-/* -*- 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.
- * 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
+ * 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>
#include <time.h>
#include <math.h>
#include "sysstuff.h"
-#include "string2.h"
+#include "gromacs/utility/cstringutil.h"
#include "network.h"
-#include "confio.h"
-#include "copyrite.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
#include "nrnb.h"
#include "main.h"
#include "force.h"
#include "macros.h"
-#include "random.h"
#include "names.h"
#include "gmx_fatal.h"
#include "txtdump.h"
#include "update.h"
#include "constr.h"
#include "vec.h"
-#include "statutil.h"
#include "tgroup.h"
#include "mdebin.h"
#include "vsite.h"
#include "force.h"
#include "mdrun.h"
#include "md_support.h"
+#include "sim_util.h"
#include "domdec.h"
-#include "partdec.h"
-#include "trnio.h"
#include "mdatoms.h"
#include "ns.h"
-#include "gmx_wallcycle.h"
#include "mtop_util.h"
-#include "gmxfio.h"
#include "pme.h"
#include "bondf.h"
#include "gmx_omp_nthreads.h"
+#include "md_logging.h"
-
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/trajectory_writing.h"
#include "gromacs/linearalgebra/mtxio.h"
#include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/imd/imd.h"
typedef struct {
- t_state s;
- rvec *f;
- real epot;
- real fnorm;
- real fmax;
- int a_fmax;
+ t_state s;
+ rvec *f;
+ real epot;
+ real fnorm;
+ real fmax;
+ int a_fmax;
} em_state_t;
static em_state_t *init_em_state()
{
- em_state_t *ems;
+ em_state_t *ems;
- snew(ems,1);
+ snew(ems, 1);
- /* does this need to be here? Should the array be declared differently (staticaly)in the state definition? */
- snew(ems->s.lambda,efptNR);
+ /* does this need to be here? Should the array be declared differently (staticaly)in the state definition? */
+ snew(ems->s.lambda, efptNR);
- return ems;
+ return ems;
}
-static void print_em_start(FILE *fplog,t_commrec *cr,gmx_runtime_t *runtime,
- gmx_wallcycle_t wcycle,
- const char *name)
+static void print_em_start(FILE *fplog,
+ t_commrec *cr,
+ gmx_walltime_accounting_t walltime_accounting,
+ gmx_wallcycle_t wcycle,
+ const char *name)
{
- char buf[STRLEN];
-
- runtime_start(runtime);
-
- sprintf(buf,"Started %s",name);
- print_date_and_time(fplog,cr->nodeid,buf,NULL);
-
- wallcycle_start(wcycle,ewcRUN);
+ walltime_accounting_start(walltime_accounting);
+ wallcycle_start(wcycle, ewcRUN);
+ print_start(fplog, cr, walltime_accounting, name);
}
-static void em_time_end(FILE *fplog,t_commrec *cr,gmx_runtime_t *runtime,
- gmx_wallcycle_t wcycle)
+static void em_time_end(gmx_walltime_accounting_t walltime_accounting,
+ gmx_wallcycle_t wcycle)
{
- wallcycle_stop(wcycle,ewcRUN);
+ wallcycle_stop(wcycle, ewcRUN);
- runtime_end(runtime);
+ walltime_accounting_end(walltime_accounting);
}
-static void sp_header(FILE *out,const char *minimizer,real ftol,int nsteps)
+static void sp_header(FILE *out, const char *minimizer, real ftol, int nsteps)
{
- fprintf(out,"\n");
- fprintf(out,"%s:\n",minimizer);
- fprintf(out," Tolerance (Fmax) = %12.5e\n",ftol);
- fprintf(out," Number of steps = %12d\n",nsteps);
+ fprintf(out, "\n");
+ fprintf(out, "%s:\n", minimizer);
+ fprintf(out, " Tolerance (Fmax) = %12.5e\n", ftol);
+ fprintf(out, " Number of steps = %12d\n", nsteps);
}
-static void warn_step(FILE *fp,real ftol,gmx_bool bLastStep,gmx_bool bConstrain)
+static void warn_step(FILE *fp, real ftol, gmx_bool bLastStep, gmx_bool bConstrain)
{
char buffer[2048];
if (bLastStep)
{
sprintf(buffer,
- "\nEnergy minimization reached the maximum number"
- "of steps before the forces reached the requested"
- "precision Fmax < %g.\n",ftol);
+ "\nEnergy minimization reached the maximum number "
+ "of steps before the forces reached the requested "
+ "precision Fmax < %g.\n", ftol);
}
else
{
sprintf(buffer,
- "\nEnergy minimization has stopped, but the forces have"
- "not converged to the requested precision Fmax < %g (which"
- "may not be possible for your system). It stopped"
- "because the algorithm tried to make a new step whose size"
- "was too small, or there was no change in the energy since"
- "last step. Either way, we regard the minimization as"
- "converged to within the available machine precision,"
+ "\nEnergy minimization has stopped, but the forces have "
+ "not converged to the requested precision Fmax < %g (which "
+ "may not be possible for your system). It stopped "
+ "because the algorithm tried to make a new step whose size "
+ "was too small, or there was no change in the energy since "
+ "last step. Either way, we regard the minimization as "
+ "converged to within the available machine precision, "
"given your starting configuration and EM parameters.\n%s%s",
ftol,
- sizeof(real)<sizeof(double) ?
- "\nDouble precision normally gives you higher accuracy, but"
- "this is often not needed for preparing to run molecular"
+ sizeof(real) < sizeof(double) ?
+ "\nDouble precision normally gives you higher accuracy, but "
+ "this is often not needed for preparing to run molecular "
"dynamics.\n" :
"",
bConstrain ?
-static void print_converged(FILE *fp,const char *alg,real ftol,
- gmx_large_int_t count,gmx_bool bDone,gmx_large_int_t nsteps,
- real epot,real fmax, int nfmax, real fnorm)
+static void print_converged(FILE *fp, const char *alg, real ftol,
+ gmx_int64_t count, gmx_bool bDone, gmx_int64_t nsteps,
+ real epot, real fmax, int nfmax, real fnorm)
{
- char buf[STEPSTRSIZE];
-
- if (bDone)
- fprintf(fp,"\n%s converged to Fmax < %g in %s steps\n",
- alg,ftol,gmx_step_str(count,buf));
- else if(count<nsteps)
- fprintf(fp,"\n%s converged to machine precision in %s steps,\n"
- "but did not reach the requested Fmax < %g.\n",
- alg,gmx_step_str(count,buf),ftol);
- else
- fprintf(fp,"\n%s did not converge to Fmax < %g in %s steps.\n",
- alg,ftol,gmx_step_str(count,buf));
+ char buf[STEPSTRSIZE];
+
+ if (bDone)
+ {
+ fprintf(fp, "\n%s converged to Fmax < %g in %s steps\n",
+ alg, ftol, gmx_step_str(count, buf));
+ }
+ else if (count < nsteps)
+ {
+ fprintf(fp, "\n%s converged to machine precision in %s steps,\n"
+ "but did not reach the requested Fmax < %g.\n",
+ alg, gmx_step_str(count, buf), ftol);
+ }
+ else
+ {
+ fprintf(fp, "\n%s did not converge to Fmax < %g in %s steps.\n",
+ alg, ftol, gmx_step_str(count, buf));
+ }
#ifdef GMX_DOUBLE
- fprintf(fp,"Potential Energy = %21.14e\n",epot);
- fprintf(fp,"Maximum force = %21.14e on atom %d\n",fmax,nfmax+1);
- fprintf(fp,"Norm of force = %21.14e\n",fnorm);
+ fprintf(fp, "Potential Energy = %21.14e\n", epot);
+ fprintf(fp, "Maximum force = %21.14e on atom %d\n", fmax, nfmax+1);
+ fprintf(fp, "Norm of force = %21.14e\n", fnorm);
#else
- fprintf(fp,"Potential Energy = %14.7e\n",epot);
- fprintf(fp,"Maximum force = %14.7e on atom %d\n",fmax,nfmax+1);
- fprintf(fp,"Norm of force = %14.7e\n",fnorm);
+ fprintf(fp, "Potential Energy = %14.7e\n", epot);
+ fprintf(fp, "Maximum force = %14.7e on atom %d\n", fmax, nfmax+1);
+ fprintf(fp, "Norm of force = %14.7e\n", fnorm);
#endif
}
static void get_f_norm_max(t_commrec *cr,
- t_grpopts *opts,t_mdatoms *mdatoms,rvec *f,
- real *fnorm,real *fmax,int *a_fmax)
+ t_grpopts *opts, t_mdatoms *mdatoms, rvec *f,
+ real *fnorm, real *fmax, int *a_fmax)
{
- double fnorm2,*sum;
- real fmax2,fmax2_0,fam;
- int la_max,a_max,start,end,i,m,gf;
-
- /* This routine finds the largest force and returns it.
- * On parallel machines the global max is taken.
- */
- fnorm2 = 0;
- fmax2 = 0;
- la_max = -1;
- gf = 0;
- start = mdatoms->start;
- end = mdatoms->homenr + start;
- if (mdatoms->cFREEZE) {
- for(i=start; i<end; i++) {
- gf = mdatoms->cFREEZE[i];
- fam = 0;
- for(m=0; m<DIM; m++)
- if (!opts->nFreeze[gf][m])
- fam += sqr(f[i][m]);
- fnorm2 += fam;
- if (fam > fmax2) {
- fmax2 = fam;
- la_max = i;
- }
- }
- } else {
- for(i=start; i<end; i++) {
- fam = norm2(f[i]);
- fnorm2 += fam;
- if (fam > fmax2) {
- fmax2 = fam;
- la_max = i;
- }
- }
- }
-
- if (la_max >= 0 && DOMAINDECOMP(cr)) {
- a_max = cr->dd->gatindex[la_max];
- } else {
- a_max = la_max;
- }
- if (PAR(cr)) {
- snew(sum,2*cr->nnodes+1);
- sum[2*cr->nodeid] = fmax2;
- sum[2*cr->nodeid+1] = a_max;
- sum[2*cr->nnodes] = fnorm2;
- gmx_sumd(2*cr->nnodes+1,sum,cr);
- fnorm2 = sum[2*cr->nnodes];
- /* Determine the global maximum */
- for(i=0; i<cr->nnodes; i++) {
- if (sum[2*i] > fmax2) {
- fmax2 = sum[2*i];
- a_max = (int)(sum[2*i+1] + 0.5);
- }
- }
- sfree(sum);
- }
-
- if (fnorm)
- *fnorm = sqrt(fnorm2);
- if (fmax)
- *fmax = sqrt(fmax2);
- if (a_fmax)
- *a_fmax = a_max;
+ double fnorm2, *sum;
+ real fmax2, fmax2_0, fam;
+ int la_max, a_max, start, end, i, m, gf;
+
+ /* This routine finds the largest force and returns it.
+ * On parallel machines the global max is taken.
+ */
+ fnorm2 = 0;
+ fmax2 = 0;
+ la_max = -1;
+ gf = 0;
+ start = 0;
+ end = mdatoms->homenr;
+ if (mdatoms->cFREEZE)
+ {
+ for (i = start; i < end; i++)
+ {
+ gf = mdatoms->cFREEZE[i];
+ fam = 0;
+ for (m = 0; m < DIM; m++)
+ {
+ if (!opts->nFreeze[gf][m])
+ {
+ fam += sqr(f[i][m]);
+ }
+ }
+ fnorm2 += fam;
+ if (fam > fmax2)
+ {
+ fmax2 = fam;
+ la_max = i;
+ }
+ }
+ }
+ else
+ {
+ for (i = start; i < end; i++)
+ {
+ fam = norm2(f[i]);
+ fnorm2 += fam;
+ if (fam > fmax2)
+ {
+ fmax2 = fam;
+ la_max = i;
+ }
+ }
+ }
+
+ if (la_max >= 0 && DOMAINDECOMP(cr))
+ {
+ a_max = cr->dd->gatindex[la_max];
+ }
+ else
+ {
+ a_max = la_max;
+ }
+ if (PAR(cr))
+ {
+ snew(sum, 2*cr->nnodes+1);
+ sum[2*cr->nodeid] = fmax2;
+ sum[2*cr->nodeid+1] = a_max;
+ sum[2*cr->nnodes] = fnorm2;
+ gmx_sumd(2*cr->nnodes+1, sum, cr);
+ fnorm2 = sum[2*cr->nnodes];
+ /* Determine the global maximum */
+ for (i = 0; i < cr->nnodes; i++)
+ {
+ if (sum[2*i] > fmax2)
+ {
+ fmax2 = sum[2*i];
+ a_max = (int)(sum[2*i+1] + 0.5);
+ }
+ }
+ sfree(sum);
+ }
+
+ if (fnorm)
+ {
+ *fnorm = sqrt(fnorm2);
+ }
+ if (fmax)
+ {
+ *fmax = sqrt(fmax2);
+ }
+ if (a_fmax)
+ {
+ *a_fmax = a_max;
+ }
}
static void get_state_f_norm_max(t_commrec *cr,
- t_grpopts *opts,t_mdatoms *mdatoms,
- em_state_t *ems)
+ t_grpopts *opts, t_mdatoms *mdatoms,
+ em_state_t *ems)
{
- get_f_norm_max(cr,opts,mdatoms,ems->f,&ems->fnorm,&ems->fmax,&ems->a_fmax);
+ get_f_norm_max(cr, opts, mdatoms, ems->f, &ems->fnorm, &ems->fmax, &ems->a_fmax);
}
-void init_em(FILE *fplog,const char *title,
- t_commrec *cr,t_inputrec *ir,
- t_state *state_global,gmx_mtop_t *top_global,
- em_state_t *ems,gmx_localtop_t **top,
- rvec **f,rvec **f_global,
- t_nrnb *nrnb,rvec mu_tot,
- t_forcerec *fr,gmx_enerdata_t **enerd,
- t_graph **graph,t_mdatoms *mdatoms,gmx_global_stat_t *gstat,
- gmx_vsite_t *vsite,gmx_constr_t constr,
- int nfile,const t_filenm fnm[],
- gmx_mdoutf_t **outf,t_mdebin **mdebin)
+void init_em(FILE *fplog, const char *title,
+ t_commrec *cr, t_inputrec *ir,
+ t_state *state_global, gmx_mtop_t *top_global,
+ em_state_t *ems, gmx_localtop_t **top,
+ rvec **f, rvec **f_global,
+ t_nrnb *nrnb, rvec mu_tot,
+ t_forcerec *fr, gmx_enerdata_t **enerd,
+ t_graph **graph, t_mdatoms *mdatoms, gmx_global_stat_t *gstat,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int nfile, const t_filenm fnm[],
+ gmx_mdoutf_t *outf, t_mdebin **mdebin,
+ int imdport, unsigned long gmx_unused Flags,
+ gmx_wallcycle_t wcycle)
{
- int start,homenr,i;
- real dvdlambda;
+ int i;
+ real dvdl_constr;
if (fplog)
{
- fprintf(fplog,"Initiating %s\n",title);
+ fprintf(fplog, "Initiating %s\n", title);
}
state_global->ngtc = 0;
/* Initialize lambda variables */
- initialize_lambdas(fplog,ir,&(state_global->fep_state),state_global->lambda,NULL);
+ initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, NULL);
init_nrnb(nrnb);
+ /* Interactive molecular dynamics */
+ init_IMD(ir, cr, top_global, fplog, 1, state_global->x,
+ nfile, fnm, NULL, imdport, Flags);
+
if (DOMAINDECOMP(cr))
{
*top = dd_init_local_top(top_global);
- dd_init_local_state(cr->dd,state_global,&ems->s);
+ dd_init_local_state(cr->dd, state_global, &ems->s);
*f = NULL;
/* Distribute the charge groups over the nodes from the master node */
- dd_partition_system(fplog,ir->init_step,cr,TRUE,1,
- state_global,top_global,ir,
- &ems->s,&ems->f,mdatoms,*top,
- fr,vsite,NULL,constr,
- nrnb,NULL,FALSE);
- dd_store_state(cr->dd,&ems->s);
+ dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
+ state_global, top_global, ir,
+ &ems->s, &ems->f, mdatoms, *top,
+ fr, vsite, NULL, constr,
+ nrnb, NULL, FALSE);
+ dd_store_state(cr->dd, &ems->s);
if (ir->nstfout)
{
- snew(*f_global,top_global->natoms);
+ snew(*f_global, top_global->natoms);
}
else
{
}
else
{
- snew(*f,top_global->natoms);
+ snew(*f, top_global->natoms);
/* Just copy the state */
ems->s = *state_global;
- snew(ems->s.x,ems->s.nalloc);
- snew(ems->f,ems->s.nalloc);
- for(i=0; i<state_global->natoms; i++)
+ snew(ems->s.x, ems->s.nalloc);
+ snew(ems->f, ems->s.nalloc);
+ for (i = 0; i < state_global->natoms; i++)
{
- copy_rvec(state_global->x[i],ems->s.x[i]);
+ copy_rvec(state_global->x[i], ems->s.x[i]);
}
- copy_mat(state_global->box,ems->s.box);
-
- if (PAR(cr) && ir->eI != eiNM)
- {
- /* Initialize the particle decomposition and split the topology */
- *top = split_system(fplog,top_global,ir,cr);
+ copy_mat(state_global->box, ems->s.box);
- pd_cg_range(cr,&fr->cg0,&fr->hcg);
- }
- else
- {
- *top = gmx_mtop_generate_local_top(top_global,ir);
- }
+ *top = gmx_mtop_generate_local_top(top_global, ir);
*f_global = *f;
- forcerec_set_excl_load(fr,*top,cr);
+ forcerec_set_excl_load(fr, *top);
+
+ setup_bonded_threading(fr, &(*top)->idef);
- init_bonded_thread_force_reduction(fr,&(*top)->idef);
-
if (ir->ePBC != epbcNONE && !fr->bMolPBC)
{
- *graph = mk_graph(fplog,&((*top)->idef),0,top_global->natoms,FALSE,FALSE);
+ *graph = mk_graph(fplog, &((*top)->idef), 0, top_global->natoms, FALSE, FALSE);
}
else
{
*graph = NULL;
}
- if (PARTDECOMP(cr))
- {
- pd_at_range(cr,&start,&homenr);
- homenr -= start;
- }
- else
- {
- start = 0;
- homenr = top_global->natoms;
- }
- atoms2md(top_global,ir,0,NULL,start,homenr,mdatoms);
- update_mdatoms(mdatoms,state_global->lambda[efptFEP]);
+ atoms2md(top_global, ir, 0, NULL, top_global->natoms, mdatoms);
+ update_mdatoms(mdatoms, state_global->lambda[efptFEP]);
if (vsite)
{
- set_vsite_top(vsite,*top,mdatoms,cr);
+ set_vsite_top(vsite, *top, mdatoms, cr);
}
}
if (constr)
{
if (ir->eConstrAlg == econtSHAKE &&
- gmx_mtop_ftype_count(top_global,F_CONSTR) > 0)
+ gmx_mtop_ftype_count(top_global, F_CONSTR) > 0)
{
- gmx_fatal(FARGS,"Can not do energy minimization with %s, use %s\n",
- econstr_names[econtSHAKE],econstr_names[econtLINCS]);
+ gmx_fatal(FARGS, "Can not do energy minimization with %s, use %s\n",
+ econstr_names[econtSHAKE], econstr_names[econtLINCS]);
}
if (!DOMAINDECOMP(cr))
{
- set_constraints(constr,*top,ir,mdatoms,cr);
+ set_constraints(constr, *top, ir, mdatoms, cr);
}
if (!ir->bContinuation)
{
/* Constrain the starting coordinates */
- dvdlambda=0;
- constrain(PAR(cr) ? NULL : fplog,TRUE,TRUE,constr,&(*top)->idef,
- ir,NULL,cr,-1,0,mdatoms,
- ems->s.x,ems->s.x,NULL,fr->bMolPBC,ems->s.box,
- ems->s.lambda[efptFEP],&dvdlambda,
- NULL,NULL,nrnb,econqCoord,FALSE,0,0);
+ dvdl_constr = 0;
+ constrain(PAR(cr) ? NULL : fplog, TRUE, TRUE, constr, &(*top)->idef,
+ ir, NULL, cr, -1, 0, 1.0, mdatoms,
+ ems->s.x, ems->s.x, NULL, fr->bMolPBC, ems->s.box,
+ ems->s.lambda[efptFEP], &dvdl_constr,
+ NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
}
}
*gstat = global_stat_init(ir);
}
- *outf = init_mdoutf(nfile,fnm,0,cr,ir,NULL);
+ *outf = init_mdoutf(fplog, nfile, fnm, 0, cr, ir, top_global, NULL, wcycle);
- snew(*enerd,1);
- init_enerdata(top_global->groups.grps[egcENER].nr,ir->fepvals->n_lambda,
+ snew(*enerd, 1);
+ init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
*enerd);
if (mdebin != NULL)
{
/* Init bin for energy stuff */
- *mdebin = init_mdebin((*outf)->fp_ene,top_global,ir,NULL);
+ *mdebin = init_mdebin(mdoutf_get_fp_ene(*outf), top_global, ir, NULL);
}
clear_rvec(mu_tot);
- calc_shifts(ems->s.box,fr->shift_vec);
+ calc_shifts(ems->s.box, fr->shift_vec);
}
-static void finish_em(FILE *fplog,t_commrec *cr,gmx_mdoutf_t *outf,
- gmx_runtime_t *runtime,gmx_wallcycle_t wcycle)
+static void finish_em(t_commrec *cr, gmx_mdoutf_t outf,
+ gmx_walltime_accounting_t walltime_accounting,
+ gmx_wallcycle_t wcycle)
{
- if (!(cr->duty & DUTY_PME)) {
- /* Tell the PME only node to finish */
- gmx_pme_send_finish(cr);
- }
+ if (!(cr->duty & DUTY_PME))
+ {
+ /* Tell the PME only node to finish */
+ gmx_pme_send_finish(cr);
+ }
- done_mdoutf(outf);
+ done_mdoutf(outf);
- em_time_end(fplog,cr,runtime,wcycle);
+ em_time_end(walltime_accounting, wcycle);
}
-static void swap_em_state(em_state_t *ems1,em_state_t *ems2)
+static void swap_em_state(em_state_t *ems1, em_state_t *ems2)
{
- em_state_t tmp;
+ em_state_t tmp;
- tmp = *ems1;
- *ems1 = *ems2;
- *ems2 = tmp;
+ tmp = *ems1;
+ *ems1 = *ems2;
+ *ems2 = tmp;
}
-static void copy_em_coords(em_state_t *ems,t_state *state)
+static void copy_em_coords(em_state_t *ems, t_state *state)
{
int i;
- for(i=0; (i<state->natoms); i++)
+ for (i = 0; (i < state->natoms); i++)
{
- copy_rvec(ems->s.x[i],state->x[i]);
+ copy_rvec(ems->s.x[i], state->x[i]);
}
}
-static void write_em_traj(FILE *fplog,t_commrec *cr,
- gmx_mdoutf_t *outf,
- gmx_bool bX,gmx_bool bF,const char *confout,
+static void write_em_traj(FILE *fplog, t_commrec *cr,
+ gmx_mdoutf_t outf,
+ gmx_bool bX, gmx_bool bF, const char *confout,
gmx_mtop_t *top_global,
- t_inputrec *ir,gmx_large_int_t step,
+ t_inputrec *ir, gmx_int64_t step,
em_state_t *state,
- t_state *state_global,rvec *f_global)
+ t_state *state_global, rvec *f_global)
{
- int mdof_flags;
+ int mdof_flags;
+ gmx_bool bIMDout = FALSE;
+
+
+ /* Shall we do IMD output? */
+ if (ir->bIMD)
+ {
+ bIMDout = do_per_step(step, IMD_get_step(ir->imd->setup));
+ }
- if ((bX || bF || confout != NULL) && !DOMAINDECOMP(cr))
+ if ((bX || bF || bIMDout || confout != NULL) && !DOMAINDECOMP(cr))
{
- copy_em_coords(state,state_global);
+ copy_em_coords(state, state_global);
f_global = state->f;
}
mdof_flags = 0;
- if (bX) { mdof_flags |= MDOF_X; }
- if (bF) { mdof_flags |= MDOF_F; }
- write_traj(fplog,cr,outf,mdof_flags,
- top_global,step,(double)step,
- &state->s,state_global,state->f,f_global,NULL,NULL);
+ if (bX)
+ {
+ mdof_flags |= MDOF_X;
+ }
+ if (bF)
+ {
+ mdof_flags |= MDOF_F;
+ }
+
+ /* If we want IMD output, set appropriate MDOF flag */
+ if (ir->bIMD)
+ {
+ mdof_flags |= MDOF_IMD;
+ }
+
+ mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
+ top_global, step, (double)step,
+ &state->s, state_global, state->f, f_global);
if (confout != NULL && MASTER(cr))
{
if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr))
{
/* Make molecules whole only for confout writing */
- do_pbc_mtop(fplog,ir->ePBC,state_global->box,top_global,
+ do_pbc_mtop(fplog, ir->ePBC, state_global->box, top_global,
state_global->x);
}
write_sto_conf_mtop(confout,
- *top_global->name,top_global,
- state_global->x,NULL,ir->ePBC,state_global->box);
+ *top_global->name, top_global,
+ state_global->x, NULL, ir->ePBC, state_global->box);
}
}
-static void do_em_step(t_commrec *cr,t_inputrec *ir,t_mdatoms *md,
+static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
gmx_bool bMolPBC,
- em_state_t *ems1,real a,rvec *f,em_state_t *ems2,
- gmx_constr_t constr,gmx_localtop_t *top,
- t_nrnb *nrnb,gmx_wallcycle_t wcycle,
- gmx_large_int_t count)
+ em_state_t *ems1, real a, rvec *f, em_state_t *ems2,
+ gmx_constr_t constr, gmx_localtop_t *top,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_int64_t count)
{
- t_state *s1,*s2;
- int i;
- int start,end;
- rvec *x1,*x2;
- real dvdlambda;
+ t_state *s1, *s2;
+ int i;
+ int start, end;
+ rvec *x1, *x2;
+ real dvdl_constr;
+ int nthreads gmx_unused;
s1 = &ems1->s;
s2 = &ems2->s;
if (s2->nalloc != s1->nalloc)
{
s2->nalloc = s1->nalloc;
- srenew(s2->x,s1->nalloc);
+ srenew(s2->x, s1->nalloc);
srenew(ems2->f, s1->nalloc);
if (s2->flags & (1<<estCGP))
{
srenew(s2->cg_p, s1->nalloc);
}
}
-
+
s2->natoms = s1->natoms;
- copy_mat(s1->box,s2->box);
+ copy_mat(s1->box, s2->box);
/* Copy free energy state */
- for (i=0;i<efptNR;i++)
+ for (i = 0; i < efptNR; i++)
{
s2->lambda[i] = s1->lambda[i];
}
- copy_mat(s1->box,s2->box);
+ copy_mat(s1->box, s2->box);
- start = md->start;
- end = md->start + md->homenr;
+ start = 0;
+ end = md->homenr;
x1 = s1->x;
x2 = s2->x;
-#pragma omp parallel num_threads(gmx_omp_nthreads_get(emntUpdate))
+ nthreads = gmx_omp_nthreads_get(emntUpdate);
+#pragma omp parallel num_threads(nthreads)
{
- int gf,i,m;
+ int gf, i, m;
gf = 0;
#pragma omp for schedule(static) nowait
- for(i=start; i<end; i++)
+ for (i = start; i < end; i++)
{
if (md->cFREEZE)
{
gf = md->cFREEZE[i];
}
- for(m=0; m<DIM; m++)
+ for (m = 0; m < DIM; m++)
{
if (ir->opts.nFreeze[gf][m])
{
x1 = s1->cg_p;
x2 = s2->cg_p;
#pragma omp for schedule(static) nowait
- for(i=start; i<end; i++)
+ for (i = start; i < end; i++)
{
- copy_rvec(x1[i],x2[i]);
+ copy_rvec(x1[i], x2[i]);
}
}
-
+
if (DOMAINDECOMP(cr))
{
s2->ddp_count = s1->ddp_count;
{
#pragma omp barrier
s2->cg_gl_nalloc = s1->cg_gl_nalloc;
- srenew(s2->cg_gl,s2->cg_gl_nalloc);
+ srenew(s2->cg_gl, s2->cg_gl_nalloc);
#pragma omp barrier
}
s2->ncg_gl = s1->ncg_gl;
#pragma omp for schedule(static) nowait
- for(i=0; i<s2->ncg_gl; i++)
+ for (i = 0; i < s2->ncg_gl; i++)
{
s2->cg_gl[i] = s1->cg_gl[i];
}
s2->ddp_count_cg_gl = s1->ddp_count_cg_gl;
}
}
-
+
if (constr)
{
- wallcycle_start(wcycle,ewcCONSTR);
- dvdlambda = 0;
- constrain(NULL,TRUE,TRUE,constr,&top->idef,
- ir,NULL,cr,count,0,md,
- s1->x,s2->x,NULL,bMolPBC,s2->box,
- s2->lambda[efptBONDED],&dvdlambda,
- NULL,NULL,nrnb,econqCoord,FALSE,0,0);
- wallcycle_stop(wcycle,ewcCONSTR);
+ wallcycle_start(wcycle, ewcCONSTR);
+ dvdl_constr = 0;
+ constrain(NULL, TRUE, TRUE, constr, &top->idef,
+ ir, NULL, cr, count, 0, 1.0, md,
+ s1->x, s2->x, NULL, bMolPBC, s2->box,
+ s2->lambda[efptBONDED], &dvdl_constr,
+ NULL, NULL, nrnb, econqCoord, FALSE, 0, 0);
+ wallcycle_stop(wcycle, ewcCONSTR);
}
}
-static void em_dd_partition_system(FILE *fplog,int step,t_commrec *cr,
- gmx_mtop_t *top_global,t_inputrec *ir,
- em_state_t *ems,gmx_localtop_t *top,
- t_mdatoms *mdatoms,t_forcerec *fr,
- gmx_vsite_t *vsite,gmx_constr_t constr,
- t_nrnb *nrnb,gmx_wallcycle_t wcycle)
+static void em_dd_partition_system(FILE *fplog, int step, t_commrec *cr,
+ gmx_mtop_t *top_global, t_inputrec *ir,
+ em_state_t *ems, gmx_localtop_t *top,
+ t_mdatoms *mdatoms, t_forcerec *fr,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle)
{
/* Repartition the domain decomposition */
- wallcycle_start(wcycle,ewcDOMDEC);
- dd_partition_system(fplog,step,cr,FALSE,1,
- NULL,top_global,ir,
- &ems->s,&ems->f,
- mdatoms,top,fr,vsite,NULL,constr,
- nrnb,wcycle,FALSE);
- dd_store_state(cr->dd,&ems->s);
- wallcycle_stop(wcycle,ewcDOMDEC);
+ wallcycle_start(wcycle, ewcDOMDEC);
+ dd_partition_system(fplog, step, cr, FALSE, 1,
+ NULL, top_global, ir,
+ &ems->s, &ems->f,
+ mdatoms, top, fr, vsite, NULL, constr,
+ nrnb, wcycle, FALSE);
+ dd_store_state(cr->dd, &ems->s);
+ wallcycle_stop(wcycle, ewcDOMDEC);
}
-static void evaluate_energy(FILE *fplog,gmx_bool bVerbose,t_commrec *cr,
- t_state *state_global,gmx_mtop_t *top_global,
- em_state_t *ems,gmx_localtop_t *top,
+static void evaluate_energy(FILE *fplog, t_commrec *cr,
+ gmx_mtop_t *top_global,
+ em_state_t *ems, gmx_localtop_t *top,
t_inputrec *inputrec,
- t_nrnb *nrnb,gmx_wallcycle_t wcycle,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_global_stat_t gstat,
- gmx_vsite_t *vsite,gmx_constr_t constr,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
t_fcdata *fcd,
- t_graph *graph,t_mdatoms *mdatoms,
- t_forcerec *fr,rvec mu_tot,
- gmx_enerdata_t *enerd,tensor vir,tensor pres,
- gmx_large_int_t count,gmx_bool bFirst)
+ t_graph *graph, t_mdatoms *mdatoms,
+ t_forcerec *fr, rvec mu_tot,
+ gmx_enerdata_t *enerd, tensor vir, tensor pres,
+ gmx_int64_t count, gmx_bool bFirst)
{
- real t;
- gmx_bool bNS;
- int nabnsb;
- tensor force_vir,shake_vir,ekin;
- real dvdlambda,prescorr,enercorr,dvdlcorr;
- real terminate=0;
-
- /* Set the time to the initial time, the time does not change during EM */
- t = inputrec->init_t;
-
- if (bFirst ||
- (DOMAINDECOMP(cr) && ems->s.ddp_count < cr->dd->ddp_count)) {
- /* This the first state or an old state used before the last ns */
- bNS = TRUE;
- } else {
- bNS = FALSE;
- if (inputrec->nstlist > 0) {
- bNS = TRUE;
- } else if (inputrec->nstlist == -1) {
- nabnsb = natoms_beyond_ns_buffer(inputrec,fr,&top->cgs,NULL,ems->s.x);
- if (PAR(cr))
- gmx_sumi(1,&nabnsb,cr);
- bNS = (nabnsb > 0);
- }
- }
-
- if (vsite)
- construct_vsites(fplog,vsite,ems->s.x,nrnb,1,NULL,
- top->idef.iparams,top->idef.il,
- fr->ePBC,fr->bMolPBC,graph,cr,ems->s.box);
-
- if (DOMAINDECOMP(cr)) {
- if (bNS) {
- /* Repartition the domain decomposition */
- em_dd_partition_system(fplog,count,cr,top_global,inputrec,
- ems,top,mdatoms,fr,vsite,constr,
- nrnb,wcycle);
- }
- }
+ real t;
+ gmx_bool bNS;
+ int nabnsb;
+ tensor force_vir, shake_vir, ekin;
+ real dvdl_constr, prescorr, enercorr, dvdlcorr;
+ real terminate = 0;
+
+ /* Set the time to the initial time, the time does not change during EM */
+ t = inputrec->init_t;
+
+ if (bFirst ||
+ (DOMAINDECOMP(cr) && ems->s.ddp_count < cr->dd->ddp_count))
+ {
+ /* This is the first state or an old state used before the last ns */
+ bNS = TRUE;
+ }
+ else
+ {
+ bNS = FALSE;
+ if (inputrec->nstlist > 0)
+ {
+ bNS = TRUE;
+ }
+ else if (inputrec->nstlist == -1)
+ {
+ nabnsb = natoms_beyond_ns_buffer(inputrec, fr, &top->cgs, NULL, ems->s.x);
+ if (PAR(cr))
+ {
+ gmx_sumi(1, &nabnsb, cr);
+ }
+ bNS = (nabnsb > 0);
+ }
+ }
+
+ if (vsite)
+ {
+ construct_vsites(vsite, ems->s.x, 1, NULL,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, cr, ems->s.box);
+ }
+
+ if (DOMAINDECOMP(cr) && bNS)
+ {
+ /* Repartition the domain decomposition */
+ em_dd_partition_system(fplog, count, cr, top_global, inputrec,
+ ems, top, mdatoms, fr, vsite, constr,
+ nrnb, wcycle);
+ }
/* Calc force & energy on new trial position */
/* do_force always puts the charge groups in the box and shifts again
* We do not unshift, so molecules are always whole in congrad.c
*/
- do_force(fplog,cr,inputrec,
- count,nrnb,wcycle,top,top_global,&top_global->groups,
- ems->s.box,ems->s.x,&ems->s.hist,
- ems->f,force_vir,mdatoms,enerd,fcd,
- ems->s.lambda,graph,fr,vsite,mu_tot,t,NULL,NULL,TRUE,
+ do_force(fplog, cr, inputrec,
+ count, nrnb, wcycle, top, &top_global->groups,
+ ems->s.box, ems->s.x, &ems->s.hist,
+ ems->f, force_vir, mdatoms, enerd, fcd,
+ ems->s.lambda, graph, fr, vsite, mu_tot, t, NULL, NULL, TRUE,
GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
- (bNS ? GMX_FORCE_NS | GMX_FORCE_DOLR : 0));
+ (bNS ? GMX_FORCE_NS | GMX_FORCE_DO_LR : 0));
/* Clear the unused shake virial and pressure */
clear_mat(shake_vir);
/* Communicate stuff when parallel */
if (PAR(cr) && inputrec->eI != eiNM)
{
- wallcycle_start(wcycle,ewcMoveE);
+ wallcycle_start(wcycle, ewcMoveE);
- global_stat(fplog,gstat,cr,enerd,force_vir,shake_vir,mu_tot,
- inputrec,NULL,NULL,NULL,1,&terminate,
- top_global,&ems->s,FALSE,
+ global_stat(fplog, gstat, cr, enerd, force_vir, shake_vir, mu_tot,
+ inputrec, NULL, NULL, NULL, 1, &terminate,
+ top_global, &ems->s, FALSE,
CGLO_ENERGY |
CGLO_PRESSURE |
CGLO_CONSTRAINT |
CGLO_FIRSTITERATE);
- wallcycle_stop(wcycle,ewcMoveE);
+ wallcycle_stop(wcycle, ewcMoveE);
}
/* Calculate long range corrections to pressure and energy */
- calc_dispcorr(fplog,inputrec,fr,count,top_global->natoms,ems->s.box,ems->s.lambda[efptVDW],
- pres,force_vir,&prescorr,&enercorr,&dvdlcorr);
+ calc_dispcorr(fplog, inputrec, fr, count, top_global->natoms, ems->s.box, ems->s.lambda[efptVDW],
+ pres, force_vir, &prescorr, &enercorr, &dvdlcorr);
enerd->term[F_DISPCORR] = enercorr;
- enerd->term[F_EPOT] += enercorr;
- enerd->term[F_PRES] += prescorr;
- enerd->term[F_DVDL] += dvdlcorr;
-
- ems->epot = enerd->term[F_EPOT];
-
- if (constr) {
- /* Project out the constraint components of the force */
- wallcycle_start(wcycle,ewcCONSTR);
- dvdlambda = 0;
- constrain(NULL,FALSE,FALSE,constr,&top->idef,
- inputrec,NULL,cr,count,0,mdatoms,
- ems->s.x,ems->f,ems->f,fr->bMolPBC,ems->s.box,
- ems->s.lambda[efptBONDED],&dvdlambda,
- NULL,&shake_vir,nrnb,econqForceDispl,FALSE,0,0);
- if (fr->bSepDVDL && fplog)
- fprintf(fplog,sepdvdlformat,"Constraints",t,dvdlambda);
- enerd->term[F_DVDL_BONDED] += dvdlambda;
- m_add(force_vir,shake_vir,vir);
- wallcycle_stop(wcycle,ewcCONSTR);
- } else {
- copy_mat(force_vir,vir);
- }
-
- clear_mat(ekin);
- enerd->term[F_PRES] =
- calc_pres(fr->ePBC,inputrec->nwall,ems->s.box,ekin,vir,pres);
-
- sum_dhdl(enerd,ems->s.lambda,inputrec->fepvals);
+ enerd->term[F_EPOT] += enercorr;
+ enerd->term[F_PRES] += prescorr;
+ enerd->term[F_DVDL] += dvdlcorr;
- if (EI_ENERGY_MINIMIZATION(inputrec->eI))
+ ems->epot = enerd->term[F_EPOT];
+
+ if (constr)
+ {
+ /* Project out the constraint components of the force */
+ wallcycle_start(wcycle, ewcCONSTR);
+ dvdl_constr = 0;
+ constrain(NULL, FALSE, FALSE, constr, &top->idef,
+ inputrec, NULL, cr, count, 0, 1.0, mdatoms,
+ ems->s.x, ems->f, ems->f, fr->bMolPBC, ems->s.box,
+ ems->s.lambda[efptBONDED], &dvdl_constr,
+ NULL, &shake_vir, nrnb, econqForceDispl, FALSE, 0, 0);
+ if (fr->bSepDVDL && fplog)
+ {
+ gmx_print_sepdvdl(fplog, "Constraints", t, dvdl_constr);
+ }
+ enerd->term[F_DVDL_CONSTR] += dvdl_constr;
+ m_add(force_vir, shake_vir, vir);
+ wallcycle_stop(wcycle, ewcCONSTR);
+ }
+ else
{
- get_state_f_norm_max(cr,&(inputrec->opts),mdatoms,ems);
+ copy_mat(force_vir, vir);
}
-}
-static double reorder_partsum(t_commrec *cr,t_grpopts *opts,t_mdatoms *mdatoms,
- gmx_mtop_t *mtop,
- em_state_t *s_min,em_state_t *s_b)
-{
- rvec *fm,*fb,*fmg;
- t_block *cgs_gl;
- int ncg,*cg_gl,*index,c,cg,i,a0,a1,a,gf,m;
- double partsum;
- unsigned char *grpnrFREEZE;
-
- if (debug)
- fprintf(debug,"Doing reorder_partsum\n");
-
- fm = s_min->f;
- fb = s_b->f;
-
- cgs_gl = dd_charge_groups_global(cr->dd);
- index = cgs_gl->index;
-
- /* Collect fm in a global vector fmg.
- * This conflicts with the spirit of domain decomposition,
- * but to fully optimize this a much more complicated algorithm is required.
- */
- snew(fmg,mtop->natoms);
-
- ncg = s_min->s.ncg_gl;
- cg_gl = s_min->s.cg_gl;
- i = 0;
- for(c=0; c<ncg; c++) {
- cg = cg_gl[c];
- a0 = index[cg];
- a1 = index[cg+1];
- for(a=a0; a<a1; a++) {
- copy_rvec(fm[i],fmg[a]);
- i++;
- }
- }
- gmx_sum(mtop->natoms*3,fmg[0],cr);
-
- /* Now we will determine the part of the sum for the cgs in state s_b */
- ncg = s_b->s.ncg_gl;
- cg_gl = s_b->s.cg_gl;
- partsum = 0;
- i = 0;
- gf = 0;
- grpnrFREEZE = mtop->groups.grpnr[egcFREEZE];
- for(c=0; c<ncg; c++) {
- cg = cg_gl[c];
- a0 = index[cg];
- a1 = index[cg+1];
- for(a=a0; a<a1; a++) {
- if (mdatoms->cFREEZE && grpnrFREEZE) {
- gf = grpnrFREEZE[i];
- }
- for(m=0; m<DIM; m++) {
- if (!opts->nFreeze[gf][m]) {
- partsum += (fb[i][m] - fmg[a][m])*fb[i][m];
- }
- }
- i++;
- }
- }
-
- sfree(fmg);
-
- return partsum;
-}
+ clear_mat(ekin);
+ enerd->term[F_PRES] =
+ calc_pres(fr->ePBC, inputrec->nwall, ems->s.box, ekin, vir, pres);
-static real pr_beta(t_commrec *cr,t_grpopts *opts,t_mdatoms *mdatoms,
- gmx_mtop_t *mtop,
- em_state_t *s_min,em_state_t *s_b)
-{
- rvec *fm,*fb;
- double sum;
- int gf,i,m;
-
- /* This is just the classical Polak-Ribiere calculation of beta;
- * it looks a bit complicated since we take freeze groups into account,
- * and might have to sum it in parallel runs.
- */
-
- if (!DOMAINDECOMP(cr) ||
- (s_min->s.ddp_count == cr->dd->ddp_count &&
- s_b->s.ddp_count == cr->dd->ddp_count)) {
- fm = s_min->f;
- fb = s_b->f;
- sum = 0;
- gf = 0;
- /* This part of code can be incorrect with DD,
- * since the atom ordering in s_b and s_min might differ.
- */
- for(i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++) {
- if (mdatoms->cFREEZE)
- gf = mdatoms->cFREEZE[i];
- for(m=0; m<DIM; m++)
- if (!opts->nFreeze[gf][m]) {
- sum += (fb[i][m] - fm[i][m])*fb[i][m];
- }
- }
- } else {
- /* We need to reorder cgs while summing */
- sum = reorder_partsum(cr,opts,mdatoms,mtop,s_min,s_b);
- }
- if (PAR(cr))
- gmx_sumd(1,&sum,cr);
-
- return sum/sqr(s_min->fnorm);
+ sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals);
+
+ if (EI_ENERGY_MINIMIZATION(inputrec->eI))
+ {
+ get_state_f_norm_max(cr, &(inputrec->opts), mdatoms, ems);
+ }
}
-double do_cg(FILE *fplog,t_commrec *cr,
- int nfile,const t_filenm fnm[],
- const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
- int nstglobalcomm,
- gmx_vsite_t *vsite,gmx_constr_t constr,
- int stepout,
- t_inputrec *inputrec,
- gmx_mtop_t *top_global,t_fcdata *fcd,
- t_state *state_global,
- t_mdatoms *mdatoms,
- t_nrnb *nrnb,gmx_wallcycle_t wcycle,
- gmx_edsam_t ed,
- t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
- gmx_membed_t membed,
- real cpt_period,real max_hours,
- const char *deviceOptions,
- unsigned long Flags,
- gmx_runtime_t *runtime)
+static double reorder_partsum(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
+ gmx_mtop_t *mtop,
+ em_state_t *s_min, em_state_t *s_b)
{
- const char *CG="Polak-Ribiere Conjugate Gradients";
-
- em_state_t *s_min,*s_a,*s_b,*s_c;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- rvec *f_global,*p,*sf,*sfm;
- double gpa,gpb,gpc,tmp,sum[2],minstep;
- real fnormn;
- real stepsize;
- real a,b,c,beta=0.0;
- real epot_repl=0;
- real pnorm;
- t_mdebin *mdebin;
- gmx_bool converged,foundlower;
- rvec mu_tot;
- gmx_bool do_log=FALSE,do_ene=FALSE,do_x,do_f;
- tensor vir,pres;
- int number_steps,neval=0,nstcg=inputrec->nstcgsteep;
- gmx_mdoutf_t *outf;
- int i,m,gf,step,nminstep;
- real terminate=0;
-
- step=0;
-
- s_min = init_em_state();
- s_a = init_em_state();
- s_b = init_em_state();
- s_c = init_em_state();
-
- /* Init em and store the local state in s_min */
- init_em(fplog,CG,cr,inputrec,
- state_global,top_global,s_min,&top,&f,&f_global,
- nrnb,mu_tot,fr,&enerd,&graph,mdatoms,&gstat,vsite,constr,
- nfile,fnm,&outf,&mdebin);
-
- /* Print to log file */
- print_em_start(fplog,cr,runtime,wcycle,CG);
-
- /* Max number of steps */
- number_steps=inputrec->nsteps;
-
- if (MASTER(cr))
- sp_header(stderr,CG,inputrec->em_tol,number_steps);
- if (fplog)
- sp_header(fplog,CG,inputrec->em_tol,number_steps);
-
- /* Call the force routine and some auxiliary (neighboursearching etc.) */
- /* do_force always puts the charge groups in the box and shifts again
- * We do not unshift, so molecules are always whole in congrad.c
- */
- evaluate_energy(fplog,bVerbose,cr,
- state_global,top_global,s_min,top,
- inputrec,nrnb,wcycle,gstat,
- vsite,constr,fcd,graph,mdatoms,fr,
- mu_tot,enerd,vir,pres,-1,TRUE);
- where();
-
- if (MASTER(cr)) {
- /* Copy stuff to the energy bin for easy printing etc. */
- upd_mdebin(mdebin,FALSE,FALSE,(double)step,
- mdatoms->tmass,enerd,&s_min->s,inputrec->fepvals,inputrec->expandedvals,s_min->s.box,
- NULL,NULL,vir,pres,NULL,mu_tot,constr);
-
- print_ebin_header(fplog,step,step,s_min->s.lambda[efptFEP]);
- print_ebin(outf->fp_ene,TRUE,FALSE,FALSE,fplog,step,step,eprNORMAL,
- TRUE,mdebin,fcd,&(top_global->groups),&(inputrec->opts));
- }
- where();
-
- /* Estimate/guess the initial stepsize */
- stepsize = inputrec->em_stepsize/s_min->fnorm;
-
- if (MASTER(cr)) {
- fprintf(stderr," F-max = %12.5e on atom %d\n",
- s_min->fmax,s_min->a_fmax+1);
- fprintf(stderr," F-Norm = %12.5e\n",
- s_min->fnorm/sqrt(state_global->natoms));
- fprintf(stderr,"\n");
- /* and copy to the log file too... */
- fprintf(fplog," F-max = %12.5e on atom %d\n",
- s_min->fmax,s_min->a_fmax+1);
- fprintf(fplog," F-Norm = %12.5e\n",
- s_min->fnorm/sqrt(state_global->natoms));
- fprintf(fplog,"\n");
- }
- /* Start the loop over CG steps.
- * Each successful step is counted, and we continue until
- * we either converge or reach the max number of steps.
- */
- converged = FALSE;
- for(step=0; (number_steps<0 || (number_steps>=0 && step<=number_steps)) && !converged;step++) {
-
- /* start taking steps in a new direction
- * First time we enter the routine, beta=0, and the direction is
- * simply the negative gradient.
- */
+ rvec *fm, *fb, *fmg;
+ t_block *cgs_gl;
+ int ncg, *cg_gl, *index, c, cg, i, a0, a1, a, gf, m;
+ double partsum;
+ unsigned char *grpnrFREEZE;
- /* Calculate the new direction in p, and the gradient in this direction, gpa */
- p = s_min->s.cg_p;
- sf = s_min->f;
- gpa = 0;
- gf = 0;
- for(i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++) {
- if (mdatoms->cFREEZE)
- gf = mdatoms->cFREEZE[i];
- for(m=0; m<DIM; m++) {
- if (!inputrec->opts.nFreeze[gf][m]) {
- p[i][m] = sf[i][m] + beta*p[i][m];
- gpa -= p[i][m]*sf[i][m];
- /* f is negative gradient, thus the sign */
- } else {
- p[i][m] = 0;
- }
- }
- }
-
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- gmx_sumd(1,&gpa,cr);
+ if (debug)
+ {
+ fprintf(debug, "Doing reorder_partsum\n");
+ }
- /* Calculate the norm of the search vector */
- get_f_norm_max(cr,&(inputrec->opts),mdatoms,p,&pnorm,NULL,NULL);
+ fm = s_min->f;
+ fb = s_b->f;
- /* Just in case stepsize reaches zero due to numerical precision... */
- if(stepsize<=0)
- stepsize = inputrec->em_stepsize/pnorm;
+ cgs_gl = dd_charge_groups_global(cr->dd);
+ index = cgs_gl->index;
- /*
- * Double check the value of the derivative in the search direction.
- * If it is positive it must be due to the old information in the
- * CG formula, so just remove that and start over with beta=0.
- * This corresponds to a steepest descent step.
+ /* Collect fm in a global vector fmg.
+ * This conflicts with the spirit of domain decomposition,
+ * but to fully optimize this a much more complicated algorithm is required.
*/
- if(gpa>0) {
- beta = 0;
- step--; /* Don't count this step since we are restarting */
- continue; /* Go back to the beginning of the big for-loop */
- }
+ snew(fmg, mtop->natoms);
- /* Calculate minimum allowed stepsize, before the average (norm)
- * relative change in coordinate is smaller than precision
- */
- minstep=0;
- for (i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++) {
- for(m=0; m<DIM; m++) {
- tmp = fabs(s_min->s.x[i][m]);
- if(tmp < 1.0)
- tmp = 1.0;
- tmp = p[i][m]/tmp;
- minstep += tmp*tmp;
- }
- }
- /* Add up from all CPUs */
- if(PAR(cr))
- gmx_sumd(1,&minstep,cr);
-
- minstep = GMX_REAL_EPS/sqrt(minstep/(3*state_global->natoms));
-
- if(stepsize<minstep) {
- converged=TRUE;
- break;
- }
-
- /* Write coordinates if necessary */
- do_x = do_per_step(step,inputrec->nstxout);
- do_f = do_per_step(step,inputrec->nstfout);
-
- write_em_traj(fplog,cr,outf,do_x,do_f,NULL,
- top_global,inputrec,step,
- s_min,state_global,f_global);
-
- /* Take a step downhill.
- * In theory, we should minimize the function along this direction.
- * That is quite possible, but it turns out to take 5-10 function evaluations
- * for each line. However, we dont really need to find the exact minimum -
- * it is much better to start a new CG step in a modified direction as soon
- * as we are close to it. This will save a lot of energy evaluations.
- *
- * In practice, we just try to take a single step.
- * If it worked (i.e. lowered the energy), we increase the stepsize but
- * the continue straight to the next CG step without trying to find any minimum.
- * If it didn't work (higher energy), there must be a minimum somewhere between
- * the old position and the new one.
- *
- * Due to the finite numerical accuracy, it turns out that it is a good idea
- * to even accept a SMALL increase in energy, if the derivative is still downhill.
- * This leads to lower final energies in the tests I've done. / Erik
- */
- s_a->epot = s_min->epot;
- a = 0.0;
- c = a + stepsize; /* reference position along line is zero */
+ ncg = s_min->s.ncg_gl;
+ cg_gl = s_min->s.cg_gl;
+ i = 0;
+ for (c = 0; c < ncg; c++)
+ {
+ cg = cg_gl[c];
+ a0 = index[cg];
+ a1 = index[cg+1];
+ for (a = a0; a < a1; a++)
+ {
+ copy_rvec(fm[i], fmg[a]);
+ i++;
+ }
+ }
+ gmx_sum(mtop->natoms*3, fmg[0], cr);
- if (DOMAINDECOMP(cr) && s_min->s.ddp_count < cr->dd->ddp_count) {
- em_dd_partition_system(fplog,step,cr,top_global,inputrec,
- s_min,top,mdatoms,fr,vsite,constr,
- nrnb,wcycle);
+ /* Now we will determine the part of the sum for the cgs in state s_b */
+ ncg = s_b->s.ncg_gl;
+ cg_gl = s_b->s.cg_gl;
+ partsum = 0;
+ i = 0;
+ gf = 0;
+ grpnrFREEZE = mtop->groups.grpnr[egcFREEZE];
+ for (c = 0; c < ncg; c++)
+ {
+ cg = cg_gl[c];
+ a0 = index[cg];
+ a1 = index[cg+1];
+ for (a = a0; a < a1; a++)
+ {
+ if (mdatoms->cFREEZE && grpnrFREEZE)
+ {
+ gf = grpnrFREEZE[i];
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ if (!opts->nFreeze[gf][m])
+ {
+ partsum += (fb[i][m] - fmg[a][m])*fb[i][m];
+ }
+ }
+ i++;
+ }
}
- /* Take a trial step (new coords in s_c) */
- do_em_step(cr,inputrec,mdatoms,fr->bMolPBC,s_min,c,s_min->s.cg_p,s_c,
- constr,top,nrnb,wcycle,-1);
+ sfree(fmg);
- neval++;
- /* Calculate energy for the trial step */
- evaluate_energy(fplog,bVerbose,cr,
- state_global,top_global,s_c,top,
- inputrec,nrnb,wcycle,gstat,
- vsite,constr,fcd,graph,mdatoms,fr,
- mu_tot,enerd,vir,pres,-1,FALSE);
-
- /* Calc derivative along line */
- p = s_c->s.cg_p;
- sf = s_c->f;
- gpc=0;
- for(i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++) {
- for(m=0; m<DIM; m++)
- gpc -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
- }
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- gmx_sumd(1,&gpc,cr);
+ return partsum;
+}
- /* This is the max amount of increase in energy we tolerate */
- tmp=sqrt(GMX_REAL_EPS)*fabs(s_a->epot);
+static real pr_beta(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
+ gmx_mtop_t *mtop,
+ em_state_t *s_min, em_state_t *s_b)
+{
+ rvec *fm, *fb;
+ double sum;
+ int gf, i, m;
- /* Accept the step if the energy is lower, or if it is not significantly higher
- * and the line derivative is still negative.
- */
- if (s_c->epot < s_a->epot || (gpc < 0 && s_c->epot < (s_a->epot + tmp))) {
- foundlower = TRUE;
- /* Great, we found a better energy. Increase step for next iteration
- * if we are still going down, decrease it otherwise
- */
- if(gpc<0)
- stepsize *= 1.618034; /* The golden section */
- else
- stepsize *= 0.618034; /* 1/golden section */
- } else {
- /* New energy is the same or higher. We will have to do some work
- * to find a smaller value in the interval. Take smaller step next time!
- */
- foundlower = FALSE;
- stepsize *= 0.618034;
- }
-
-
-
-
- /* OK, if we didn't find a lower value we will have to locate one now - there must
- * be one in the interval [a=0,c].
- * The same thing is valid here, though: Don't spend dozens of iterations to find
- * the line minimum. We try to interpolate based on the derivative at the endpoints,
- * and only continue until we find a lower value. In most cases this means 1-2 iterations.
- *
- * I also have a safeguard for potentially really patological functions so we never
- * take more than 20 steps before we give up ...
- *
- * If we already found a lower value we just skip this step and continue to the update.
- */
- if (!foundlower) {
- nminstep=0;
-
- do {
- /* Select a new trial point.
- * If the derivatives at points a & c have different sign we interpolate to zero,
- * otherwise just do a bisection.
- */
- if(gpa<0 && gpc>0)
- b = a + gpa*(a-c)/(gpc-gpa);
- else
- b = 0.5*(a+c);
-
- /* safeguard if interpolation close to machine accuracy causes errors:
- * never go outside the interval
- */
- if(b<=a || b>=c)
- b = 0.5*(a+c);
-
- if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count) {
- /* Reload the old state */
- em_dd_partition_system(fplog,-1,cr,top_global,inputrec,
- s_min,top,mdatoms,fr,vsite,constr,
- nrnb,wcycle);
- }
-
- /* Take a trial step to this new point - new coords in s_b */
- do_em_step(cr,inputrec,mdatoms,fr->bMolPBC,s_min,b,s_min->s.cg_p,s_b,
- constr,top,nrnb,wcycle,-1);
-
- neval++;
- /* Calculate energy for the trial step */
- evaluate_energy(fplog,bVerbose,cr,
- state_global,top_global,s_b,top,
- inputrec,nrnb,wcycle,gstat,
- vsite,constr,fcd,graph,mdatoms,fr,
- mu_tot,enerd,vir,pres,-1,FALSE);
-
- /* p does not change within a step, but since the domain decomposition
- * might change, we have to use cg_p of s_b here.
- */
- p = s_b->s.cg_p;
- sf = s_b->f;
- gpb=0;
- for(i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++) {
- for(m=0; m<DIM; m++)
- gpb -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
- }
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- gmx_sumd(1,&gpb,cr);
-
- if (debug)
- fprintf(debug,"CGE: EpotA %f EpotB %f EpotC %f gpb %f\n",
- s_a->epot,s_b->epot,s_c->epot,gpb);
-
- epot_repl = s_b->epot;
-
- /* Keep one of the intervals based on the value of the derivative at the new point */
- if (gpb > 0) {
- /* Replace c endpoint with b */
- swap_em_state(s_b,s_c);
- c = b;
- gpc = gpb;
- } else {
- /* Replace a endpoint with b */
- swap_em_state(s_b,s_a);
- a = b;
- gpa = gpb;
- }
-
- /*
- * Stop search as soon as we find a value smaller than the endpoints.
- * Never run more than 20 steps, no matter what.
- */
- nminstep++;
- } while ((epot_repl > s_a->epot || epot_repl > s_c->epot) &&
- (nminstep < 20));
-
- if (fabs(epot_repl - s_min->epot) < fabs(s_min->epot)*GMX_REAL_EPS ||
- nminstep >= 20) {
- /* OK. We couldn't find a significantly lower energy.
- * If beta==0 this was steepest descent, and then we give up.
- * If not, set beta=0 and restart with steepest descent before quitting.
- */
- if (beta == 0.0) {
- /* Converged */
- converged = TRUE;
- break;
- } else {
- /* Reset memory before giving up */
- beta = 0.0;
- continue;
- }
- }
-
- /* Select min energy state of A & C, put the best in B.
- */
- if (s_c->epot < s_a->epot) {
- if (debug)
- fprintf(debug,"CGE: C (%f) is lower than A (%f), moving C to B\n",
- s_c->epot,s_a->epot);
- swap_em_state(s_b,s_c);
- gpb = gpc;
- b = c;
- } else {
- if (debug)
- fprintf(debug,"CGE: A (%f) is lower than C (%f), moving A to B\n",
- s_a->epot,s_c->epot);
- swap_em_state(s_b,s_a);
- gpb = gpa;
- b = a;
- }
-
- } else {
- if (debug)
- fprintf(debug,"CGE: Found a lower energy %f, moving C to B\n",
- s_c->epot);
- swap_em_state(s_b,s_c);
- gpb = gpc;
- b = c;
- }
-
- /* new search direction */
- /* beta = 0 means forget all memory and restart with steepest descents. */
- if (nstcg && ((step % nstcg)==0))
- beta = 0.0;
- else {
- /* s_min->fnorm cannot be zero, because then we would have converged
- * and broken out.
- */
-
- /* Polak-Ribiere update.
- * Change to fnorm2/fnorm2_old for Fletcher-Reeves
- */
- beta = pr_beta(cr,&inputrec->opts,mdatoms,top_global,s_min,s_b);
- }
- /* Limit beta to prevent oscillations */
- if (fabs(beta) > 5.0)
- beta = 0.0;
-
-
- /* update positions */
- swap_em_state(s_min,s_b);
- gpa = gpb;
-
- /* Print it if necessary */
- if (MASTER(cr)) {
- if(bVerbose)
- fprintf(stderr,"\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
- step,s_min->epot,s_min->fnorm/sqrt(state_global->natoms),
- s_min->fmax,s_min->a_fmax+1);
- /* Store the new (lower) energies */
- upd_mdebin(mdebin,FALSE,FALSE,(double)step,
- mdatoms->tmass,enerd,&s_min->s,inputrec->fepvals,inputrec->expandedvals,s_min->s.box,
- NULL,NULL,vir,pres,NULL,mu_tot,constr);
-
- do_log = do_per_step(step,inputrec->nstlog);
- do_ene = do_per_step(step,inputrec->nstenergy);
- if(do_log)
- print_ebin_header(fplog,step,step,s_min->s.lambda[efptFEP]);
- print_ebin(outf->fp_ene,do_ene,FALSE,FALSE,
- do_log ? fplog : NULL,step,step,eprNORMAL,
- TRUE,mdebin,fcd,&(top_global->groups),&(inputrec->opts));
- }
-
- /* Stop when the maximum force lies below tolerance.
- * If we have reached machine precision, converged is already set to true.
+ /* This is just the classical Polak-Ribiere calculation of beta;
+ * it looks a bit complicated since we take freeze groups into account,
+ * and might have to sum it in parallel runs.
*/
- converged = converged || (s_min->fmax < inputrec->em_tol);
-
- } /* End of the loop */
- if (converged)
- step--; /* we never took that last step in this case */
-
- if (s_min->fmax > inputrec->em_tol)
+ if (!DOMAINDECOMP(cr) ||
+ (s_min->s.ddp_count == cr->dd->ddp_count &&
+ s_b->s.ddp_count == cr->dd->ddp_count))
{
- if (MASTER(cr))
+ fm = s_min->f;
+ fb = s_b->f;
+ sum = 0;
+ gf = 0;
+ /* This part of code can be incorrect with DD,
+ * since the atom ordering in s_b and s_min might differ.
+ */
+ for (i = 0; i < mdatoms->homenr; i++)
{
- warn_step(stderr,inputrec->em_tol,step-1==number_steps,FALSE);
- warn_step(fplog ,inputrec->em_tol,step-1==number_steps,FALSE);
+ if (mdatoms->cFREEZE)
+ {
+ gf = mdatoms->cFREEZE[i];
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ if (!opts->nFreeze[gf][m])
+ {
+ sum += (fb[i][m] - fm[i][m])*fb[i][m];
+ }
+ }
}
- converged = FALSE;
}
-
- if (MASTER(cr)) {
- /* If we printed energy and/or logfile last step (which was the last step)
- * we don't have to do it again, but otherwise print the final values.
- */
- if(!do_log) {
- /* Write final value to log since we didn't do anything the last step */
- print_ebin_header(fplog,step,step,s_min->s.lambda[efptFEP]);
+ else
+ {
+ /* We need to reorder cgs while summing */
+ sum = reorder_partsum(cr, opts, mdatoms, mtop, s_min, s_b);
}
- if (!do_ene || !do_log) {
- /* Write final energy file entries */
- print_ebin(outf->fp_ene,!do_ene,FALSE,FALSE,
- !do_log ? fplog : NULL,step,step,eprNORMAL,
- TRUE,mdebin,fcd,&(top_global->groups),&(inputrec->opts));
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &sum, cr);
}
- }
-
- /* Print some stuff... */
- if (MASTER(cr))
- fprintf(stderr,"\nwriting lowest energy coordinates.\n");
-
- /* IMPORTANT!
- * For accurate normal mode calculation it is imperative that we
- * store the last conformation into the full precision binary trajectory.
- *
- * However, we should only do it if we did NOT already write this step
- * above (which we did if do_x or do_f was true).
- */
- do_x = !do_per_step(step,inputrec->nstxout);
- do_f = (inputrec->nstfout > 0 && !do_per_step(step,inputrec->nstfout));
-
- write_em_traj(fplog,cr,outf,do_x,do_f,ftp2fn(efSTO,nfile,fnm),
- top_global,inputrec,step,
- s_min,state_global,f_global);
-
- fnormn = s_min->fnorm/sqrt(state_global->natoms);
-
- if (MASTER(cr)) {
- print_converged(stderr,CG,inputrec->em_tol,step,converged,number_steps,
- s_min->epot,s_min->fmax,s_min->a_fmax,fnormn);
- print_converged(fplog,CG,inputrec->em_tol,step,converged,number_steps,
- s_min->epot,s_min->fmax,s_min->a_fmax,fnormn);
-
- fprintf(fplog,"\nPerformed %d energy evaluations in total.\n",neval);
- }
-
- finish_em(fplog,cr,outf,runtime,wcycle);
-
- /* To print the actual number of steps we needed somewhere */
- runtime->nsteps_done = step;
-
- return 0;
-} /* That's all folks */
+ return sum/sqr(s_min->fnorm);
+}
-double do_lbfgs(FILE *fplog,t_commrec *cr,
- int nfile,const t_filenm fnm[],
- const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
- int nstglobalcomm,
- gmx_vsite_t *vsite,gmx_constr_t constr,
- int stepout,
- t_inputrec *inputrec,
- gmx_mtop_t *top_global,t_fcdata *fcd,
- t_state *state,
- t_mdatoms *mdatoms,
- t_nrnb *nrnb,gmx_wallcycle_t wcycle,
- gmx_edsam_t ed,
- t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
- gmx_membed_t membed,
- real cpt_period,real max_hours,
- const char *deviceOptions,
- unsigned long Flags,
- gmx_runtime_t *runtime)
+double do_cg(FILE *fplog, t_commrec *cr,
+ int nfile, const t_filenm fnm[],
+ const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
+ int gmx_unused nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int gmx_unused stepout,
+ t_inputrec *inputrec,
+ gmx_mtop_t *top_global, t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t gmx_unused ed,
+ t_forcerec *fr,
+ int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused membed,
+ real gmx_unused cpt_period, real gmx_unused max_hours,
+ const char gmx_unused *deviceOptions,
+ int imdport,
+ unsigned long gmx_unused Flags,
+ gmx_walltime_accounting_t walltime_accounting)
{
- static const char *LBFGS="Low-Memory BFGS Minimizer";
- em_state_t ems;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- rvec *f_global;
- int ncorr,nmaxcorr,point,cp,neval,nminstep;
- double stepsize,gpa,gpb,gpc,tmp,minstep;
- real *rho,*alpha,*ff,*xx,*p,*s,*lastx,*lastf,**dx,**dg;
- real *xa,*xb,*xc,*fa,*fb,*fc,*xtmp,*ftmp;
- real a,b,c,maxdelta,delta;
- real diag,Epot0,Epot,EpotA,EpotB,EpotC;
- real dgdx,dgdg,sq,yr,beta;
- t_mdebin *mdebin;
- gmx_bool converged,first;
- rvec mu_tot;
- real fnorm,fmax;
- gmx_bool do_log,do_ene,do_x,do_f,foundlower,*frozen;
- tensor vir,pres;
- int start,end,number_steps;
- gmx_mdoutf_t *outf;
- int i,k,m,n,nfmax,gf,step;
- int mdof_flags;
- /* not used */
- real terminate;
-
- if (PAR(cr))
- gmx_fatal(FARGS,"Cannot do parallel L-BFGS Minimization - yet.\n");
-
- n = 3*state->natoms;
- nmaxcorr = inputrec->nbfgscorr;
-
- /* Allocate memory */
- /* Use pointers to real so we dont have to loop over both atoms and
- * dimensions all the time...
- * x/f are allocated as rvec *, so make new x0/f0 pointers-to-real
- * that point to the same memory.
- */
- snew(xa,n);
- snew(xb,n);
- snew(xc,n);
- snew(fa,n);
- snew(fb,n);
- snew(fc,n);
- snew(frozen,n);
-
- snew(p,n);
- snew(lastx,n);
- snew(lastf,n);
- snew(rho,nmaxcorr);
- snew(alpha,nmaxcorr);
-
- snew(dx,nmaxcorr);
- for(i=0;i<nmaxcorr;i++)
- snew(dx[i],n);
-
- snew(dg,nmaxcorr);
- for(i=0;i<nmaxcorr;i++)
- snew(dg[i],n);
-
- step = 0;
- neval = 0;
-
- /* Init em */
- init_em(fplog,LBFGS,cr,inputrec,
- state,top_global,&ems,&top,&f,&f_global,
- nrnb,mu_tot,fr,&enerd,&graph,mdatoms,&gstat,vsite,constr,
- nfile,fnm,&outf,&mdebin);
- /* Do_lbfgs is not completely updated like do_steep and do_cg,
- * so we free some memory again.
- */
- sfree(ems.s.x);
- sfree(ems.f);
-
- xx = (real *)state->x;
- ff = (real *)f;
-
- start = mdatoms->start;
- end = mdatoms->homenr + start;
-
- /* Print to log file */
- print_em_start(fplog,cr,runtime,wcycle,LBFGS);
-
- do_log = do_ene = do_x = do_f = TRUE;
-
- /* Max number of steps */
- number_steps=inputrec->nsteps;
-
- /* Create a 3*natoms index to tell whether each degree of freedom is frozen */
- gf = 0;
- for(i=start; i<end; i++) {
- if (mdatoms->cFREEZE)
- gf = mdatoms->cFREEZE[i];
- for(m=0; m<DIM; m++)
- frozen[3*i+m]=inputrec->opts.nFreeze[gf][m];
- }
- if (MASTER(cr))
- sp_header(stderr,LBFGS,inputrec->em_tol,number_steps);
- if (fplog)
- sp_header(fplog,LBFGS,inputrec->em_tol,number_steps);
-
- if (vsite)
- construct_vsites(fplog,vsite,state->x,nrnb,1,NULL,
- top->idef.iparams,top->idef.il,
- fr->ePBC,fr->bMolPBC,graph,cr,state->box);
-
- /* Call the force routine and some auxiliary (neighboursearching etc.) */
- /* do_force always puts the charge groups in the box and shifts again
- * We do not unshift, so molecules are always whole
- */
- neval++;
- ems.s.x = state->x;
- ems.f = f;
- evaluate_energy(fplog,bVerbose,cr,
- state,top_global,&ems,top,
- inputrec,nrnb,wcycle,gstat,
- vsite,constr,fcd,graph,mdatoms,fr,
- mu_tot,enerd,vir,pres,-1,TRUE);
- where();
-
- if (MASTER(cr)) {
- /* Copy stuff to the energy bin for easy printing etc. */
- upd_mdebin(mdebin,FALSE,FALSE,(double)step,
- mdatoms->tmass,enerd,state,inputrec->fepvals,inputrec->expandedvals,state->box,
- NULL,NULL,vir,pres,NULL,mu_tot,constr);
-
- print_ebin_header(fplog,step,step,state->lambda[efptFEP]);
- print_ebin(outf->fp_ene,TRUE,FALSE,FALSE,fplog,step,step,eprNORMAL,
- TRUE,mdebin,fcd,&(top_global->groups),&(inputrec->opts));
- }
- where();
-
- /* This is the starting energy */
- Epot = enerd->term[F_EPOT];
-
- fnorm = ems.fnorm;
- fmax = ems.fmax;
- nfmax = ems.a_fmax;
-
- /* Set the initial step.
- * since it will be multiplied by the non-normalized search direction
- * vector (force vector the first time), we scale it by the
- * norm of the force.
- */
-
- if (MASTER(cr)) {
- fprintf(stderr,"Using %d BFGS correction steps.\n\n",nmaxcorr);
- fprintf(stderr," F-max = %12.5e on atom %d\n",fmax,nfmax+1);
- fprintf(stderr," F-Norm = %12.5e\n",fnorm/sqrt(state->natoms));
- fprintf(stderr,"\n");
- /* and copy to the log file too... */
- fprintf(fplog,"Using %d BFGS correction steps.\n\n",nmaxcorr);
- fprintf(fplog," F-max = %12.5e on atom %d\n",fmax,nfmax+1);
- fprintf(fplog," F-Norm = %12.5e\n",fnorm/sqrt(state->natoms));
- fprintf(fplog,"\n");
- }
-
- point=0;
- for(i=0;i<n;i++)
- if(!frozen[i])
- dx[point][i] = ff[i]; /* Initial search direction */
- else
- dx[point][i] = 0;
-
- stepsize = 1.0/fnorm;
- converged = FALSE;
-
- /* Start the loop over BFGS steps.
- * Each successful step is counted, and we continue until
- * we either converge or reach the max number of steps.
- */
+ const char *CG = "Polak-Ribiere Conjugate Gradients";
- ncorr=0;
-
- /* Set the gradient from the force */
- converged = FALSE;
- for(step=0; (number_steps<0 || (number_steps>=0 && step<=number_steps)) && !converged; step++) {
-
- /* Write coordinates if necessary */
- do_x = do_per_step(step,inputrec->nstxout);
- do_f = do_per_step(step,inputrec->nstfout);
+ em_state_t *s_min, *s_a, *s_b, *s_c;
+ gmx_localtop_t *top;
+ gmx_enerdata_t *enerd;
+ rvec *f;
+ gmx_global_stat_t gstat;
+ t_graph *graph;
+ rvec *f_global, *p, *sf, *sfm;
+ double gpa, gpb, gpc, tmp, sum[2], minstep;
+ real fnormn;
+ real stepsize;
+ real a, b, c, beta = 0.0;
+ real epot_repl = 0;
+ real pnorm;
+ t_mdebin *mdebin;
+ gmx_bool converged, foundlower;
+ rvec mu_tot;
+ gmx_bool do_log = FALSE, do_ene = FALSE, do_x, do_f;
+ tensor vir, pres;
+ int number_steps, neval = 0, nstcg = inputrec->nstcgsteep;
+ gmx_mdoutf_t outf;
+ int i, m, gf, step, nminstep;
+ real terminate = 0;
+
+ step = 0;
+
+ s_min = init_em_state();
+ s_a = init_em_state();
+ s_b = init_em_state();
+ s_c = init_em_state();
+
+ /* Init em and store the local state in s_min */
+ init_em(fplog, CG, cr, inputrec,
+ state_global, top_global, s_min, &top, &f, &f_global,
+ nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
+ nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
+
+ /* Print to log file */
+ print_em_start(fplog, cr, walltime_accounting, wcycle, CG);
+
+ /* Max number of steps */
+ number_steps = inputrec->nsteps;
- mdof_flags = 0;
- if (do_x)
+ if (MASTER(cr))
{
- mdof_flags |= MDOF_X;
+ sp_header(stderr, CG, inputrec->em_tol, number_steps);
}
-
- if (do_f)
+ if (fplog)
{
- mdof_flags |= MDOF_F;
+ sp_header(fplog, CG, inputrec->em_tol, number_steps);
}
- write_traj(fplog,cr,outf,mdof_flags,
- top_global,step,(real)step,state,state,f,f,NULL,NULL);
-
- /* Do the linesearching in the direction dx[point][0..(n-1)] */
-
- /* pointer to current direction - point=0 first time here */
- s=dx[point];
-
- /* calculate line gradient */
- for(gpa=0,i=0;i<n;i++)
- gpa-=s[i]*ff[i];
-
- /* Calculate minimum allowed stepsize, before the average (norm)
- * relative change in coordinate is smaller than precision
+ /* Call the force routine and some auxiliary (neighboursearching etc.) */
+ /* do_force always puts the charge groups in the box and shifts again
+ * We do not unshift, so molecules are always whole in congrad.c
*/
- for(minstep=0,i=0;i<n;i++) {
- tmp=fabs(xx[i]);
- if(tmp<1.0)
- tmp=1.0;
- tmp = s[i]/tmp;
- minstep += tmp*tmp;
- }
- minstep = GMX_REAL_EPS/sqrt(minstep/n);
+ evaluate_energy(fplog, cr,
+ top_global, s_min, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, -1, TRUE);
+ where();
- if(stepsize<minstep) {
- converged=TRUE;
- break;
- }
+ if (MASTER(cr))
+ {
+ /* Copy stuff to the energy bin for easy printing etc. */
+ upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+ mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
+ NULL, NULL, vir, pres, NULL, mu_tot, constr);
- /* Store old forces and coordinates */
- for(i=0;i<n;i++) {
- lastx[i]=xx[i];
- lastf[i]=ff[i];
+ print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
+ print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
+ TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
}
- Epot0=Epot;
-
- first=TRUE;
+ where();
- for(i=0;i<n;i++)
- xa[i]=xx[i];
+ /* Estimate/guess the initial stepsize */
+ stepsize = inputrec->em_stepsize/s_min->fnorm;
- /* Take a step downhill.
- * In theory, we should minimize the function along this direction.
- * That is quite possible, but it turns out to take 5-10 function evaluations
- * for each line. However, we dont really need to find the exact minimum -
- * it is much better to start a new BFGS step in a modified direction as soon
- * as we are close to it. This will save a lot of energy evaluations.
- *
- * In practice, we just try to take a single step.
- * If it worked (i.e. lowered the energy), we increase the stepsize but
- * the continue straight to the next BFGS step without trying to find any minimum.
- * If it didn't work (higher energy), there must be a minimum somewhere between
- * the old position and the new one.
- *
- * Due to the finite numerical accuracy, it turns out that it is a good idea
- * to even accept a SMALL increase in energy, if the derivative is still downhill.
- * This leads to lower final energies in the tests I've done. / Erik
+ if (MASTER(cr))
+ {
+ fprintf(stderr, " F-max = %12.5e on atom %d\n",
+ s_min->fmax, s_min->a_fmax+1);
+ fprintf(stderr, " F-Norm = %12.5e\n",
+ s_min->fnorm/sqrt(state_global->natoms));
+ fprintf(stderr, "\n");
+ /* and copy to the log file too... */
+ fprintf(fplog, " F-max = %12.5e on atom %d\n",
+ s_min->fmax, s_min->a_fmax+1);
+ fprintf(fplog, " F-Norm = %12.5e\n",
+ s_min->fnorm/sqrt(state_global->natoms));
+ fprintf(fplog, "\n");
+ }
+ /* Start the loop over CG steps.
+ * Each successful step is counted, and we continue until
+ * we either converge or reach the max number of steps.
*/
- foundlower=FALSE;
- EpotA = Epot0;
- a = 0.0;
- c = a + stepsize; /* reference position along line is zero */
+ converged = FALSE;
+ for (step = 0; (number_steps < 0 || (number_steps >= 0 && step <= number_steps)) && !converged; step++)
+ {
- /* Check stepsize first. We do not allow displacements
- * larger than emstep.
- */
- do {
- c = a + stepsize;
- maxdelta=0;
- for(i=0;i<n;i++) {
- delta=c*s[i];
- if(delta>maxdelta)
- maxdelta=delta;
- }
- if(maxdelta>inputrec->em_stepsize)
- stepsize*=0.1;
- } while(maxdelta>inputrec->em_stepsize);
-
- /* Take a trial step */
- for (i=0; i<n; i++)
- xc[i] = lastx[i] + c*s[i];
+ /* start taking steps in a new direction
+ * First time we enter the routine, beta=0, and the direction is
+ * simply the negative gradient.
+ */
- neval++;
- /* Calculate energy for the trial step */
- ems.s.x = (rvec *)xc;
- ems.f = (rvec *)fc;
- evaluate_energy(fplog,bVerbose,cr,
- state,top_global,&ems,top,
- inputrec,nrnb,wcycle,gstat,
- vsite,constr,fcd,graph,mdatoms,fr,
- mu_tot,enerd,vir,pres,step,FALSE);
- EpotC = ems.epot;
-
- /* Calc derivative along line */
- for(gpc=0,i=0; i<n; i++) {
- gpc -= s[i]*fc[i]; /* f is negative gradient, thus the sign */
- }
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- gmx_sumd(1,&gpc,cr);
+ /* Calculate the new direction in p, and the gradient in this direction, gpa */
+ p = s_min->s.cg_p;
+ sf = s_min->f;
+ gpa = 0;
+ gf = 0;
+ for (i = 0; i < mdatoms->homenr; i++)
+ {
+ if (mdatoms->cFREEZE)
+ {
+ gf = mdatoms->cFREEZE[i];
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ if (!inputrec->opts.nFreeze[gf][m])
+ {
+ p[i][m] = sf[i][m] + beta*p[i][m];
+ gpa -= p[i][m]*sf[i][m];
+ /* f is negative gradient, thus the sign */
+ }
+ else
+ {
+ p[i][m] = 0;
+ }
+ }
+ }
- /* This is the max amount of increase in energy we tolerate */
- tmp=sqrt(GMX_REAL_EPS)*fabs(EpotA);
+ /* Sum the gradient along the line across CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &gpa, cr);
+ }
- /* Accept the step if the energy is lower, or if it is not significantly higher
- * and the line derivative is still negative.
- */
- if(EpotC<EpotA || (gpc<0 && EpotC<(EpotA+tmp))) {
- foundlower = TRUE;
- /* Great, we found a better energy. Increase step for next iteration
- * if we are still going down, decrease it otherwise
- */
- if(gpc<0)
- stepsize *= 1.618034; /* The golden section */
- else
- stepsize *= 0.618034; /* 1/golden section */
- } else {
- /* New energy is the same or higher. We will have to do some work
- * to find a smaller value in the interval. Take smaller step next time!
- */
- foundlower = FALSE;
- stepsize *= 0.618034;
- }
-
- /* OK, if we didn't find a lower value we will have to locate one now - there must
- * be one in the interval [a=0,c].
- * The same thing is valid here, though: Don't spend dozens of iterations to find
- * the line minimum. We try to interpolate based on the derivative at the endpoints,
- * and only continue until we find a lower value. In most cases this means 1-2 iterations.
- *
- * I also have a safeguard for potentially really patological functions so we never
- * take more than 20 steps before we give up ...
+ /* Calculate the norm of the search vector */
+ get_f_norm_max(cr, &(inputrec->opts), mdatoms, p, &pnorm, NULL, NULL);
+
+ /* Just in case stepsize reaches zero due to numerical precision... */
+ if (stepsize <= 0)
+ {
+ stepsize = inputrec->em_stepsize/pnorm;
+ }
+
+ /*
+ * Double check the value of the derivative in the search direction.
+ * If it is positive it must be due to the old information in the
+ * CG formula, so just remove that and start over with beta=0.
+ * This corresponds to a steepest descent step.
+ */
+ if (gpa > 0)
+ {
+ beta = 0;
+ step--; /* Don't count this step since we are restarting */
+ continue; /* Go back to the beginning of the big for-loop */
+ }
+
+ /* Calculate minimum allowed stepsize, before the average (norm)
+ * relative change in coordinate is smaller than precision
+ */
+ minstep = 0;
+ for (i = 0; i < mdatoms->homenr; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ tmp = fabs(s_min->s.x[i][m]);
+ if (tmp < 1.0)
+ {
+ tmp = 1.0;
+ }
+ tmp = p[i][m]/tmp;
+ minstep += tmp*tmp;
+ }
+ }
+ /* Add up from all CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &minstep, cr);
+ }
+
+ minstep = GMX_REAL_EPS/sqrt(minstep/(3*state_global->natoms));
+
+ if (stepsize < minstep)
+ {
+ converged = TRUE;
+ break;
+ }
+
+ /* Write coordinates if necessary */
+ do_x = do_per_step(step, inputrec->nstxout);
+ do_f = do_per_step(step, inputrec->nstfout);
+
+ write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
+ top_global, inputrec, step,
+ s_min, state_global, f_global);
+
+ /* Take a step downhill.
+ * In theory, we should minimize the function along this direction.
+ * That is quite possible, but it turns out to take 5-10 function evaluations
+ * for each line. However, we dont really need to find the exact minimum -
+ * it is much better to start a new CG step in a modified direction as soon
+ * as we are close to it. This will save a lot of energy evaluations.
+ *
+ * In practice, we just try to take a single step.
+ * If it worked (i.e. lowered the energy), we increase the stepsize but
+ * the continue straight to the next CG step without trying to find any minimum.
+ * If it didn't work (higher energy), there must be a minimum somewhere between
+ * the old position and the new one.
+ *
+ * Due to the finite numerical accuracy, it turns out that it is a good idea
+ * to even accept a SMALL increase in energy, if the derivative is still downhill.
+ * This leads to lower final energies in the tests I've done. / Erik
+ */
+ s_a->epot = s_min->epot;
+ a = 0.0;
+ c = a + stepsize; /* reference position along line is zero */
+
+ if (DOMAINDECOMP(cr) && s_min->s.ddp_count < cr->dd->ddp_count)
+ {
+ em_dd_partition_system(fplog, step, cr, top_global, inputrec,
+ s_min, top, mdatoms, fr, vsite, constr,
+ nrnb, wcycle);
+ }
+
+ /* Take a trial step (new coords in s_c) */
+ do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, c, s_min->s.cg_p, s_c,
+ constr, top, nrnb, wcycle, -1);
+
+ neval++;
+ /* Calculate energy for the trial step */
+ evaluate_energy(fplog, cr,
+ top_global, s_c, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, -1, FALSE);
+
+ /* Calc derivative along line */
+ p = s_c->s.cg_p;
+ sf = s_c->f;
+ gpc = 0;
+ for (i = 0; i < mdatoms->homenr; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ gpc -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
+ }
+ }
+ /* Sum the gradient along the line across CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &gpc, cr);
+ }
+
+ /* This is the max amount of increase in energy we tolerate */
+ tmp = sqrt(GMX_REAL_EPS)*fabs(s_a->epot);
+
+ /* Accept the step if the energy is lower, or if it is not significantly higher
+ * and the line derivative is still negative.
+ */
+ if (s_c->epot < s_a->epot || (gpc < 0 && s_c->epot < (s_a->epot + tmp)))
+ {
+ foundlower = TRUE;
+ /* Great, we found a better energy. Increase step for next iteration
+ * if we are still going down, decrease it otherwise
+ */
+ if (gpc < 0)
+ {
+ stepsize *= 1.618034; /* The golden section */
+ }
+ else
+ {
+ stepsize *= 0.618034; /* 1/golden section */
+ }
+ }
+ else
+ {
+ /* New energy is the same or higher. We will have to do some work
+ * to find a smaller value in the interval. Take smaller step next time!
+ */
+ foundlower = FALSE;
+ stepsize *= 0.618034;
+ }
+
+
+
+
+ /* OK, if we didn't find a lower value we will have to locate one now - there must
+ * be one in the interval [a=0,c].
+ * The same thing is valid here, though: Don't spend dozens of iterations to find
+ * the line minimum. We try to interpolate based on the derivative at the endpoints,
+ * and only continue until we find a lower value. In most cases this means 1-2 iterations.
+ *
+ * I also have a safeguard for potentially really patological functions so we never
+ * take more than 20 steps before we give up ...
+ *
+ * If we already found a lower value we just skip this step and continue to the update.
+ */
+ if (!foundlower)
+ {
+ nminstep = 0;
+
+ do
+ {
+ /* Select a new trial point.
+ * If the derivatives at points a & c have different sign we interpolate to zero,
+ * otherwise just do a bisection.
+ */
+ if (gpa < 0 && gpc > 0)
+ {
+ b = a + gpa*(a-c)/(gpc-gpa);
+ }
+ else
+ {
+ b = 0.5*(a+c);
+ }
+
+ /* safeguard if interpolation close to machine accuracy causes errors:
+ * never go outside the interval
+ */
+ if (b <= a || b >= c)
+ {
+ b = 0.5*(a+c);
+ }
+
+ if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
+ {
+ /* Reload the old state */
+ em_dd_partition_system(fplog, -1, cr, top_global, inputrec,
+ s_min, top, mdatoms, fr, vsite, constr,
+ nrnb, wcycle);
+ }
+
+ /* Take a trial step to this new point - new coords in s_b */
+ do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, b, s_min->s.cg_p, s_b,
+ constr, top, nrnb, wcycle, -1);
+
+ neval++;
+ /* Calculate energy for the trial step */
+ evaluate_energy(fplog, cr,
+ top_global, s_b, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, -1, FALSE);
+
+ /* p does not change within a step, but since the domain decomposition
+ * might change, we have to use cg_p of s_b here.
+ */
+ p = s_b->s.cg_p;
+ sf = s_b->f;
+ gpb = 0;
+ for (i = 0; i < mdatoms->homenr; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ gpb -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
+ }
+ }
+ /* Sum the gradient along the line across CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &gpb, cr);
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n",
+ s_a->epot, s_b->epot, s_c->epot, gpb);
+ }
+
+ epot_repl = s_b->epot;
+
+ /* Keep one of the intervals based on the value of the derivative at the new point */
+ if (gpb > 0)
+ {
+ /* Replace c endpoint with b */
+ swap_em_state(s_b, s_c);
+ c = b;
+ gpc = gpb;
+ }
+ else
+ {
+ /* Replace a endpoint with b */
+ swap_em_state(s_b, s_a);
+ a = b;
+ gpa = gpb;
+ }
+
+ /*
+ * Stop search as soon as we find a value smaller than the endpoints.
+ * Never run more than 20 steps, no matter what.
+ */
+ nminstep++;
+ }
+ while ((epot_repl > s_a->epot || epot_repl > s_c->epot) &&
+ (nminstep < 20));
+
+ if (fabs(epot_repl - s_min->epot) < fabs(s_min->epot)*GMX_REAL_EPS ||
+ nminstep >= 20)
+ {
+ /* OK. We couldn't find a significantly lower energy.
+ * If beta==0 this was steepest descent, and then we give up.
+ * If not, set beta=0 and restart with steepest descent before quitting.
+ */
+ if (beta == 0.0)
+ {
+ /* Converged */
+ converged = TRUE;
+ break;
+ }
+ else
+ {
+ /* Reset memory before giving up */
+ beta = 0.0;
+ continue;
+ }
+ }
+
+ /* Select min energy state of A & C, put the best in B.
+ */
+ if (s_c->epot < s_a->epot)
+ {
+ if (debug)
+ {
+ fprintf(debug, "CGE: C (%f) is lower than A (%f), moving C to B\n",
+ s_c->epot, s_a->epot);
+ }
+ swap_em_state(s_b, s_c);
+ gpb = gpc;
+ b = c;
+ }
+ else
+ {
+ if (debug)
+ {
+ fprintf(debug, "CGE: A (%f) is lower than C (%f), moving A to B\n",
+ s_a->epot, s_c->epot);
+ }
+ swap_em_state(s_b, s_a);
+ gpb = gpa;
+ b = a;
+ }
+
+ }
+ else
+ {
+ if (debug)
+ {
+ fprintf(debug, "CGE: Found a lower energy %f, moving C to B\n",
+ s_c->epot);
+ }
+ swap_em_state(s_b, s_c);
+ gpb = gpc;
+ b = c;
+ }
+
+ /* new search direction */
+ /* beta = 0 means forget all memory and restart with steepest descents. */
+ if (nstcg && ((step % nstcg) == 0))
+ {
+ beta = 0.0;
+ }
+ else
+ {
+ /* s_min->fnorm cannot be zero, because then we would have converged
+ * and broken out.
+ */
+
+ /* Polak-Ribiere update.
+ * Change to fnorm2/fnorm2_old for Fletcher-Reeves
+ */
+ beta = pr_beta(cr, &inputrec->opts, mdatoms, top_global, s_min, s_b);
+ }
+ /* Limit beta to prevent oscillations */
+ if (fabs(beta) > 5.0)
+ {
+ beta = 0.0;
+ }
+
+
+ /* update positions */
+ swap_em_state(s_min, s_b);
+ gpa = gpb;
+
+ /* Print it if necessary */
+ if (MASTER(cr))
+ {
+ if (bVerbose)
+ {
+ fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
+ step, s_min->epot, s_min->fnorm/sqrt(state_global->natoms),
+ s_min->fmax, s_min->a_fmax+1);
+ }
+ /* Store the new (lower) energies */
+ upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+ mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
+ NULL, NULL, vir, pres, NULL, mu_tot, constr);
+
+ do_log = do_per_step(step, inputrec->nstlog);
+ do_ene = do_per_step(step, inputrec->nstenergy);
+
+ /* Prepare IMD energy record, if bIMD is TRUE. */
+ IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, step, TRUE);
+
+ if (do_log)
+ {
+ print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
+ }
+ print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
+ do_log ? fplog : NULL, step, step, eprNORMAL,
+ TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ }
+
+ /* Send energies and positions to the IMD client if bIMD is TRUE. */
+ if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
+ {
+ IMD_send_positions(inputrec->imd);
+ }
+
+ /* Stop when the maximum force lies below tolerance.
+ * If we have reached machine precision, converged is already set to true.
+ */
+ converged = converged || (s_min->fmax < inputrec->em_tol);
+
+ } /* End of the loop */
+
+ /* IMD cleanup, if bIMD is TRUE. */
+ IMD_finalize(inputrec->bIMD, inputrec->imd);
+
+ if (converged)
+ {
+ step--; /* we never took that last step in this case */
+
+ }
+ if (s_min->fmax > inputrec->em_tol)
+ {
+ if (MASTER(cr))
+ {
+ warn_step(stderr, inputrec->em_tol, step-1 == number_steps, FALSE);
+ warn_step(fplog, inputrec->em_tol, step-1 == number_steps, FALSE);
+ }
+ converged = FALSE;
+ }
+
+ if (MASTER(cr))
+ {
+ /* If we printed energy and/or logfile last step (which was the last step)
+ * we don't have to do it again, but otherwise print the final values.
+ */
+ if (!do_log)
+ {
+ /* Write final value to log since we didn't do anything the last step */
+ print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
+ }
+ if (!do_ene || !do_log)
+ {
+ /* Write final energy file entries */
+ print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
+ !do_log ? fplog : NULL, step, step, eprNORMAL,
+ TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ }
+ }
+
+ /* Print some stuff... */
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+ }
+
+ /* IMPORTANT!
+ * For accurate normal mode calculation it is imperative that we
+ * store the last conformation into the full precision binary trajectory.
*
- * If we already found a lower value we just skip this step and continue to the update.
+ * However, we should only do it if we did NOT already write this step
+ * above (which we did if do_x or do_f was true).
+ */
+ do_x = !do_per_step(step, inputrec->nstxout);
+ do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout));
+
+ write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
+ top_global, inputrec, step,
+ s_min, state_global, f_global);
+
+ fnormn = s_min->fnorm/sqrt(state_global->natoms);
+
+ if (MASTER(cr))
+ {
+ print_converged(stderr, CG, inputrec->em_tol, step, converged, number_steps,
+ s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+ print_converged(fplog, CG, inputrec->em_tol, step, converged, number_steps,
+ s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+
+ fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
+ }
+
+ finish_em(cr, outf, walltime_accounting, wcycle);
+
+ /* To print the actual number of steps we needed somewhere */
+ walltime_accounting_set_nsteps_done(walltime_accounting, step);
+
+ return 0;
+} /* That's all folks */
+
+
+double do_lbfgs(FILE *fplog, t_commrec *cr,
+ int nfile, const t_filenm fnm[],
+ const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
+ int gmx_unused nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int gmx_unused stepout,
+ t_inputrec *inputrec,
+ gmx_mtop_t *top_global, t_fcdata *fcd,
+ t_state *state,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t gmx_unused ed,
+ t_forcerec *fr,
+ int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused membed,
+ real gmx_unused cpt_period, real gmx_unused max_hours,
+ const char gmx_unused *deviceOptions,
+ int imdport,
+ unsigned long gmx_unused Flags,
+ gmx_walltime_accounting_t walltime_accounting)
+{
+ static const char *LBFGS = "Low-Memory BFGS Minimizer";
+ em_state_t ems;
+ gmx_localtop_t *top;
+ gmx_enerdata_t *enerd;
+ rvec *f;
+ gmx_global_stat_t gstat;
+ t_graph *graph;
+ rvec *f_global;
+ int ncorr, nmaxcorr, point, cp, neval, nminstep;
+ double stepsize, gpa, gpb, gpc, tmp, minstep;
+ real *rho, *alpha, *ff, *xx, *p, *s, *lastx, *lastf, **dx, **dg;
+ real *xa, *xb, *xc, *fa, *fb, *fc, *xtmp, *ftmp;
+ real a, b, c, maxdelta, delta;
+ real diag, Epot0, Epot, EpotA, EpotB, EpotC;
+ real dgdx, dgdg, sq, yr, beta;
+ t_mdebin *mdebin;
+ gmx_bool converged, first;
+ rvec mu_tot;
+ real fnorm, fmax;
+ gmx_bool do_log, do_ene, do_x, do_f, foundlower, *frozen;
+ tensor vir, pres;
+ int start, end, number_steps;
+ gmx_mdoutf_t outf;
+ int i, k, m, n, nfmax, gf, step;
+ int mdof_flags;
+ /* not used */
+ real terminate;
+
+ if (PAR(cr))
+ {
+ gmx_fatal(FARGS, "Cannot do parallel L-BFGS Minimization - yet.\n");
+ }
+
+ if (NULL != constr)
+ {
+ gmx_fatal(FARGS, "The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent).");
+ }
+
+ n = 3*state->natoms;
+ nmaxcorr = inputrec->nbfgscorr;
+
+ /* Allocate memory */
+ /* Use pointers to real so we dont have to loop over both atoms and
+ * dimensions all the time...
+ * x/f are allocated as rvec *, so make new x0/f0 pointers-to-real
+ * that point to the same memory.
+ */
+ snew(xa, n);
+ snew(xb, n);
+ snew(xc, n);
+ snew(fa, n);
+ snew(fb, n);
+ snew(fc, n);
+ snew(frozen, n);
+
+ snew(p, n);
+ snew(lastx, n);
+ snew(lastf, n);
+ snew(rho, nmaxcorr);
+ snew(alpha, nmaxcorr);
+
+ snew(dx, nmaxcorr);
+ for (i = 0; i < nmaxcorr; i++)
+ {
+ snew(dx[i], n);
+ }
+
+ snew(dg, nmaxcorr);
+ for (i = 0; i < nmaxcorr; i++)
+ {
+ snew(dg[i], n);
+ }
+
+ step = 0;
+ neval = 0;
+
+ /* Init em */
+ init_em(fplog, LBFGS, cr, inputrec,
+ state, top_global, &ems, &top, &f, &f_global,
+ nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
+ nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
+ /* Do_lbfgs is not completely updated like do_steep and do_cg,
+ * so we free some memory again.
+ */
+ sfree(ems.s.x);
+ sfree(ems.f);
+
+ xx = (real *)state->x;
+ ff = (real *)f;
+
+ start = 0;
+ end = mdatoms->homenr;
+
+ /* Print to log file */
+ print_em_start(fplog, cr, walltime_accounting, wcycle, LBFGS);
+
+ do_log = do_ene = do_x = do_f = TRUE;
+
+ /* Max number of steps */
+ number_steps = inputrec->nsteps;
+
+ /* Create a 3*natoms index to tell whether each degree of freedom is frozen */
+ gf = 0;
+ for (i = start; i < end; i++)
+ {
+ if (mdatoms->cFREEZE)
+ {
+ gf = mdatoms->cFREEZE[i];
+ }
+ for (m = 0; m < DIM; m++)
+ {
+ frozen[3*i+m] = inputrec->opts.nFreeze[gf][m];
+ }
+ }
+ if (MASTER(cr))
+ {
+ sp_header(stderr, LBFGS, inputrec->em_tol, number_steps);
+ }
+ if (fplog)
+ {
+ sp_header(fplog, LBFGS, inputrec->em_tol, number_steps);
+ }
+
+ if (vsite)
+ {
+ construct_vsites(vsite, state->x, 1, NULL,
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, cr, state->box);
+ }
+
+ /* Call the force routine and some auxiliary (neighboursearching etc.) */
+ /* do_force always puts the charge groups in the box and shifts again
+ * We do not unshift, so molecules are always whole
*/
+ neval++;
+ ems.s.x = state->x;
+ ems.f = f;
+ evaluate_energy(fplog, cr,
+ top_global, &ems, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, -1, TRUE);
+ where();
+
+ if (MASTER(cr))
+ {
+ /* Copy stuff to the energy bin for easy printing etc. */
+ upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+ mdatoms->tmass, enerd, state, inputrec->fepvals, inputrec->expandedvals, state->box,
+ NULL, NULL, vir, pres, NULL, mu_tot, constr);
+
+ print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
+ print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
+ TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ }
+ where();
+
+ /* This is the starting energy */
+ Epot = enerd->term[F_EPOT];
+
+ fnorm = ems.fnorm;
+ fmax = ems.fmax;
+ nfmax = ems.a_fmax;
+
+ /* Set the initial step.
+ * since it will be multiplied by the non-normalized search direction
+ * vector (force vector the first time), we scale it by the
+ * norm of the force.
+ */
+
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "Using %d BFGS correction steps.\n\n", nmaxcorr);
+ fprintf(stderr, " F-max = %12.5e on atom %d\n", fmax, nfmax+1);
+ fprintf(stderr, " F-Norm = %12.5e\n", fnorm/sqrt(state->natoms));
+ fprintf(stderr, "\n");
+ /* and copy to the log file too... */
+ fprintf(fplog, "Using %d BFGS correction steps.\n\n", nmaxcorr);
+ fprintf(fplog, " F-max = %12.5e on atom %d\n", fmax, nfmax+1);
+ fprintf(fplog, " F-Norm = %12.5e\n", fnorm/sqrt(state->natoms));
+ fprintf(fplog, "\n");
+ }
+
+ point = 0;
+ for (i = 0; i < n; i++)
+ {
+ if (!frozen[i])
+ {
+ dx[point][i] = ff[i]; /* Initial search direction */
+ }
+ else
+ {
+ dx[point][i] = 0;
+ }
+ }
+
+ stepsize = 1.0/fnorm;
+ converged = FALSE;
+
+ /* Start the loop over BFGS steps.
+ * Each successful step is counted, and we continue until
+ * we either converge or reach the max number of steps.
+ */
+
+ ncorr = 0;
+
+ /* Set the gradient from the force */
+ converged = FALSE;
+ for (step = 0; (number_steps < 0 || (number_steps >= 0 && step <= number_steps)) && !converged; step++)
+ {
+
+ /* Write coordinates if necessary */
+ do_x = do_per_step(step, inputrec->nstxout);
+ do_f = do_per_step(step, inputrec->nstfout);
+
+ mdof_flags = 0;
+ if (do_x)
+ {
+ mdof_flags |= MDOF_X;
+ }
+
+ if (do_f)
+ {
+ mdof_flags |= MDOF_F;
+ }
+
+ if (inputrec->bIMD)
+ {
+ mdof_flags |= MDOF_IMD;
+ }
+
+ mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
+ top_global, step, (real)step, state, state, f, f);
+
+ /* Do the linesearching in the direction dx[point][0..(n-1)] */
+
+ /* pointer to current direction - point=0 first time here */
+ s = dx[point];
+
+ /* calculate line gradient */
+ for (gpa = 0, i = 0; i < n; i++)
+ {
+ gpa -= s[i]*ff[i];
+ }
+
+ /* Calculate minimum allowed stepsize, before the average (norm)
+ * relative change in coordinate is smaller than precision
+ */
+ for (minstep = 0, i = 0; i < n; i++)
+ {
+ tmp = fabs(xx[i]);
+ if (tmp < 1.0)
+ {
+ tmp = 1.0;
+ }
+ tmp = s[i]/tmp;
+ minstep += tmp*tmp;
+ }
+ minstep = GMX_REAL_EPS/sqrt(minstep/n);
+
+ if (stepsize < minstep)
+ {
+ converged = TRUE;
+ break;
+ }
+
+ /* Store old forces and coordinates */
+ for (i = 0; i < n; i++)
+ {
+ lastx[i] = xx[i];
+ lastf[i] = ff[i];
+ }
+ Epot0 = Epot;
+
+ first = TRUE;
- if(!foundlower) {
-
- nminstep=0;
- do {
- /* Select a new trial point.
- * If the derivatives at points a & c have different sign we interpolate to zero,
- * otherwise just do a bisection.
- */
-
- if(gpa<0 && gpc>0)
- b = a + gpa*(a-c)/(gpc-gpa);
- else
- b = 0.5*(a+c);
-
- /* safeguard if interpolation close to machine accuracy causes errors:
- * never go outside the interval
- */
- if(b<=a || b>=c)
- b = 0.5*(a+c);
-
- /* Take a trial step */
- for (i=0; i<n; i++)
- xb[i] = lastx[i] + b*s[i];
-
- neval++;
- /* Calculate energy for the trial step */
- ems.s.x = (rvec *)xb;
- ems.f = (rvec *)fb;
- evaluate_energy(fplog,bVerbose,cr,
- state,top_global,&ems,top,
- inputrec,nrnb,wcycle,gstat,
- vsite,constr,fcd,graph,mdatoms,fr,
- mu_tot,enerd,vir,pres,step,FALSE);
- EpotB = ems.epot;
-
- fnorm = ems.fnorm;
-
- for(gpb=0,i=0; i<n; i++)
- gpb -= s[i]*fb[i]; /* f is negative gradient, thus the sign */
-
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- gmx_sumd(1,&gpb,cr);
-
- /* Keep one of the intervals based on the value of the derivative at the new point */
- if(gpb>0) {
- /* Replace c endpoint with b */
- EpotC = EpotB;
- c = b;
- gpc = gpb;
- /* swap coord pointers b/c */
- xtmp = xb;
- ftmp = fb;
- xb = xc;
- fb = fc;
- xc = xtmp;
- fc = ftmp;
- } else {
- /* Replace a endpoint with b */
- EpotA = EpotB;
- a = b;
- gpa = gpb;
- /* swap coord pointers a/b */
- xtmp = xb;
- ftmp = fb;
- xb = xa;
- fb = fa;
- xa = xtmp;
- fa = ftmp;
- }
-
- /*
- * Stop search as soon as we find a value smaller than the endpoints,
- * or if the tolerance is below machine precision.
- * Never run more than 20 steps, no matter what.
- */
- nminstep++;
- } while((EpotB>EpotA || EpotB>EpotC) && (nminstep<20));
-
- if(fabs(EpotB-Epot0)<GMX_REAL_EPS || nminstep>=20) {
- /* OK. We couldn't find a significantly lower energy.
- * If ncorr==0 this was steepest descent, and then we give up.
- * If not, reset memory to restart as steepest descent before quitting.
+ for (i = 0; i < n; i++)
+ {
+ xa[i] = xx[i];
+ }
+
+ /* Take a step downhill.
+ * In theory, we should minimize the function along this direction.
+ * That is quite possible, but it turns out to take 5-10 function evaluations
+ * for each line. However, we dont really need to find the exact minimum -
+ * it is much better to start a new BFGS step in a modified direction as soon
+ * as we are close to it. This will save a lot of energy evaluations.
+ *
+ * In practice, we just try to take a single step.
+ * If it worked (i.e. lowered the energy), we increase the stepsize but
+ * the continue straight to the next BFGS step without trying to find any minimum.
+ * If it didn't work (higher energy), there must be a minimum somewhere between
+ * the old position and the new one.
+ *
+ * Due to the finite numerical accuracy, it turns out that it is a good idea
+ * to even accept a SMALL increase in energy, if the derivative is still downhill.
+ * This leads to lower final energies in the tests I've done. / Erik
*/
- if(ncorr==0) {
- /* Converged */
- converged=TRUE;
- break;
- } else {
- /* Reset memory */
- ncorr=0;
- /* Search in gradient direction */
- for(i=0;i<n;i++)
- dx[point][i]=ff[i];
- /* Reset stepsize */
- stepsize = 1.0/fnorm;
- continue;
- }
- }
-
- /* Select min energy state of A & C, put the best in xx/ff/Epot
- */
- if(EpotC<EpotA) {
- Epot = EpotC;
- /* Use state C */
- for(i=0;i<n;i++) {
- xx[i]=xc[i];
- ff[i]=fc[i];
- }
- stepsize=c;
- } else {
- Epot = EpotA;
- /* Use state A */
- for(i=0;i<n;i++) {
- xx[i]=xa[i];
- ff[i]=fa[i];
- }
- stepsize=a;
- }
-
- } else {
- /* found lower */
- Epot = EpotC;
- /* Use state C */
- for(i=0;i<n;i++) {
- xx[i]=xc[i];
- ff[i]=fc[i];
- }
- stepsize=c;
- }
-
- /* Update the memory information, and calculate a new
- * approximation of the inverse hessian
- */
+ foundlower = FALSE;
+ EpotA = Epot0;
+ a = 0.0;
+ c = a + stepsize; /* reference position along line is zero */
- /* Have new data in Epot, xx, ff */
- if(ncorr<nmaxcorr)
- ncorr++;
+ /* Check stepsize first. We do not allow displacements
+ * larger than emstep.
+ */
+ do
+ {
+ c = a + stepsize;
+ maxdelta = 0;
+ for (i = 0; i < n; i++)
+ {
+ delta = c*s[i];
+ if (delta > maxdelta)
+ {
+ maxdelta = delta;
+ }
+ }
+ if (maxdelta > inputrec->em_stepsize)
+ {
+ stepsize *= 0.1;
+ }
+ }
+ while (maxdelta > inputrec->em_stepsize);
- for(i=0;i<n;i++) {
- dg[point][i]=lastf[i]-ff[i];
- dx[point][i]*=stepsize;
- }
+ /* Take a trial step */
+ for (i = 0; i < n; i++)
+ {
+ xc[i] = lastx[i] + c*s[i];
+ }
- dgdg=0;
- dgdx=0;
- for(i=0;i<n;i++) {
- dgdg+=dg[point][i]*dg[point][i];
- dgdx+=dg[point][i]*dx[point][i];
- }
+ neval++;
+ /* Calculate energy for the trial step */
+ ems.s.x = (rvec *)xc;
+ ems.f = (rvec *)fc;
+ evaluate_energy(fplog, cr,
+ top_global, &ems, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, step, FALSE);
+ EpotC = ems.epot;
+
+ /* Calc derivative along line */
+ for (gpc = 0, i = 0; i < n; i++)
+ {
+ gpc -= s[i]*fc[i]; /* f is negative gradient, thus the sign */
+ }
+ /* Sum the gradient along the line across CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &gpc, cr);
+ }
- diag=dgdx/dgdg;
+ /* This is the max amount of increase in energy we tolerate */
+ tmp = sqrt(GMX_REAL_EPS)*fabs(EpotA);
- rho[point]=1.0/dgdx;
- point++;
+ /* Accept the step if the energy is lower, or if it is not significantly higher
+ * and the line derivative is still negative.
+ */
+ if (EpotC < EpotA || (gpc < 0 && EpotC < (EpotA+tmp)))
+ {
+ foundlower = TRUE;
+ /* Great, we found a better energy. Increase step for next iteration
+ * if we are still going down, decrease it otherwise
+ */
+ if (gpc < 0)
+ {
+ stepsize *= 1.618034; /* The golden section */
+ }
+ else
+ {
+ stepsize *= 0.618034; /* 1/golden section */
+ }
+ }
+ else
+ {
+ /* New energy is the same or higher. We will have to do some work
+ * to find a smaller value in the interval. Take smaller step next time!
+ */
+ foundlower = FALSE;
+ stepsize *= 0.618034;
+ }
- if(point>=nmaxcorr)
- point=0;
+ /* OK, if we didn't find a lower value we will have to locate one now - there must
+ * be one in the interval [a=0,c].
+ * The same thing is valid here, though: Don't spend dozens of iterations to find
+ * the line minimum. We try to interpolate based on the derivative at the endpoints,
+ * and only continue until we find a lower value. In most cases this means 1-2 iterations.
+ *
+ * I also have a safeguard for potentially really patological functions so we never
+ * take more than 20 steps before we give up ...
+ *
+ * If we already found a lower value we just skip this step and continue to the update.
+ */
- /* Update */
- for(i=0;i<n;i++)
- p[i]=ff[i];
+ if (!foundlower)
+ {
- cp=point;
+ nminstep = 0;
+ do
+ {
+ /* Select a new trial point.
+ * If the derivatives at points a & c have different sign we interpolate to zero,
+ * otherwise just do a bisection.
+ */
- /* Recursive update. First go back over the memory points */
- for(k=0;k<ncorr;k++) {
- cp--;
- if(cp<0)
- cp=ncorr-1;
+ if (gpa < 0 && gpc > 0)
+ {
+ b = a + gpa*(a-c)/(gpc-gpa);
+ }
+ else
+ {
+ b = 0.5*(a+c);
+ }
- sq=0;
- for(i=0;i<n;i++)
- sq+=dx[cp][i]*p[i];
+ /* safeguard if interpolation close to machine accuracy causes errors:
+ * never go outside the interval
+ */
+ if (b <= a || b >= c)
+ {
+ b = 0.5*(a+c);
+ }
- alpha[cp]=rho[cp]*sq;
+ /* Take a trial step */
+ for (i = 0; i < n; i++)
+ {
+ xb[i] = lastx[i] + b*s[i];
+ }
- for(i=0;i<n;i++)
- p[i] -= alpha[cp]*dg[cp][i];
- }
+ neval++;
+ /* Calculate energy for the trial step */
+ ems.s.x = (rvec *)xb;
+ ems.f = (rvec *)fb;
+ evaluate_energy(fplog, cr,
+ top_global, &ems, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, step, FALSE);
+ EpotB = ems.epot;
- for(i=0;i<n;i++)
- p[i] *= diag;
+ fnorm = ems.fnorm;
- /* And then go forward again */
- for(k=0;k<ncorr;k++) {
- yr = 0;
- for(i=0;i<n;i++)
- yr += p[i]*dg[cp][i];
+ for (gpb = 0, i = 0; i < n; i++)
+ {
+ gpb -= s[i]*fb[i]; /* f is negative gradient, thus the sign */
- beta = rho[cp]*yr;
- beta = alpha[cp]-beta;
+ }
+ /* Sum the gradient along the line across CPUs */
+ if (PAR(cr))
+ {
+ gmx_sumd(1, &gpb, cr);
+ }
- for(i=0;i<n;i++)
- p[i] += beta*dx[cp][i];
+ /* Keep one of the intervals based on the value of the derivative at the new point */
+ if (gpb > 0)
+ {
+ /* Replace c endpoint with b */
+ EpotC = EpotB;
+ c = b;
+ gpc = gpb;
+ /* swap coord pointers b/c */
+ xtmp = xb;
+ ftmp = fb;
+ xb = xc;
+ fb = fc;
+ xc = xtmp;
+ fc = ftmp;
+ }
+ else
+ {
+ /* Replace a endpoint with b */
+ EpotA = EpotB;
+ a = b;
+ gpa = gpb;
+ /* swap coord pointers a/b */
+ xtmp = xb;
+ ftmp = fb;
+ xb = xa;
+ fb = fa;
+ xa = xtmp;
+ fa = ftmp;
+ }
- cp++;
- if(cp>=ncorr)
- cp=0;
- }
+ /*
+ * Stop search as soon as we find a value smaller than the endpoints,
+ * or if the tolerance is below machine precision.
+ * Never run more than 20 steps, no matter what.
+ */
+ nminstep++;
+ }
+ while ((EpotB > EpotA || EpotB > EpotC) && (nminstep < 20));
- for(i=0;i<n;i++)
- if(!frozen[i])
- dx[point][i] = p[i];
- else
- dx[point][i] = 0;
+ if (fabs(EpotB-Epot0) < GMX_REAL_EPS || nminstep >= 20)
+ {
+ /* OK. We couldn't find a significantly lower energy.
+ * If ncorr==0 this was steepest descent, and then we give up.
+ * If not, reset memory to restart as steepest descent before quitting.
+ */
+ if (ncorr == 0)
+ {
+ /* Converged */
+ converged = TRUE;
+ break;
+ }
+ else
+ {
+ /* Reset memory */
+ ncorr = 0;
+ /* Search in gradient direction */
+ for (i = 0; i < n; i++)
+ {
+ dx[point][i] = ff[i];
+ }
+ /* Reset stepsize */
+ stepsize = 1.0/fnorm;
+ continue;
+ }
+ }
+
+ /* Select min energy state of A & C, put the best in xx/ff/Epot
+ */
+ if (EpotC < EpotA)
+ {
+ Epot = EpotC;
+ /* Use state C */
+ for (i = 0; i < n; i++)
+ {
+ xx[i] = xc[i];
+ ff[i] = fc[i];
+ }
+ stepsize = c;
+ }
+ else
+ {
+ Epot = EpotA;
+ /* Use state A */
+ for (i = 0; i < n; i++)
+ {
+ xx[i] = xa[i];
+ ff[i] = fa[i];
+ }
+ stepsize = a;
+ }
- stepsize=1.0;
+ }
+ else
+ {
+ /* found lower */
+ Epot = EpotC;
+ /* Use state C */
+ for (i = 0; i < n; i++)
+ {
+ xx[i] = xc[i];
+ ff[i] = fc[i];
+ }
+ stepsize = c;
+ }
- /* Test whether the convergence criterion is met */
- get_f_norm_max(cr,&(inputrec->opts),mdatoms,f,&fnorm,&fmax,&nfmax);
+ /* Update the memory information, and calculate a new
+ * approximation of the inverse hessian
+ */
- /* Print it if necessary */
- if (MASTER(cr)) {
- if(bVerbose)
- fprintf(stderr,"\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
- step,Epot,fnorm/sqrt(state->natoms),fmax,nfmax+1);
- /* Store the new (lower) energies */
- upd_mdebin(mdebin,FALSE,FALSE,(double)step,
- mdatoms->tmass,enerd,state,inputrec->fepvals,inputrec->expandedvals,state->box,
- NULL,NULL,vir,pres,NULL,mu_tot,constr);
- do_log = do_per_step(step,inputrec->nstlog);
- do_ene = do_per_step(step,inputrec->nstenergy);
- if(do_log)
- print_ebin_header(fplog,step,step,state->lambda[efptFEP]);
- print_ebin(outf->fp_ene,do_ene,FALSE,FALSE,
- do_log ? fplog : NULL,step,step,eprNORMAL,
- TRUE,mdebin,fcd,&(top_global->groups),&(inputrec->opts));
- }
+ /* Have new data in Epot, xx, ff */
+ if (ncorr < nmaxcorr)
+ {
+ ncorr++;
+ }
- /* Stop when the maximum force lies below tolerance.
- * If we have reached machine precision, converged is already set to true.
- */
+ for (i = 0; i < n; i++)
+ {
+ dg[point][i] = lastf[i]-ff[i];
+ dx[point][i] *= stepsize;
+ }
+
+ dgdg = 0;
+ dgdx = 0;
+ for (i = 0; i < n; i++)
+ {
+ dgdg += dg[point][i]*dg[point][i];
+ dgdx += dg[point][i]*dx[point][i];
+ }
+
+ diag = dgdx/dgdg;
+
+ rho[point] = 1.0/dgdx;
+ point++;
+
+ if (point >= nmaxcorr)
+ {
+ point = 0;
+ }
+
+ /* Update */
+ for (i = 0; i < n; i++)
+ {
+ p[i] = ff[i];
+ }
+
+ cp = point;
+
+ /* Recursive update. First go back over the memory points */
+ for (k = 0; k < ncorr; k++)
+ {
+ cp--;
+ if (cp < 0)
+ {
+ cp = ncorr-1;
+ }
+
+ sq = 0;
+ for (i = 0; i < n; i++)
+ {
+ sq += dx[cp][i]*p[i];
+ }
+
+ alpha[cp] = rho[cp]*sq;
+
+ for (i = 0; i < n; i++)
+ {
+ p[i] -= alpha[cp]*dg[cp][i];
+ }
+ }
+
+ for (i = 0; i < n; i++)
+ {
+ p[i] *= diag;
+ }
+
+ /* And then go forward again */
+ for (k = 0; k < ncorr; k++)
+ {
+ yr = 0;
+ for (i = 0; i < n; i++)
+ {
+ yr += p[i]*dg[cp][i];
+ }
+
+ beta = rho[cp]*yr;
+ beta = alpha[cp]-beta;
- converged = converged || (fmax < inputrec->em_tol);
+ for (i = 0; i < n; i++)
+ {
+ p[i] += beta*dx[cp][i];
+ }
+
+ cp++;
+ if (cp >= ncorr)
+ {
+ cp = 0;
+ }
+ }
+
+ for (i = 0; i < n; i++)
+ {
+ if (!frozen[i])
+ {
+ dx[point][i] = p[i];
+ }
+ else
+ {
+ dx[point][i] = 0;
+ }
+ }
+
+ stepsize = 1.0;
+
+ /* Test whether the convergence criterion is met */
+ get_f_norm_max(cr, &(inputrec->opts), mdatoms, f, &fnorm, &fmax, &nfmax);
- } /* End of the loop */
+ /* Print it if necessary */
+ if (MASTER(cr))
+ {
+ if (bVerbose)
+ {
+ fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
+ step, Epot, fnorm/sqrt(state->natoms), fmax, nfmax+1);
+ }
+ /* Store the new (lower) energies */
+ upd_mdebin(mdebin, FALSE, FALSE, (double)step,
+ mdatoms->tmass, enerd, state, inputrec->fepvals, inputrec->expandedvals, state->box,
+ NULL, NULL, vir, pres, NULL, mu_tot, constr);
+ do_log = do_per_step(step, inputrec->nstlog);
+ do_ene = do_per_step(step, inputrec->nstenergy);
+ if (do_log)
+ {
+ print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
+ }
+ print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
+ do_log ? fplog : NULL, step, step, eprNORMAL,
+ TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ }
+
+ /* Send x and E to IMD client, if bIMD is TRUE. */
+ if (do_IMD(inputrec->bIMD, step, cr, TRUE, state->box, state->x, inputrec, 0, wcycle) && MASTER(cr))
+ {
+ IMD_send_positions(inputrec->imd);
+ }
+
+ /* Stop when the maximum force lies below tolerance.
+ * If we have reached machine precision, converged is already set to true.
+ */
- if(converged)
- step--; /* we never took that last step in this case */
+ converged = converged || (fmax < inputrec->em_tol);
+
+ } /* End of the loop */
+
+ /* IMD cleanup, if bIMD is TRUE. */
+ IMD_finalize(inputrec->bIMD, inputrec->imd);
+
+ if (converged)
+ {
+ step--; /* we never took that last step in this case */
- if(fmax>inputrec->em_tol)
+ }
+ if (fmax > inputrec->em_tol)
{
if (MASTER(cr))
{
- warn_step(stderr,inputrec->em_tol,step-1==number_steps,FALSE);
- warn_step(fplog ,inputrec->em_tol,step-1==number_steps,FALSE);
+ warn_step(stderr, inputrec->em_tol, step-1 == number_steps, FALSE);
+ warn_step(fplog, inputrec->em_tol, step-1 == number_steps, FALSE);
}
converged = FALSE;
}
- /* If we printed energy and/or logfile last step (which was the last step)
- * we don't have to do it again, but otherwise print the final values.
- */
- if(!do_log) /* Write final value to log since we didn't do anythin last step */
- print_ebin_header(fplog,step,step,state->lambda[efptFEP]);
- if(!do_ene || !do_log) /* Write final energy file entries */
- print_ebin(outf->fp_ene,!do_ene,FALSE,FALSE,
- !do_log ? fplog : NULL,step,step,eprNORMAL,
- TRUE,mdebin,fcd,&(top_global->groups),&(inputrec->opts));
-
- /* Print some stuff... */
- if (MASTER(cr))
- fprintf(stderr,"\nwriting lowest energy coordinates.\n");
-
- /* IMPORTANT!
- * For accurate normal mode calculation it is imperative that we
- * store the last conformation into the full precision binary trajectory.
- *
- * However, we should only do it if we did NOT already write this step
- * above (which we did if do_x or do_f was true).
- */
- do_x = !do_per_step(step,inputrec->nstxout);
- do_f = !do_per_step(step,inputrec->nstfout);
- write_em_traj(fplog,cr,outf,do_x,do_f,ftp2fn(efSTO,nfile,fnm),
- top_global,inputrec,step,
- &ems,state,f);
-
- if (MASTER(cr)) {
- print_converged(stderr,LBFGS,inputrec->em_tol,step,converged,
- number_steps,Epot,fmax,nfmax,fnorm/sqrt(state->natoms));
- print_converged(fplog,LBFGS,inputrec->em_tol,step,converged,
- number_steps,Epot,fmax,nfmax,fnorm/sqrt(state->natoms));
-
- fprintf(fplog,"\nPerformed %d energy evaluations in total.\n",neval);
- }
-
- finish_em(fplog,cr,outf,runtime,wcycle);
-
- /* To print the actual number of steps we needed somewhere */
- runtime->nsteps_done = step;
-
- return 0;
+ /* If we printed energy and/or logfile last step (which was the last step)
+ * we don't have to do it again, but otherwise print the final values.
+ */
+ if (!do_log) /* Write final value to log since we didn't do anythin last step */
+ {
+ print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
+ }
+ if (!do_ene || !do_log) /* Write final energy file entries */
+ {
+ print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
+ !do_log ? fplog : NULL, step, step, eprNORMAL,
+ TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ }
+
+ /* Print some stuff... */
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+ }
+
+ /* IMPORTANT!
+ * For accurate normal mode calculation it is imperative that we
+ * store the last conformation into the full precision binary trajectory.
+ *
+ * However, we should only do it if we did NOT already write this step
+ * above (which we did if do_x or do_f was true).
+ */
+ do_x = !do_per_step(step, inputrec->nstxout);
+ do_f = !do_per_step(step, inputrec->nstfout);
+ write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
+ top_global, inputrec, step,
+ &ems, state, f);
+
+ if (MASTER(cr))
+ {
+ print_converged(stderr, LBFGS, inputrec->em_tol, step, converged,
+ number_steps, Epot, fmax, nfmax, fnorm/sqrt(state->natoms));
+ print_converged(fplog, LBFGS, inputrec->em_tol, step, converged,
+ number_steps, Epot, fmax, nfmax, fnorm/sqrt(state->natoms));
+
+ fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
+ }
+
+ finish_em(cr, outf, walltime_accounting, wcycle);
+
+ /* To print the actual number of steps we needed somewhere */
+ walltime_accounting_set_nsteps_done(walltime_accounting, step);
+
+ return 0;
} /* That's all folks */
-double do_steep(FILE *fplog,t_commrec *cr,
+double do_steep(FILE *fplog, t_commrec *cr,
int nfile, const t_filenm fnm[],
- const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
- int nstglobalcomm,
- gmx_vsite_t *vsite,gmx_constr_t constr,
- int stepout,
+ const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
+ int gmx_unused nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int gmx_unused stepout,
t_inputrec *inputrec,
- gmx_mtop_t *top_global,t_fcdata *fcd,
+ gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
t_mdatoms *mdatoms,
- t_nrnb *nrnb,gmx_wallcycle_t wcycle,
- gmx_edsam_t ed,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
- gmx_membed_t membed,
- real cpt_period,real max_hours,
- const char *deviceOptions,
- unsigned long Flags,
- gmx_runtime_t *runtime)
+ int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused membed,
+ real gmx_unused cpt_period, real gmx_unused max_hours,
+ const char gmx_unused *deviceOptions,
+ int imdport,
+ unsigned long gmx_unused Flags,
+ gmx_walltime_accounting_t walltime_accounting)
{
- const char *SD="Steepest Descents";
- em_state_t *s_min,*s_try;
- rvec *f_global;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- real stepsize,constepsize;
- real ustep,dvdlambda,fnormn;
- gmx_mdoutf_t *outf;
- t_mdebin *mdebin;
- gmx_bool bDone,bAbort,do_x,do_f;
- tensor vir,pres;
- rvec mu_tot;
- int nsteps;
- int count=0;
- int steps_accepted=0;
- /* not used */
- real terminate=0;
-
- s_min = init_em_state();
- s_try = init_em_state();
-
- /* Init em and store the local state in s_try */
- init_em(fplog,SD,cr,inputrec,
- state_global,top_global,s_try,&top,&f,&f_global,
- nrnb,mu_tot,fr,&enerd,&graph,mdatoms,&gstat,vsite,constr,
- nfile,fnm,&outf,&mdebin);
-
- /* Print to log file */
- print_em_start(fplog,cr,runtime,wcycle,SD);
-
- /* Set variables for stepsize (in nm). This is the largest
- * step that we are going to make in any direction.
- */
- ustep = inputrec->em_stepsize;
- stepsize = 0;
-
- /* Max number of steps */
- nsteps = inputrec->nsteps;
-
- if (MASTER(cr))
- /* Print to the screen */
- sp_header(stderr,SD,inputrec->em_tol,nsteps);
- if (fplog)
- sp_header(fplog,SD,inputrec->em_tol,nsteps);
-
- /**** HERE STARTS THE LOOP ****
- * count is the counter for the number of steps
- * bDone will be TRUE when the minimization has converged
- * bAbort will be TRUE when nsteps steps have been performed or when
- * the stepsize becomes smaller than is reasonable for machine precision
- */
- count = 0;
- bDone = FALSE;
- bAbort = FALSE;
- while( !bDone && !bAbort ) {
- bAbort = (nsteps >= 0) && (count == nsteps);
-
- /* set new coordinates, except for first step */
- if (count > 0) {
- do_em_step(cr,inputrec,mdatoms,fr->bMolPBC,
- s_min,stepsize,s_min->f,s_try,
- constr,top,nrnb,wcycle,count);
- }
-
- evaluate_energy(fplog,bVerbose,cr,
- state_global,top_global,s_try,top,
- inputrec,nrnb,wcycle,gstat,
- vsite,constr,fcd,graph,mdatoms,fr,
- mu_tot,enerd,vir,pres,count,count==0);
+ const char *SD = "Steepest Descents";
+ em_state_t *s_min, *s_try;
+ rvec *f_global;
+ gmx_localtop_t *top;
+ gmx_enerdata_t *enerd;
+ rvec *f;
+ gmx_global_stat_t gstat;
+ t_graph *graph;
+ real stepsize, constepsize;
+ real ustep, fnormn;
+ gmx_mdoutf_t outf;
+ t_mdebin *mdebin;
+ gmx_bool bDone, bAbort, do_x, do_f;
+ tensor vir, pres;
+ rvec mu_tot;
+ int nsteps;
+ int count = 0;
+ int steps_accepted = 0;
+ /* not used */
+ real terminate = 0;
+
+ s_min = init_em_state();
+ s_try = init_em_state();
+
+ /* Init em and store the local state in s_try */
+ init_em(fplog, SD, cr, inputrec,
+ state_global, top_global, s_try, &top, &f, &f_global,
+ nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
+ nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
+
+ /* Print to log file */
+ print_em_start(fplog, cr, walltime_accounting, wcycle, SD);
+
+ /* Set variables for stepsize (in nm). This is the largest
+ * step that we are going to make in any direction.
+ */
+ ustep = inputrec->em_stepsize;
+ stepsize = 0;
+
+ /* Max number of steps */
+ nsteps = inputrec->nsteps;
if (MASTER(cr))
- print_ebin_header(fplog,count,count,s_try->s.lambda[efptFEP]);
-
- if (count == 0)
- s_min->epot = s_try->epot + 1;
-
- /* Print it if necessary */
- if (MASTER(cr)) {
- if (bVerbose) {
- fprintf(stderr,"Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
- count,ustep,s_try->epot,s_try->fmax,s_try->a_fmax+1,
- (s_try->epot < s_min->epot) ? '\n' : '\r');
- }
-
- if (s_try->epot < s_min->epot) {
- /* Store the new (lower) energies */
- upd_mdebin(mdebin,FALSE,FALSE,(double)count,
- mdatoms->tmass,enerd,&s_try->s,inputrec->fepvals,inputrec->expandedvals,
- s_try->s.box, NULL,NULL,vir,pres,NULL,mu_tot,constr);
- print_ebin(outf->fp_ene,TRUE,
- do_per_step(steps_accepted,inputrec->nstdisreout),
- do_per_step(steps_accepted,inputrec->nstorireout),
- fplog,count,count,eprNORMAL,TRUE,
- mdebin,fcd,&(top_global->groups),&(inputrec->opts));
- fflush(fplog);
- }
- }
-
- /* Now if the new energy is smaller than the previous...
- * or if this is the first step!
- * or if we did random steps!
+ {
+ /* Print to the screen */
+ sp_header(stderr, SD, inputrec->em_tol, nsteps);
+ }
+ if (fplog)
+ {
+ sp_header(fplog, SD, inputrec->em_tol, nsteps);
+ }
+
+ /**** HERE STARTS THE LOOP ****
+ * count is the counter for the number of steps
+ * bDone will be TRUE when the minimization has converged
+ * bAbort will be TRUE when nsteps steps have been performed or when
+ * the stepsize becomes smaller than is reasonable for machine precision
*/
+ count = 0;
+ bDone = FALSE;
+ bAbort = FALSE;
+ while (!bDone && !bAbort)
+ {
+ bAbort = (nsteps >= 0) && (count == nsteps);
- if ( (count==0) || (s_try->epot < s_min->epot) ) {
- steps_accepted++;
+ /* set new coordinates, except for first step */
+ if (count > 0)
+ {
+ do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
+ s_min, stepsize, s_min->f, s_try,
+ constr, top, nrnb, wcycle, count);
+ }
- /* Test whether the convergence criterion is met... */
- bDone = (s_try->fmax < inputrec->em_tol);
+ evaluate_energy(fplog, cr,
+ top_global, s_try, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, count, count == 0);
- /* Copy the arrays for force, positions and energy */
- /* The 'Min' array always holds the coords and forces of the minimal
- sampled energy */
- swap_em_state(s_min,s_try);
- if (count > 0)
- ustep *= 1.2;
+ if (MASTER(cr))
+ {
+ print_ebin_header(fplog, count, count, s_try->s.lambda[efptFEP]);
+ }
- /* Write to trn, if necessary */
- do_x = do_per_step(steps_accepted,inputrec->nstxout);
- do_f = do_per_step(steps_accepted,inputrec->nstfout);
- write_em_traj(fplog,cr,outf,do_x,do_f,NULL,
- top_global,inputrec,count,
- s_min,state_global,f_global);
- }
- else {
- /* If energy is not smaller make the step smaller... */
- ustep *= 0.5;
+ if (count == 0)
+ {
+ s_min->epot = s_try->epot + 1;
+ }
- if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count) {
- /* Reload the old state */
- em_dd_partition_system(fplog,count,cr,top_global,inputrec,
- s_min,top,mdatoms,fr,vsite,constr,
- nrnb,wcycle);
- }
- }
+ /* Print it if necessary */
+ if (MASTER(cr))
+ {
+ if (bVerbose)
+ {
+ fprintf(stderr, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
+ count, ustep, s_try->epot, s_try->fmax, s_try->a_fmax+1,
+ (s_try->epot < s_min->epot) ? '\n' : '\r');
+ }
+
+ if (s_try->epot < s_min->epot)
+ {
+ /* Store the new (lower) energies */
+ upd_mdebin(mdebin, FALSE, FALSE, (double)count,
+ mdatoms->tmass, enerd, &s_try->s, inputrec->fepvals, inputrec->expandedvals,
+ s_try->s.box, NULL, NULL, vir, pres, NULL, mu_tot, constr);
+
+ /* Prepare IMD energy record, if bIMD is TRUE. */
+ IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, count, TRUE);
+
+ print_ebin(mdoutf_get_fp_ene(outf), TRUE,
+ do_per_step(steps_accepted, inputrec->nstdisreout),
+ do_per_step(steps_accepted, inputrec->nstorireout),
+ fplog, count, count, eprNORMAL, TRUE,
+ mdebin, fcd, &(top_global->groups), &(inputrec->opts));
+ fflush(fplog);
+ }
+ }
+
+ /* Now if the new energy is smaller than the previous...
+ * or if this is the first step!
+ * or if we did random steps!
+ */
+
+ if ( (count == 0) || (s_try->epot < s_min->epot) )
+ {
+ steps_accepted++;
+
+ /* Test whether the convergence criterion is met... */
+ bDone = (s_try->fmax < inputrec->em_tol);
+
+ /* Copy the arrays for force, positions and energy */
+ /* The 'Min' array always holds the coords and forces of the minimal
+ sampled energy */
+ swap_em_state(s_min, s_try);
+ if (count > 0)
+ {
+ ustep *= 1.2;
+ }
+
+ /* Write to trn, if necessary */
+ do_x = do_per_step(steps_accepted, inputrec->nstxout);
+ do_f = do_per_step(steps_accepted, inputrec->nstfout);
+ write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
+ top_global, inputrec, count,
+ s_min, state_global, f_global);
+ }
+ else
+ {
+ /* If energy is not smaller make the step smaller... */
+ ustep *= 0.5;
- /* Determine new step */
- stepsize = ustep/s_min->fmax;
+ if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
+ {
+ /* Reload the old state */
+ em_dd_partition_system(fplog, count, cr, top_global, inputrec,
+ s_min, top, mdatoms, fr, vsite, constr,
+ nrnb, wcycle);
+ }
+ }
+
+ /* Determine new step */
+ stepsize = ustep/s_min->fmax;
- /* Check if stepsize is too small, with 1 nm as a characteristic length */
+ /* Check if stepsize is too small, with 1 nm as a characteristic length */
#ifdef GMX_DOUBLE
if (count == nsteps || ustep < 1e-12)
#else
{
if (MASTER(cr))
{
- warn_step(stderr,inputrec->em_tol,count==nsteps,constr!=NULL);
- warn_step(fplog ,inputrec->em_tol,count==nsteps,constr!=NULL);
+ warn_step(stderr, inputrec->em_tol, count == nsteps, constr != NULL);
+ warn_step(fplog, inputrec->em_tol, count == nsteps, constr != NULL);
}
- bAbort=TRUE;
+ bAbort = TRUE;
}
- count++;
- } /* End of the loop */
+ /* Send IMD energies and positions, if bIMD is TRUE. */
+ if (do_IMD(inputrec->bIMD, count, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
+ {
+ IMD_send_positions(inputrec->imd);
+ }
+
+ count++;
+ } /* End of the loop */
+
+ /* IMD cleanup, if bIMD is TRUE. */
+ IMD_finalize(inputrec->bIMD, inputrec->imd);
- /* Print some shit... */
- if (MASTER(cr))
- fprintf(stderr,"\nwriting lowest energy coordinates.\n");
- write_em_traj(fplog,cr,outf,TRUE,inputrec->nstfout,ftp2fn(efSTO,nfile,fnm),
- top_global,inputrec,count,
- s_min,state_global,f_global);
+ /* Print some data... */
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "\nwriting lowest energy coordinates.\n");
+ }
+ write_em_traj(fplog, cr, outf, TRUE, inputrec->nstfout, ftp2fn(efSTO, nfile, fnm),
+ top_global, inputrec, count,
+ s_min, state_global, f_global);
- fnormn = s_min->fnorm/sqrt(state_global->natoms);
+ fnormn = s_min->fnorm/sqrt(state_global->natoms);
- if (MASTER(cr)) {
- print_converged(stderr,SD,inputrec->em_tol,count,bDone,nsteps,
- s_min->epot,s_min->fmax,s_min->a_fmax,fnormn);
- print_converged(fplog,SD,inputrec->em_tol,count,bDone,nsteps,
- s_min->epot,s_min->fmax,s_min->a_fmax,fnormn);
- }
+ if (MASTER(cr))
+ {
+ print_converged(stderr, SD, inputrec->em_tol, count, bDone, nsteps,
+ s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+ print_converged(fplog, SD, inputrec->em_tol, count, bDone, nsteps,
+ s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+ }
- finish_em(fplog,cr,outf,runtime,wcycle);
+ finish_em(cr, outf, walltime_accounting, wcycle);
- /* To print the actual number of steps we needed somewhere */
- inputrec->nsteps=count;
+ /* To print the actual number of steps we needed somewhere */
+ inputrec->nsteps = count;
- runtime->nsteps_done = count;
+ walltime_accounting_set_nsteps_done(walltime_accounting, count);
- return 0;
+ return 0;
} /* That's all folks */
-double do_nm(FILE *fplog,t_commrec *cr,
- int nfile,const t_filenm fnm[],
- const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
- int nstglobalcomm,
- gmx_vsite_t *vsite,gmx_constr_t constr,
- int stepout,
+double do_nm(FILE *fplog, t_commrec *cr,
+ int nfile, const t_filenm fnm[],
+ const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
+ int gmx_unused nstglobalcomm,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ int gmx_unused stepout,
t_inputrec *inputrec,
- gmx_mtop_t *top_global,t_fcdata *fcd,
+ gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
t_mdatoms *mdatoms,
- t_nrnb *nrnb,gmx_wallcycle_t wcycle,
- gmx_edsam_t ed,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
- gmx_membed_t membed,
- real cpt_period,real max_hours,
- const char *deviceOptions,
- unsigned long Flags,
- gmx_runtime_t *runtime)
+ int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ gmx_membed_t gmx_unused membed,
+ real gmx_unused cpt_period, real gmx_unused max_hours,
+ const char gmx_unused *deviceOptions,
+ int imdport,
+ unsigned long gmx_unused Flags,
+ gmx_walltime_accounting_t walltime_accounting)
{
- const char *NM = "Normal Mode Analysis";
- gmx_mdoutf_t *outf;
- int natoms,atom,d;
- int nnodes,node;
- rvec *f_global;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- real t,t0,lambda,lam0;
- gmx_bool bNS;
- tensor vir,pres;
- rvec mu_tot;
- rvec *fneg,*dfdx;
- gmx_bool bSparse; /* use sparse matrix storage format */
- size_t sz;
- gmx_sparsematrix_t * sparse_matrix = NULL;
- real * full_matrix = NULL;
- em_state_t * state_work;
+ const char *NM = "Normal Mode Analysis";
+ gmx_mdoutf_t outf;
+ int natoms, atom, d;
+ int nnodes, node;
+ rvec *f_global;
+ gmx_localtop_t *top;
+ gmx_enerdata_t *enerd;
+ rvec *f;
+ gmx_global_stat_t gstat;
+ t_graph *graph;
+ real t, t0, lambda, lam0;
+ gmx_bool bNS;
+ tensor vir, pres;
+ rvec mu_tot;
+ rvec *fneg, *dfdx;
+ gmx_bool bSparse; /* use sparse matrix storage format */
+ size_t sz = 0;
+ gmx_sparsematrix_t * sparse_matrix = NULL;
+ real * full_matrix = NULL;
+ em_state_t * state_work;
/* added with respect to mdrun */
- int i,j,k,row,col;
- real der_range=10.0*sqrt(GMX_REAL_EPS);
+ int i, j, k, row, col;
+ real der_range = 10.0*sqrt(GMX_REAL_EPS);
real x_min;
- real fnorm,fmax;
+ real fnorm, fmax;
if (constr != NULL)
{
- gmx_fatal(FARGS,"Constraints present with Normal Mode Analysis, this combination is not supported");
+ gmx_fatal(FARGS, "Constraints present with Normal Mode Analysis, this combination is not supported");
}
state_work = init_em_state();
/* Init em and store the local state in state_minimum */
- init_em(fplog,NM,cr,inputrec,
- state_global,top_global,state_work,&top,
- &f,&f_global,
- nrnb,mu_tot,fr,&enerd,&graph,mdatoms,&gstat,vsite,constr,
- nfile,fnm,&outf,NULL);
+ init_em(fplog, NM, cr, inputrec,
+ state_global, top_global, state_work, &top,
+ &f, &f_global,
+ nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
+ nfile, fnm, &outf, NULL, imdport, Flags, wcycle);
natoms = top_global->natoms;
- snew(fneg,natoms);
- snew(dfdx,natoms);
+ snew(fneg, natoms);
+ snew(dfdx, natoms);
#ifndef GMX_DOUBLE
if (MASTER(cr))
/* Check if we can/should use sparse storage format.
*
* Sparse format is only useful when the Hessian itself is sparse, which it
- * will be when we use a cutoff.
- * For small systems (n<1000) it is easier to always use full matrix format, though.
- */
- if(EEL_FULL(fr->eeltype) || fr->rlist==0.0)
+ * will be when we use a cutoff.
+ * For small systems (n<1000) it is easier to always use full matrix format, though.
+ */
+ if (EEL_FULL(fr->eeltype) || fr->rlist == 0.0)
{
- fprintf(stderr,"Non-cutoff electrostatics used, forcing full Hessian format.\n");
+ md_print_info(cr, fplog, "Non-cutoff electrostatics used, forcing full Hessian format.\n");
bSparse = FALSE;
}
- else if(top_global->natoms < 1000)
+ else if (top_global->natoms < 1000)
{
- fprintf(stderr,"Small system size (N=%d), using full Hessian format.\n",top_global->natoms);
+ md_print_info(cr, fplog, "Small system size (N=%d), using full Hessian format.\n", top_global->natoms);
bSparse = FALSE;
}
else
{
- fprintf(stderr,"Using compressed symmetric sparse Hessian format.\n");
+ md_print_info(cr, fplog, "Using compressed symmetric sparse Hessian format.\n");
bSparse = TRUE;
}
- sz = DIM*top_global->natoms;
+ if (MASTER(cr))
+ {
+ sz = DIM*top_global->natoms;
- fprintf(stderr,"Allocating Hessian memory...\n\n");
+ fprintf(stderr, "Allocating Hessian memory...\n\n");
- if(bSparse)
- {
- sparse_matrix=gmx_sparsematrix_init(sz);
- sparse_matrix->compressed_symmetric = TRUE;
- }
- else
- {
- snew(full_matrix,sz*sz);
+ if (bSparse)
+ {
+ sparse_matrix = gmx_sparsematrix_init(sz);
+ sparse_matrix->compressed_symmetric = TRUE;
+ }
+ else
+ {
+ snew(full_matrix, sz*sz);
+ }
}
/* Initial values */
where();
/* Write start time and temperature */
- print_em_start(fplog,cr,runtime,wcycle,NM);
+ print_em_start(fplog, cr, walltime_accounting, wcycle, NM);
/* fudge nr of steps to nr of atoms */
inputrec->nsteps = natoms*2;
if (MASTER(cr))
{
- fprintf(stderr,"starting normal mode calculation '%s'\n%d steps.\n\n",
- *(top_global->name),(int)inputrec->nsteps);
+ fprintf(stderr, "starting normal mode calculation '%s'\n%d steps.\n\n",
+ *(top_global->name), (int)inputrec->nsteps);
}
nnodes = cr->nnodes;
/* Make evaluate_energy do a single node force calculation */
cr->nnodes = 1;
- evaluate_energy(fplog,bVerbose,cr,
- state_global,top_global,state_work,top,
- inputrec,nrnb,wcycle,gstat,
- vsite,constr,fcd,graph,mdatoms,fr,
- mu_tot,enerd,vir,pres,-1,TRUE);
+ evaluate_energy(fplog, cr,
+ top_global, state_work, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, -1, TRUE);
cr->nnodes = nnodes;
/* if forces are not small, warn user */
- get_state_f_norm_max(cr,&(inputrec->opts),mdatoms,state_work);
+ get_state_f_norm_max(cr, &(inputrec->opts), mdatoms, state_work);
- if (MASTER(cr))
+ md_print_info(cr, fplog, "Maximum force:%12.5e\n", state_work->fmax);
+ if (state_work->fmax > 1.0e-3)
{
- fprintf(stderr,"Maximum force:%12.5e\n",state_work->fmax);
- if (state_work->fmax > 1.0e-3)
- {
- fprintf(stderr,"Maximum force probably not small enough to");
- fprintf(stderr," ensure that you are in an \nenergy well. ");
- fprintf(stderr,"Be aware that negative eigenvalues may occur");
- fprintf(stderr," when the\nresulting matrix is diagonalized.\n");
- }
+ md_print_info(cr, fplog,
+ "The force is probably not small enough to "
+ "ensure that you are at a minimum.\n"
+ "Be aware that negative eigenvalues may occur\n"
+ "when the resulting matrix is diagonalized.\n\n");
}
/***********************************************************
************************************************************/
/* Steps are divided one by one over the nodes */
- for(atom=cr->nodeid; atom<natoms; atom+=nnodes)
+ for (atom = cr->nodeid; atom < natoms; atom += nnodes)
{
- for (d=0; d<DIM; d++)
+ for (d = 0; d < DIM; d++)
{
x_min = state_work->s.x[atom][d];
/* Make evaluate_energy do a single node force calculation */
cr->nnodes = 1;
- evaluate_energy(fplog,bVerbose,cr,
- state_global,top_global,state_work,top,
- inputrec,nrnb,wcycle,gstat,
- vsite,constr,fcd,graph,mdatoms,fr,
- mu_tot,enerd,vir,pres,atom*2,FALSE);
+ evaluate_energy(fplog, cr,
+ top_global, state_work, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, atom*2, FALSE);
- for(i=0; i<natoms; i++)
+ for (i = 0; i < natoms; i++)
{
copy_rvec(state_work->f[i], fneg[i]);
}
state_work->s.x[atom][d] = x_min + der_range;
- evaluate_energy(fplog,bVerbose,cr,
- state_global,top_global,state_work,top,
- inputrec,nrnb,wcycle,gstat,
- vsite,constr,fcd,graph,mdatoms,fr,
- mu_tot,enerd,vir,pres,atom*2+1,FALSE);
+ evaluate_energy(fplog, cr,
+ top_global, state_work, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph, mdatoms, fr,
+ mu_tot, enerd, vir, pres, atom*2+1, FALSE);
cr->nnodes = nnodes;
/* x is restored to original */
state_work->s.x[atom][d] = x_min;
- for(j=0; j<natoms; j++)
+ for (j = 0; j < natoms; j++)
{
- for (k=0; (k<DIM); k++)
+ for (k = 0; (k < DIM); k++)
{
dfdx[j][k] =
-(state_work->f[j][k] - fneg[j][k])/(2*der_range);
#else
#define mpi_type MPI_FLOAT
#endif
- MPI_Send(dfdx[0],natoms*DIM,mpi_type,MASTERNODE(cr),cr->nodeid,
+ MPI_Send(dfdx[0], natoms*DIM, mpi_type, MASTERNODE(cr), cr->nodeid,
cr->mpi_comm_mygroup);
#endif
}
else
{
- for(node=0; (node<nnodes && atom+node<natoms); node++)
+ for (node = 0; (node < nnodes && atom+node < natoms); node++)
{
if (node > 0)
{
#ifdef GMX_MPI
MPI_Status stat;
- MPI_Recv(dfdx[0],natoms*DIM,mpi_type,node,node,
- cr->mpi_comm_mygroup,&stat);
+ MPI_Recv(dfdx[0], natoms*DIM, mpi_type, node, node,
+ cr->mpi_comm_mygroup, &stat);
#undef mpi_type
#endif
}
row = (atom + node)*DIM + d;
- for(j=0; j<natoms; j++)
+ for (j = 0; j < natoms; j++)
{
- for(k=0; k<DIM; k++)
+ for (k = 0; k < DIM; k++)
{
col = j*DIM + k;
if (col >= row && dfdx[j][k] != 0.0)
{
gmx_sparsematrix_increment_value(sparse_matrix,
- row,col,dfdx[j][k]);
+ row, col, dfdx[j][k]);
}
}
else
/* write progress */
if (MASTER(cr) && bVerbose)
{
- fprintf(stderr,"\rFinished step %d out of %d",
- min(atom+nnodes,natoms),natoms);
+ fprintf(stderr, "\rFinished step %d out of %d",
+ min(atom+nnodes, natoms), natoms);
fflush(stderr);
}
}
if (MASTER(cr))
{
- fprintf(stderr,"\n\nWriting Hessian...\n");
- gmx_mtxio_write(ftp2fn(efMTX,nfile,fnm),sz,sz,full_matrix,sparse_matrix);
+ fprintf(stderr, "\n\nWriting Hessian...\n");
+ gmx_mtxio_write(ftp2fn(efMTX, nfile, fnm), sz, sz, full_matrix, sparse_matrix);
}
- finish_em(fplog,cr,outf,runtime,wcycle);
+ finish_em(cr, outf, walltime_accounting, wcycle);
- runtime->nsteps_done = natoms*2;
+ walltime_accounting_set_nsteps_done(walltime_accounting, natoms*2);
return 0;
}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff