-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
- *
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, 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.
+ *
+ * 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.
*
- * If you want to redistribute modifications, 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 www.gromacs.org.
+ * 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.
*
- * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
+ * 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.
*
- * For more info, check our website at http://www.gromacs.org
+ * 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.
*
- * And Hey:
- * GROwing Monsters And Cloning Shrimps
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/ns.h"
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "maths.h"
-#include "vec.h"
-#include "network.h"
-#include "nsgrid.h"
-#include "force.h"
-#include "nonbonded.h"
-#include "ns.h"
-#include "pbc.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "nrnb.h"
-#include "txtdump.h"
-#include "mtop_util.h"
-
-#include "domdec.h"
-#include "adress.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nonbonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "adress.h"
/*
* E X C L U S I O N H A N D L I N G
*
************************************************/
-static void reallocate_nblist(t_nblist *nl)
+void reallocate_nblist(t_nblist *nl)
{
if (gmx_debug_at)
{
int maxsr, int maxlr,
int ivdw, int ivdwmod,
int ielec, int ielecmod,
- int igeometry, int type)
+ int igeometry, int type,
+ gmx_bool bElecAndVdwSwitchDiffers)
{
t_nblist *nl;
int homenr;
}
/* This will also set the simd_padding_width field */
- gmx_nonbonded_set_kernel_pointers( (i == 0) ? log : NULL, nl);
+ gmx_nonbonded_set_kernel_pointers( (i == 0) ? log : NULL, nl, bElecAndVdwSwitchDiffers);
/* maxnri is influenced by the number of shifts (maximum is 8)
* and the number of energy groups.
*/
nl->maxnri = homenr*4;
nl->maxnrj = 0;
- nl->maxlen = 0;
nl->nri = -1;
nl->nrj = 0;
nl->iinr = NULL;
nl->gid = NULL;
nl->shift = NULL;
nl->jindex = NULL;
+ nl->jjnr = NULL;
+ nl->excl_fep = NULL;
reallocate_nblist(nl);
nl->jindex[0] = 0;
* cache trashing.
*/
int maxsr, maxsr_wat, maxlr, maxlr_wat;
- int ielec, ielecf, ivdw, ielecmod, ielecmodf, ivdwmod, type;
+ int ielec, ivdw, ielecmod, ivdwmod, type;
int solvent;
int igeometry_def, igeometry_w, igeometry_ww;
int i;
+ gmx_bool bElecAndVdwSwitchDiffers;
t_nblists *nbl;
/* maxsr = homenr-fr->nWatMol*3; */
}
/* Determine the values for ielec/ivdw. */
- ielec = fr->nbkernel_elec_interaction;
- ivdw = fr->nbkernel_vdw_interaction;
- ielecmod = fr->nbkernel_elec_modifier;
- ivdwmod = fr->nbkernel_vdw_modifier;
- type = GMX_NBLIST_INTERACTION_STANDARD;
+ ielec = fr->nbkernel_elec_interaction;
+ ivdw = fr->nbkernel_vdw_interaction;
+ ielecmod = fr->nbkernel_elec_modifier;
+ ivdwmod = fr->nbkernel_vdw_modifier;
+ type = GMX_NBLIST_INTERACTION_STANDARD;
+ bElecAndVdwSwitchDiffers = ( (fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw));
fr->ns.bCGlist = (getenv("GMX_NBLISTCG") != 0);
if (!fr->ns.bCGlist)
type = GMX_NBLIST_INTERACTION_ADRESS;
}
init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ], &nbl->nlist_lr[eNL_VDWQQ],
- maxsr, maxlr, ivdw, ivdwmod, ielec, ielecmod, igeometry_def, type);
+ maxsr, maxlr, ivdw, ivdwmod, ielec, ielecmod, igeometry_def, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_VDW], &nbl->nlist_lr[eNL_VDW],
- maxsr, maxlr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, igeometry_def, type);
+ maxsr, maxlr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, igeometry_def, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_QQ], &nbl->nlist_lr[eNL_QQ],
- maxsr, maxlr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_def, type);
+ maxsr, maxlr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_def, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_WATER], &nbl->nlist_lr[eNL_VDWQQ_WATER],
- maxsr_wat, maxlr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_w, type);
+ maxsr_wat, maxlr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_w, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_QQ_WATER], &nbl->nlist_lr[eNL_QQ_WATER],
- maxsr_wat, maxlr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_w, type);
+ maxsr_wat, maxlr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_w, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_WATERWATER], &nbl->nlist_lr[eNL_VDWQQ_WATERWATER],
- maxsr_wat, maxlr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_ww, type);
+ maxsr_wat, maxlr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_ww, type, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_QQ_WATERWATER], &nbl->nlist_lr[eNL_QQ_WATERWATER],
- maxsr_wat, maxlr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_ww, type);
+ maxsr_wat, maxlr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_ww, type, bElecAndVdwSwitchDiffers);
/* Did we get the solvent loops so we can use optimized water kernels? */
if (nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf == NULL
|| nbl->nlist_sr[eNL_QQ_WATER].kernelptr_vf == NULL
-#ifndef DISABLE_WATERWATER_NLIST
|| nbl->nlist_sr[eNL_VDWQQ_WATERWATER].kernelptr_vf == NULL
- || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == NULL
-#endif
- )
+ || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == NULL)
{
fr->solvent_opt = esolNO;
- fprintf(log, "Note: The available nonbonded kernels do not support water optimization - disabling.\n");
+ if (log != NULL)
+ {
+ fprintf(log, "Note: The available nonbonded kernels do not support water optimization - disabling.\n");
+ }
}
if (fr->efep != efepNO)
{
- if ((fr->bEwald) && (fr->sc_alphacoul > 0)) /* need to handle long range differently if using softcore */
- {
- ielecf = GMX_NBKERNEL_ELEC_EWALD;
- ielecmodf = eintmodNONE;
- }
- else
- {
- ielecf = ielec;
- ielecmodf = ielecmod;
- }
-
init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_FREE], &nbl->nlist_lr[eNL_VDWQQ_FREE],
- maxsr, maxlr, ivdw, ivdwmod, ielecf, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
+ maxsr, maxlr, ivdw, ivdwmod, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_VDW_FREE], &nbl->nlist_lr[eNL_VDW_FREE],
- maxsr, maxlr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
+ maxsr, maxlr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
init_nblist(log, &nbl->nlist_sr[eNL_QQ_FREE], &nbl->nlist_lr[eNL_QQ_FREE],
- maxsr, maxlr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielecf, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY);
+ maxsr, maxlr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
}
}
/* QMMM MM list */
if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
{
init_nblist(log, &fr->QMMMlist, NULL,
- maxsr, maxlr, 0, 0, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_STANDARD);
+ maxsr, maxlr, 0, 0, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_STANDARD, bElecAndVdwSwitchDiffers);
}
if (log != NULL)
{
nl->nri = -1;
nl->nrj = 0;
- nl->maxlen = 0;
if (nl->jindex)
{
nl->jindex[0] = 0;
-static inline void new_i_nblist(t_nblist *nlist,
- gmx_bool bLR, atom_id i_atom, int shift, int gid)
+static gmx_inline void new_i_nblist(t_nblist *nlist, atom_id i_atom, int shift, int gid)
{
int i, k, nri, nshift;
nlist->gid[nri] = gid;
nlist->shift[nri] = shift;
}
+ else
+ {
+ /* Adding to previous list. First remove possible previous padding */
+ if (nlist->simd_padding_width > 1)
+ {
+ while (nlist->nrj > 0 && nlist->jjnr[nlist->nrj-1] < 0)
+ {
+ nlist->nrj--;
+ }
+ }
+ }
}
-static inline void close_i_nblist(t_nblist *nlist)
+static gmx_inline void close_i_nblist(t_nblist *nlist)
{
int nri = nlist->nri;
int len;
nlist->jindex[nri+1] = nlist->nrj;
len = nlist->nrj - nlist->jindex[nri];
-
- /* nlist length for water i molecules is treated statically
- * in the innerloops
- */
- if (len > nlist->maxlen)
- {
- nlist->maxlen = len;
- }
}
}
-static inline void close_nblist(t_nblist *nlist)
+static gmx_inline void close_nblist(t_nblist *nlist)
{
/* Only close this nblist when it has been initialized.
* Avoid the creation of i-lists with no j-particles.
}
}
-static inline void close_neighbor_lists(t_forcerec *fr, gmx_bool bMakeQMMMnblist)
+static gmx_inline void close_neighbor_lists(t_forcerec *fr, gmx_bool bMakeQMMMnblist)
{
int n, i;
}
-static inline void add_j_to_nblist(t_nblist *nlist, atom_id j_atom, gmx_bool bLR)
+static gmx_inline void add_j_to_nblist(t_nblist *nlist, atom_id j_atom, gmx_bool bLR)
{
int nrj = nlist->nrj;
nlist->nrj++;
}
-static inline void add_j_to_nblist_cg(t_nblist *nlist,
- atom_id j_start, int j_end,
- t_excl *bexcl, gmx_bool i_is_j,
- gmx_bool bLR)
+static gmx_inline void add_j_to_nblist_cg(t_nblist *nlist,
+ atom_id j_start, int j_end,
+ t_excl *bexcl, gmx_bool i_is_j,
+ gmx_bool bLR)
{
int nrj = nlist->nrj;
int j;
if (iwater != esolNO)
{
- vdwc = &nlist[eNL_VDWQQ_WATER];
- vdw = &nlist[eNL_VDW];
- coul = &nlist[eNL_QQ_WATER];
-#ifndef DISABLE_WATERWATER_NLIST
+ vdwc = &nlist[eNL_VDWQQ_WATER];
+ vdw = &nlist[eNL_VDW];
+ coul = &nlist[eNL_QQ_WATER];
vdwc_ww = &nlist[eNL_VDWQQ_WATERWATER];
coul_ww = &nlist[eNL_QQ_WATERWATER];
-#endif
}
else
{
/* Create new i_atom for each energy group */
if (bDoCoul && bDoVdW)
{
- new_i_nblist(vdwc, bLR, i_atom, shift, gid);
-#ifndef DISABLE_WATERWATER_NLIST
- new_i_nblist(vdwc_ww, bLR, i_atom, shift, gid);
-#endif
+ new_i_nblist(vdwc, i_atom, shift, gid);
+ new_i_nblist(vdwc_ww, i_atom, shift, gid);
}
if (bDoVdW)
{
- new_i_nblist(vdw, bLR, i_atom, shift, gid);
+ new_i_nblist(vdw, i_atom, shift, gid);
}
if (bDoCoul)
{
- new_i_nblist(coul, bLR, i_atom, shift, gid);
-#ifndef DISABLE_WATERWATER_NLIST
- new_i_nblist(coul_ww, bLR, i_atom, shift, gid);
-#endif
+ new_i_nblist(coul, i_atom, shift, gid);
+ new_i_nblist(coul_ww, i_atom, shift, gid);
}
/* Loop over the j charge groups */
for (j = 0; (j < nj); j++)
}
else
{
-#ifdef DISABLE_WATERWATER_NLIST
- /* Add entries for the three atoms - only do VdW if we need to */
- if (!bDoVdW)
- {
- add_j_to_nblist(coul, jj0, bLR);
- }
- else
- {
- add_j_to_nblist(vdwc, jj0, bLR);
- }
- add_j_to_nblist(coul, jj0+1, bLR);
- add_j_to_nblist(coul, jj0+2, bLR);
-#else
/* One entry for the entire water-water interaction */
if (!bDoVdW)
{
{
add_j_to_nblist(vdwc_ww, jj0, bLR);
}
-#endif
}
}
else if (iwater == esolTIP4P && jwater == esolTIP4P)
}
else
{
-#ifdef DISABLE_WATERWATER_NLIST
- /* Add entries for the four atoms - only do VdW if we need to */
- if (bDoVdW)
- {
- add_j_to_nblist(vdw, jj0, bLR);
- }
- add_j_to_nblist(coul, jj0+1, bLR);
- add_j_to_nblist(coul, jj0+2, bLR);
- add_j_to_nblist(coul, jj0+3, bLR);
-#else
/* One entry for the entire water-water interaction */
if (!bDoVdW)
{
{
add_j_to_nblist(vdwc_ww, jj0, bLR);
}
-#endif
}
}
else
close_i_nblist(vdw);
close_i_nblist(coul);
close_i_nblist(vdwc);
-#ifndef DISABLE_WATERWATER_NLIST
close_i_nblist(coul_ww);
close_i_nblist(vdwc_ww);
-#endif
}
else
{
/* Create new i_atom for each energy group */
if (bDoVdW && bDoCoul)
{
- new_i_nblist(vdwc, bLR, i_atom, shift, gid);
+ new_i_nblist(vdwc, i_atom, shift, gid);
}
if (bDoVdW)
{
- new_i_nblist(vdw, bLR, i_atom, shift, gid);
+ new_i_nblist(vdw, i_atom, shift, gid);
}
if (bDoCoul)
{
- new_i_nblist(coul, bLR, i_atom, shift, gid);
+ new_i_nblist(coul, i_atom, shift, gid);
}
bDoVdW_i = (bDoVdW && bHaveVdW[type[i_atom]]);
bDoCoul_i = (bDoCoul && qi != 0);
/* Create new i_atom for each energy group */
if (bDoVdW && bDoCoul)
{
- new_i_nblist(vdwc, bLR, i_atom, shift, gid);
+ new_i_nblist(vdwc, i_atom, shift, gid);
}
if (bDoVdW)
{
- new_i_nblist(vdw, bLR, i_atom, shift, gid);
+ new_i_nblist(vdw, i_atom, shift, gid);
}
if (bDoCoul)
{
- new_i_nblist(coul, bLR, i_atom, shift, gid);
+ new_i_nblist(coul, i_atom, shift, gid);
}
- new_i_nblist(vdw_free, bLR, i_atom, shift, gid);
- new_i_nblist(coul_free, bLR, i_atom, shift, gid);
- new_i_nblist(vdwc_free, bLR, i_atom, shift, gid);
+ new_i_nblist(vdw_free, i_atom, shift, gid);
+ new_i_nblist(coul_free, i_atom, shift, gid);
+ new_i_nblist(vdwc_free, i_atom, shift, gid);
bDoVdW_i = (bDoVdW &&
(bHaveVdW[type[i_atom]] || bHaveVdW[typeB[i_atom]]));
/* Create new i_atom for each energy group */
if (bDoVdW && bDoCoul)
{
- new_i_nblist(vdwc, bLR, i_atom, shift, gid);
- new_i_nblist(vdwc_adress, bLR, i_atom, shift, gid);
+ new_i_nblist(vdwc, i_atom, shift, gid);
+ new_i_nblist(vdwc_adress, i_atom, shift, gid);
}
if (bDoVdW)
{
- new_i_nblist(vdw, bLR, i_atom, shift, gid);
- new_i_nblist(vdw_adress, bLR, i_atom, shift, gid);
+ new_i_nblist(vdw, i_atom, shift, gid);
+ new_i_nblist(vdw_adress, i_atom, shift, gid);
}
if (bDoCoul)
{
- new_i_nblist(coul, bLR, i_atom, shift, gid);
- new_i_nblist(coul_adress, bLR, i_atom, shift, gid);
+ new_i_nblist(coul, i_atom, shift, gid);
+ new_i_nblist(coul_adress, i_atom, shift, gid);
}
bDoVdW_i = (bDoVdW && bHaveVdW[type[i_atom]]);
bDoCoul_i = (bDoCoul && qi != 0);
* processed by the generic AdResS kernel.
*/
if ( (bEnergyGroupCG &&
- wf[i_atom] >= 1-GMX_REAL_EPS && wf[jj] >= 1-GMX_REAL_EPS ) ||
- ( !bEnergyGroupCG && wf[jj] <= GMX_REAL_EPS ) )
+ wf[i_atom] >= 1-GMX_REAL_EPS && wf[jj] >= 1-GMX_REAL_EPS ) ||
+ ( !bEnergyGroupCG && wf[jj] <= GMX_REAL_EPS ) )
{
continue;
}
b_hybrid = !((wf[i_atom] >= 1-GMX_REAL_EPS && wf[jj] >= 1-GMX_REAL_EPS) ||
- (wf[i_atom] <= GMX_REAL_EPS && wf[jj] <= GMX_REAL_EPS));
+ (wf[i_atom] <= GMX_REAL_EPS && wf[jj] <= GMX_REAL_EPS));
if (bNotEx)
{
}
static void
-put_in_list_qmmm(gmx_bool bHaveVdW[],
- int ngid,
- t_mdatoms * md,
- int icg,
- int jgid,
- int nj,
- atom_id jjcg[],
- atom_id index[],
- t_excl bExcl[],
- int shift,
- t_forcerec * fr,
- gmx_bool bLR,
- gmx_bool bDoVdW,
- gmx_bool bDoCoul,
- int solvent_opt)
+put_in_list_qmmm(gmx_bool gmx_unused bHaveVdW[],
+ int ngid,
+ t_mdatoms gmx_unused * md,
+ int icg,
+ int jgid,
+ int nj,
+ atom_id jjcg[],
+ atom_id index[],
+ t_excl bExcl[],
+ int shift,
+ t_forcerec * fr,
+ gmx_bool bLR,
+ gmx_bool gmx_unused bDoVdW,
+ gmx_bool gmx_unused bDoCoul,
+ int gmx_unused solvent_opt)
{
t_nblist * coul;
int i, j, jcg, igid, gid;
i_atom = i0+i;
gid = GID(igid, jgid, ngid);
/* Create new i_atom for each energy group */
- new_i_nblist(coul, bLR, i_atom, shift, gid);
+ new_i_nblist(coul, i_atom, shift, gid);
/* Loop over the j charge groups */
for (j = 0; j < nj; j++)
}
static void
-put_in_list_cg(gmx_bool bHaveVdW[],
- int ngid,
- t_mdatoms * md,
- int icg,
- int jgid,
- int nj,
- atom_id jjcg[],
- atom_id index[],
- t_excl bExcl[],
- int shift,
- t_forcerec * fr,
- gmx_bool bLR,
- gmx_bool bDoVdW,
- gmx_bool bDoCoul,
- int solvent_opt)
+put_in_list_cg(gmx_bool gmx_unused bHaveVdW[],
+ int ngid,
+ t_mdatoms gmx_unused * md,
+ int icg,
+ int jgid,
+ int nj,
+ atom_id jjcg[],
+ atom_id index[],
+ t_excl bExcl[],
+ int shift,
+ t_forcerec * fr,
+ gmx_bool bLR,
+ gmx_bool gmx_unused bDoVdW,
+ gmx_bool gmx_unused bDoCoul,
+ int gmx_unused solvent_opt)
{
int cginfo;
int igid, gid, nbl_ind;
* If required, zero interactions could be removed here
* or in the force loop.
*/
- new_i_nblist(vdwc, bLR, index[icg], shift, gid);
+ new_i_nblist(vdwc, index[icg], shift, gid);
vdwc->iinr_end[vdwc->nri] = index[icg+1];
for (j = 0; (j < nj); j++)
*
************************************************/
-static inline void get_dx(int Nx, real gridx, real rc2, int xgi, real x,
- int *dx0, int *dx1, real *dcx2)
+static gmx_inline void get_dx(int Nx, real gridx, real rc2, int xgi, real x,
+ int *dx0, int *dx1, real *dcx2)
{
real dcx, tmp;
int xgi0, xgi1, i;
}
}
-static inline void get_dx_dd(int Nx, real gridx, real rc2, int xgi, real x,
- int ncpddc, int shift_min, int shift_max,
- int *g0, int *g1, real *dcx2)
+static gmx_inline void get_dx_dd(int Nx, real gridx, real rc2, int xgi, real x,
+ int ncpddc, int shift_min, int shift_max,
+ int *g0, int *g1, real *dcx2)
{
real dcx, tmp;
int g_min, g_max, shift_home;
if (bDoLongRange && fr->bTwinRange)
{
- /* The VdW and elec. LR cut-off's could be different,
+ /* With plain cut-off or RF we need to make the list exactly
+ * up to the cut-off and the cut-off's can be different,
* so we can not simply set them to rlistlong.
+ * To keep this code compatible with (exotic) old cases,
+ * we also create lists up to rvdw/rcoulomb for PME and Ewald.
+ * The interaction check should correspond to:
+ * !ir_vdw/coulomb_might_be_zero_at_cutoff from inputrec.c.
*/
- if (EVDW_MIGHT_BE_ZERO_AT_CUTOFF(fr->vdwtype) &&
- fr->rvdw > fr->rlist)
+ if (((fr->vdwtype == evdwCUT || fr->vdwtype == evdwPME) &&
+ fr->vdw_modifier == eintmodNONE) ||
+ fr->rvdw <= fr->rlist)
{
- *rvdw2 = sqr(fr->rlistlong);
+ *rvdw2 = sqr(fr->rvdw);
}
else
{
- *rvdw2 = sqr(fr->rvdw);
+ *rvdw2 = sqr(fr->rlistlong);
}
- if (EEL_MIGHT_BE_ZERO_AT_CUTOFF(fr->eeltype) &&
- fr->rcoulomb > fr->rlist)
+ if (((fr->eeltype == eelCUT ||
+ (EEL_RF(fr->eeltype) && fr->eeltype != eelRF_ZERO) ||
+ fr->eeltype == eelPME ||
+ fr->eeltype == eelEWALD) &&
+ fr->coulomb_modifier == eintmodNONE) ||
+ fr->rcoulomb <= fr->rlist)
{
- *rcoul2 = sqr(fr->rlistlong);
+ *rcoul2 = sqr(fr->rcoulomb);
}
else
{
- *rcoul2 = sqr(fr->rcoulomb);
+ *rcoul2 = sqr(fr->rlistlong);
}
}
else
}
}
-static int nsgrid_core(FILE *log, t_commrec *cr, t_forcerec *fr,
- matrix box, rvec box_size, int ngid,
+static int nsgrid_core(t_commrec *cr, t_forcerec *fr,
+ matrix box, int ngid,
gmx_localtop_t *top,
- t_grid *grid, rvec x[],
+ t_grid *grid,
t_excl bexcl[], gmx_bool *bExcludeAlleg,
- t_nrnb *nrnb, t_mdatoms *md,
- real *lambda, real *dvdlambda,
- gmx_grppairener_t *grppener,
+ t_mdatoms *md,
put_in_list_t *put_in_list,
gmx_bool bHaveVdW[],
gmx_bool bDoLongRange, gmx_bool bMakeQMMMnblist)
gmx_ns_t *ns;
atom_id **nl_lr_ljc, **nl_lr_one, **nl_sr;
int *nlr_ljc, *nlr_one, *nsr;
- gmx_domdec_t *dd = NULL;
+ gmx_domdec_t *dd;
t_block *cgs = &(top->cgs);
int *cginfo = fr->cginfo;
/* atom_id *i_atoms,*cgsindex=cgs->index; */
ns = &fr->ns;
bDomDec = DOMAINDECOMP(cr);
- if (bDomDec)
- {
- dd = cr->dd;
- }
+ dd = cr->dd;
bTriclinicX = ((YY < grid->npbcdim &&
(!bDomDec || dd->nc[YY] == 1) && box[YY][XX] != 0) ||
void init_ns(FILE *fplog, const t_commrec *cr,
gmx_ns_t *ns, t_forcerec *fr,
- const gmx_mtop_t *mtop,
- matrix box)
+ const gmx_mtop_t *mtop)
{
int mt, icg, nr_in_cg, maxcg, i, j, jcg, ngid, ncg;
t_block *cgs;
ns->bexcl = NULL;
if (!DOMAINDECOMP(cr))
{
- /* This could be reduced with particle decomposition */
ns_realloc_natoms(ns, mtop->natoms);
}
int search_neighbours(FILE *log, t_forcerec *fr,
- rvec x[], matrix box,
+ matrix box,
gmx_localtop_t *top,
gmx_groups_t *groups,
t_commrec *cr,
t_nrnb *nrnb, t_mdatoms *md,
- real *lambda, real *dvdlambda,
- gmx_grppairener_t *grppener,
gmx_bool bFillGrid,
- gmx_bool bDoLongRangeNS,
- gmx_bool bPadListsForKernels)
+ gmx_bool bDoLongRangeNS)
{
t_block *cgs = &(top->cgs);
rvec box_size, grid_x0, grid_x1;
get_nsgrid_boundaries(grid->nboundeddim, box, NULL, NULL, NULL, NULL,
cgs->nr, fr->cg_cm, grid_x0, grid_x1, &grid_dens);
- grid_first(log, grid, NULL, NULL, fr->ePBC, box, grid_x0, grid_x1,
+ grid_first(log, grid, NULL, NULL, box, grid_x0, grid_x1,
fr->rlistlong, grid_dens);
}
debug_gmx();
- /* Don't know why this all is... (DvdS 3/99) */
-#ifndef SEGV
start = 0;
end = cgs->nr;
-#else
- start = fr->cg0;
- end = (cgs->nr+1)/2;
-#endif
if (DOMAINDECOMP(cr))
{
end = cgs->nr;
- fill_grid(log, dd_zones, grid, end, -1, end, fr->cg_cm);
+ fill_grid(dd_zones, grid, end, -1, end, fr->cg_cm);
grid->icg0 = 0;
grid->icg1 = dd_zones->izone[dd_zones->nizone-1].cg1;
}
else
{
- fill_grid(log, NULL, grid, cgs->nr, fr->cg0, fr->hcg, fr->cg_cm);
+ fill_grid(NULL, grid, cgs->nr, fr->cg0, fr->hcg, fr->cg_cm);
grid->icg0 = fr->cg0;
grid->icg1 = fr->hcg;
debug_gmx();
-
- if (PARTDECOMP(cr))
- {
- mv_grid(cr, grid);
- }
- debug_gmx();
}
- calc_elemnr(log, grid, start, end, cgs->nr);
+ calc_elemnr(grid, start, end, cgs->nr);
calc_ptrs(grid);
- grid_last(log, grid, start, end, cgs->nr);
+ grid_last(grid, start, end, cgs->nr);
if (gmx_debug_at)
{
- check_grid(debug, grid);
+ check_grid(grid);
print_grid(debug, grid);
}
}
/* Set the grid cell index for the test particle only.
* The cell to cg index is not corrected, but that does not matter.
*/
- fill_grid(log, NULL, ns->grid, fr->hcg, fr->hcg-1, fr->hcg, fr->cg_cm);
+ fill_grid(NULL, ns->grid, fr->hcg, fr->hcg-1, fr->hcg, fr->cg_cm);
}
debug_gmx();
if (bGrid)
{
grid = ns->grid;
- nsearch = nsgrid_core(log, cr, fr, box, box_size, ngid, top,
- grid, x, ns->bexcl, ns->bExcludeAlleg,
- nrnb, md, lambda, dvdlambda, grppener,
- put_in_list, ns->bHaveVdW,
+ nsearch = nsgrid_core(cr, fr, box, ngid, top,
+ grid, ns->bexcl, ns->bExcludeAlleg,
+ md, put_in_list, ns->bHaveVdW,
bDoLongRangeNS, FALSE);
/* neighbour searching withouth QMMM! QM atoms have zero charge in
*/
if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
{
- nsearch += nsgrid_core(log, cr, fr, box, box_size, ngid, top,
- grid, x, ns->bexcl, ns->bExcludeAlleg,
- nrnb, md, lambda, dvdlambda, grppener,
- put_in_list_qmmm, ns->bHaveVdW,
+ nsearch += nsgrid_core(cr, fr, box, ngid, top,
+ grid, ns->bexcl, ns->bExcludeAlleg,
+ md, put_in_list_qmmm, ns->bHaveVdW,
bDoLongRangeNS, TRUE);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff