-/* -*- 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
- *
- * 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.
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-
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- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2012,2013,2014, 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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* of the License, or (at your option) any later version.
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+ * in the README & COPYING files - if they are missing, get the
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* 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.
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include "typedefs.h"
-#include "mdatoms.h"
-#include "smalloc.h"
-#include "main.h"
-#include "qmmm.h"
-#include "mtop_util.h"
-#include "gmx_omp_nthreads.h"
+#include "gmxpre.h"
+
+#include <math.h>
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
#define ALMOST_ZERO 1e-30
-t_mdatoms *init_mdatoms(FILE *fp,gmx_mtop_t *mtop,gmx_bool bFreeEnergy)
+t_mdatoms *init_mdatoms(FILE *fp, gmx_mtop_t *mtop, gmx_bool bFreeEnergy)
{
- int mb,a,g,nmol;
- double tmA,tmB;
- t_atom *atom;
- t_mdatoms *md;
- gmx_mtop_atomloop_all_t aloop;
- t_ilist *ilist;
-
- snew(md,1);
-
- md->nenergrp = mtop->groups.grps[egcENER].nr;
- md->bVCMgrps = FALSE;
- tmA = 0.0;
- tmB = 0.0;
-
- aloop = gmx_mtop_atomloop_all_init(mtop);
- while(gmx_mtop_atomloop_all_next(aloop,&a,&atom)) {
- if (ggrpnr(&mtop->groups,egcVCM,a) > 0)
- md->bVCMgrps = TRUE;
-
- if (bFreeEnergy && PERTURBED(*atom)) {
- md->nPerturbed++;
- if (atom->mB != atom->m)
- md->nMassPerturbed++;
- if (atom->qB != atom->q)
- md->nChargePerturbed++;
+ int mb, a, g, nmol;
+ double tmA, tmB;
+ t_atom *atom;
+ t_mdatoms *md;
+ gmx_mtop_atomloop_all_t aloop;
+ t_ilist *ilist;
+
+ snew(md, 1);
+
+ md->nenergrp = mtop->groups.grps[egcENER].nr;
+ md->bVCMgrps = FALSE;
+ tmA = 0.0;
+ tmB = 0.0;
+
+ aloop = gmx_mtop_atomloop_all_init(mtop);
+ while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
+ {
+ if (ggrpnr(&mtop->groups, egcVCM, a) > 0)
+ {
+ md->bVCMgrps = TRUE;
+ }
+
+ if (bFreeEnergy && PERTURBED(*atom))
+ {
+ md->nPerturbed++;
+ if (atom->mB != atom->m)
+ {
+ md->nMassPerturbed++;
+ }
+ if (atom->qB != atom->q)
+ {
+ md->nChargePerturbed++;
+ }
+ if (atom->typeB != atom->type)
+ {
+ md->nTypePerturbed++;
+ }
+ }
+
+ tmA += atom->m;
+ tmB += atom->mB;
}
-
- tmA += atom->m;
- tmB += atom->mB;
- }
-
- md->tmassA = tmA;
- md->tmassB = tmB;
-
- if (bFreeEnergy && fp)
- fprintf(fp,
- "There are %d atoms and %d charges for free energy perturbation\n",
- md->nPerturbed,md->nChargePerturbed);
-
- md->bOrires = gmx_mtop_ftype_count(mtop,F_ORIRES);
-
- return md;
+
+ md->tmassA = tmA;
+ md->tmassB = tmB;
+
+ if (bFreeEnergy && fp)
+ {
+ fprintf(fp,
+ "There are %d atoms and %d charges for free energy perturbation\n",
+ md->nPerturbed, md->nChargePerturbed);
+ }
+
+ md->bOrires = gmx_mtop_ftype_count(mtop, F_ORIRES);
+
+ return md;
}
-void atoms2md(gmx_mtop_t *mtop,t_inputrec *ir,
- int nindex,int *index,
- int start,int homenr,
- t_mdatoms *md)
+void atoms2md(gmx_mtop_t *mtop, t_inputrec *ir,
+ int nindex, int *index,
+ int homenr,
+ t_mdatoms *md)
{
- gmx_mtop_atomlookup_t alook;
- int i;
- t_grpopts *opts;
- gmx_groups_t *groups;
- gmx_molblock_t *molblock;
-
- opts = &ir->opts;
-
- groups = &mtop->groups;
-
- molblock = mtop->molblock;
-
- /* Index==NULL indicates particle decomposition,
- * unless we have an empty DD node, so also check for homenr and start.
- * This should be signaled properly with an extra parameter or nindex==-1.
- */
- if (index == NULL && (homenr > 0 || start > 0)) {
- md->nr = mtop->natoms;
- } else {
- md->nr = nindex;
- }
-
- if (md->nr > md->nalloc) {
- md->nalloc = over_alloc_dd(md->nr);
-
- if (md->nMassPerturbed) {
- srenew(md->massA,md->nalloc);
- srenew(md->massB,md->nalloc);
- }
- srenew(md->massT,md->nalloc);
- srenew(md->invmass,md->nalloc);
- srenew(md->chargeA,md->nalloc);
- if (md->nPerturbed) {
- srenew(md->chargeB,md->nalloc);
- }
- srenew(md->typeA,md->nalloc);
- if (md->nPerturbed) {
- srenew(md->typeB,md->nalloc);
+ gmx_bool bLJPME;
+ gmx_mtop_atomlookup_t alook;
+ int i;
+ t_grpopts *opts;
+ gmx_groups_t *groups;
+ gmx_molblock_t *molblock;
+
+ bLJPME = EVDW_PME(ir->vdwtype);
+
+ opts = &ir->opts;
+
+ groups = &mtop->groups;
+
+ molblock = mtop->molblock;
+
+ /* Index==NULL indicates no DD (unless we have a DD node with no
+ * atoms), so also check for homenr. This should be
+ * signaled properly with an extra parameter or nindex==-1.
+ */
+ if (index == NULL && (homenr > 0))
+ {
+ md->nr = mtop->natoms;
}
- srenew(md->ptype,md->nalloc);
- if (opts->ngtc > 1) {
- srenew(md->cTC,md->nalloc);
- /* We always copy cTC with domain decomposition */
+ else
+ {
+ md->nr = nindex;
}
- srenew(md->cENER,md->nalloc);
- if (opts->ngacc > 1)
- srenew(md->cACC,md->nalloc);
- if (opts->nFreeze &&
- (opts->ngfrz > 1 ||
- opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
- srenew(md->cFREEZE,md->nalloc);
- if (md->bVCMgrps)
- srenew(md->cVCM,md->nalloc);
- if (md->bOrires)
- srenew(md->cORF,md->nalloc);
- if (md->nPerturbed)
- srenew(md->bPerturbed,md->nalloc);
-
- /* Note that these user t_mdatoms array pointers are NULL
- * when there is only one group present.
- * Therefore, when adding code, the user should use something like:
- * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
- */
- if (mtop->groups.grpnr[egcUser1] != NULL)
- srenew(md->cU1,md->nalloc);
- if (mtop->groups.grpnr[egcUser2] != NULL)
- srenew(md->cU2,md->nalloc);
-
- if (ir->bQMMM)
- srenew(md->bQM,md->nalloc);
- if (ir->bAdress) {
- srenew(md->wf,md->nalloc);
- srenew(md->tf_table_index,md->nalloc);
+
+ if (md->nr > md->nalloc)
+ {
+ md->nalloc = over_alloc_dd(md->nr);
+
+ if (md->nMassPerturbed)
+ {
+ srenew(md->massA, md->nalloc);
+ srenew(md->massB, md->nalloc);
+ }
+ srenew(md->massT, md->nalloc);
+ srenew(md->invmass, md->nalloc);
+ srenew(md->chargeA, md->nalloc);
+ if (bLJPME)
+ {
+ srenew(md->sqrt_c6A, md->nalloc);
+ srenew(md->sigmaA, md->nalloc);
+ srenew(md->sigma3A, md->nalloc);
+ }
+ if (md->nPerturbed)
+ {
+ srenew(md->chargeB, md->nalloc);
+ if (bLJPME)
+ {
+ srenew(md->sqrt_c6B, md->nalloc);
+ srenew(md->sigmaB, md->nalloc);
+ srenew(md->sigma3B, md->nalloc);
+ }
+ }
+ srenew(md->typeA, md->nalloc);
+ if (md->nPerturbed)
+ {
+ srenew(md->typeB, md->nalloc);
+ }
+ srenew(md->ptype, md->nalloc);
+ if (opts->ngtc > 1)
+ {
+ srenew(md->cTC, md->nalloc);
+ /* We always copy cTC with domain decomposition */
+ }
+ srenew(md->cENER, md->nalloc);
+ if (opts->ngacc > 1)
+ {
+ srenew(md->cACC, md->nalloc);
+ }
+ if (opts->nFreeze &&
+ (opts->ngfrz > 1 ||
+ opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
+ {
+ srenew(md->cFREEZE, md->nalloc);
+ }
+ if (md->bVCMgrps)
+ {
+ srenew(md->cVCM, md->nalloc);
+ }
+ if (md->bOrires)
+ {
+ srenew(md->cORF, md->nalloc);
+ }
+ if (md->nPerturbed)
+ {
+ srenew(md->bPerturbed, md->nalloc);
+ }
+
+ /* Note that these user t_mdatoms array pointers are NULL
+ * when there is only one group present.
+ * Therefore, when adding code, the user should use something like:
+ * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
+ */
+ if (mtop->groups.grpnr[egcUser1] != NULL)
+ {
+ srenew(md->cU1, md->nalloc);
+ }
+ if (mtop->groups.grpnr[egcUser2] != NULL)
+ {
+ srenew(md->cU2, md->nalloc);
+ }
+
+ if (ir->bQMMM)
+ {
+ srenew(md->bQM, md->nalloc);
+ }
+ if (ir->bAdress)
+ {
+ srenew(md->wf, md->nalloc);
+ srenew(md->tf_table_index, md->nalloc);
+ }
}
- }
- alook = gmx_mtop_atomlookup_init(mtop);
+ alook = gmx_mtop_atomlookup_init(mtop);
#pragma omp parallel for num_threads(gmx_omp_nthreads_get(emntDefault)) schedule(static)
- for(i=0; i<md->nr; i++) {
- int g,ag,molb;
- real mA,mB,fac;
- t_atom *atom;
-
- if (index == NULL) {
- ag = i;
- } else {
- ag = index[i];
- }
- gmx_mtop_atomnr_to_atom(alook,ag,&atom);
+ for (i = 0; i < md->nr; i++)
+ {
+ int g, ag, molb;
+ real mA, mB, fac;
+ real c6, c12;
+ t_atom *atom;
- if (md->cFREEZE) {
- md->cFREEZE[i] = ggrpnr(groups,egcFREEZE,ag);
- }
+ if (index == NULL)
+ {
+ ag = i;
+ }
+ else
+ {
+ ag = index[i];
+ }
+ gmx_mtop_atomnr_to_atom(alook, ag, &atom);
+
+ if (md->cFREEZE)
+ {
+ md->cFREEZE[i] = ggrpnr(groups, egcFREEZE, ag);
+ }
if (EI_ENERGY_MINIMIZATION(ir->eI))
{
/* Displacement is proportional to F, masses used for constraints */
{
/* The friction coefficient is mass/tau_t */
fac = ir->delta_t/opts->tau_t[md->cTC ? groups->grpnr[egcTC][ag] : 0];
- mA = 0.5*atom->m*fac;
- mB = 0.5*atom->mB*fac;
+ mA = 0.5*atom->m*fac;
+ mB = 0.5*atom->mB*fac;
}
}
else
mA = atom->m;
mB = atom->mB;
}
- if (md->nMassPerturbed) {
- md->massA[i] = mA;
- md->massB[i] = mB;
- }
- md->massT[i] = mA;
- if (mA == 0.0) {
- md->invmass[i] = 0;
- } else if (md->cFREEZE) {
- g = md->cFREEZE[i];
- if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
- /* Set the mass of completely frozen particles to ALMOST_ZERO iso 0
- * to avoid div by zero in lincs or shake.
- * Note that constraints can still move a partially frozen particle.
- */
- md->invmass[i] = ALMOST_ZERO;
- else
- md->invmass[i] = 1.0/mA;
- } else {
- md->invmass[i] = 1.0/mA;
- }
- md->chargeA[i] = atom->q;
- md->typeA[i] = atom->type;
- if (md->nPerturbed) {
- md->chargeB[i] = atom->qB;
- md->typeB[i] = atom->typeB;
- md->bPerturbed[i] = PERTURBED(*atom);
- }
- md->ptype[i] = atom->ptype;
- if (md->cTC)
- md->cTC[i] = groups->grpnr[egcTC][ag];
- md->cENER[i] =
- (groups->grpnr[egcENER] ? groups->grpnr[egcENER][ag] : 0);
- if (md->cACC)
- md->cACC[i] = groups->grpnr[egcACC][ag];
- if (md->cVCM)
- md->cVCM[i] = groups->grpnr[egcVCM][ag];
- if (md->cORF)
- md->cORF[i] = groups->grpnr[egcORFIT][ag];
-
- if (md->cU1)
- md->cU1[i] = groups->grpnr[egcUser1][ag];
- if (md->cU2)
- md->cU2[i] = groups->grpnr[egcUser2][ag];
-
- if (ir->bQMMM) {
- if (groups->grpnr[egcQMMM] == 0 ||
- groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1) {
- md->bQM[i] = TRUE;
- } else {
- md->bQM[i] = FALSE;
- }
- }
- /* Initialize AdResS weighting functions to adressw */
- if (ir->bAdress){
- md->wf[i] = 1.0;
- /* if no tf table groups specified, use default table */
- md->tf_table_index[i] = DEFAULT_TF_TABLE;
- if (ir->adress->n_tf_grps > 0){
- /* if tf table groups specified, tf is only applied to thoose energy groups*/
- md->tf_table_index[i] = NO_TF_TABLE;
- /* check wether atom is in one of the relevant energy groups and assign a table index */
- for (g=0; g<ir->adress->n_tf_grps; g++){
- if (md->cENER[i] == ir->adress->tf_table_index[g]){
- md->tf_table_index[i] = g;
+ if (md->nMassPerturbed)
+ {
+ md->massA[i] = mA;
+ md->massB[i] = mB;
+ }
+ md->massT[i] = mA;
+ if (mA == 0.0)
+ {
+ md->invmass[i] = 0;
+ }
+ else if (md->cFREEZE)
+ {
+ g = md->cFREEZE[i];
+ if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
+ {
+ /* Set the mass of completely frozen particles to ALMOST_ZERO iso 0
+ * to avoid div by zero in lincs or shake.
+ * Note that constraints can still move a partially frozen particle.
+ */
+ md->invmass[i] = ALMOST_ZERO;
+ }
+ else
+ {
+ md->invmass[i] = 1.0/mA;
+ }
+ }
+ else
+ {
+ md->invmass[i] = 1.0/mA;
+ }
+ md->chargeA[i] = atom->q;
+ md->typeA[i] = atom->type;
+ if (bLJPME)
+ {
+ c6 = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c6;
+ c12 = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c12;
+ md->sqrt_c6A[i] = sqrt(c6);
+ if (c6 == 0.0 || c12 == 0)
+ {
+ md->sigmaA[i] = 1.0;
+ }
+ else
+ {
+ md->sigmaA[i] = pow(c12/c6, 1.0/6.0);
+ }
+ md->sigma3A[i] = 1/(md->sigmaA[i]*md->sigmaA[i]*md->sigmaA[i]);
+ }
+ if (md->nPerturbed)
+ {
+ md->bPerturbed[i] = PERTURBED(*atom);
+ md->chargeB[i] = atom->qB;
+ md->typeB[i] = atom->typeB;
+ if (bLJPME)
+ {
+ c6 = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c6;
+ c12 = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c12;
+ md->sqrt_c6B[i] = sqrt(c6);
+ if (c6 == 0.0 || c12 == 0)
+ {
+ md->sigmaB[i] = 1.0;
+ }
+ else
+ {
+ md->sigmaB[i] = pow(c12/c6, 1.0/6.0);
+ }
+ md->sigma3B[i] = 1/(md->sigmaB[i]*md->sigmaB[i]*md->sigmaB[i]);
+ }
+ }
+ md->ptype[i] = atom->ptype;
+ if (md->cTC)
+ {
+ md->cTC[i] = groups->grpnr[egcTC][ag];
+ }
+ md->cENER[i] =
+ (groups->grpnr[egcENER] ? groups->grpnr[egcENER][ag] : 0);
+ if (md->cACC)
+ {
+ md->cACC[i] = groups->grpnr[egcACC][ag];
+ }
+ if (md->cVCM)
+ {
+ md->cVCM[i] = groups->grpnr[egcVCM][ag];
+ }
+ if (md->cORF)
+ {
+ md->cORF[i] = groups->grpnr[egcORFIT][ag];
+ }
+
+ if (md->cU1)
+ {
+ md->cU1[i] = groups->grpnr[egcUser1][ag];
+ }
+ if (md->cU2)
+ {
+ md->cU2[i] = groups->grpnr[egcUser2][ag];
+ }
+
+ if (ir->bQMMM)
+ {
+ if (groups->grpnr[egcQMMM] == 0 ||
+ groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1)
+ {
+ md->bQM[i] = TRUE;
+ }
+ else
+ {
+ md->bQM[i] = FALSE;
+ }
+ }
+ /* Initialize AdResS weighting functions to adressw */
+ if (ir->bAdress)
+ {
+ md->wf[i] = 1.0;
+ /* if no tf table groups specified, use default table */
+ md->tf_table_index[i] = DEFAULT_TF_TABLE;
+ if (ir->adress->n_tf_grps > 0)
+ {
+ /* if tf table groups specified, tf is only applied to thoose energy groups*/
+ md->tf_table_index[i] = NO_TF_TABLE;
+ /* check wether atom is in one of the relevant energy groups and assign a table index */
+ for (g = 0; g < ir->adress->n_tf_grps; g++)
+ {
+ if (md->cENER[i] == ir->adress->tf_table_index[g])
+ {
+ md->tf_table_index[i] = g;
+ }
}
}
}
}
- }
- gmx_mtop_atomlookup_destroy(alook);
+ gmx_mtop_atomlookup_destroy(alook);
- md->start = start;
- md->homenr = homenr;
- md->lambda = 0;
+ md->homenr = homenr;
+ md->lambda = 0;
}
-void update_mdatoms(t_mdatoms *md,real lambda)
+void update_mdatoms(t_mdatoms *md, real lambda)
{
- int al,end;
- real L1=1.0-lambda;
-
- end=md->nr;
-
- if (md->nMassPerturbed) {
- for(al=0; (al<end); al++) {
- if (md->bPerturbed[al]) {
- md->massT[al] = L1*md->massA[al]+ lambda*md->massB[al];
- if (md->invmass[al] > 1.1*ALMOST_ZERO)
- md->invmass[al] = 1.0/md->massT[al];
- }
+ int al, end;
+ real L1 = 1.0-lambda;
+
+ end = md->nr;
+
+ if (md->nMassPerturbed)
+ {
+ for (al = 0; (al < end); al++)
+ {
+ if (md->bPerturbed[al])
+ {
+ md->massT[al] = L1*md->massA[al]+ lambda*md->massB[al];
+ if (md->invmass[al] > 1.1*ALMOST_ZERO)
+ {
+ md->invmass[al] = 1.0/md->massT[al];
+ }
+ }
+ }
+ md->tmass = L1*md->tmassA + lambda*md->tmassB;
+ }
+ else
+ {
+ md->tmass = md->tmassA;
}
- md->tmass = L1*md->tmassA + lambda*md->tmassB;
- } else {
- md->tmass = md->tmassA;
- }
- md->lambda = lambda;
+ md->lambda = lambda;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff