&aadata, top->idef.il, mdatoms->nr,
- TRUE, TRUE, TRUE);
- *((gmx_allvsallgb2_data_t **)work) = aadata;
- }
-
- for (i = 0; i < born->nr; i++)
- {
- born->gpol_hct_work[i] = 0;
- }
-
- for (i = ni0; i < ni1; i++)
- {
- /* We assume shifts are NOT used for all-vs-all interactions */
-
- /* Load i atom data */
- ix = x[3*i];
- iy = x[3*i+1];
- iz = x[3*i+2];
-
- rai = top->atomtypes.gb_radius[mdatoms->typeA[i]]-doffset;
- rai_inv = 1.0/rai;
-
- sk_ai = born->param[i];
- sk2_ai = sk_ai*sk_ai;
-
- sum_ai = 0;
-
- /* Load limits for loop over neighbors */
- nj0 = aadata->jindex_gb[3*i];
- nj1 = aadata->jindex_gb[3*i+1];
- nj2 = aadata->jindex_gb[3*i+2];
-
- mask = aadata->exclusion_mask_gb[i];
-
- /* Prologue part, including exclusion mask */
- for (j = nj0; j < nj1; j++, mask++)
- {
- if (*mask != 0)
- {
- k = j%natoms;
-
- /* load j atom coordinates */
- jx = x[3*k];
- jy = x[3*k+1];
- jz = x[3*k+2];
-
- /* Calculate distance */
- dx = ix - jx;
- dy = iy - jy;
- dz = iz - jz;
- rsq = dx*dx+dy*dy+dz*dz;
-
- /* Calculate 1/r and 1/r2 */
- rinv = gmx::invsqrt(rsq);
- dr = rsq*rinv;
-
- /* sk is precalculated in init_gb() */
- sk = born->param[k];
- raj = top->atomtypes.gb_radius[mdatoms->typeA[k]]-doffset;
-
- /* aj -> ai interaction */
-
-
- if (rai < dr+sk)
- {
- lij = 1.0/(dr-sk);
- dlij = 1.0;
-
- if (rai > dr-sk)
- {
- lij = rai_inv;
- dlij = 0.0;
- }
-
- uij = 1.0/(dr+sk);
- lij2 = lij * lij;
- lij3 = lij2 * lij;
- uij2 = uij * uij;
- uij3 = uij2 * uij;
-
- diff2 = uij2-lij2;
-
- lij_inv = gmx::invsqrt(lij2);
- sk2 = sk*sk;
- sk2_rinv = sk2*rinv;
- prod = 0.25*sk2_rinv;
-
- log_term = std::log(uij*lij_inv);
- /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */
- tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2);
-
- if (rai < sk-dr)
- {
- tmp = tmp + 2.0 * (rai_inv-lij);
- }
-
- t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
- t2 = -0.5*uij2 - prod*uij3 + 0.25*(uij*rinv+uij3*dr);
-
- t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
-
- dadxi = (dlij*t1+t2+t3)*rinv;
-
- sum_ai += 0.5*tmp;
- }
- else
- {
- dadxi = 0.0;
- }
-
- /* ai -> aj interaction */
- if (raj < dr + sk_ai)
- {
- lij = 1.0/(dr-sk_ai);
- dlij = 1.0;
- raj_inv = 1.0/raj;
-
- if (raj > dr-sk_ai)
- {
- lij = raj_inv;
- dlij = 0.0;
- }
-
- lij2 = lij * lij;
- lij3 = lij2 * lij;
-
- uij = 1.0/(dr+sk_ai);
- uij2 = uij * uij;
- uij3 = uij2 * uij;
-
- diff2 = uij2-lij2;
-
- lij_inv = gmx::invsqrt(lij2);
- sk2 = sk2_ai; /* sk2_ai = sk_ai * sk_ai in i loop above */
- sk2_rinv = sk2*rinv;
- prod = 0.25 * sk2_rinv;
-
- /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */
- log_term = std::log(uij*lij_inv);
-
- tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2);
-
- if (raj < sk_ai-dr)
- {
- tmp = tmp + 2.0 * (raj_inv-lij);
- }
-
- t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
- t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
- t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
-
- dadxj = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
-
- born->gpol_hct_work[k] += 0.5*tmp;
- }
- else
- {
- dadxj = 0.0;
- }
- fr->dadx[n++] = dadxi;
- fr->dadx[n++] = dadxj;
-
- }
- }
-
- /* Main part, no exclusions */
- for (j = nj1; j < nj2; j++)
- {
- k = j%natoms;
-
- /* load j atom coordinates */
- jx = x[3*k];
- jy = x[3*k+1];
- jz = x[3*k+2];
-
- /* Calculate distance */
- dx = ix - jx;
- dy = iy - jy;
- dz = iz - jz;
- rsq = dx*dx+dy*dy+dz*dz;
-
- /* Calculate 1/r and 1/r2 */
- rinv = gmx::invsqrt(rsq);
- dr = rsq*rinv;
-
- /* sk is precalculated in init_gb() */
- sk = born->param[k];
- raj = top->atomtypes.gb_radius[mdatoms->typeA[k]]-doffset;
-
- /* aj -> ai interaction */
- if (rai < dr+sk)
- {
- lij = 1.0/(dr-sk);
- dlij = 1.0;
-
- if (rai > dr-sk)
- {
- lij = rai_inv;
- dlij = 0.0;
- }
-
- uij = 1.0/(dr+sk);
- lij2 = lij * lij;
- lij3 = lij2 * lij;
- uij2 = uij * uij;
- uij3 = uij2 * uij;
-
- diff2 = uij2-lij2;
-
- lij_inv = gmx::invsqrt(lij2);
- sk2 = sk*sk;
- sk2_rinv = sk2*rinv;
- prod = 0.25*sk2_rinv;
-
- log_term = std::log(uij*lij_inv);
- /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */
- tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2);
-
- if (rai < sk-dr)
- {
- tmp = tmp + 2.0 * (rai_inv-lij);
- }
-
- /* duij = 1.0; */
- t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
- t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
- t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
-
- dadxi = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
-
- sum_ai += 0.5*tmp;
- }
- else
- {
- dadxi = 0.0;
- }
-
- /* ai -> aj interaction */
- if (raj < dr + sk_ai)
- {
- lij = 1.0/(dr-sk_ai);
- dlij = 1.0;
- raj_inv = 1.0/raj;
-
- if (raj > dr-sk_ai)
- {
- lij = raj_inv;
- dlij = 0.0;
- }
-
- lij2 = lij * lij;
- lij3 = lij2 * lij;
-
- uij = 1.0/(dr+sk_ai);
- uij2 = uij * uij;
- uij3 = uij2 * uij;
-
- diff2 = uij2-lij2;
-
- lij_inv = gmx::invsqrt(lij2);
- sk2 = sk2_ai; /* sk2_ai = sk_ai * sk_ai in i loop above */
- sk2_rinv = sk2*rinv;
- prod = 0.25 * sk2_rinv;
-
- /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */
- log_term = std::log(uij*lij_inv);
-
- tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2);
-
- if (raj < sk_ai-dr)
- {
- tmp = tmp + 2.0 * (raj_inv-lij);
- }
-
- t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr);
- t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr);
- t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv;
-
- dadxj = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */
-
- born->gpol_hct_work[k] += 0.5*tmp;
- }
- else
- {
- dadxj = 0.0;
- }
- fr->dadx[n++] = dadxi;
- fr->dadx[n++] = dadxj;
- }
- born->gpol_hct_work[i] += sum_ai;
- }
-
- /* Parallel summations would go here if ever implemented with DD */
-
- if (gb_algorithm == egbHCT)
- {
- /* HCT */
- for (i = 0; i < natoms; i++)
- {
- if (born->use[i] != 0)
- {
- rai = top->atomtypes.gb_radius[mdatoms->typeA[i]]-born->gb_doffset;
- sum_ai = 1.0/rai - born->gpol_hct_work[i];
- min_rad = rai + born->gb_doffset;
- rad = 1.0/sum_ai;
-
- born->bRad[i] = std::max(rad, min_rad);
- fr->invsqrta[i] = gmx::invsqrt(born->bRad[i]);
- }
- }
-
- }
- else
- {
- /* OBC */
- /* Calculate the radii */
- for (i = 0; i < natoms; i++)
- {
- if (born->use[i] != 0)
- {
- rai = top->atomtypes.gb_radius[mdatoms->typeA[i]];
- rai_inv2 = 1.0/rai;
- rai = rai-doffset;
- rai_inv = 1.0/rai;
- sum_ai = rai * born->gpol_hct_work[i];
- sum_ai2 = sum_ai * sum_ai;
- sum_ai3 = sum_ai2 * sum_ai;
-
- tsum = tanh(born->obc_alpha*sum_ai-born->obc_beta*sum_ai2+born->obc_gamma*sum_ai3);
- born->bRad[i] = rai_inv - tsum*rai_inv2;
- born->bRad[i] = 1.0 / born->bRad[i];
-
- fr->invsqrta[i] = gmx::invsqrt(born->bRad[i]);
-
- tchain = rai * (born->obc_alpha-2*born->obc_beta*sum_ai+3*born->obc_gamma*sum_ai2);
- born->drobc[i] = (1.0-tsum*tsum)*tchain*rai_inv2;
- }
- }
- }
- return 0;
-}
-
-
-
-
-
-int
-genborn_allvsall_calc_chainrule(t_forcerec * fr,
- t_mdatoms * mdatoms,
- gmx_genborn_t * born,
- real * x,
- real * f,
- int gb_algorithm,
- void * work)
-{
- gmx_allvsallgb2_data_t *aadata;
- int natoms;
- int ni0, ni1;
- int nj0, nj1, nj2;
- int i, j, k, n;
- int idx;
- int * mask;
-
- real ix, iy, iz;
- real fix, fiy, fiz;
- real jx, jy, jz;
- real dx, dy, dz;
- real tx, ty, tz;
- real rbai, rbaj, fgb, fgb_ai, rbi;
- real * rb;
- real * dadx;
-
- natoms = mdatoms->nr;
- ni0 = 0;
- ni1 = mdatoms->homenr;
- dadx = fr->dadx;
-
- aadata = (gmx_allvsallgb2_data_t *)work;
-
- n = 0;
- rb = born->work;
-
- /* Loop to get the proper form for the Born radius term */
- if (gb_algorithm == egbSTILL)
- {
- for (i = 0; i < natoms; i++)
- {
- rbi = born->bRad[i];
- rb[i] = (2 * rbi * rbi * fr->dvda[i])/ONE_4PI_EPS0;
- }
- }
- else if (gb_algorithm == egbHCT)
- {
- for (i = 0; i < natoms; i++)
- {
- rbi = born->bRad[i];
- rb[i] = rbi * rbi * fr->dvda[i];
- }
- }
- else if (gb_algorithm == egbOBC)
- {
- for (idx = 0; idx < natoms; idx++)
- {
- rbi = born->bRad[idx];
- rb[idx] = rbi * rbi * born->drobc[idx] * fr->dvda[idx];
- }
- }
-
- for (i = ni0; i < ni1; i++)
- {
- /* We assume shifts are NOT used for all-vs-all interactions */
-
- /* Load i atom data */
- ix = x[3*i];
- iy = x[3*i+1];
- iz = x[3*i+2];
-
- fix = 0;
- fiy = 0;
- fiz = 0;
-
- rbai = rb[i];
-
- /* Load limits for loop over neighbors */
- nj0 = aadata->jindex_gb[3*i];
- nj1 = aadata->jindex_gb[3*i+1];
- nj2 = aadata->jindex_gb[3*i+2];
-
- mask = aadata->exclusion_mask_gb[i];
-
- /* Prologue part, including exclusion mask */
- for (j = nj0; j < nj1; j++, mask++)
- {
- if (*mask != 0)
- {
- k = j%natoms;
-
- /* load j atom coordinates */
- jx = x[3*k];
- jy = x[3*k+1];
- jz = x[3*k+2];
-
- /* Calculate distance */
- dx = ix - jx;
- dy = iy - jy;
- dz = iz - jz;
-
- rbaj = rb[k];
-
- fgb = rbai*dadx[n++];
- fgb_ai = rbaj*dadx[n++];
-
- /* Total force between ai and aj is the sum of ai->aj and aj->ai */
- fgb = fgb + fgb_ai;
-
- tx = fgb * dx;
- ty = fgb * dy;
- tz = fgb * dz;
-
- fix = fix + tx;
- fiy = fiy + ty;
- fiz = fiz + tz;
-
- /* Update force on atom aj */
- f[3*k] = f[3*k] - tx;
- f[3*k+1] = f[3*k+1] - ty;
- f[3*k+2] = f[3*k+2] - tz;
- }
- }
-
- /* Main part, no exclusions */
- for (j = nj1; j < nj2; j++)
- {
- k = j%natoms;
-
- /* load j atom coordinates */
- jx = x[3*k];
- jy = x[3*k+1];
- jz = x[3*k+2];
-
- /* Calculate distance */
- dx = ix - jx;
- dy = iy - jy;
- dz = iz - jz;
-
- rbaj = rb[k];
-
- fgb = rbai*dadx[n++];
- fgb_ai = rbaj*dadx[n++];
-
- /* Total force between ai and aj is the sum of ai->aj and aj->ai */
- fgb = fgb + fgb_ai;
-
- tx = fgb * dx;
- ty = fgb * dy;
- tz = fgb * dz;
-
- fix = fix + tx;
- fiy = fiy + ty;
- fiz = fiz + tz;
-
- /* Update force on atom aj */
- f[3*k] = f[3*k] - tx;
- f[3*k+1] = f[3*k+1] - ty;
- f[3*k+2] = f[3*k+2] - tz;
- }
- /* Update force and shift forces on atom ai */
- f[3*i] = f[3*i] + fix;
- f[3*i+1] = f[3*i+1] + fiy;
- f[3*i+2] = f[3*i+2] + fiz;
- }
-
- return 0;
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team.
- * Copyright (c) 2010,2014,2015, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef _GENBORN_ALLVSALL_H
-#define _GENBORN_ALLVSALL_H
-
-#include "gromacs/utility/real.h"
-
-struct gmx_genborn_t;
-struct gmx_localtop_t;
-struct t_forcerec;
-struct t_mdatoms;
-
-int
-genborn_allvsall_calc_still_radii(struct t_forcerec * fr,
- t_mdatoms * mdatoms,
- gmx_genborn_t * born,
- gmx_localtop_t * top,
- real * x,
- void * work);
-
-int
-genborn_allvsall_calc_hct_obc_radii(struct t_forcerec * fr,
- t_mdatoms * mdatoms,
- gmx_genborn_t * born,
- int gb_algorithm,
- gmx_localtop_t * top,
- real * x,
- void * work);
-
-int
-genborn_allvsall_calc_chainrule(struct t_forcerec * fr,
- t_mdatoms * mdatoms,
- gmx_genborn_t * born,
- real * x,
- real * f,
- int gb_algorithm,
- void * work);
-
-#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
md->bEner[i] = TRUE;
}
- else if ((i == F_GBPOL) && ir->implicit_solvent == eisGBSA)
- {
- md->bEner[i] = TRUE;
- }
- else if ((i == F_NPSOLVATION) && ir->implicit_solvent == eisGBSA && (ir->sa_algorithm != esaNO))
- {
- md->bEner[i] = TRUE;
- }
- else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
- {
- md->bEner[i] = FALSE;
- }
else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
{
md->bEner[i] = EI_DYNAMICS(ir->eI);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
count, nrnb, wcycle, top, &top_global->groups,
ems->s.box, ems->s.x, &ems->s.hist,
ems->f, force_vir, mdAtoms->mdatoms(), enerd, fcd,
- ems->s.lambda, graph, fr, vsite, mu_tot, t, nullptr, TRUE,
+ ems->s.lambda, graph, fr, vsite, mu_tot, t, nullptr,
GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
(bNS ? GMX_FORCE_NS : 0),
size_t atom = atom_index[aid];
for (size_t d = 0; d < DIM; d++)
{
- gmx_bool bBornRadii = FALSE;
gmx_int64_t step = 0;
int force_flags = GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES;
double t = 0;
constr, enerd, fcd,
&state_work.s, &state_work.f, vir, mdatoms,
nrnb, wcycle, graph, &top_global->groups,
- shellfc, fr, bBornRadii, t, mu_tot,
+ shellfc, fr, t, mu_tot,
vsite,
DdOpenBalanceRegionBeforeForceComputation::no,
DdCloseBalanceRegionAfterForceComputation::no);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_groups_t *groups,
gmx_shellfc_t *shfc,
t_forcerec *fr,
- gmx_bool bBornRadii,
double t, rvec mu_tot,
gmx_vsite_t *vsite,
DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
state->box, state->x, &state->hist,
force[Min], force_vir, md, enerd, fcd,
state->lambda, graph,
- fr, vsite, mu_tot, t, nullptr, bBornRadii,
+ fr, vsite, mu_tot, t, nullptr,
(bDoNS ? GMX_FORCE_NS : 0) | force_flags,
ddOpenBalanceRegion, ddCloseBalanceRegion);
top, groups, state->box, pos[Try], &state->hist,
force[Try], force_vir,
md, enerd, fcd, state->lambda, graph,
- fr, vsite, mu_tot, t, nullptr, bBornRadii,
+ fr, vsite, mu_tot, t, nullptr,
force_flags,
ddOpenBalanceRegion, ddCloseBalanceRegion);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_groups_t *groups,
gmx_shellfc_t *shfc,
t_forcerec *fr,
- gmx_bool bBornRadii,
double t, rvec mu_tot,
gmx_vsite_t *vsite,
DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/forcerec.h"
-#include "gromacs/mdlib/genborn.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/nb_verlet.h"
t_forcerec *fr, interaction_const_t *ic,
gmx_vsite_t *vsite, rvec mu_tot,
double t, gmx_edsam_t ed,
- gmx_bool bBornRadii,
int flags,
DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion)
/* Compute the bonded and non-bonded energies and optionally forces */
do_force_lowlevel(fr, inputrec, &(top->idef),
cr, nrnb, wcycle, mdatoms,
- as_rvec_array(x.data()), hist, f, &forceWithVirial, enerd, fcd, top, fr->born,
- bBornRadii, box,
- inputrec->fepvals, lambda, graph, &(top->excls), fr->mu_tot,
+ as_rvec_array(x.data()), hist, f, &forceWithVirial, enerd, fcd,
+ box, inputrec->fepvals, lambda, graph, &(top->excls), fr->mu_tot,
flags, &cycles_pme);
wallcycle_stop(wcycle, ewcFORCE);
real *lambda, t_graph *graph,
t_forcerec *fr, gmx_vsite_t *vsite, rvec mu_tot,
double t, gmx_edsam_t ed,
- gmx_bool bBornRadii,
int flags,
DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion)
wallcycle_stop(wcycle, ewcNS);
}
- if (inputrec->implicit_solvent && bNS)
- {
- make_gb_nblist(cr, inputrec->gb_algorithm,
- as_rvec_array(x.data()), box, fr, &top->idef, graph, fr->born);
- }
-
if (DOMAINDECOMP(cr) && !thisRankHasDuty(cr, DUTY_PME))
{
wallcycle_start(wcycle, ewcPPDURINGPME);
/* Compute the bonded and non-bonded energies and optionally forces */
do_force_lowlevel(fr, inputrec, &(top->idef),
cr, nrnb, wcycle, mdatoms,
- as_rvec_array(x.data()), hist, f, &forceWithVirial, enerd, fcd, top, fr->born,
- bBornRadii, box,
- inputrec->fepvals, lambda,
+ as_rvec_array(x.data()), hist, f, &forceWithVirial, enerd, fcd,
+ box, inputrec->fepvals, lambda,
graph, &(top->excls), fr->mu_tot,
flags,
&cycles_pme);
t_forcerec *fr,
gmx_vsite_t *vsite, rvec mu_tot,
double t, gmx_edsam_t ed,
- gmx_bool bBornRadii,
int flags,
DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion)
fr, fr->ic,
vsite, mu_tot,
t, ed,
- bBornRadii,
flags,
ddOpenBalanceRegion,
ddCloseBalanceRegion);
lambda.data(), graph,
fr, vsite, mu_tot,
t, ed,
- bBornRadii,
flags,
ddOpenBalanceRegion,
ddCloseBalanceRegion);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
state_global->box, state_global->x, &state_global->hist,
f, force_vir, mdatoms, enerd, fcd,
state_global->lambda,
- nullptr, fr, nullptr, mu_tot, t, nullptr, FALSE,
+ nullptr, fr, nullptr, mu_tot, t, nullptr,
GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
(bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS : 0) |
(bStateChanged ? GMX_FORCE_STATECHANGED : 0),
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct ForceProviders;
/* Abstract type for PME that is defined only in the routine that use them. */
-struct gmx_genborn_t;
struct gmx_ns_t;
struct gmx_pme_t;
struct nonbonded_verlet_t;
enum {
enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
};
-/* OOR is "one over r" -- standard coul */
-enum {
- enbcoulNONE, enbcoulOOR, enbcoulRF, enbcoulTAB, enbcoulGB, enbcoulFEWALD, enbcoulNR
-};
enum {
egCOULSR, egLJSR, egBHAMSR,
- egCOUL14, egLJ14, egGB, egNR
+ egCOUL14, egLJ14, egNR
};
extern const char *egrp_nm[egNR+1];
gmx_bool bAllvsAll;
/* Private work data */
void *AllvsAll_work;
- void *AllvsAll_workgb;
/* Cut-Off stuff.
* Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
/* Shell molecular dynamics flexible constraints */
real fc_stepsize;
- /* Generalized born implicit solvent */
- gmx_bool bGB;
- /* Generalized born stuff */
- real gb_epsilon_solvent;
- /* Table data for GB */
- struct t_forcetable *gbtab;
- /* VdW radius for each atomtype (dim is thus ntype) */
- real *atype_radius;
- /* Effective radius (derived from effective volume) for each type */
- real *atype_vol;
- /* Implicit solvent - surface tension for each atomtype */
- real *atype_surftens;
- /* Implicit solvent - radius for GB calculation */
- real *atype_gb_radius;
- /* Implicit solvent - overlap for HCT model */
- real *atype_S_hct;
- /* Generalized born interaction data */
- struct gmx_genborn_t *born;
-
- /* Table scale for GB */
- real gbtabscale;
- /* Table range for GB */
- real gbtabr;
- /* GB neighborlists (the sr list will contain for each atom all other atoms
- * (for use in the SA calculation) and the lr list will contain
- * for each atom all atoms 1-4 or greater (for use in the GB calculation)
- */
- struct t_nblist *gblist_sr;
- struct t_nblist *gblist_lr;
- struct t_nblist *gblist;
-
- /* Inverse square root of the Born radii for implicit solvent */
- real *invsqrta;
- /* Derivatives of the potential with respect to the Born radii */
- real *dvda;
- /* Derivatives of the Born radii with respect to coordinates */
- real *dadx;
- real *dadx_rawptr;
- int nalloc_dadx; /* Allocated size of dadx */
-
/* If > 0 signals Test Particle Insertion,
* the value is the number of atoms of the molecule to insert
* Only the energy difference due to the addition of the last molecule
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2010, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
PR("ewald-geometry", ir->ewald_geometry);
PR("epsilon-surface", ir->epsilon_surface);
- /* Implicit solvent */
- PS("implicit-solvent", EIMPLICITSOL(ir->implicit_solvent));
-
- /* Generalized born electrostatics */
- PS("gb-algorithm", EGBALGORITHM(ir->gb_algorithm));
- PI("nstgbradii", ir->nstgbradii);
- PR("rgbradii", ir->rgbradii);
- PR("gb-epsilon-solvent", ir->gb_epsilon_solvent);
- PR("gb-saltconc", ir->gb_saltconc);
- PR("gb-obc-alpha", ir->gb_obc_alpha);
- PR("gb-obc-beta", ir->gb_obc_beta);
- PR("gb-obc-gamma", ir->gb_obc_gamma);
- PR("gb-dielectric-offset", ir->gb_dielectric_offset);
- PS("sa-algorithm", ESAALGORITHM(ir->sa_algorithm));
- PR("sa-surface-tension", ir->sa_surface_tension);
-
/* Options for weak coupling algorithms */
PS("tcoupl", ETCOUPLTYPE(ir->etc));
PI("nsttcouple", ir->nsttcouple);
cmp_real(fp, "inputrec->epsilon_r", -1, ir1->epsilon_r, ir2->epsilon_r, ftol, abstol);
cmp_real(fp, "inputrec->epsilon_rf", -1, ir1->epsilon_rf, ir2->epsilon_rf, ftol, abstol);
cmp_real(fp, "inputrec->tabext", -1, ir1->tabext, ir2->tabext, ftol, abstol);
- cmp_int(fp, "inputrec->implicit_solvent", -1, ir1->implicit_solvent, ir2->implicit_solvent);
- cmp_int(fp, "inputrec->gb_algorithm", -1, ir1->gb_algorithm, ir2->gb_algorithm);
- cmp_int(fp, "inputrec->nstgbradii", -1, ir1->nstgbradii, ir2->nstgbradii);
- cmp_real(fp, "inputrec->rgbradii", -1, ir1->rgbradii, ir2->rgbradii, ftol, abstol);
- cmp_real(fp, "inputrec->gb_saltconc", -1, ir1->gb_saltconc, ir2->gb_saltconc, ftol, abstol);
- cmp_real(fp, "inputrec->gb_epsilon_solvent", -1, ir1->gb_epsilon_solvent, ir2->gb_epsilon_solvent, ftol, abstol);
- cmp_real(fp, "inputrec->gb_obc_alpha", -1, ir1->gb_obc_alpha, ir2->gb_obc_alpha, ftol, abstol);
- cmp_real(fp, "inputrec->gb_obc_beta", -1, ir1->gb_obc_beta, ir2->gb_obc_beta, ftol, abstol);
- cmp_real(fp, "inputrec->gb_obc_gamma", -1, ir1->gb_obc_gamma, ir2->gb_obc_gamma, ftol, abstol);
- cmp_real(fp, "inputrec->gb_dielectric_offset", -1, ir1->gb_dielectric_offset, ir2->gb_dielectric_offset, ftol, abstol);
- cmp_int(fp, "inputrec->sa_algorithm", -1, ir1->sa_algorithm, ir2->sa_algorithm);
- cmp_real(fp, "inputrec->sa_surface_tension", -1, ir1->sa_surface_tension, ir2->sa_surface_tension, ftol, abstol);
cmp_int(fp, "inputrec->eDispCorr", -1, ir1->eDispCorr, ir2->eDispCorr);
cmp_real(fp, "inputrec->shake_tol", -1, ir1->shake_tol, ir2->shake_tol, ftol, abstol);
gmx_bool inputrecExclForces(const t_inputrec *ir)
{
- return (EEL_FULL(ir->coulombtype) || (EEL_RF(ir->coulombtype)) ||
- ir->implicit_solvent != eisNO);
+ return (EEL_FULL(ir->coulombtype) || (EEL_RF(ir->coulombtype)));
}
gmx_bool inputrecNptTrotter(const t_inputrec *ir)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real rcoulomb; /* Coulomb cutoff (nm) */
real epsilon_r; /* relative dielectric constant */
real epsilon_rf; /* relative dielectric constant of the RF */
- int implicit_solvent; /* No (=explicit water), or GBSA solvent models */
- int gb_algorithm; /* Algorithm to use for calculation Born radii */
- int nstgbradii; /* Frequency of updating Generalized Born radii */
- real rgbradii; /* Cutoff for GB radii calculation */
- real gb_saltconc; /* Salt concentration (M) for GBSA models */
- real gb_epsilon_solvent; /* dielectric coeff. of implicit solvent */
- real gb_obc_alpha; /* 1st scaling factor for Bashford-Case GB */
- real gb_obc_beta; /* 2nd scaling factor for Bashford-Case GB */
- real gb_obc_gamma; /* 3rd scaling factor for Bashford-Case GB */
- real gb_dielectric_offset; /* Dielectric offset for Still/HCT/OBC */
- int sa_algorithm; /* Algorithm for SA part of GBSA */
- real sa_surface_tension; /* Energy factor for SA part of GBSA */
+ bool implicit_solvent; /* Always false (no longer supported */
int vdwtype; /* Type of Van der Waals treatment */
int vdw_modifier; /* Modify the VdW interaction */
real rvdw_switch; /* Van der Waals switch range start (nm) */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const char *eel_names[eelNR+1] = {
"Cut-off", "Reaction-Field", "Generalized-Reaction-Field",
"PME", "Ewald", "P3M-AD", "Poisson", "Switch", "Shift", "User",
- "Generalized-Born", "Reaction-Field-nec", "Encad-shift",
+ "Generalized-Born (unused)", "Reaction-Field-nec", "Encad-shift",
"PME-User", "PME-Switch", "PME-User-Switch",
"Reaction-Field-zero", nullptr
};
"No", "Single", "Periodic", nullptr
};
-const char *eis_names[eisNR+1] = {
- "No", "GBSA", nullptr
-};
-
-const char *egb_names[egbNR+1] = {
- "Still", "HCT", "OBC", nullptr
-};
-
-const char *esa_names[esaNR+1] = {
- "Ace-approximation", "None", "Still", nullptr
-};
-
const char *ewt_names[ewtNR+1] = {
"9-3", "10-4", "table", "12-6", nullptr
};
const char *gmx_nbkernel_elec_names[GMX_NBKERNEL_ELEC_NR+1] =
{
- "None", "Coulomb", "Reaction-Field", "Cubic-Spline-Table", "Generalized-Born", "Ewald", nullptr
+ "None", "Coulomb", "Reaction-Field", "Cubic-Spline-Table", "Ewald", nullptr
};
const char *gmx_nbkernel_vdw_names[GMX_NBKERNEL_VDW_NR+1] =
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Macro to select the correct string for modifiers
#define INTMODIFIER(e) enum_name(e, eintmodNR, eintmod_names)
-/*! \brief Cut-off treatment for Coulomb
- *
- * eelNOTUSED1 used to be GB, but to enable generalized born with different
- * forms of electrostatics (RF, switch, etc.) in the future it is now selected
- * separately (through the implicit_solvent option).
- */
+/*! \brief Cut-off treatment for Coulomb */
enum {
eelCUT, eelRF, eelGRF, eelPME, eelEWALD, eelP3M_AD,
eelPOISSON, eelSWITCH, eelSHIFT, eelUSER, eelGB_NOTUSED, eelRF_NEC_UNSUPPORTED, eelENCADSHIFT,
//! And macro for simulated annealing string
#define EANNEAL(e) enum_name(e, eannNR, eann_names)
-//! Implicit solvent algorithms.
-enum {
- eisNO, eisGBSA, eisNR
-};
-//! String corresponding to implicit solvent.
-extern const char *eis_names[eisNR+1];
-//! Macro for implicit solvent string.
-#define EIMPLICITSOL(e) enum_name(e, eisNR, eis_names)
-
-//! Algorithms for calculating GB radii.
-enum {
- egbSTILL, egbHCT, egbOBC, egbNR
-};
-//! String for GB algorithm name.
-extern const char *egb_names[egbNR+1];
-//! Macro for GB string.
-#define EGBALGORITHM(e) enum_name(e, egbNR, egb_names)
-
-//! Surface area algorithm for implicit solvent.
-enum {
- esaAPPROX, esaNO, esaSTILL, esaNR
-};
-//! String corresponding to surface area algorithm.
-extern const char *esa_names[esaNR+1];
-//! brief Macro for SA algorithm string.
-#define ESAALGORITHM(e) enum_name(e, esaNR, esa_names)
-
//! Wall types.
enum {
ewt93, ewt104, ewtTABLE, ewt126, ewtNR
GMX_NBKERNEL_ELEC_COULOMB,
GMX_NBKERNEL_ELEC_REACTIONFIELD,
GMX_NBKERNEL_ELEC_CUBICSPLINETABLE,
- GMX_NBKERNEL_ELEC_GENERALIZEDBORN,
GMX_NBKERNEL_ELEC_EWALD,
GMX_NBKERNEL_ELEC_NR
};
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return table;
}
-t_forcetable *make_gb_table(const t_forcerec *fr)
-{
- t_tabledata *td;
- int nx0;
- double r, r2, Vtab, Ftab, expterm;
-
- t_forcetable *table;
-
- /* Set the table dimensions for GB, not really necessary to
- * use etiNR (since we only have one table, but ...)
- */
- snew(table, 1);
- snew(td, 1);
- table->interaction = GMX_TABLE_INTERACTION_ELEC;
- table->format = GMX_TABLE_FORMAT_CUBICSPLINE_YFGH;
- table->r = fr->gbtabr;
- table->scale = fr->gbtabscale;
- table->n = static_cast<int>(table->scale*table->r);
- table->formatsize = 4;
- table->ninteractions = 1;
- table->stride = table->formatsize*table->ninteractions;
- nx0 = 0;
-
- /* Each table type (e.g. coul,lj6,lj12) requires four numbers per
- * datapoint. For performance reasons we want the table data to be
- * aligned on a 32-byte boundary. This new pointer must not be
- * used in a free() call, but thankfully we're sloppy enough not
- * to do this :-)
- */
-
- snew_aligned(table->data, table->stride*table->n, 32);
-
- init_table(table->n, nx0, table->scale, &(td[0]), TRUE);
-
- /* Local implementation so we don't have to use the etabGB
- * enum above, which will cause problems later when
- * making the other tables (right now even though we are using
- * GB, the normal Coulomb tables will be created, but this
- * will cause a problem since fr->eeltype==etabGB which will not
- * be defined in fill_table and set_table_type
- */
-
- for (int i = nx0; i < table->n; i++)
- {
- r = td->x[i];
- r2 = r*r;
- expterm = exp(-0.25*r2);
-
- Vtab = 1/sqrt(r2+expterm);
- Ftab = (r-0.25*r*expterm)/((r2+expterm)*sqrt(r2+expterm));
-
- /* Convert to single precision when we store to mem */
- td->x[i] = i/table->scale;
- td->v[i] = Vtab;
- td->f[i] = Ftab;
-
- }
-
- copy2table(table->n, 0, table->stride, td[0].x, td[0].v, td[0].f, 1.0, table->data);
-
- done_tabledata(&(td[0]));
- sfree(td);
-
- return table;
-
-
-}
-
bondedtable_t make_bonded_table(FILE *fplog, const char *fn, int angle)
{
t_tabledata td;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
bondedtable_t make_bonded_table(FILE *fplog, const char *fn, int angle);
-/*! \brief Return a table for GB calculations
- *
- * \param fr Force record
- * \return Pointer to new gb table structure
- */
-t_forcetable *make_gb_table(const t_forcerec *fr);
-
/*! \brief Construct and return tabulated dispersion and repulsion interactions
*
* This table can be used to compute long-range dispersion corrections */
{
"Run", "Step", "PP during PME", "Domain decomp.", "DD comm. load",
"DD comm. bounds", "Vsite constr.", "Send X to PME", "Neighbor search", "Launch GPU ops.",
- "Comm. coord.", "Born radii", "Force", "Wait + Comm. F", "PME mesh",
+ "Comm. coord.", "Force", "Wait + Comm. F", "PME mesh",
"PME redist. X/F", "PME spread", "PME gather", "PME 3D-FFT", "PME 3D-FFT Comm.", "PME solve LJ", "PME solve Elec",
"PME wait for PP", "Wait + Recv. PME F",
"Wait PME GPU spread", "PME 3D-FFT", "PME solve", /* the strings for FFT/solve are repeated here for mixed mode counters */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
enum {
ewcRUN, ewcSTEP, ewcPPDURINGPME, ewcDOMDEC, ewcDDCOMMLOAD,
ewcDDCOMMBOUND, ewcVSITECONSTR, ewcPP_PMESENDX, ewcNS, ewcLAUNCH_GPU,
- ewcMOVEX, ewcGB, ewcFORCE, ewcMOVEF, ewcPMEMESH,
+ ewcMOVEX, ewcFORCE, ewcMOVEF, ewcPMEMESH,
ewcPME_REDISTXF, ewcPME_SPREAD, ewcPME_GATHER, ewcPME_FFT, ewcPME_FFTCOMM, ewcLJPME, ewcPME_SOLVE,
ewcPMEWAITCOMM, ewcPP_PMEWAITRECVF,
ewcWAIT_GPU_PME_SPREAD, ewcPME_FFT_MIXED_MODE, ewcPME_SOLVE_MIXED_MODE,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void init_atomtypes(t_atomtypes *at)
{
at->nr = 0;
- at->radius = nullptr;
- at->vol = nullptr;
at->atomnumber = nullptr;
- at->gb_radius = nullptr;
- at->S_hct = nullptr;
}
void done_atom(t_atoms *at)
void done_atomtypes(t_atomtypes *atype)
{
atype->nr = 0;
- sfree(atype->radius);
- sfree(atype->vol);
- sfree(atype->surftens);
sfree(atype->atomnumber);
- sfree(atype->gb_radius);
- sfree(atype->S_hct);
}
void add_t_atoms(t_atoms *atoms, int natom_extra, int nres_extra)
{
pr_indent(fp, indent);
fprintf(fp,
- "atomtype[%3d]={radius=%12.5e, volume=%12.5e, gb_radius=%12.5e, surftens=%12.5e, atomnumber=%4d, S_hct=%12.5e)}\n",
- bShowNumbers ? i : -1, atomtypes->radius[i], atomtypes->vol[i],
- atomtypes->gb_radius[i],
- atomtypes->surftens[i], atomtypes->atomnumber[i], atomtypes->S_hct[i]);
+ "atomtype[%3d]={atomnumber=%4d}\n",
+ bShowNumbers ? i : -1, atomtypes->atomnumber[i]);
}
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
typedef struct t_atomtypes
{
int nr; /* number of atomtypes */
- real *radius; /* GBSA radius for each atomtype */
- real *vol; /* GBSA efective volume for each atomtype */
- real *surftens; /* implicit solvent surftens for each atomtype */
- real *gb_radius; /* GB radius for each atom type */
- real *S_hct; /* Overlap factors for HCT/OBC GB models */
int *atomnumber; /* Atomic number, used for QM/MM */
} t_atomtypes;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
case F_VSITEN:
fprintf(fp, "n=%2d, a=%15.8e\n", iparams->vsiten.n, iparams->vsiten.a);
break;
- case F_GB12:
- case F_GB13:
- case F_GB14:
- fprintf(fp, "sar=%15.8e, st=%15.8e, pi=%15.8e, gbr=%15.8e, bmlt=%15.8e\n", iparams->gb.sar, iparams->gb.st, iparams->gb.pi, iparams->gb.gbr, iparams->gb.bmlt);
+ case F_GB12_NOLONGERUSED:
+ case F_GB13_NOLONGERUSED:
+ case F_GB14_NOLONGERUSED:
+ // These could only be generated by grompp, not written in
+ // a .top file. Now that implicit solvent is not
+ // supported, they can't be generated, and the values are
+ // ignored if read from an old .tpr file. So there is
+ // nothing to print.
break;
case F_CMAP:
fprintf(fp, "cmapA=%1d, cmapB=%1d\n", iparams->cmap.cmapA, iparams->cmap.cmapB);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
F_PIDIHS,
F_TABDIHS,
F_CMAP,
- F_GB12,
- F_GB13,
- F_GB14,
- F_GBPOL,
- F_NPSOLVATION,
+ F_GB12_NOLONGERUSED,
+ F_GB13_NOLONGERUSED,
+ F_GB14_NOLONGERUSED,
+ F_GBPOL_NOLONGERUSED,
+ F_NPSOLVATION_NOLONGERUSED,
F_LJ14,
F_COUL14,
F_LJC14_Q,
struct {
int table; real kA; real kB;
} tab;
- struct {
- real sar, st, pi, gbr, bmlt;
- } gb;
struct {
int cmapA, cmapB;
} cmap;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
def_bonded ("PIDIHS", "Improper Dih.", 4, 3, 3, eNR_IMPROPER, pdihs ),
def_bondedt ("TABDIHS", "Tab. Dih.", 4, 2, 2, eNR_TABDIHS, tab_dihs ),
def_bonded ("CMAP", "CMAP Dih.", 5, -1, -1, eNR_CMAP, unimplemented ),
- def_bonded ("GB12", "GB 1-2 Pol.", 2, 4, 0, eNR_GB, unimplemented ),
- def_bonded ("GB13", "GB 1-3 Pol.", 2, 4, 0, eNR_GB, unimplemented ),
- def_bonded ("GB14", "GB 1-4 Pol.", 2, 4, 0, eNR_GB, unimplemented ),
- def_nofc ("GBPOL", "GB Polarization" ),
- def_nofc ("NPSOLVATION", "Nonpolar Sol." ),
+ def_nofc ("GB12", "GB 1-2 Pol. (unused)" ),
+ def_nofc ("GB13", "GB 1-3 Pol. (unused)" ),
+ def_nofc ("GB14", "GB 1-4 Pol. (unused)" ),
+ def_nofc ("GBPOL", "GB Polarization (unused)" ),
+ def_nofc ("NPSOLVATION", "Nonpolar Sol. (unused)" ),
def_bondedz ("LJ14", "LJ-14", 2, 2, 2, eNR_NB14, unimplemented ),
def_nofc ("COUL14", "Coulomb-14" ),
def_bondedz ("LJC14_Q", "LJC-14 q", 2, 5, 0, eNR_NB14, unimplemented ),
gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
gmx_bool bNS, bNStList, bSimAnn, bStopCM,
bFirstStep, bInitStep, bLastStep = FALSE,
- bBornRadii, bUsingEnsembleRestraints;
+ bUsingEnsembleRestraints;
gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
bForceUpdate = FALSE, bCPT;
bLastStep = TRUE;
}
- /* Determine whether or not to update the Born radii if doing GB */
- bBornRadii = bFirstStep;
- if (ir->implicit_solvent && (step % ir->nstgbradii == 0))
- {
- bBornRadii = TRUE;
- }
-
/* do_log triggers energy and virial calculation. Because this leads
* to different code paths, forces can be different. Thus for exact
* continuation we should avoid extra log output.
constr, enerd, fcd,
state, &f, force_vir, mdatoms,
nrnb, wcycle, graph, groups,
- shellfc, fr, bBornRadii, t, mu_tot,
+ shellfc, fr, t, mu_tot,
vsite,
ddOpenBalanceRegion, ddCloseBalanceRegion);
}
state->box, state->x, &state->hist,
f, force_vir, mdatoms, enerd, fcd,
state->lambda, graph,
- fr, vsite, mu_tot, t, ed, bBornRadii,
+ fr, vsite, mu_tot, t, ed,
(bNS ? GMX_FORCE_NS : 0) | force_flags,
ddOpenBalanceRegion, ddCloseBalanceRegion);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff