-/* -*- 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
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+ * 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
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*
- * 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:
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+ * 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>
#include <math.h>
#include <string.h>
#include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
#include "macros.h"
-#include "maths.h"
+#include "gromacs/math/utilities.h"
#include "vec.h"
+#include "types/commrec.h"
#include "network.h"
#include "nsgrid.h"
#include "force.h"
*
************************************************/
-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
)
{
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, 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 there are no j-particles we have to reduce the
+ * number of i-particles again, to prevent errors in the
+ * kernel functions.
*/
- if (len > nlist->maxlen)
+ if ((len == 0) && (nlist->nri > 0))
{
- nlist->maxlen = len;
+ nlist->nri--;
}
}
}
-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;
*
************************************************/
-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
ns->bexcl = NULL;
if (!DOMAINDECOMP(cr))
{
- /* This could be reduced with particle decomposition */
ns_realloc_natoms(ns, mtop->natoms);
}
}
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))
{
grid->icg0 = fr->cg0;
grid->icg1 = fr->hcg;
debug_gmx();
-
- if (PARTDECOMP(cr))
- {
- mv_grid(cr, grid);
- }
- debug_gmx();
}
calc_elemnr(grid, start, end, cgs->nr);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff