-/* -*- 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
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
* 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.
+ *
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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
+ * official version at http://www.gromacs.org.
+ *
* 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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+ * the research papers on the package. Check out http://www.gromacs.org.
*/
/* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
+#include "gmxpre.h"
#include <math.h>
-#include "macros.h"
-#include "main.h"
-#include "smalloc.h"
-#include "futil.h"
-#include "tgroup.h"
-#include "vec.h"
-#include "network.h"
-#include "smalloc.h"
-#include "update.h"
-#include "rbin.h"
-#include "mtop_util.h"
-
-static void init_grptcstat(int ngtc,t_grp_tcstat tcstat[])
-{
- int i,j;
-
- for(i=0; (i<ngtc); i++) {
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/tgroup.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/rbin.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+
+static void init_grptcstat(int ngtc, t_grp_tcstat tcstat[])
+{
+ int i, j;
+
+ for (i = 0; (i < ngtc); i++)
+ {
tcstat[i].T = 0;
clear_mat(tcstat[i].ekinh);
clear_mat(tcstat[i].ekinh_old);
}
}
-static void init_grpstat(FILE *log,
- gmx_mtop_t *mtop,int ngacc,t_grp_acc gstat[])
+static void init_grpstat(gmx_mtop_t *mtop, int ngacc, t_grp_acc gstat[])
{
- gmx_groups_t *groups;
+ gmx_groups_t *groups;
gmx_mtop_atomloop_all_t aloop;
- int i,grp;
- t_atom *atom;
-
- if (ngacc > 0) {
+ int i, grp;
+ t_atom *atom;
+
+ if (ngacc > 0)
+ {
groups = &mtop->groups;
- aloop = gmx_mtop_atomloop_all_init(mtop);
- while (gmx_mtop_atomloop_all_next(aloop,&i,&atom))
+ aloop = gmx_mtop_atomloop_all_init(mtop);
+ while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
- grp = ggrpnr(groups,egcACC,i);
+ grp = ggrpnr(groups, egcACC, i);
if ((grp < 0) && (grp >= ngacc))
{
gmx_incons("Input for acceleration groups wrong");
}
}
-void init_ekindata(FILE *log,gmx_mtop_t *mtop,t_grpopts *opts,
+void init_ekindata(FILE gmx_unused *log, gmx_mtop_t *mtop, t_grpopts *opts,
gmx_ekindata_t *ekind)
{
- int i;
+ int i;
+ int nthread, thread;
#ifdef DEBUG
- fprintf(log,"ngtc: %d, ngacc: %d, ngener: %d\n",opts->ngtc,opts->ngacc,
- opts->ngener);
+ fprintf(log, "ngtc: %d, ngacc: %d, ngener: %d\n", opts->ngtc, opts->ngacc,
+ opts->ngener);
#endif
- /* bNEMD tells if we should remove remove the COM velocity
- * from the velocities during velocity scaling in T-coupling.
- * Turn this on when we have multiple acceleration groups
- * or one accelerated group.
- */
- ekind->bNEMD = (opts->ngacc > 1 || norm(opts->acc[0]) > 0);
-
- ekind->ngtc = opts->ngtc;
- snew(ekind->tcstat,opts->ngtc);
- init_grptcstat(opts->ngtc,ekind->tcstat);
- /* Set Berendsen tcoupl lambda's to 1,
- * so runs without Berendsen coupling are not affected.
- */
- for(i=0; i<opts->ngtc; i++)
- {
- ekind->tcstat[i].lambda = 1.0;
- ekind->tcstat[i].vscale_nhc = 1.0;
- ekind->tcstat[i].ekinscaleh_nhc = 1.0;
- ekind->tcstat[i].ekinscalef_nhc = 1.0;
- }
-
- ekind->ngacc = opts->ngacc;
- snew(ekind->grpstat,opts->ngacc);
- init_grpstat(log,mtop,opts->ngacc,ekind->grpstat);
+ /* bNEMD tells if we should remove remove the COM velocity
+ * from the velocities during velocity scaling in T-coupling.
+ * Turn this on when we have multiple acceleration groups
+ * or one accelerated group.
+ */
+ ekind->bNEMD = (opts->ngacc > 1 || norm(opts->acc[0]) > 0);
+
+ ekind->ngtc = opts->ngtc;
+ snew(ekind->tcstat, opts->ngtc);
+ init_grptcstat(opts->ngtc, ekind->tcstat);
+ /* Set Berendsen tcoupl lambda's to 1,
+ * so runs without Berendsen coupling are not affected.
+ */
+ for (i = 0; i < opts->ngtc; i++)
+ {
+ ekind->tcstat[i].lambda = 1.0;
+ ekind->tcstat[i].vscale_nhc = 1.0;
+ ekind->tcstat[i].ekinscaleh_nhc = 1.0;
+ ekind->tcstat[i].ekinscalef_nhc = 1.0;
+ }
+
+ nthread = gmx_omp_nthreads_get(emntUpdate);
+
+ snew(ekind->ekin_work_alloc, nthread);
+ snew(ekind->ekin_work, nthread);
+ snew(ekind->dekindl_work, nthread);
+#pragma omp parallel for num_threads(nthread) schedule(static)
+ for (thread = 0; thread < nthread; thread++)
+ {
+#define EKIN_WORK_BUFFER_SIZE 2
+ /* Allocate 2 extra elements on both sides, so in single
+ * precision we have
+ * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
+ * buffer on both sides to avoid cache pollution.
+ */
+ snew(ekind->ekin_work_alloc[thread], ekind->ngtc+2*EKIN_WORK_BUFFER_SIZE);
+ ekind->ekin_work[thread] = ekind->ekin_work_alloc[thread] + EKIN_WORK_BUFFER_SIZE;
+ /* Nasty hack so we can have the per-thread accumulation
+ * variable for dekindl in the same thread-local cache lines
+ * as the per-thread accumulation tensors for ekin[fh],
+ * because they are accumulated in the same loop. */
+ ekind->dekindl_work[thread] = &(ekind->ekin_work[thread][ekind->ngtc][0][0]);
+#undef EKIN_WORK_BUFFER_SIZE
+ }
+
+ ekind->ngacc = opts->ngacc;
+ snew(ekind->grpstat, opts->ngacc);
+ init_grpstat(mtop, opts->ngacc, ekind->grpstat);
}
-void accumulate_u(t_commrec *cr,t_grpopts *opts,gmx_ekindata_t *ekind)
+void accumulate_u(t_commrec *cr, t_grpopts *opts, gmx_ekindata_t *ekind)
{
/* This routine will only be called when it's necessary */
t_bin *rb;
- int g;
-
+ int g;
+
rb = mk_bin();
-
- for(g=0; (g<opts->ngacc); g++)
+
+ for (g = 0; (g < opts->ngacc); g++)
{
- add_binr(rb,DIM,ekind->grpstat[g].u);
+ add_binr(rb, DIM, ekind->grpstat[g].u);
}
- sum_bin(rb,cr);
-
- for(g=0; (g<opts->ngacc); g++)
+ sum_bin(rb, cr);
+
+ for (g = 0; (g < opts->ngacc); g++)
{
- extract_binr(rb,DIM*g,DIM,ekind->grpstat[g].u);
+ extract_binr(rb, DIM*g, DIM, ekind->grpstat[g].u);
}
destroy_bin(rb);
-}
+}
/* I don't think accumulate_ekin is used anymore? */
#if 0
-static void accumulate_ekin(t_commrec *cr,t_grpopts *opts,
- gmx_ekindata_t *ekind)
+static void accumulate_ekin(t_commrec *cr, t_grpopts *opts,
+ gmx_ekindata_t *ekind)
{
int g;
- if(PAR(cr))
+ if (PAR(cr))
{
- for(g=0; (g<opts->ngtc); g++)
+ for (g = 0; (g < opts->ngtc); g++)
{
- gmx_sum(DIM*DIM,ekind->tcstat[g].ekinf[0],cr);
+ gmx_sum(DIM*DIM, ekind->tcstat[g].ekinf[0], cr);
}
}
-}
-#endif
+}
+#endif
-void update_ekindata(int start,int homenr,gmx_ekindata_t *ekind,
- t_grpopts *opts,rvec v[],t_mdatoms *md,real lambda)
+void update_ekindata(int start, int homenr, gmx_ekindata_t *ekind,
+ t_grpopts *opts, rvec v[], t_mdatoms *md, real lambda)
{
- int d,g,n;
- real mv;
-
- /* calculate mean velocities at whole timestep */
- for(g=0; (g<opts->ngtc); g++) {
- ekind->tcstat[g].T = 0;
- }
-
- if (ekind->bNEMD) {
- for (g=0; (g<opts->ngacc); g++)
- clear_rvec(ekind->grpstat[g].u);
-
- g = 0;
- for(n=start; (n<start+homenr); n++) {
- if (md->cACC)
- g = md->cACC[n];
- for(d=0; (d<DIM);d++) {
- mv = md->massT[n]*v[n][d];
- ekind->grpstat[g].u[d] += mv;
- }
+ int d, g, n;
+ real mv;
+
+ /* calculate mean velocities at whole timestep */
+ for (g = 0; (g < opts->ngtc); g++)
+ {
+ ekind->tcstat[g].T = 0;
}
- for (g=0; (g < opts->ngacc); g++) {
- for(d=0; (d<DIM);d++) {
- ekind->grpstat[g].u[d] /=
- (1-lambda)*ekind->grpstat[g].mA + lambda*ekind->grpstat[g].mB;
- }
+ if (ekind->bNEMD)
+ {
+ for (g = 0; (g < opts->ngacc); g++)
+ {
+ clear_rvec(ekind->grpstat[g].u);
+ }
+
+ g = 0;
+ for (n = start; (n < start+homenr); n++)
+ {
+ if (md->cACC)
+ {
+ g = md->cACC[n];
+ }
+ for (d = 0; (d < DIM); d++)
+ {
+ mv = md->massT[n]*v[n][d];
+ ekind->grpstat[g].u[d] += mv;
+ }
+ }
+
+ for (g = 0; (g < opts->ngacc); g++)
+ {
+ for (d = 0; (d < DIM); d++)
+ {
+ ekind->grpstat[g].u[d] /=
+ (1-lambda)*ekind->grpstat[g].mA + lambda*ekind->grpstat[g].mB;
+ }
+ }
}
- }
}
-real sum_ekin(t_grpopts *opts,gmx_ekindata_t *ekind,real *dekindlambda,
- gmx_bool bEkinAveVel, gmx_bool bSaveEkinOld, gmx_bool bScaleEkin)
+real sum_ekin(t_grpopts *opts, gmx_ekindata_t *ekind, real *dekindlambda,
+ gmx_bool bEkinAveVel, gmx_bool bScaleEkin)
{
- int i,j,m,ngtc;
- real T,ek;
+ int i, j, m, ngtc;
+ real T, ek;
t_grp_tcstat *tcstat;
- real nrdf,nd,*ndf;
-
+ real nrdf, nd, *ndf;
+
ngtc = opts->ngtc;
ndf = opts->nrdf;
-
- T = 0;
+
+ T = 0;
nrdf = 0;
clear_mat(ekind->ekin);
- for(i=0; (i<ngtc); i++)
+ for (i = 0; (i < ngtc); i++)
{
- nd = ndf[i];
+ nd = ndf[i];
tcstat = &ekind->tcstat[i];
/* Sometimes a group does not have degrees of freedom, e.g.
* when it consists of shells and virtual sites, then we just
* set the temperatue to 0 and also neglect the kinetic
* energy, which should be zero anyway.
*/
-
- if (nd > 0) {
+
+ if (nd > 0)
+ {
if (bEkinAveVel)
{
if (!bScaleEkin)
{
/* in this case, kinetic energy is from the current velocities already */
- msmul(tcstat->ekinf,tcstat->ekinscalef_nhc,tcstat->ekinf);
+ msmul(tcstat->ekinf, tcstat->ekinscalef_nhc, tcstat->ekinf);
}
- }
+ }
else
-
{
/* Calculate the full step Ekin as the average of the half steps */
- for(j=0; (j<DIM); j++)
+ for (j = 0; (j < DIM); j++)
{
- for(m=0; (m<DIM); m++)
+ for (m = 0; (m < DIM); m++)
{
tcstat->ekinf[j][m] =
0.5*(tcstat->ekinh[j][m]*tcstat->ekinscaleh_nhc + tcstat->ekinh_old[j][m]);
}
}
}
- m_add(tcstat->ekinf,ekind->ekin,ekind->ekin);
-
- tcstat->Th = calc_temp(trace(tcstat->ekinh),nd);
- tcstat->T = calc_temp(trace(tcstat->ekinf),nd);
+ m_add(tcstat->ekinf, ekind->ekin, ekind->ekin);
+
+ tcstat->Th = calc_temp(trace(tcstat->ekinh), nd);
+ tcstat->T = calc_temp(trace(tcstat->ekinf), nd);
/* after the scaling factors have been multiplied in, we can remove them */
- if (bEkinAveVel)
+ if (bEkinAveVel)
{
tcstat->ekinscalef_nhc = 1.0;
- }
- else
+ }
+ else
{
tcstat->ekinscaleh_nhc = 1.0;
}
}
- else
+ else
{
tcstat->T = 0;
tcstat->Th = 0;
}
if (nrdf > 0)
{
- T/=nrdf;
+ T /= nrdf;
}
- if (dekindlambda)
+ if (dekindlambda)
{
- *dekindlambda = 0.5*(ekind->dekindl + ekind->dekindl_old);
+ if (bEkinAveVel)
+ {
+ *dekindlambda = ekind->dekindl;
+ }
+ else
+ {
+ *dekindlambda = 0.5*(ekind->dekindl + ekind->dekindl_old);
+ }
}
return T;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff