/*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
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/*! \internal \file
*
* \brief This file defines integrators for energy minimization
*
* \author Berk Hess <hess@kth.se>
* \author Erik Lindahl <erik@kth.se>
* \ingroup module_mdlib
*/
#include "gmxpre.h"
#include "minimize.h"
#include "config.h"
#include <cmath>
#include <cstring>
#include <ctime>
#include <algorithm>
#include <vector>
#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/mtxio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/imd/imd.h"
#include "gromacs/linearalgebra/sparsematrix.h"
#include "gromacs/listed-forces/manage-threading.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/mdsetup.h"
#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/shellfc.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdlib/trajectory_writing.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
//! Utility structure for manipulating states during EM
typedef struct {
//! Copy of the global state
t_state s;
//! Force array
PaddedRVecVector f;
//! Potential energy
real epot;
//! Norm of the force
real fnorm;
//! Maximum force
real fmax;
//! Direction
int a_fmax;
} em_state_t;
//! Print the EM starting conditions
static void print_em_start(FILE *fplog,
t_commrec *cr,
gmx_walltime_accounting_t walltime_accounting,
gmx_wallcycle_t wcycle,
const char *name)
{
walltime_accounting_start(walltime_accounting);
wallcycle_start(wcycle, ewcRUN);
print_start(fplog, cr, walltime_accounting, name);
}
//! Stop counting time for EM
static void em_time_end(gmx_walltime_accounting_t walltime_accounting,
gmx_wallcycle_t wcycle)
{
wallcycle_stop(wcycle, ewcRUN);
walltime_accounting_end(walltime_accounting);
}
//! Printing a log file and console header
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);
}
//! Print warning message
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);
}
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, "
"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 "
"dynamics.\n" :
"",
bConstrain ?
"You might need to increase your constraint accuracy, or turn\n"
"off constraints altogether (set constraints = none in mdp file)\n" :
"");
}
fputs(wrap_lines(buffer, 78, 0, FALSE), fp);
}
//! Print message about convergence of the EM
static void print_converged(FILE *fp, const char *alg, real ftol,
gmx_int64_t count, gmx_bool bDone, gmx_int64_t nsteps,
const em_state_t *ems, double sqrtNumAtoms)
{
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));
}
#if GMX_DOUBLE
fprintf(fp, "Potential Energy = %21.14e\n", ems->epot);
fprintf(fp, "Maximum force = %21.14e on atom %d\n", ems->fmax, ems->a_fmax + 1);
fprintf(fp, "Norm of force = %21.14e\n", ems->fnorm/sqrtNumAtoms);
#else
fprintf(fp, "Potential Energy = %14.7e\n", ems->epot);
fprintf(fp, "Maximum force = %14.7e on atom %d\n", ems->fmax, ems->a_fmax + 1);
fprintf(fp, "Norm of force = %14.7e\n", ems->fnorm/sqrtNumAtoms);
#endif
}
//! Compute the norm and max of the force array in parallel
static void get_f_norm_max(t_commrec *cr,
t_grpopts *opts, t_mdatoms *mdatoms, const rvec *f,
real *fnorm, real *fmax, int *a_fmax)
{
double fnorm2, *sum;
real fmax2, 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;
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 += gmx::square(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;
}
}
//! Compute the norm of the force
static void get_state_f_norm_max(t_commrec *cr,
t_grpopts *opts, t_mdatoms *mdatoms,
em_state_t *ems)
{
get_f_norm_max(cr, opts, mdatoms, as_rvec_array(ems->f.data()),
&ems->fnorm, &ems->fmax, &ems->a_fmax);
}
//! Initialize the energy minimization
static void init_em(FILE *fplog, const char *title,
t_commrec *cr, gmx::IMDOutputProvider *outputProvider,
t_inputrec *ir,
const MdrunOptions &mdrunOptions,
t_state *state_global, gmx_mtop_t *top_global,
em_state_t *ems, gmx_localtop_t **top,
t_nrnb *nrnb, rvec mu_tot,
t_forcerec *fr, gmx_enerdata_t **enerd,
t_graph **graph, gmx::MDAtoms *mdAtoms, gmx_global_stat_t *gstat,
gmx_vsite_t *vsite, gmx_constr_t constr, gmx_shellfc_t **shellfc,
int nfile, const t_filenm fnm[],
gmx_mdoutf_t *outf, t_mdebin **mdebin,
gmx_wallcycle_t wcycle)
{
real dvdl_constr;
if (fplog)
{
fprintf(fplog, "Initiating %s\n", title);
}
if (MASTER(cr))
{
state_global->ngtc = 0;
/* Initialize lambda variables */
initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, nullptr);
}
init_nrnb(nrnb);
/* Interactive molecular dynamics */
init_IMD(ir, cr, top_global, fplog, 1,
MASTER(cr) ? as_rvec_array(state_global->x.data()) : nullptr,
nfile, fnm, nullptr, mdrunOptions);
if (ir->eI == eiNM)
{
GMX_ASSERT(shellfc != nullptr, "With NM we always support shells");
*shellfc = init_shell_flexcon(stdout,
top_global,
n_flexible_constraints(constr),
ir->nstcalcenergy,
DOMAINDECOMP(cr));
}
else
{
GMX_ASSERT(EI_ENERGY_MINIMIZATION(ir->eI), "This else currently only handles energy minimizers, consider if your algorithm needs shell/flexible-constraint support");
/* With energy minimization, shells and flexible constraints are
* automatically minimized when treated like normal DOFS.
*/
if (shellfc != nullptr)
{
*shellfc = nullptr;
}
}
auto mdatoms = mdAtoms->mdatoms();
if (DOMAINDECOMP(cr))
{
*top = dd_init_local_top(top_global);
dd_init_local_state(cr->dd, state_global, &ems->s);
/* 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, constr,
nrnb, nullptr, FALSE);
dd_store_state(cr->dd, &ems->s);
*graph = nullptr;
}
else
{
state_change_natoms(state_global, state_global->natoms);
/* Just copy the state */
ems->s = *state_global;
state_change_natoms(&ems->s, ems->s.natoms);
/* We need to allocate one element extra, since we might use
* (unaligned) 4-wide SIMD loads to access rvec entries.
*/
ems->f.resize(gmx::paddedRVecVectorSize(ems->s.natoms));
snew(*top, 1);
mdAlgorithmsSetupAtomData(cr, ir, top_global, *top, fr,
graph, mdAtoms,
vsite, shellfc ? *shellfc : nullptr);
if (vsite)
{
set_vsite_top(vsite, *top, mdatoms);
}
}
update_mdatoms(mdAtoms->mdatoms(), ems->s.lambda[efptMASS]);
if (constr)
{
if (ir->eConstrAlg == econtSHAKE &&
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]);
}
if (!DOMAINDECOMP(cr))
{
set_constraints(constr, *top, ir, mdatoms, cr);
}
if (!ir->bContinuation)
{
/* Constrain the starting coordinates */
dvdl_constr = 0;
constrain(PAR(cr) ? nullptr : fplog, TRUE, TRUE, constr, &(*top)->idef,
ir, cr, -1, 0, 1.0, mdatoms,
as_rvec_array(ems->s.x.data()),
as_rvec_array(ems->s.x.data()),
nullptr,
fr->bMolPBC, ems->s.box,
ems->s.lambda[efptFEP], &dvdl_constr,
nullptr, nullptr, nrnb, econqCoord);
}
}
if (PAR(cr))
{
*gstat = global_stat_init(ir);
}
else
{
*gstat = nullptr;
}
*outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, nullptr, wcycle);
snew(*enerd, 1);
init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
*enerd);
if (mdebin != nullptr)
{
/* Init bin for energy stuff */
*mdebin = init_mdebin(mdoutf_get_fp_ene(*outf), top_global, ir, nullptr);
}
clear_rvec(mu_tot);
calc_shifts(ems->s.box, fr->shift_vec);
}
//! Finalize the minimization
static void finish_em(t_commrec *cr, gmx_mdoutf_t outf,
gmx_walltime_accounting_t walltime_accounting,
gmx_wallcycle_t wcycle)
{
if (!thisRankHasDuty(cr, DUTY_PME))
{
/* Tell the PME only node to finish */
gmx_pme_send_finish(cr);
}
done_mdoutf(outf);
em_time_end(walltime_accounting, wcycle);
}
//! Swap two different EM states during minimization
static void swap_em_state(em_state_t **ems1, em_state_t **ems2)
{
em_state_t *tmp;
tmp = *ems1;
*ems1 = *ems2;
*ems2 = tmp;
}
//! Save the EM trajectory
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_int64_t step,
em_state_t *state,
t_state *state_global,
ObservablesHistory *observablesHistory)
{
int mdof_flags = 0;
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, observablesHistory,
state->f);
if (confout != nullptr)
{
if (DOMAINDECOMP(cr))
{
/* If bX=true, x was collected to state_global in the call above */
if (!bX)
{
gmx::ArrayRef<gmx::RVec> globalXRef = MASTER(cr) ? gmx::makeArrayRef(state_global->x) : gmx::EmptyArrayRef();
dd_collect_vec(cr->dd, &state->s, state->s.x, globalXRef);
}
}
else
{
/* Copy the local state pointer */
state_global = &state->s;
}
if (MASTER(cr))
{
if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr))
{
/* Make molecules whole only for confout writing */
do_pbc_mtop(fplog, ir->ePBC, state->s.box, top_global,
as_rvec_array(state_global->x.data()));
}
write_sto_conf_mtop(confout,
*top_global->name, top_global,
as_rvec_array(state_global->x.data()), nullptr, ir->ePBC, state->s.box);
}
}
}
//! \brief Do one minimization step
//
// \returns true when the step succeeded, false when a constraint error occurred
static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
gmx_bool bMolPBC,
em_state_t *ems1, real a, const PaddedRVecVector *force,
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 start, end;
real dvdl_constr;
int nthreads gmx_unused;
bool validStep = true;
s1 = &ems1->s;
s2 = &ems2->s;
if (DOMAINDECOMP(cr) && s1->ddp_count != cr->dd->ddp_count)
{
gmx_incons("state mismatch in do_em_step");
}
s2->flags = s1->flags;
if (s2->natoms != s1->natoms)
{
state_change_natoms(s2, s1->natoms);
/* We need to allocate one element extra, since we might use
* (unaligned) 4-wide SIMD loads to access rvec entries.
*/
ems2->f.resize(gmx::paddedRVecVectorSize(s2->natoms));
}
if (DOMAINDECOMP(cr) && s2->cg_gl.size() != s1->cg_gl.size())
{
s2->cg_gl.resize(s1->cg_gl.size());
}
copy_mat(s1->box, s2->box);
/* Copy free energy state */
s2->lambda = s1->lambda;
copy_mat(s1->box, s2->box);
start = 0;
end = md->homenr;
// cppcheck-suppress unreadVariable
nthreads = gmx_omp_nthreads_get(emntUpdate);
#pragma omp parallel num_threads(nthreads)
{
const rvec *x1 = as_rvec_array(s1->x.data());
rvec *x2 = as_rvec_array(s2->x.data());
const rvec *f = as_rvec_array(force->data());
int gf = 0;
#pragma omp for schedule(static) nowait
for (int i = start; i < end; i++)
{
try
{
if (md->cFREEZE)
{
gf = md->cFREEZE[i];
}
for (int m = 0; m < DIM; m++)
{
if (ir->opts.nFreeze[gf][m])
{
x2[i][m] = x1[i][m];
}
else
{
x2[i][m] = x1[i][m] + a*f[i][m];
}
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
if (s2->flags & (1<<estCGP))
{
/* Copy the CG p vector */
const rvec *p1 = as_rvec_array(s1->cg_p.data());
rvec *p2 = as_rvec_array(s2->cg_p.data());
#pragma omp for schedule(static) nowait
for (int i = start; i < end; i++)
{
// Trivial OpenMP block that does not throw
copy_rvec(p1[i], p2[i]);
}
}
if (DOMAINDECOMP(cr))
{
s2->ddp_count = s1->ddp_count;
/* OpenMP does not supported unsigned loop variables */
#pragma omp for schedule(static) nowait
for (int i = 0; i < static_cast<int>(s2->cg_gl.size()); 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);
dvdl_constr = 0;
validStep =
constrain(nullptr, TRUE, TRUE, constr, &top->idef,
ir, cr, count, 0, 1.0, md,
as_rvec_array(s1->x.data()), as_rvec_array(s2->x.data()),
nullptr, bMolPBC, s2->box,
s2->lambda[efptBONDED], &dvdl_constr,
nullptr, nullptr, nrnb, econqCoord);
wallcycle_stop(wcycle, ewcCONSTR);
if (cr->nnodes > 1)
{
/* This global reduction will affect performance at high
* parallelization, but we can not really avoid it.
* But usually EM is not run at high parallelization.
*/
int reductionBuffer = !validStep;
gmx_sumi(1, &reductionBuffer, cr);
validStep = (reductionBuffer == 0);
}
// We should move this check to the different minimizers
if (!validStep && ir->eI != eiSteep)
{
gmx_fatal(FARGS, "The coordinates could not be constrained. Minimizer '%s' can not handle constraint failures, use minimizer '%s' before using '%s'.",
EI(ir->eI), EI(eiSteep), EI(ir->eI));
}
}
return validStep;
}
//! Prepare EM for using domain decomposition parallellization
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,
gmx::MDAtoms *mdAtoms, t_forcerec *fr,
gmx_vsite_t *vsite, gmx_constr_t constr,
t_nrnb *nrnb, gmx_wallcycle_t wcycle)
{
/* Repartition the domain decomposition */
dd_partition_system(fplog, step, cr, FALSE, 1,
nullptr, top_global, ir,
&ems->s, &ems->f,
mdAtoms, top, fr, vsite, constr,
nrnb, wcycle, FALSE);
dd_store_state(cr->dd, &ems->s);
}
//! De one energy evaluation
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,
gmx_global_stat_t gstat,
gmx_vsite_t *vsite, gmx_constr_t constr,
t_fcdata *fcd,
t_graph *graph, gmx::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;
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;
}
}
if (vsite)
{
construct_vsites(vsite, as_rvec_array(ems->s.x.data()), 1, nullptr,
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->groups,
ems->s.box, ems->s.x, &ems->s.hist,
ems->f, force_vir, mdAtoms->mdatoms(), enerd, fcd,
ems->s.lambda, graph, fr, vsite, mu_tot, t, nullptr, TRUE,
GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
(bNS ? GMX_FORCE_NS : 0),
DOMAINDECOMP(cr) ?
DdOpenBalanceRegionBeforeForceComputation::yes :
DdOpenBalanceRegionBeforeForceComputation::no,
DOMAINDECOMP(cr) ?
DdCloseBalanceRegionAfterForceComputation::yes :
DdCloseBalanceRegionAfterForceComputation::no);
/* Clear the unused shake virial and pressure */
clear_mat(shake_vir);
clear_mat(pres);
/* Communicate stuff when parallel */
if (PAR(cr) && inputrec->eI != eiNM)
{
wallcycle_start(wcycle, ewcMoveE);
global_stat(gstat, cr, enerd, force_vir, shake_vir, mu_tot,
inputrec, nullptr, nullptr, nullptr, 1, &terminate,
nullptr, FALSE,
CGLO_ENERGY |
CGLO_PRESSURE |
CGLO_CONSTRAINT);
wallcycle_stop(wcycle, ewcMoveE);
}
/* Calculate long range corrections to pressure and energy */
calc_dispcorr(inputrec, fr, 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);
dvdl_constr = 0;
rvec *f_rvec = as_rvec_array(ems->f.data());
constrain(nullptr, FALSE, FALSE, constr, &top->idef,
inputrec, cr, count, 0, 1.0, mdAtoms->mdatoms(),
as_rvec_array(ems->s.x.data()), f_rvec, f_rvec,
fr->bMolPBC, ems->s.box,
ems->s.lambda[efptBONDED], &dvdl_constr,
nullptr, &shake_vir, nrnb, econqForceDispl);
enerd->term[F_DVDL_CONSTR] += dvdl_constr;
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);
if (EI_ENERGY_MINIMIZATION(inputrec->eI))
{
get_state_f_norm_max(cr, &(inputrec->opts), mdAtoms->mdatoms(), ems);
}
}
//! Parallel utility summing energies and forces
static double reorder_partsum(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
gmx_mtop_t *top_global,
em_state_t *s_min, em_state_t *s_b)
{
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");
}
const rvec *fm = as_rvec_array(s_min->f.data());
const rvec *fb = as_rvec_array(s_b->f.data());
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.
*/
rvec *fmg;
snew(fmg, top_global->natoms);
ncg = s_min->s.cg_gl.size();
cg_gl = s_min->s.cg_gl.data();
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(top_global->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.cg_gl.size();
cg_gl = s_b->s.cg_gl.data();
partsum = 0;
i = 0;
gf = 0;
grpnrFREEZE = top_global->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;
}
//! Print some stuff, like beta, whatever that means.
static real pr_beta(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
gmx_mtop_t *top_global,
em_state_t *s_min, em_state_t *s_b)
{
double sum;
/* 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))
{
const rvec *fm = as_rvec_array(s_min->f.data());
const rvec *fb = as_rvec_array(s_b->f.data());
sum = 0;
int gf = 0;
/* This part of code can be incorrect with DD,
* since the atom ordering in s_b and s_min might differ.
*/
for (int i = 0; i < mdatoms->homenr; i++)
{
if (mdatoms->cFREEZE)
{
gf = mdatoms->cFREEZE[i];
}
for (int 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, top_global, s_min, s_b);
}
if (PAR(cr))
{
gmx_sumd(1, &sum, cr);
}
return sum/gmx::square(s_min->fnorm);
}
namespace gmx
{
/*! \brief Do conjugate gradients minimization
\copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
int nfile, const t_filenm fnm[],
const gmx_output_env_t *oenv,
const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
gmx::MDAtoms *mdAtoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_t ed,
t_forcerec *fr,
const ReplicaExchangeParameters &replExParams,
gmx_membed_t gmx_unused *membed,
gmx_walltime_accounting_t walltime_accounting)
*/
double do_cg(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
int nfile, const t_filenm fnm[],
const gmx_output_env_t gmx_unused *oenv,
const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
ObservablesHistory *observablesHistory,
gmx::MDAtoms *mdAtoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_forcerec *fr,
const ReplicaExchangeParameters gmx_unused &replExParams,
gmx_membed_t gmx_unused *membed,
gmx_walltime_accounting_t walltime_accounting)
{
const char *CG = "Polak-Ribiere Conjugate Gradients";
gmx_localtop_t *top;
gmx_enerdata_t *enerd;
gmx_global_stat_t gstat;
t_graph *graph;
double tmp, minstep;
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 m, step, nminstep;
auto mdatoms = mdAtoms->mdatoms();
step = 0;
if (MASTER(cr))
{
// In CG, the state is extended with a search direction
state_global->flags |= (1<<estCGP);
// Ensure the extra per-atom state array gets allocated
state_change_natoms(state_global, state_global->natoms);
// Initialize the search direction to zero
for (RVec &cg_p : state_global->cg_p)
{
cg_p = { 0, 0, 0 };
}
}
/* Create 4 states on the stack and extract pointers that we will swap */
em_state_t s0 {}, s1 {}, s2 {}, s3 {};
em_state_t *s_min = &s0;
em_state_t *s_a = &s1;
em_state_t *s_b = &s2;
em_state_t *s_c = &s3;
/* Init em and store the local state in s_min */
init_em(fplog, CG, cr, outputProvider, inputrec, mdrunOptions,
state_global, top_global, s_min, &top,
nrnb, mu_tot, fr, &enerd, &graph, mdAtoms, &gstat,
vsite, constr, nullptr,
nfile, fnm, &outf, &mdebin, wcycle);
/* Print to log file */
print_em_start(fplog, cr, walltime_accounting, 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, 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 (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,
nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
print_ebin_header(fplog, step, step);
print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
where();
/* Estimate/guess the initial stepsize */
stepsize = inputrec->em_stepsize/s_min->fnorm;
if (MASTER(cr))
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
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/sqrtNumAtoms);
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/sqrtNumAtoms);
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 || 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.
*/
/* Calculate the new direction in p, and the gradient in this direction, gpa */
rvec *pm = as_rvec_array(s_min->s.cg_p.data());
const rvec *sfm = as_rvec_array(s_min->f.data());
double gpa = 0;
int gf = 0;
for (int 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])
{
pm[i][m] = sfm[i][m] + beta*pm[i][m];
gpa -= pm[i][m]*sfm[i][m];
/* f is negative gradient, thus the sign */
}
else
{
pm[i][m] = 0;
}
}
}
/* Sum the gradient along the line across CPUs */
if (PAR(cr))
{
gmx_sumd(1, &gpa, cr);
}
/* Calculate the norm of the search vector */
get_f_norm_max(cr, &(inputrec->opts), mdatoms, pm, &pnorm, nullptr, nullptr);
/* 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 (int 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 = pm[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*top_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, nullptr,
top_global, inputrec, step,
s_min, state_global, observablesHistory);
/* 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 */
const rvec *pc = as_rvec_array(s_c->s.cg_p.data());
const rvec *sfc = as_rvec_array(s_c->f.data());
double gpc = 0;
for (int i = 0; i < mdatoms->homenr; i++)
{
for (m = 0; m < DIM; m++)
{
gpc -= pc[i][m]*sfc[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 pathological 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.
*/
double gpb;
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.
*/
const rvec *pb = as_rvec_array(s_b->s.cg_p.data());
const rvec *sfb = as_rvec_array(s_b->f.data());
gpb = 0;
for (int i = 0; i < mdatoms->homenr; i++)
{
for (m = 0; m < DIM; m++)
{
gpb -= pb[i][m]*sfb[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;
}
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;
}
}
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;
}
/* 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 (mdrunOptions.verbose)
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
step, s_min->epot, s_min->fnorm/sqrtNumAtoms,
s_min->fmax, s_min->a_fmax+1);
fflush(stderr);
}
/* 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,
nullptr, nullptr, vir, pres, nullptr, 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);
}
print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
do_log ? fplog : nullptr, step, step, eprNORMAL,
mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
/* Send energies and positions to the IMD client if bIMD is TRUE. */
if (MASTER(cr) && do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, as_rvec_array(state_global->x.data()), inputrec, 0, wcycle))
{
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);
}
if (!do_ene || !do_log)
{
/* Write final energy file entries */
print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
!do_log ? fplog : nullptr, step, step, eprNORMAL,
mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
}
/* 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).
*/
/* Note that with 0 < nstfout != nstxout we can end up with two frames
* in the trajectory with the same step number.
*/
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, observablesHistory);
if (MASTER(cr))
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
print_converged(stderr, CG, inputrec->em_tol, step, converged, number_steps,
s_min, sqrtNumAtoms);
print_converged(fplog, CG, inputrec->em_tol, step, converged, number_steps,
s_min, sqrtNumAtoms);
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 */
/*! \brief Do L-BFGS conjugate gradients minimization
\copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
int nfile, const t_filenm fnm[],
const gmx_output_env_t *oenv,
const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
gmx::MDAtoms *mdAtoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_t ed,
t_forcerec *fr,
const ReplicaExchangeParameters &replExParams,
gmx_membed_t gmx_unused *membed,
gmx_walltime_accounting_t walltime_accounting)
*/
double do_lbfgs(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
int nfile, const t_filenm fnm[],
const gmx_output_env_t gmx_unused *oenv,
const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
ObservablesHistory *observablesHistory,
gmx::MDAtoms *mdAtoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_forcerec *fr,
const ReplicaExchangeParameters gmx_unused &replExParams,
gmx_membed_t gmx_unused *membed,
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;
gmx_global_stat_t gstat;
t_graph *graph;
int ncorr, nmaxcorr, point, cp, neval, nminstep;
double stepsize, step_taken, gpa, gpb, gpc, tmp, minstep;
real *rho, *alpha, *p, *s, **dx, **dg;
real a, b, c, maxdelta, delta;
real diag, Epot0;
real dgdx, dgdg, sq, yr, beta;
t_mdebin *mdebin;
gmx_bool converged;
rvec mu_tot;
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, gf, step;
int mdof_flags;
auto mdatoms = mdAtoms->mdatoms();
if (PAR(cr))
{
gmx_fatal(FARGS, "Cannot do parallel L-BFGS Minimization - yet.\n");
}
if (nullptr != 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_global->natoms;
nmaxcorr = inputrec->nbfgscorr;
snew(frozen, n);
snew(p, 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, outputProvider, inputrec, mdrunOptions,
state_global, top_global, &ems, &top,
nrnb, mu_tot, fr, &enerd, &graph, mdAtoms, &gstat,
vsite, constr, nullptr,
nfile, fnm, &outf, &mdebin, wcycle);
start = 0;
end = mdatoms->homenr;
/* We need 4 working states */
em_state_t s0 {}, s1 {}, s2 {}, s3 {};
em_state_t *sa = &s0;
em_state_t *sb = &s1;
em_state_t *sc = &s2;
em_state_t *last = &s3;
/* Initialize by copying the state from ems (we could skip x and f here) */
*sa = ems;
*sb = ems;
*sc = ems;
/* 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, as_rvec_array(state_global->x.data()), 1, nullptr,
top->idef.iparams, top->idef.il,
fr->ePBC, fr->bMolPBC, cr, state_global->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++;
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_global, inputrec->fepvals, inputrec->expandedvals, state_global->box,
nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
print_ebin_header(fplog, step, step);
print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
where();
/* 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))
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
fprintf(stderr, "Using %d BFGS correction steps.\n\n", nmaxcorr);
fprintf(stderr, " F-max = %12.5e on atom %d\n", ems.fmax, ems.a_fmax + 1);
fprintf(stderr, " F-Norm = %12.5e\n", ems.fnorm/sqrtNumAtoms);
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", ems.fmax, ems.a_fmax + 1);
fprintf(fplog, " F-Norm = %12.5e\n", ems.fnorm/sqrtNumAtoms);
fprintf(fplog, "\n");
}
// Point is an index to the memory of search directions, where 0 is the first one.
point = 0;
// Set initial search direction to the force (-gradient), or 0 for frozen particles.
real *fInit = static_cast<real *>(as_rvec_array(ems.f.data())[0]);
for (i = 0; i < n; i++)
{
if (!frozen[i])
{
dx[point][i] = fInit[i]; /* Initial search direction */
}
else
{
dx[point][i] = 0;
}
}
// Stepsize will be modified during the search, and actually it is not critical
// (the main efficiency in the algorithm comes from changing directions), but
// we still need an initial value, so estimate it as the inverse of the norm
// so we take small steps where the potential fluctuates a lot.
stepsize = 1.0/ems.fnorm;
/* 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 || 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, &ems.s, state_global, observablesHistory, ems.f);
/* Do the linesearching in the direction dx[point][0..(n-1)] */
/* make s a pointer to current search direction - point=0 first time we get here */
s = dx[point];
real *xx = static_cast<real *>(as_rvec_array(ems.s.x.data())[0]);
real *ff = static_cast<real *>(as_rvec_array(ems.f.data())[0]);
// calculate line gradient in position A
for (gpa = 0, i = 0; i < n; i++)
{
gpa -= s[i]*ff[i];
}
/* Calculate minimum allowed stepsize along the line, 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;
}
// Before taking any steps along the line, store the old position
*last = ems;
real *lastx = static_cast<real *>(as_rvec_array(last->s.x.data())[0]);
real *lastf = static_cast<real *>(as_rvec_array(last->f.data())[0]);
Epot0 = ems.epot;
*sa = ems;
/* Take a step downhill.
* In theory, we should find the actual minimum of the function in this
* direction, somewhere along the line.
* 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
* continue straight to the next BFGS step without trying to find any minimum,
* i.e. we change the search direction too. If the line was smooth, it is
* likely we are in a smooth region, and then it makes sense to take longer
* steps in the modified search direction too.
*
* If it didn't work (higher energy), there must be a minimum somewhere between
* the old position and the new one. Then we need to start by finding a lower
* value before we change search direction. Since the energy was apparently
* quite rough, we need to decrease the step size.
*
* Due to the finite numerical accuracy, it turns out that it is a good idea
* to 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
*/
// State "A" is the first position along the line.
// reference position along line is initially zero
a = 0.0;
// Check stepsize first. We do not allow displacements
// larger than emstep.
//
do
{
// Pick a new position C by adding stepsize to A.
c = a + stepsize;
// Calculate what the largest change in any individual coordinate
// would be (translation along line * gradient along line)
maxdelta = 0;
for (i = 0; i < n; i++)
{
delta = c*s[i];
if (delta > maxdelta)
{
maxdelta = delta;
}
}
// If any displacement is larger than the stepsize limit, reduce the step
if (maxdelta > inputrec->em_stepsize)
{
stepsize *= 0.1;
}
}
while (maxdelta > inputrec->em_stepsize);
// Take a trial step and move the coordinate array xc[] to position C
real *xc = static_cast<real *>(as_rvec_array(sc->s.x.data())[0]);
for (i = 0; i < n; i++)
{
xc[i] = lastx[i] + c*s[i];
}
neval++;
// Calculate energy for the trial step in position C
evaluate_energy(fplog, cr,
top_global, sc, top,
inputrec, nrnb, wcycle, gstat,
vsite, constr, fcd, graph, mdAtoms, fr,
mu_tot, enerd, vir, pres, step, FALSE);
// Calc line gradient in position C
real *fc = static_cast<real *>(as_rvec_array(sc->f.data())[0]);
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);
}
// This is the max amount of increase in energy we tolerate.
// By allowing VERY small changes (close to numerical precision) we
// frequently find even better (lower) final energies.
tmp = sqrt(GMX_REAL_EPS)*fabs(sa->epot);
// Accept the step if the energy is lower in the new position C (compared to A),
// or if it is not significantly higher and the line derivative is still negative.
if (sc->epot < sa->epot || (gpc < 0 && sc->epot < (sa->epot + tmp)))
{
// Great, we found a better energy. We no longer try to alter the
// stepsize, but simply accept this new better position. The we select a new
// search direction instead, which will be much more efficient than continuing
// to take smaller steps along a line. Set fnorm based on the new C position,
// which will be used to update the stepsize to 1/fnorm further down.
foundlower = TRUE;
}
else
{
// If we got here, the energy is NOT lower in point C, i.e. it will be the same
// or higher than in point A. In this case it is pointless to move to point C,
// so we will have to do more iterations along the same line to find a smaller
// value in the interval [A=0.0,C].
// Here, A is still 0.0, but that will change when we do a search in the interval
// [0.0,C] below. That search we will do by interpolation or bisection rather
// than with the stepsize, so no need to modify it. For the next search direction
// it will be reset to 1/fnorm anyway.
foundlower = FALSE;
}
if (!foundlower)
{
// OK, if we didn't find a lower value we will have to locate one now - there must
// be one in the interval [a,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 pathological 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.
real fnorm = 0;
nminstep = 0;
do
{
// Select a new trial point B in the interval [A,C].
// If the derivatives at points a & c have different sign we interpolate to zero,
// otherwise just do a bisection since there might be multiple minima/maxima
// inside the interval.
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 to point B
real *xb = static_cast<real *>(as_rvec_array(sb->s.x.data())[0]);
for (i = 0; i < n; i++)
{
xb[i] = lastx[i] + b*s[i];
}
neval++;
// Calculate energy for the trial step in point B
evaluate_energy(fplog, cr,
top_global, sb, top,
inputrec, nrnb, wcycle, gstat,
vsite, constr, fcd, graph, mdAtoms, fr,
mu_tot, enerd, vir, pres, step, FALSE);
fnorm = sb->fnorm;
// Calculate gradient in point B
real *fb = static_cast<real *>(as_rvec_array(sb->f.data())[0]);
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 [A,B] or [B,C] based on the value of the derivative
// at the new point B, and rename the endpoints of this new interval A and C.
if (gpb > 0)
{
/* Replace c endpoint with b */
c = b;
/* swap states b and c */
swap_em_state(&sb, &sc);
}
else
{
/* Replace a endpoint with b */
a = b;
/* swap states a and b */
swap_em_state(&sa, &sb);
}
/*
* 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 ((sb->epot > sa->epot || sb->epot > sc->epot) && (nminstep < 20));
if (fabs(sb->epot - 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 (sc->epot < sa->epot)
{
/* Use state C */
ems = *sc;
step_taken = c;
}
else
{
/* Use state A */
ems = *sa;
step_taken = a;
}
}
else
{
/* found lower */
/* Use state C */
ems = *sc;
step_taken = c;
}
/* Update the memory information, and calculate a new
* approximation of the inverse hessian
*/
/* Have new data in Epot, xx, ff */
if (ncorr < nmaxcorr)
{
ncorr++;
}
for (i = 0; i < n; i++)
{
dg[point][i] = lastf[i]-ff[i];
dx[point][i] *= step_taken;
}
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;
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;
}
}
/* Print it if necessary */
if (MASTER(cr))
{
if (mdrunOptions.verbose)
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
step, ems.epot, ems.fnorm/sqrtNumAtoms, ems.fmax, ems.a_fmax + 1);
fflush(stderr);
}
/* Store the new (lower) energies */
upd_mdebin(mdebin, FALSE, FALSE, (double)step,
mdatoms->tmass, enerd, state_global, inputrec->fepvals, inputrec->expandedvals, state_global->box,
nullptr, nullptr, vir, pres, nullptr, 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);
}
print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
do_log ? fplog : nullptr, step, step, eprNORMAL,
mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
/* Send x and E to IMD client, if bIMD is TRUE. */
if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, as_rvec_array(state_global->x.data()), inputrec, 0, wcycle) && MASTER(cr))
{
IMD_send_positions(inputrec->imd);
}
// Reset stepsize in we are doing more iterations
stepsize = 1.0/ems.fnorm;
/* Stop when the maximum force lies below tolerance.
* If we have reached machine precision, converged is already set to true.
*/
converged = converged || (ems.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 (ems.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 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);
}
if (!do_ene || !do_log) /* Write final energy file entries */
{
print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
!do_log ? fplog : nullptr, step, step, eprNORMAL,
mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
}
/* 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_global, observablesHistory);
if (MASTER(cr))
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
print_converged(stderr, LBFGS, inputrec->em_tol, step, converged,
number_steps, &ems, sqrtNumAtoms);
print_converged(fplog, LBFGS, inputrec->em_tol, step, converged,
number_steps, &ems, sqrtNumAtoms);
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 */
/*! \brief Do steepest descents minimization
\copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
int nfile, const t_filenm fnm[],
const gmx_output_env_t *oenv,
const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
gmx::MDAtoms *mdAtoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_t ed,
t_forcerec *fr,
const ReplicaExchangeParameters &replExParams,
gmx_walltime_accounting_t walltime_accounting)
*/
double do_steep(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
int nfile, const t_filenm fnm[],
const gmx_output_env_t gmx_unused *oenv,
const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
ObservablesHistory *observablesHistory,
gmx::MDAtoms *mdAtoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_forcerec *fr,
const ReplicaExchangeParameters gmx_unused &replExParams,
gmx_membed_t gmx_unused *membed,
gmx_walltime_accounting_t walltime_accounting)
{
const char *SD = "Steepest Descents";
gmx_localtop_t *top;
gmx_enerdata_t *enerd;
gmx_global_stat_t gstat;
t_graph *graph;
real stepsize;
real ustep;
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;
auto mdatoms = mdAtoms->mdatoms();
/* Create 2 states on the stack and extract pointers that we will swap */
em_state_t s0 {}, s1 {};
em_state_t *s_min = &s0;
em_state_t *s_try = &s1;
/* Init em and store the local state in s_try */
init_em(fplog, SD, cr, outputProvider, inputrec, mdrunOptions,
state_global, top_global, s_try, &top,
nrnb, mu_tot, fr, &enerd, &graph, mdAtoms, &gstat,
vsite, constr, nullptr,
nfile, fnm, &outf, &mdebin, 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 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 */
bool validStep = true;
if (count > 0)
{
validStep =
do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
s_min, stepsize, &s_min->f, s_try,
constr, top, nrnb, wcycle, count);
}
if (validStep)
{
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);
}
else
{
// Signal constraint error during stepping with energy=inf
s_try->epot = std::numeric_limits<real>::infinity();
}
if (MASTER(cr))
{
print_ebin_header(fplog, count, count);
}
if (count == 0)
{
s_min->epot = s_try->epot;
}
/* Print it if necessary */
if (MASTER(cr))
{
if (mdrunOptions.verbose)
{
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,
( (count == 0) || (s_try->epot < s_min->epot) ) ? '\n' : '\r');
fflush(stderr);
}
if ( (count == 0) || (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, nullptr, nullptr, vir, pres, nullptr, 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,
mdebin, fcd, &(top_global->groups), &(inputrec->opts), nullptr);
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, nullptr,
top_global, inputrec, count,
s_min, state_global, observablesHistory);
}
else
{
/* If energy is not smaller make the step smaller... */
ustep *= 0.5;
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 */
#if GMX_DOUBLE
if (count == nsteps || ustep < 1e-12)
#else
if (count == nsteps || ustep < 1e-6)
#endif
{
if (MASTER(cr))
{
warn_step(stderr, inputrec->em_tol, count == nsteps, constr != nullptr);
warn_step(fplog, inputrec->em_tol, count == nsteps, constr != nullptr);
}
bAbort = TRUE;
}
/* Send IMD energies and positions, if bIMD is TRUE. */
if (do_IMD(inputrec->bIMD, count, cr, TRUE, state_global->box,
MASTER(cr) ? as_rvec_array(state_global->x.data()) : nullptr,
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 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, observablesHistory);
if (MASTER(cr))
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
print_converged(stderr, SD, inputrec->em_tol, count, bDone, nsteps,
s_min, sqrtNumAtoms);
print_converged(fplog, SD, inputrec->em_tol, count, bDone, nsteps,
s_min, sqrtNumAtoms);
}
finish_em(cr, outf, walltime_accounting, wcycle);
/* To print the actual number of steps we needed somewhere */
inputrec->nsteps = count;
walltime_accounting_set_nsteps_done(walltime_accounting, count);
return 0;
} /* That's all folks */
/*! \brief Do normal modes analysis
\copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
int nfile, const t_filenm fnm[],
const gmx_output_env_t *oenv,
const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
gmx::MDAtoms *mdAtoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_t ed,
t_forcerec *fr,
const ReplicaExchangeParameters &replExParams,
gmx_walltime_accounting_t walltime_accounting)
*/
double do_nm(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
int nfile, const t_filenm fnm[],
const gmx_output_env_t gmx_unused *oenv,
const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
ObservablesHistory gmx_unused *observablesHistory,
gmx::MDAtoms *mdAtoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_forcerec *fr,
const ReplicaExchangeParameters gmx_unused &replExParams,
gmx_membed_t gmx_unused *membed,
gmx_walltime_accounting_t walltime_accounting)
{
const char *NM = "Normal Mode Analysis";
gmx_mdoutf_t outf;
int nnodes, node;
gmx_localtop_t *top;
gmx_enerdata_t *enerd;
gmx_global_stat_t gstat;
t_graph *graph;
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 = nullptr;
real * full_matrix = nullptr;
/* added with respect to mdrun */
int row, col;
real der_range = 10.0*sqrt(GMX_REAL_EPS);
real x_min;
bool bIsMaster = MASTER(cr);
auto mdatoms = mdAtoms->mdatoms();
if (constr != nullptr)
{
gmx_fatal(FARGS, "Constraints present with Normal Mode Analysis, this combination is not supported");
}
gmx_shellfc_t *shellfc;
em_state_t state_work {};
/* Init em and store the local state in state_minimum */
init_em(fplog, NM, cr, outputProvider, inputrec, mdrunOptions,
state_global, top_global, &state_work, &top,
nrnb, mu_tot, fr, &enerd, &graph, mdAtoms, &gstat,
vsite, constr, &shellfc,
nfile, fnm, &outf, nullptr, wcycle);
std::vector<size_t> atom_index = get_atom_index(top_global);
snew(fneg, atom_index.size());
snew(dfdx, atom_index.size());
#if !GMX_DOUBLE
if (bIsMaster)
{
fprintf(stderr,
"NOTE: This version of GROMACS has been compiled in single precision,\n"
" which MIGHT not be accurate enough for normal mode analysis.\n"
" GROMACS now uses sparse matrix storage, so the memory requirements\n"
" are fairly modest even if you recompile in double precision.\n\n");
}
#endif
/* 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->ic->eeltype) || fr->rlist == 0.0)
{
GMX_LOG(mdlog.warning).appendText("Non-cutoff electrostatics used, forcing full Hessian format.");
bSparse = FALSE;
}
else if (atom_index.size() < 1000)
{
GMX_LOG(mdlog.warning).appendTextFormatted("Small system size (N=%d), using full Hessian format.",
atom_index.size());
bSparse = FALSE;
}
else
{
GMX_LOG(mdlog.warning).appendText("Using compressed symmetric sparse Hessian format.");
bSparse = TRUE;
}
/* Number of dimensions, based on real atoms, that is not vsites or shell */
sz = DIM*atom_index.size();
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);
}
init_nrnb(nrnb);
where();
/* Write start time and temperature */
print_em_start(fplog, cr, walltime_accounting, wcycle, NM);
/* fudge nr of steps to nr of atoms */
inputrec->nsteps = atom_index.size()*2;
if (bIsMaster)
{
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, 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);
GMX_LOG(mdlog.warning).appendTextFormatted("Maximum force:%12.5e", state_work.fmax);
if (state_work.fmax > 1.0e-3)
{
GMX_LOG(mdlog.warning).appendText(
"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.");
}
/***********************************************************
*
* Loop over all pairs in matrix
*
* do_force called twice. Once with positive and
* once with negative displacement
*
************************************************************/
/* Steps are divided one by one over the nodes */
bool bNS = true;
for (unsigned int aid = cr->nodeid; aid < atom_index.size(); aid += nnodes)
{
size_t atom = atom_index[aid];
for (size_t d = 0; d < DIM; d++)
{
gmx_bool bBornRadii = FALSE;
gmx_int64_t step = 0;
int force_flags = GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES;
double t = 0;
x_min = state_work.s.x[atom][d];
for (unsigned int dx = 0; (dx < 2); dx++)
{
if (dx == 0)
{
state_work.s.x[atom][d] = x_min - der_range;
}
else
{
state_work.s.x[atom][d] = x_min + der_range;
}
/* Make evaluate_energy do a single node force calculation */
cr->nnodes = 1;
if (shellfc)
{
/* Now is the time to relax the shells */
(void) relax_shell_flexcon(fplog, cr, mdrunOptions.verbose, step,
inputrec, bNS, force_flags,
top,
constr, enerd, fcd,
&state_work.s, &state_work.f, vir, mdatoms,
nrnb, wcycle, graph, &top_global->groups,
shellfc, fr, bBornRadii, t, mu_tot,
vsite,
DdOpenBalanceRegionBeforeForceComputation::no,
DdCloseBalanceRegionAfterForceComputation::no);
bNS = false;
step++;
}
else
{
evaluate_energy(fplog, cr,
top_global, &state_work, top,
inputrec, nrnb, wcycle, gstat,
vsite, constr, fcd, graph, mdAtoms, fr,
mu_tot, enerd, vir, pres, aid*2+dx, FALSE);
}
cr->nnodes = nnodes;
if (dx == 0)
{
for (size_t i = 0; i < atom_index.size(); i++)
{
copy_rvec(state_work.f[atom_index[i]], fneg[i]);
}
}
}
/* x is restored to original */
state_work.s.x[atom][d] = x_min;
for (size_t j = 0; j < atom_index.size(); j++)
{
for (size_t k = 0; (k < DIM); k++)
{
dfdx[j][k] =
-(state_work.f[atom_index[j]][k] - fneg[j][k])/(2*der_range);
}
}
if (!bIsMaster)
{
#if GMX_MPI
#define mpi_type GMX_MPI_REAL
MPI_Send(dfdx[0], atom_index.size()*DIM, mpi_type, MASTER(cr),
cr->nodeid, cr->mpi_comm_mygroup);
#endif
}
else
{
for (node = 0; (node < nnodes && aid+node < atom_index.size()); node++)
{
if (node > 0)
{
#if GMX_MPI
MPI_Status stat;
MPI_Recv(dfdx[0], atom_index.size()*DIM, mpi_type, node, node,
cr->mpi_comm_mygroup, &stat);
#undef mpi_type
#endif
}
row = (aid + node)*DIM + d;
for (size_t j = 0; j < atom_index.size(); j++)
{
for (size_t k = 0; k < DIM; k++)
{
col = j*DIM + k;
if (bSparse)
{
if (col >= row && dfdx[j][k] != 0.0)
{
gmx_sparsematrix_increment_value(sparse_matrix,
row, col, dfdx[j][k]);
}
}
else
{
full_matrix[row*sz+col] = dfdx[j][k];
}
}
}
}
}
if (mdrunOptions.verbose && fplog)
{
fflush(fplog);
}
}
/* write progress */
if (bIsMaster && mdrunOptions.verbose)
{
fprintf(stderr, "\rFinished step %d out of %d",
static_cast<int>(std::min(atom+nnodes, atom_index.size())),
static_cast<int>(atom_index.size()));
fflush(stderr);
}
}
if (bIsMaster)
{
fprintf(stderr, "\n\nWriting Hessian...\n");
gmx_mtxio_write(ftp2fn(efMTX, nfile, fnm), sz, sz, full_matrix, sparse_matrix);
}
finish_em(cr, outf, walltime_accounting, wcycle);
walltime_accounting_set_nsteps_done(walltime_accounting, atom_index.size()*2);
return 0;
}
} // namespace gmx