-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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-
- * This program is free software; you can redistribute it and/or
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- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2008, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
+ *
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*
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+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
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+ * 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.
*
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * To help us fund GROMACS development, we humbly ask that you cite
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
#include <string.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "genborn.h"
-#include "vec.h"
-#include "grompp.h"
-#include "pdbio.h"
-#include "names.h"
-#include "physics.h"
-#include "partdec.h"
-#include "domdec.h"
-#include "network.h"
-#include "gmx_fatal.h"
-#include "mtop_util.h"
-#include "pbc.h"
-#include "nrnb.h"
-#include "bondf.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/genborn.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/units.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/legacyheaders/nrnb.h"
+
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
-#ifdef GMX_X86_SSE2
+#ifdef GMX_SIMD_X86_SSE2_OR_HIGHER
# ifdef GMX_DOUBLE
# include "genborn_sse2_double.h"
# include "genborn_allvsall_sse2_double.h"
int list_nalloc;
} t_gbtmpnbls;
-/* This function is exactly the same as the one in bondfree.c. The reason
+/* This function is exactly the same as the one in bonded/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
*/
}
}
-int init_gb_nblist(int natoms, t_nblist *nl)
+static int init_gb_nblist(int natoms, t_nblist *nl)
{
nl->maxnri = natoms*4;
nl->maxnrj = 0;
- nl->maxlen = 0;
nl->nri = 0;
nl->nrj = 0;
nl->iinr = NULL;
return 0;
}
-void gb_pd_send(t_commrec *cr, real *send_data, int nr)
-{
-#ifdef GMX_MPI
- int i, cur;
- int *index, *sendc, *disp;
-
- snew(sendc, cr->nnodes);
- snew(disp, cr->nnodes);
-
- index = pd_index(cr);
- cur = cr->nodeid;
-
- /* Setup count/index arrays */
- for (i = 0; i < cr->nnodes; i++)
- {
- sendc[i] = index[i+1]-index[i];
- disp[i] = index[i];
- }
-
- /* Do communication */
- MPI_Gatherv(send_data+index[cur], sendc[cur], GMX_MPI_REAL, send_data, sendc,
- disp, GMX_MPI_REAL, 0, cr->mpi_comm_mygroup);
- MPI_Bcast(send_data, nr, GMX_MPI_REAL, 0, cr->mpi_comm_mygroup);
-
-#endif
-}
-
-
-int init_gb_plist(t_params *p_list)
-{
- p_list->nr = 0;
- p_list->param = NULL;
-
- return 0;
-}
-
-
-int init_gb_still(const t_commrec *cr,
- const t_atomtypes *atype, t_idef *idef, t_atoms *atoms,
- gmx_genborn_t *born, int natoms)
+static int init_gb_still(const t_atomtypes *atype, t_idef *idef, t_atoms *atoms,
+ gmx_genborn_t *born, int natoms)
{
int i, j, i1, i2, k, m, nbond, nang, ia, ib, ic, id, nb, idx, idx2, at;
snew(gp, natoms);
snew(born->gpol_still_work, natoms+3);
- if (PAR(cr))
- {
- if (PARTDECOMP(cr))
- {
- pd_at_range(cr, &at0, &at1);
-
- for (i = 0; i < natoms; i++)
- {
- vsol[i] = gp[i] = 0;
- }
- }
- else
- {
- at0 = 0;
- at1 = natoms;
- }
- }
- else
- {
- at0 = 0;
- at1 = natoms;
- }
+ at0 = 0;
+ at1 = natoms;
doffset = born->gb_doffset;
h = ri*(1+ratio);
term = (M_PI/3.0)*h*h*(3.0*ri-h);
- if (PARTDECOMP(cr))
- {
- vsol[ia] += term;
- }
- else
- {
- born->vsolv_globalindex[ia] -= term;
- }
+ 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);
- if (PARTDECOMP(cr))
- {
- vsol[ib] += term;
- }
- else
- {
- born->vsolv_globalindex[ib] -= term;
- }
- }
-
- if (PARTDECOMP(cr))
- {
- gmx_sum(natoms, vsol, cr);
-
- for (i = 0; i < natoms; i++)
- {
- born->vsolv_globalindex[i] = born->vsolv_globalindex[i]-vsol[i];
- }
+ born->vsolv_globalindex[ib] -= term;
}
/* Get the self-, 1-2 and 1-3 polarization energies for analytical Still
r4 = r*r*r*r;
- if (PARTDECOMP(cr))
- {
- gp[ia] += STILL_P2*born->vsolv_globalindex[ib]/r4;
- gp[ib] += STILL_P2*born->vsolv_globalindex[ia]/r4;
- }
- else
- {
- 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;
- }
+ 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 */
r = idef->iparams[m].gb.st;
r4 = r*r*r*r;
- if (PARTDECOMP(cr))
- {
- gp[ia] += STILL_P3*born->vsolv[ib]/r4;
- gp[ib] += STILL_P3*born->vsolv[ia]/r4;
- }
- else
- {
- 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;
- }
- }
-
- if (PARTDECOMP(cr))
- {
- gmx_sum(natoms, gp, cr);
-
- for (i = 0; i < natoms; i++)
- {
- born->gpol_globalindex[i] = born->gpol_globalindex[i]+gp[i];
- }
+ 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);
/* Initialize all GB datastructs and compute polarization energies */
int init_gb(gmx_genborn_t **p_born,
- const t_commrec *cr, t_forcerec *fr, const t_inputrec *ir,
+ t_forcerec *fr, const t_inputrec *ir,
const gmx_mtop_t *mtop, int gb_algorithm)
{
int i, j, m, ai, aj, jj, natoms, nalloc;
/* If Still model, initialise the polarisation energies */
if (gb_algorithm == egbSTILL)
{
- init_gb_still(cr, &(mtop->atomtypes), &(localtop->idef), &atoms,
+ init_gb_still(&(mtop->atomtypes), &(localtop->idef), &atoms,
born, natoms);
}
static int
-calc_gb_rad_still(t_commrec *cr, t_forcerec *fr, int natoms, gmx_localtop_t *top,
+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)
{
}
/* Parallel summations */
- if (PARTDECOMP(cr))
- {
- gmx_sum(natoms, born->gpol_still_work, cr);
- }
- else if (DOMAINDECOMP(cr))
+ if (DOMAINDECOMP(cr))
{
dd_atom_sum_real(cr->dd, born->gpol_still_work);
}
static int
-calc_gb_rad_hct(t_commrec *cr, t_forcerec *fr, int natoms, gmx_localtop_t *top,
+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)
{
}
/* Parallel summations */
- if (PARTDECOMP(cr))
- {
- gmx_sum(natoms, born->gpol_hct_work, cr);
- }
- else if (DOMAINDECOMP(cr))
+ if (DOMAINDECOMP(cr))
{
dd_atom_sum_real(cr->dd, born->gpol_hct_work);
}
}
static int
-calc_gb_rad_obc(t_commrec *cr, t_forcerec *fr, int natoms, gmx_localtop_t *top,
+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, at0, at1;
}
/* Parallel summations */
- if (PARTDECOMP(cr))
- {
- gmx_sum(natoms, born->gpol_hct_work, cr);
- }
- else if (DOMAINDECOMP(cr))
+ if (DOMAINDECOMP(cr))
{
dd_atom_sum_real(cr->dd, born->gpol_hct_work);
}
if (ir->gb_algorithm == egbSTILL)
{
-#if 0 && defined (GMX_X86_SSE2)
- if (fr->use_acceleration)
+#if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
+ if (fr->use_simd_kernels)
{
# ifdef GMX_DOUBLE
genborn_allvsall_calc_still_radii_sse2_double(fr, md, born, top, x[0], cr, &fr->AllvsAll_workgb);
genborn_allvsall_calc_still_radii(fr, md, born, top, x[0], cr, &fr->AllvsAll_workgb);
}
#else
- genborn_allvsall_calc_still_radii(fr, md, born, top, x[0], cr, &fr->AllvsAll_workgb);
+ genborn_allvsall_calc_still_radii(fr, md, born, top, x[0], &fr->AllvsAll_workgb);
#endif
/* 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)
{
-#if 0 && defined (GMX_X86_SSE2)
- if (fr->use_acceleration)
+#if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
+ if (fr->use_simd_kernels)
{
# ifdef GMX_DOUBLE
genborn_allvsall_calc_hct_obc_radii_sse2_double(fr, md, born, ir->gb_algorithm, top, x[0], cr, &fr->AllvsAll_workgb);
genborn_allvsall_calc_hct_obc_radii(fr, md, born, ir->gb_algorithm, top, x[0], cr, &fr->AllvsAll_workgb);
}
#else
- genborn_allvsall_calc_hct_obc_radii(fr, md, born, ir->gb_algorithm, top, x[0], cr, &fr->AllvsAll_workgb);
+ genborn_allvsall_calc_hct_obc_radii(fr, md, born, ir->gb_algorithm, top, x[0], &fr->AllvsAll_workgb);
#endif
/* 24 flops in outer loop, 183 in inner */
inc_nrnb(nrnb, eNR_BORN_AVA_RADII_HCT_OBC, md->homenr*24+cnt*183);
/* Switch for determining which algorithm to use for Born radii calculation */
#ifdef GMX_DOUBLE
-#if 0 && defined (GMX_X86_SSE2)
+#if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
/* x86 or x86-64 with GCC inline assembly and/or SSE intrinsics */
switch (ir->gb_algorithm)
{
case egbSTILL:
- if (fr->use_acceleration)
+ if (fr->use_simd_kernels)
{
calc_gb_rad_still_sse2_double(cr, fr, born->nr, top, atype, x[0], nl, born);
}
else
{
- calc_gb_rad_still(cr, fr, born->nr, top, atype, x, nl, born, md);
+ calc_gb_rad_still(cr, fr, top, x, nl, born, md);
}
break;
case egbHCT:
- if (fr->use_acceleration)
+ if (fr->use_simd_kernels)
{
calc_gb_rad_hct_obc_sse2_double(cr, fr, born->nr, top, atype, x[0], nl, born, md, ir->gb_algorithm);
}
else
{
- calc_gb_rad_hct(cr, fr, born->nr, top, atype, x, nl, born, md);
+ calc_gb_rad_hct(cr, fr, top, x, nl, born, md);
}
break;
case egbOBC:
- if (fr->use_acceleration)
+ if (fr->use_simd_kernels)
{
calc_gb_rad_hct_obc_sse2_double(cr, fr, born->nr, top, atype, x[0], nl, born, md, ir->gb_algorithm);
}
else
{
- calc_gb_rad_obc(cr, fr, born->nr, top, atype, x, nl, born, md);
+ calc_gb_rad_obc(cr, fr, born->nr, top, x, nl, born, md);
}
break;
switch (ir->gb_algorithm)
{
case egbSTILL:
- calc_gb_rad_still(cr, fr, born->nr, top, x, nl, born, md);
+ calc_gb_rad_still(cr, fr, top, x, nl, born, md);
break;
case egbHCT:
- calc_gb_rad_hct(cr, fr, born->nr, top, x, nl, born, md);
+ calc_gb_rad_hct(cr, fr, top, x, nl, born, md);
break;
case egbOBC:
- calc_gb_rad_obc(cr, fr, born->nr, top, x, nl, born, md);
+ calc_gb_rad_obc(cr, fr, top, x, nl, born, md);
break;
default:
#else
-#if 0 && defined (GMX_X86_SSE2)
+#if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
/* x86 or x86-64 with GCC inline assembly and/or SSE intrinsics */
switch (ir->gb_algorithm)
{
case egbSTILL:
- if (fr->use_acceleration)
+ if (fr->use_simd_kernels)
{
calc_gb_rad_still_sse2_single(cr, fr, born->nr, top, x[0], nl, born);
}
else
{
- calc_gb_rad_still(cr, fr, born->nr, top, x, nl, born, md);
+ calc_gb_rad_still(cr, fr, top, x, nl, born, md);
}
break;
case egbHCT:
- if (fr->use_acceleration)
+ if (fr->use_simd_kernels)
{
calc_gb_rad_hct_obc_sse2_single(cr, fr, born->nr, top, x[0], nl, born, md, ir->gb_algorithm);
}
else
{
- calc_gb_rad_hct(cr, fr, born->nr, top, x, nl, born, md);
+ calc_gb_rad_hct(cr, fr, top, x, nl, born, md);
}
break;
case egbOBC:
- if (fr->use_acceleration)
+ if (fr->use_simd_kernels)
{
calc_gb_rad_hct_obc_sse2_single(cr, fr, born->nr, top, x[0], nl, born, md, ir->gb_algorithm);
}
switch (ir->gb_algorithm)
{
case egbSTILL:
- calc_gb_rad_still(cr, fr, born->nr, top, x, nl, born, md);
+ calc_gb_rad_still(cr, fr, top, x, nl, born, md);
break;
case egbHCT:
- calc_gb_rad_hct(cr, fr, born->nr, top, x, nl, born, md);
+ calc_gb_rad_hct(cr, fr, top, x, nl, born, md);
break;
case egbOBC:
- calc_gb_rad_obc(cr, fr, born->nr, top, x, nl, born, md);
+ calc_gb_rad_obc(cr, fr, top, x, nl, born, md);
break;
default:
int i, ai, at0, at1;
real rai, e, derb, q, q2, fi, rai_inv, vtot;
- if (PARTDECOMP(cr))
- {
- pd_at_range(cr, &at0, &at1);
- }
- else if (DOMAINDECOMP(cr))
+ if (DOMAINDECOMP(cr))
{
at0 = 0;
at1 = cr->dd->nat_home;
/* To keep the compiler happy */
factor = 0;
- if (PARTDECOMP(cr))
- {
- pd_at_range(cr, &at0, &at1);
- }
- else if (DOMAINDECOMP(cr))
+ if (DOMAINDECOMP(cr))
{
at0 = 0;
at1 = cr->dd->nat_home;
fr->invsqrta, fr->dvda, fr->gbtab.data, idef, born->epsilon_r, born->gb_epsilon_solvent, fr->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->epsfac);
+ enerd->term[F_GBPOL] += calc_gb_selfcorrections(cr, born->nr, md->chargeA, born, fr->dvda, fr->epsfac);
/* If parallel, sum the derivative of the potential w.r.t the born radii */
- if (PARTDECOMP(cr))
- {
- gmx_sum(md->nr, fr->dvda, cr);
- }
- else if (DOMAINDECOMP(cr))
+ if (DOMAINDECOMP(cr))
{
dd_atom_sum_real(cr->dd, fr->dvda);
dd_atom_spread_real(cr->dd, fr->dvda);
if (fr->bAllvsAll)
{
-#if 0 && defined (GMX_X86_SSE2)
- if (fr->use_acceleration)
+#if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
+ if (fr->use_simd_kernels)
{
# ifdef GMX_DOUBLE
genborn_allvsall_calc_chainrule_sse2_double(fr, md, born, x[0], f[0], gb_algorithm, fr->AllvsAll_workgb);
return;
}
-#if 0 && defined (GMX_X86_SSE2)
- if (fr->use_acceleration)
+#if 0 && defined (GMX_SIMD_X86_SSE2_OR_HIGHER)
+ if (fr->use_simd_kernels)
{
# ifdef GMX_DOUBLE
calc_gb_chainrule_sse2_double(fr->natoms_force, &(fr->gblist), fr->dadx, fr->dvda, x[0],
}
else
{
- /* Single node or particle decomp (global==local), just copy pointers and return */
+ /* Single node, just copy pointers and return */
if (gb_algorithm == egbSTILL)
{
born->gpol = born->gpol_globalindex;
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff