--- /dev/null
- energyEvaluator.run(&state_work, mu_tot, vir, pres, atom*2+dx, FALSE);
+/*
+ * 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.
+ *
+ * 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.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * 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.
+ *
+ * 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.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file defines integrators for energy minimization
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Erik Lindahl <erik@kth.se>
+ * \ingroup module_mdrun
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <cmath>
+#include <cstring>
+#include <ctime>
+
+#include <algorithm>
+#include <vector>
+
+#include "gromacs/commandline/filenm.h"
+#include "gromacs/domdec/collect.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/domdec/partition.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"
+
+#include "integrator.h"
+
+//! Utility structure for manipulating states during EM
+typedef struct {
+ //! Copy of the global state
+ t_state s;
+ //! Force array
+ PaddedVector<gmx::RVec> 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,
+ const t_commrec *cr,
+ gmx_walltime_accounting_t walltime_accounting,
+ gmx_wallcycle_t wcycle,
+ const char *name)
+{
+ walltime_accounting_start_time(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_time(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,
+ real fmax,
+ gmx_bool bLastStep,
+ gmx_bool bConstrain)
+{
+ constexpr bool realIsDouble = GMX_DOUBLE;
+ char buffer[2048];
+
+ if (!std::isfinite(fmax))
+ {
+ sprintf(buffer,
+ "\nEnergy minimization has stopped because the force "
+ "on at least one atom is not finite. This usually means "
+ "atoms are overlapping. Modify the input coordinates to "
+ "remove atom overlap or use soft-core potentials with "
+ "the free energy code to avoid infinite forces.\n%s",
+ !realIsDouble ?
+ "You could also be lucky that switching to double precision "
+ "is sufficient to obtain finite forces.\n" :
+ "");
+ }
+ else 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,
+ !realIsDouble ?
+ "\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), stderr);
+ 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,
+ int64_t count, gmx_bool bDone, 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(const 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->globalAtomIndices[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 = gmx::roundToInt(sum[2*i+1]);
+ }
+ }
+ 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(const t_commrec *cr,
+ t_grpopts *opts, t_mdatoms *mdatoms,
+ em_state_t *ems)
+{
+ get_f_norm_max(cr, opts, mdatoms, ems->f.rvec_array(),
+ &ems->fnorm, &ems->fmax, &ems->a_fmax);
+}
+
+//! Initialize the energy minimization
+static void init_em(FILE *fplog,
+ const gmx::MDLogger &mdlog,
+ const char *title,
+ const t_commrec *cr,
+ const gmx_multisim_t *ms,
+ 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::Constraints *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, ms, top_global, fplog, 1,
+ MASTER(cr) ? state_global->x.rvec_array() : 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,
+ constr ? constr->numFlexibleConstraints() : 0,
+ 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, mdlog, 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);
+ ems->f.resizeWithPadding(ems->s.natoms);
+
+ snew(*top, 1);
+ mdAlgorithmsSetupAtomData(cr, ir, top_global, *top, fr,
+ graph, mdAtoms,
+ constr, vsite, shellfc ? *shellfc : nullptr);
+
+ if (vsite)
+ {
+ set_vsite_top(vsite, *top, mdatoms);
+ }
+ }
+
+ update_mdatoms(mdAtoms->mdatoms(), ems->s.lambda[efptMASS]);
+
+ if (constr)
+ {
+ // TODO how should this cross-module support dependency be managed?
+ 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 (!ir->bContinuation)
+ {
+ /* Constrain the starting coordinates */
+ dvdl_constr = 0;
+ constr->apply(TRUE, TRUE,
+ -1, 0, 1.0,
+ ems->s.x.rvec_array(),
+ ems->s.x.rvec_array(),
+ nullptr,
+ ems->s.box,
+ ems->s.lambda[efptFEP], &dvdl_constr,
+ nullptr, nullptr, gmx::ConstraintVariable::Positions);
+ }
+ }
+
+ 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(const 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, const t_commrec *cr,
+ gmx_mdoutf_t outf,
+ gmx_bool bX, gmx_bool bF, const char *confout,
+ gmx_mtop_t *top_global,
+ t_inputrec *ir, 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, static_cast<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) ? makeArrayRef(state_global->x) : gmx::EmptyArrayRef();
+ dd_collect_vec(cr->dd, &state->s, makeArrayRef(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,
+ state_global->x.rvec_array());
+ }
+
+ write_sto_conf_mtop(confout,
+ *top_global->name, top_global,
+ state_global->x.rvec_array(), 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(const t_commrec *cr,
+ t_inputrec *ir, t_mdatoms *md,
+ em_state_t *ems1, real a, const PaddedVector<gmx::RVec> *force,
+ em_state_t *ems2,
+ gmx::Constraints *constr,
+ 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);
+ ems2->f.resizeWithPadding(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;
+
+ nthreads = gmx_omp_nthreads_get(emntUpdate);
+#pragma omp parallel num_threads(nthreads)
+ {
+ const rvec *x1 = s1->x.rvec_array();
+ rvec *x2 = s2->x.rvec_array();
+ const rvec *f = force->rvec_array();
+
+ 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 = s1->cg_p.rvec_array();
+ rvec *p2 = s2->cg_p.rvec_array();
+#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)
+ {
+ dvdl_constr = 0;
+ validStep =
+ constr->apply(TRUE, TRUE,
+ count, 0, 1.0,
+ s1->x.rvec_array(), s2->x.rvec_array(),
+ nullptr, s2->box,
+ s2->lambda[efptBONDED], &dvdl_constr,
+ nullptr, nullptr, gmx::ConstraintVariable::Positions);
+
+ 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 = static_cast<int>(!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,
+ const gmx::MDLogger &mdlog,
+ int step, const 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::Constraints *constr,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle)
+{
+ /* Repartition the domain decomposition */
+ dd_partition_system(fplog, mdlog, 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);
+}
+
+namespace
+{
+
+/*! \brief Class to handle the work of setting and doing an energy evaluation.
+ *
+ * This class is a mere aggregate of parameters to pass to evaluate an
+ * energy, so that future changes to names and types of them consume
+ * less time when refactoring other code.
+ *
+ * Aggregate initialization is used, for which the chief risk is that
+ * if a member is added at the end and not all initializer lists are
+ * updated, then the member will be value initialized, which will
+ * typically mean initialization to zero.
+ *
+ * We only want to construct one of these with an initializer list, so
+ * we explicitly delete the default constructor. */
+class EnergyEvaluator
+{
+ public:
+ //! We only intend to construct such objects with an initializer list.
+#if __GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 9)
+ // Aspects of the C++11 spec changed after GCC 4.8.5, and
+ // compilation of the initializer list construction in
+ // runner.cpp fails in GCC 4.8.5.
+ EnergyEvaluator() = delete;
+#endif
+ /*! \brief Evaluates an energy on the state in \c ems.
+ *
+ * \todo In practice, the same objects mu_tot, vir, and pres
+ * are always passed to this function, so we would rather have
+ * them as data members. However, their C-array types are
+ * unsuited for aggregate initialization. When the types
+ * improve, the call signature of this method can be reduced.
+ */
+ void run(em_state_t *ems, rvec mu_tot,
+ tensor vir, tensor pres,
+ int64_t count, gmx_bool bFirst);
+ //! Handles logging (deprecated).
+ FILE *fplog;
+ //! Handles logging.
+ const gmx::MDLogger &mdlog;
+ //! Handles communication.
+ const t_commrec *cr;
+ //! Coordinates multi-simulations.
+ const gmx_multisim_t *ms;
+ //! Holds the simulation topology.
+ gmx_mtop_t *top_global;
+ //! Holds the domain topology.
+ gmx_localtop_t *top;
+ //! User input options.
+ t_inputrec *inputrec;
+ //! Manages flop accounting.
+ t_nrnb *nrnb;
+ //! Manages wall cycle accounting.
+ gmx_wallcycle_t wcycle;
+ //! Coordinates global reduction.
+ gmx_global_stat_t gstat;
+ //! Handles virtual sites.
+ gmx_vsite_t *vsite;
+ //! Handles constraints.
+ gmx::Constraints *constr;
+ //! Handles strange things.
+ t_fcdata *fcd;
+ //! Molecular graph for SHAKE.
+ t_graph *graph;
+ //! Per-atom data for this domain.
+ gmx::MDAtoms *mdAtoms;
+ //! Handles how to calculate the forces.
+ t_forcerec *fr;
+ //! Stores the computed energies.
+ gmx_enerdata_t *enerd;
+};
+
+void
+EnergyEvaluator::run(em_state_t *ems, rvec mu_tot,
+ tensor vir, tensor pres,
+ 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, ems->s.x.rvec_array(), 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, mdlog, 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, ms, inputrec, nullptr, nullptr,
+ count, nrnb, wcycle, top, &top_global->groups,
+ ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
+ ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd,
+ ems->s.lambda, graph, fr, vsite, mu_tot, t, nullptr,
+ 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 */
+ dvdl_constr = 0;
+ rvec *f_rvec = ems->f.rvec_array();
+ constr->apply(FALSE, FALSE,
+ count, 0, 1.0,
+ ems->s.x.rvec_array(), f_rvec, f_rvec,
+ ems->s.box,
+ ems->s.lambda[efptBONDED], &dvdl_constr,
+ nullptr, &shake_vir, gmx::ConstraintVariable::ForceDispl);
+ enerd->term[F_DVDL_CONSTR] += dvdl_constr;
+ m_add(force_vir, shake_vir, vir);
+ }
+ 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);
+ }
+}
+
+} // namespace
+
+//! Parallel utility summing energies and forces
+static double reorder_partsum(const 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 = s_min->f.rvec_array();
+ const rvec *fb = s_b->f.rvec_array();
+
+ 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(const 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 = s_min->f.rvec_array();
+ const rvec *fb = s_b->f.rvec_array();
+ 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
+{
+
+void
+Integrator::do_cg()
+{
+ 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();
+
+ GMX_LOG(mdlog.info).asParagraph().
+ appendText("Note that activating conjugate gradient energy minimization via the "
+ "integrator .mdp option and the command gmx mdrun may "
+ "be available in a different form in a future version of GROMACS, "
+ "e.g. gmx minimize and an .mdp option.");
+
+ 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, mdlog, CG, cr, ms, 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);
+ }
+
+ EnergyEvaluator energyEvaluator {
+ fplog, mdlog, cr, ms,
+ top_global, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph,
+ mdAtoms, fr, enerd
+ };
+ /* 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
+ */
+ energyEvaluator.run(s_min, mu_tot, vir, pres, -1, TRUE);
+
+ if (MASTER(cr))
+ {
+ /* Copy stuff to the energy bin for easy printing etc. */
+ matrix nullBox = {};
+ upd_mdebin(mdebin, FALSE, FALSE, static_cast<double>(step),
+ mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
+ 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);
+ }
+
+ /* 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 = s_min->s.cg_p.rvec_array();
+ const rvec *sfm = s_min->f.rvec_array();
+ 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;
+ auto s_min_x = makeArrayRef(s_min->s.x);
+ for (int i = 0; i < mdatoms->homenr; i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ tmp = fabs(s_min_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, mdlog, 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, s_min, c, &s_min->s.cg_p, s_c,
+ constr, -1);
+
+ neval++;
+ /* Calculate energy for the trial step */
+ energyEvaluator.run(s_c, mu_tot, vir, pres, -1, FALSE);
+
+ /* Calc derivative along line */
+ const rvec *pc = s_c->s.cg_p.rvec_array();
+ const rvec *sfc = s_c->f.rvec_array();
+ 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 = std::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, mdlog, -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, s_min, b, &s_min->s.cg_p, s_b,
+ constr, -1);
+
+ neval++;
+ /* Calculate energy for the trial step */
+ energyEvaluator.run(s_b, mu_tot, 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 = s_b->s.cg_p.rvec_array();
+ const rvec *sfb = s_b->f.rvec_array();
+ 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 (std::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 */
+ matrix nullBox = {};
+ upd_mdebin(mdebin, FALSE, FALSE, static_cast<double>(step),
+ mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
+ 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, state_global->x.rvec_array(), 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(fplog, inputrec->em_tol, s_min->fmax,
+ 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);
+}
+
+
+void
+Integrator::do_lbfgs()
+{
+ 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();
+
+ GMX_LOG(mdlog.info).asParagraph().
+ appendText("Note that activating L-BFGS energy minimization via the "
+ "integrator .mdp option and the command gmx mdrun may "
+ "be available in a different form in a future version of GROMACS, "
+ "e.g. gmx minimize and an .mdp option.");
+
+ if (PAR(cr))
+ {
+ gmx_fatal(FARGS, "L-BFGS minimization only supports a single rank");
+ }
+
+ 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, mdlog, LBFGS, cr, ms, 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] != 0);
+ }
+ }
+ 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_global->x.rvec_array(), 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++;
+ EnergyEvaluator energyEvaluator {
+ fplog, mdlog, cr, ms,
+ top_global, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph,
+ mdAtoms, fr, enerd
+ };
+ energyEvaluator.run(&ems, mu_tot, vir, pres, -1, TRUE);
+
+ if (MASTER(cr))
+ {
+ /* Copy stuff to the energy bin for easy printing etc. */
+ matrix nullBox = {};
+ upd_mdebin(mdebin, FALSE, FALSE, static_cast<double>(step),
+ mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
+ 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);
+ }
+
+ /* 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 *>(ems.f.rvec_array()[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, static_cast<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 *>(ems.s.x.rvec_array()[0]);
+ real *ff = static_cast<real *>(ems.f.rvec_array()[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 *>(last->s.x.data()[0]);
+ real *lastf = static_cast<real *>(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 *>(sc->s.x.rvec_array()[0]);
+ for (i = 0; i < n; i++)
+ {
+ xc[i] = lastx[i] + c*s[i];
+ }
+
+ neval++;
+ // Calculate energy for the trial step in position C
+ energyEvaluator.run(sc, mu_tot, vir, pres, step, FALSE);
+
+ // Calc line gradient in position C
+ real *fc = static_cast<real *>(sc->f.rvec_array()[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 = std::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.
+ foundlower = sc->epot < sa->epot || (gpc < 0 && sc->epot < (sa->epot + tmp));
+ // If true, 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.
+
+ // If false, 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.
+
+ 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 *>(sb->s.x.rvec_array()[0]);
+ for (i = 0; i < n; i++)
+ {
+ xb[i] = lastx[i] + b*s[i];
+ }
+
+ neval++;
+ // Calculate energy for the trial step in point B
+ energyEvaluator.run(sb, mu_tot, vir, pres, step, FALSE);
+ fnorm = sb->fnorm;
+
+ // Calculate gradient in point B
+ real *fb = static_cast<real *>(sb->f.rvec_array()[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 (std::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 */
+ matrix nullBox = {};
+ upd_mdebin(mdebin, FALSE, FALSE, static_cast<double>(step),
+ mdatoms->tmass, enerd, nullptr, nullptr, nullptr, nullBox,
+ 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, state_global->x.rvec_array(), 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(fplog, inputrec->em_tol, ems.fmax,
+ 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);
+}
+
+void
+Integrator::do_steep()
+{
+ 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();
+
+ GMX_LOG(mdlog.info).asParagraph().
+ appendText("Note that activating steepest-descent energy minimization via the "
+ "integrator .mdp option and the command gmx mdrun may "
+ "be available in a different form in a future version of GROMACS, "
+ "e.g. gmx minimize and an .mdp option.");
+
+ /* 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, mdlog, SD, cr, ms, 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);
+ }
+ EnergyEvaluator energyEvaluator {
+ fplog, mdlog, cr, ms,
+ top_global, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph,
+ mdAtoms, fr, enerd
+ };
+
+ /**** 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,
+ s_min, stepsize, &s_min->f, s_try,
+ constr, count);
+ }
+
+ if (validStep)
+ {
+ energyEvaluator.run(s_try, mu_tot, 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 */
+ matrix nullBox = {};
+ upd_mdebin(mdebin, FALSE, FALSE, static_cast<double>(count),
+ mdatoms->tmass, enerd, nullptr, nullptr, nullptr,
+ nullBox, 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, mdlog, 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(fplog, inputrec->em_tol, s_min->fmax,
+ 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) ? state_global->x.rvec_array() : 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 != 0, 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);
+}
+
+void
+Integrator::do_nm()
+{
+ 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 *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*std::sqrt(GMX_REAL_EPS);
+ real x_min;
+ bool bIsMaster = MASTER(cr);
+ auto mdatoms = mdAtoms->mdatoms();
+
+ GMX_LOG(mdlog.info).asParagraph().
+ appendText("Note that activating normal-mode analysis via the integrator "
+ ".mdp option and the command gmx mdrun may "
+ "be available in a different form in a future version of GROMACS, "
+ "e.g. gmx normal-modes.");
+
+ 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, mdlog, NM, cr, ms, 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<int> atom_index = get_atom_index(top_global);
+ std::vector<gmx::RVec> fneg(atom_index.size(), {0, 0, 0});
+ 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=%zu), 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);
+
+
+ /* 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%" PRId64 " steps.\n\n",
+ *(top_global->name), inputrec->nsteps);
+ }
+
+ nnodes = cr->nnodes;
+
+ /* Make evaluate_energy do a single node force calculation */
+ cr->nnodes = 1;
+ EnergyEvaluator energyEvaluator {
+ fplog, mdlog, cr, ms,
+ top_global, top,
+ inputrec, nrnb, wcycle, gstat,
+ vsite, constr, fcd, graph,
+ mdAtoms, fr, enerd
+ };
+ energyEvaluator.run(&state_work, mu_tot, 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;
+ auto state_work_x = makeArrayRef(state_work.s.x);
+ auto state_work_f = makeArrayRef(state_work.f);
+ 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++)
+ {
+ int64_t step = 0;
+ int force_flags = GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES;
+ double t = 0;
+
+ x_min = state_work_x[atom][d];
+
+ for (unsigned int dx = 0; (dx < 2); dx++)
+ {
+ if (dx == 0)
+ {
+ state_work_x[atom][d] = x_min - der_range;
+ }
+ else
+ {
+ state_work_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 */
+ relax_shell_flexcon(fplog,
+ cr,
+ ms,
+ mdrunOptions.verbose,
+ nullptr,
+ step,
+ inputrec,
+ bNS,
+ force_flags,
+ top,
+ constr,
+ enerd,
+ fcd,
+ &state_work.s,
+ state_work.f.arrayRefWithPadding(),
+ vir,
+ mdatoms,
+ nrnb,
+ wcycle,
+ graph,
+ &top_global->groups,
+ shellfc,
+ fr,
+ t,
+ mu_tot,
+ vsite,
+ DdOpenBalanceRegionBeforeForceComputation::no,
+ DdCloseBalanceRegionAfterForceComputation::no);
+ bNS = false;
+ step++;
+ }
+ else
+ {
- for (node = 0; (node < nnodes && atom+node < atom_index.size()); node++)
++ energyEvaluator.run(&state_work, mu_tot, vir, pres, aid*2+dx, FALSE);
+ }
+
+ cr->nnodes = nnodes;
+
+ if (dx == 0)
+ {
+ std::copy(state_work_f.begin(), state_work_f.begin()+atom_index.size(), fneg.begin());
+ }
+ }
+
+ /* x is restored to original */
+ state_work_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
+ {
- row = (atom + node)*DIM + d;
++ 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);
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 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.
+ *
+ * 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.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * 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.
+ *
+ * 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.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief Implements the loop for simulation reruns
+ *
+ * \author Pascal Merz <pascal.merz@colorado.edu>
+ * \ingroup module_mdrun
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include <cinttypes>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+
+#include <algorithm>
+#include <memory>
+
+#include "gromacs/awh/awh.h"
+#include "gromacs/commandline/filenm.h"
+#include "gromacs/compat/make_unique.h"
+#include "gromacs/domdec/collect.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_network.h"
+#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/domdec/partition.h"
+#include "gromacs/essentialdynamics/edsam.h"
+#include "gromacs/ewald/pme.h"
+#include "gromacs/ewald/pme-load-balancing.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/gpu_utils/gpu_utils.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdlib/checkpointhandler.h"
+#include "gromacs/mdlib/compute_io.h"
+#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/ebin.h"
+#include "gromacs/mdlib/expanded.h"
+#include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/force_flags.h"
+#include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/md_support.h"
+#include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/mdoutf.h"
+#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/mdsetup.h"
+#include "gromacs/mdlib/membed.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
+#include "gromacs/mdlib/ns.h"
+#include "gromacs/mdlib/resethandler.h"
+#include "gromacs/mdlib/shellfc.h"
+#include "gromacs/mdlib/sighandler.h"
+#include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/simulationsignal.h"
+#include "gromacs/mdlib/stophandler.h"
+#include "gromacs/mdlib/tgroup.h"
+#include "gromacs/mdlib/trajectory_writing.h"
+#include "gromacs/mdlib/update.h"
+#include "gromacs/mdlib/vcm.h"
+#include "gromacs/mdlib/vsite.h"
+#include "gromacs/mdtypes/awh-history.h"
+#include "gromacs/mdtypes/awh-params.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/df_history.h"
+#include "gromacs/mdtypes/energyhistory.h"
+#include "gromacs/mdtypes/fcdata.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/group.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/interaction_const.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/observableshistory.h"
+#include "gromacs/mdtypes/state.h"
+#include "gromacs/mimic/MimicUtils.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/swap/swapcoords.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/trajectory/trajectoryframe.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "integrator.h"
+#include "replicaexchange.h"
+
+using gmx::SimulationSignaller;
+
+/*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
+ *
+ * \param[in] rerunFrame The trajectory frame to compute energy/forces for
+ * \param[in,out] globalState The global state container
+ * \param[in] constructVsites When true, vsite coordinates are constructed
+ * \param[in] vsite Vsite setup, can be nullptr when \p constructVsites = false
+ * \param[in] idef Topology parameters, used for constructing vsites
+ * \param[in] timeStep Time step, used for constructing vsites
+ * \param[in] forceRec Force record, used for constructing vsites
+ * \param[in,out] graph The molecular graph, used for constructing vsites when != nullptr
+ */
+static void prepareRerunState(const t_trxframe &rerunFrame,
+ t_state *globalState,
+ bool constructVsites,
+ const gmx_vsite_t *vsite,
+ const t_idef &idef,
+ double timeStep,
+ const t_forcerec &forceRec,
+ t_graph *graph)
+{
+ auto x = makeArrayRef(globalState->x);
+ auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec *>(rerunFrame.x), globalState->natoms);
+ std::copy(rerunX.begin(), rerunX.end(), x.begin());
+ copy_mat(rerunFrame.box, globalState->box);
+
+ if (constructVsites)
+ {
+ GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
+
+ if (graph)
+ {
+ /* Following is necessary because the graph may get out of sync
+ * with the coordinates if we only have every N'th coordinate set
+ */
+ mk_mshift(nullptr, graph, forceRec.ePBC, globalState->box, globalState->x.rvec_array());
+ shift_self(graph, globalState->box, as_rvec_array(globalState->x.data()));
+ }
+ construct_vsites(vsite, globalState->x.rvec_array(), timeStep, globalState->v.rvec_array(),
+ idef.iparams, idef.il,
+ forceRec.ePBC, forceRec.bMolPBC, nullptr, globalState->box);
+ if (graph)
+ {
+ unshift_self(graph, globalState->box, globalState->x.rvec_array());
+ }
+ }
+}
+
+void gmx::Integrator::do_rerun()
+{
+ // TODO Historically, the EM and MD "integrators" used different
+ // names for the t_inputrec *parameter, but these must have the
+ // same name, now that it's a member of a struct. We use this ir
+ // alias to avoid a large ripple of nearly useless changes.
+ // t_inputrec is being replaced by IMdpOptionsProvider, so this
+ // will go away eventually.
+ t_inputrec *ir = inputrec;
+ gmx_mdoutf *outf = nullptr;
+ int64_t step, step_rel;
+ double t, lam0[efptNR];
+ bool isLastStep = false;
+ bool doFreeEnergyPerturbation = false;
+ int force_flags;
+ tensor force_vir, shake_vir, total_vir, pres;
+ t_trxstatus *status;
+ rvec mu_tot;
+ t_trxframe rerun_fr;
+ gmx_localtop_t *top;
+ t_mdebin *mdebin = nullptr;
+ gmx_enerdata_t *enerd;
+ PaddedVector<gmx::RVec> f {};
+ gmx_global_stat_t gstat;
+ t_graph *graph = nullptr;
+ gmx_groups_t *groups;
+ gmx_ekindata_t *ekind;
+ gmx_shellfc_t *shellfc;
+
+ double cycles;
+
+ /* Domain decomposition could incorrectly miss a bonded
+ interaction, but checking for that requires a global
+ communication stage, which does not otherwise happen in DD
+ code. So we do that alongside the first global energy reduction
+ after a new DD is made. These variables handle whether the
+ check happens, and the result it returns. */
+ bool shouldCheckNumberOfBondedInteractions = false;
+ int totalNumberOfBondedInteractions = -1;
+
+ SimulationSignals signals;
+ // Most global communnication stages don't propagate mdrun
+ // signals, and will use this object to achieve that.
+ SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
+
+ GMX_LOG(mdlog.info).asParagraph().
+ appendText("Note that it is planned that the command gmx mdrun -rerun will "
+ "be available in a different form in a future version of GROMACS, "
+ "e.g. gmx rerun -f.");
+
+ if (ir->bExpanded)
+ {
+ gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
+ }
+ if (ir->bSimTemp)
+ {
+ gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
+ }
+ if (ir->bDoAwh)
+ {
+ gmx_fatal(FARGS, "AWH not supported by rerun.");
+ }
+ if (replExParams.exchangeInterval > 0)
+ {
+ gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
+ }
+ if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
+ {
+ gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
+ }
+ if (ir->bIMD)
+ {
+ gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
+ }
+ if (isMultiSim(ms))
+ {
+ gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
+ }
+ if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
+ [](int i){return i != eannNO; }))
+ {
+ gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
+ }
+
++ /* Rerun can't work if an output file name is the same as the input file name.
++ * If this is the case, the user will get an error telling them what the issue is.
++ */
++ if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0 ||
++ strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
++ {
++ gmx_fatal(FARGS, "When using mdrun -rerun, the name of the input trajectory file "
++ "%s cannot be identical to the name of an output file (whether "
++ "given explicitly with -o or -x, or by default)",
++ opt2fn("-rerun", nfile, fnm));
++ }
++
+ /* Settings for rerun */
+ ir->nstlist = 1;
+ ir->nstcalcenergy = 1;
+ int nstglobalcomm = 1;
+ const bool bNS = true;
+
+ ir->nstxout_compressed = 0;
+ groups = &top_global->groups;
+ if (ir->eI == eiMimic)
+ {
+ top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
+ }
+
+ /* Initial values */
+ init_rerun(fplog, cr, outputProvider, ir, oenv, mdrunOptions,
+ state_global, lam0, nrnb, top_global,
+ nfile, fnm, &outf, &mdebin, wcycle);
+
+ /* Energy terms and groups */
+ snew(enerd, 1);
+ init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
+ enerd);
+
+ /* Kinetic energy data */
+ snew(ekind, 1);
+ init_ekindata(fplog, top_global, &(ir->opts), ekind);
+ /* Copy the cos acceleration to the groups struct */
+ ekind->cosacc.cos_accel = ir->cos_accel;
+
+ gstat = global_stat_init(ir);
+
+ /* Check for polarizable models and flexible constraints */
+ shellfc = init_shell_flexcon(fplog,
+ top_global, constr ? constr->numFlexibleConstraints() : 0,
+ ir->nstcalcenergy, DOMAINDECOMP(cr));
+
+ {
+ double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
+ if ((io > 2000) && MASTER(cr))
+ {
+ fprintf(stderr,
+ "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
+ io);
+ }
+ }
+
+ // Local state only becomes valid now.
+ std::unique_ptr<t_state> stateInstance;
+ t_state * state;
+
+ if (DOMAINDECOMP(cr))
+ {
+ top = dd_init_local_top(top_global);
+
+ stateInstance = compat::make_unique<t_state>();
+ state = stateInstance.get();
+ dd_init_local_state(cr->dd, state_global, state);
+
+ /* Distribute the charge groups over the nodes from the master node */
+ dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
+ state_global, top_global, ir,
+ state, &f, mdAtoms, top, fr,
+ vsite, constr,
+ nrnb, nullptr, FALSE);
+ shouldCheckNumberOfBondedInteractions = true;
+ }
+ else
+ {
+ state_change_natoms(state_global, state_global->natoms);
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries.
+ */
+ f.resizeWithPadding(state_global->natoms);
+ /* Copy the pointer to the global state */
+ state = state_global;
+
+ snew(top, 1);
+ mdAlgorithmsSetupAtomData(cr, ir, top_global, top, fr,
+ &graph, mdAtoms, constr, vsite, shellfc);
+ }
+
+ auto mdatoms = mdAtoms->mdatoms();
+
+ // NOTE: The global state is no longer used at this point.
+ // But state_global is still used as temporary storage space for writing
+ // the global state to file and potentially for replica exchange.
+ // (Global topology should persist.)
+
+ update_mdatoms(mdatoms, state->lambda[efptMASS]);
+
+ if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
+ {
+ doFreeEnergyPerturbation = true;
+ }
+
+ {
+ int cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
+ (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
+ bool bSumEkinhOld = false;
+ t_vcm *vcm = nullptr;
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
+ nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, &nullSignaller, state->box,
+ &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
+ }
+ checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
+ top_global, top, state,
+ &shouldCheckNumberOfBondedInteractions);
+
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "starting md rerun '%s', reading coordinates from"
+ " input trajectory '%s'\n\n",
+ *(top_global->name), opt2fn("-rerun", nfile, fnm));
+ if (mdrunOptions.verbose)
+ {
+ fprintf(stderr, "Calculated time to finish depends on nsteps from "
+ "run input file,\nwhich may not correspond to the time "
+ "needed to process input trajectory.\n\n");
+ }
+ fprintf(fplog, "\n");
+ }
+
+ walltime_accounting_start_time(walltime_accounting);
+ wallcycle_start(wcycle, ewcRUN);
+ print_start(fplog, cr, walltime_accounting, "mdrun");
+
+ /***********************************************************
+ *
+ * Loop over MD steps
+ *
+ ************************************************************/
+
+ if (constr)
+ {
+ GMX_LOG(mdlog.info).asParagraph().
+ appendText("Simulations has constraints. Rerun does not recalculate constraints.");
+ }
+
+ rerun_fr.natoms = 0;
+ if (MASTER(cr))
+ {
+ isLastStep = !read_first_frame(oenv, &status,
+ opt2fn("-rerun", nfile, fnm),
+ &rerun_fr, TRX_NEED_X);
+ if (rerun_fr.natoms != top_global->natoms)
+ {
+ gmx_fatal(FARGS,
+ "Number of atoms in trajectory (%d) does not match the "
+ "run input file (%d)\n",
+ rerun_fr.natoms, top_global->natoms);
+ }
+
+ if (ir->ePBC != epbcNONE)
+ {
+ if (!rerun_fr.bBox)
+ {
+ gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
+ "does not contain a box, while pbc is used",
+ rerun_fr.step, rerun_fr.time);
+ }
+ if (max_cutoff2(ir->ePBC, rerun_fr.box) < gmx::square(fr->rlist))
+ {
+ gmx_fatal(FARGS, "Rerun trajectory frame step %" PRId64 " time %f "
+ "has too small box dimensions", rerun_fr.step, rerun_fr.time);
+ }
+ }
+ }
+
+ GMX_LOG(mdlog.info).asParagraph().
+ appendText("Rerun does not report kinetic energy, total energy, temperature, virial and pressure.");
+
+ if (PAR(cr))
+ {
+ rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
+ }
+
+ if (ir->ePBC != epbcNONE)
+ {
+ /* Set the shift vectors.
+ * Necessary here when have a static box different from the tpr box.
+ */
+ calc_shifts(rerun_fr.box, fr->shift_vec);
+ }
+
+ auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
+ compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
+ MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
+ mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
+
+ // we don't do counter resetting in rerun - finish will always be valid
+ walltime_accounting_set_valid_finish(walltime_accounting);
+
+ DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion = (DOMAINDECOMP(cr) ? DdOpenBalanceRegionBeforeForceComputation::yes : DdOpenBalanceRegionBeforeForceComputation::no);
+ DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion = (DOMAINDECOMP(cr) ? DdCloseBalanceRegionAfterForceComputation::yes : DdCloseBalanceRegionAfterForceComputation::no);
+
+ step = ir->init_step;
+ step_rel = 0;
+
+ /* and stop now if we should */
+ isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
+ while (!isLastStep)
+ {
+ wallcycle_start(wcycle, ewcSTEP);
+
+ if (rerun_fr.bStep)
+ {
+ step = rerun_fr.step;
+ step_rel = step - ir->init_step;
+ }
+ if (rerun_fr.bTime)
+ {
+ t = rerun_fr.time;
+ }
+ else
+ {
+ t = step;
+ }
+
+ if (ir->efep != efepNO && MASTER(cr))
+ {
+ setCurrentLambdasRerun(step, ir->fepvals, &rerun_fr, lam0, state_global);
+ }
+
+ if (MASTER(cr))
+ {
+ const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
+ if (constructVsites && DOMAINDECOMP(cr))
+ {
+ gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
+ "use a single rank");
+ }
+ prepareRerunState(rerun_fr, state_global, constructVsites, vsite, top->idef, ir->delta_t, *fr, graph);
+ }
+
+ isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
+
+ if (DOMAINDECOMP(cr))
+ {
+ /* Repartition the domain decomposition */
+ const bool bMasterState = true;
+ dd_partition_system(fplog, mdlog, step, cr,
+ bMasterState, nstglobalcomm,
+ state_global, top_global, ir,
+ state, &f, mdAtoms, top, fr,
+ vsite, constr,
+ nrnb, wcycle,
+ mdrunOptions.verbose);
+ shouldCheckNumberOfBondedInteractions = true;
+ }
+
+ if (MASTER(cr))
+ {
+ print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
+ }
+
+ if (ir->efep != efepNO)
+ {
+ update_mdatoms(mdatoms, state->lambda[efptMASS]);
+ }
+
+ force_flags = (GMX_FORCE_STATECHANGED |
+ GMX_FORCE_DYNAMICBOX |
+ GMX_FORCE_ALLFORCES |
+ (GMX_GPU ? GMX_FORCE_VIRIAL : 0) | // TODO: Get rid of this once #2649 is solved
+ GMX_FORCE_ENERGY |
+ (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
+
+ if (shellfc)
+ {
+ /* Now is the time to relax the shells */
+ relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
+ enforcedRotation, step,
+ ir, bNS, force_flags, top,
+ constr, enerd, fcd,
+ state, f.arrayRefWithPadding(), force_vir, mdatoms,
+ nrnb, wcycle, graph, groups,
+ shellfc, fr, t, mu_tot,
+ vsite,
+ ddOpenBalanceRegion, ddCloseBalanceRegion);
+ }
+ else
+ {
+ /* The coordinates (x) are shifted (to get whole molecules)
+ * in do_force.
+ * This is parallellized as well, and does communication too.
+ * Check comments in sim_util.c
+ */
+ Awh *awh = nullptr;
+ gmx_edsam *ed = nullptr;
+ do_force(fplog, cr, ms, ir, awh, enforcedRotation,
+ step, nrnb, wcycle, top, groups,
+ state->box, state->x.arrayRefWithPadding(), &state->hist,
+ f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
+ state->lambda, graph,
+ fr, vsite, mu_tot, t, ed,
+ GMX_FORCE_NS | force_flags,
+ ddOpenBalanceRegion, ddCloseBalanceRegion);
+ }
+
+ /* Now we have the energies and forces corresponding to the
+ * coordinates at time t.
+ */
+ {
+ const bool isCheckpointingStep = false;
+ const bool doRerun = true;
+ const bool bSumEkinhOld = false;
+ do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
+ ir, state, state_global, observablesHistory,
+ top_global, fr,
+ outf, mdebin, ekind, f,
+ isCheckpointingStep, doRerun, isLastStep,
+ mdrunOptions.writeConfout,
+ bSumEkinhOld);
+ }
+
+ stopHandler->setSignal();
+
+ if (graph)
+ {
+ /* Need to unshift here */
+ unshift_self(graph, state->box, as_rvec_array(state->x.data()));
+ }
+
+ if (vsite != nullptr)
+ {
+ wallcycle_start(wcycle, ewcVSITECONSTR);
+ if (graph != nullptr)
+ {
+ shift_self(graph, state->box, as_rvec_array(state->x.data()));
+ }
+ construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
+ top->idef.iparams, top->idef.il,
+ fr->ePBC, fr->bMolPBC, cr, state->box);
+
+ if (graph != nullptr)
+ {
+ unshift_self(graph, state->box, as_rvec_array(state->x.data()));
+ }
+ wallcycle_stop(wcycle, ewcVSITECONSTR);
+ }
+
+ {
+ const bool doInterSimSignal = false;
+ const bool doIntraSimSignal = true;
+ bool bSumEkinhOld = false;
+ t_vcm *vcm = nullptr;
+ SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
+
+ compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
+ wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ constr, &signaller,
+ state->box,
+ &totalNumberOfBondedInteractions, &bSumEkinhOld,
+ CGLO_GSTAT | CGLO_ENERGY
+ | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
+ );
+ checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
+ top_global, top, state,
+ &shouldCheckNumberOfBondedInteractions);
+ }
+
+ /* Note: this is OK, but there are some numerical precision issues with using the convergence of
+ the virial that should probably be addressed eventually. state->veta has better properies,
+ but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
+ generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
+
+ if (ir->efep != efepNO)
+ {
+ /* Sum up the foreign energy and dhdl terms for md and sd.
+ Currently done every step so that dhdl is correct in the .edr */
+ sum_dhdl(enerd, state->lambda, ir->fepvals);
+ }
+
+ /* Output stuff */
+ if (MASTER(cr))
+ {
+ const bool bCalcEnerStep = true;
+ upd_mdebin(mdebin, doFreeEnergyPerturbation, bCalcEnerStep,
+ t, mdatoms->tmass, enerd, state,
+ ir->fepvals, ir->expandedvals, rerun_fr.box,
+ shake_vir, force_vir, total_vir, pres,
+ ekind, mu_tot, constr);
+
+ const bool do_ene = true;
+ const bool do_log = true;
+ Awh *awh = nullptr;
+ const bool do_dr = ir->nstdisreout != 0;
+ const bool do_or = ir->nstorireout != 0;
+
+ print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
+ step, t,
+ eprNORMAL, mdebin, fcd, groups, &(ir->opts), awh);
+
+ if (do_per_step(step, ir->nstlog))
+ {
+ if (fflush(fplog) != 0)
+ {
+ gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
+ }
+ }
+ }
+
+ /* Print the remaining wall clock time for the run */
+ if (isMasterSimMasterRank(ms, cr) &&
+ (mdrunOptions.verbose || gmx_got_usr_signal()))
+ {
+ if (shellfc)
+ {
+ fprintf(stderr, "\n");
+ }
+ print_time(stderr, walltime_accounting, step, ir, cr);
+ }
+
+ /* Ion/water position swapping.
+ * Not done in last step since trajectory writing happens before this call
+ * in the MD loop and exchanges would be lost anyway. */
+ if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep &&
+ do_per_step(step, ir->swap->nstswap))
+ {
+ const bool doRerun = true;
+ do_swapcoords(cr, step, t, ir, wcycle,
+ rerun_fr.x,
+ rerun_fr.box,
+ MASTER(cr) && mdrunOptions.verbose,
+ doRerun);
+ }
+
+ if (MASTER(cr))
+ {
+ /* read next frame from input trajectory */
+ isLastStep = !read_next_frame(oenv, status, &rerun_fr);
+ }
+
+ if (PAR(cr))
+ {
+ rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
+ }
+
+ cycles = wallcycle_stop(wcycle, ewcSTEP);
+ if (DOMAINDECOMP(cr) && wcycle)
+ {
+ dd_cycles_add(cr->dd, cycles, ddCyclStep);
+ }
+
+ if (!rerun_fr.bStep)
+ {
+ /* increase the MD step number */
+ step++;
+ step_rel++;
+ }
+ }
+ /* End of main MD loop */
+
+ /* Closing TNG files can include compressing data. Therefore it is good to do that
+ * before stopping the time measurements. */
+ mdoutf_tng_close(outf);
+
+ /* Stop measuring walltime */
+ walltime_accounting_end_time(walltime_accounting);
+
+ if (MASTER(cr))
+ {
+ close_trx(status);
+ }
+
+ if (!thisRankHasDuty(cr, DUTY_PME))
+ {
+ /* Tell the PME only node to finish */
+ gmx_pme_send_finish(cr);
+ }
+
+ done_mdebin(mdebin);
+ done_mdoutf(outf);
+
+ done_shellfc(fplog, shellfc, step_rel);
+
+ // Clean up swapcoords
+ if (ir->eSwapCoords != eswapNO)
+ {
+ finish_swapcoords(ir->swap);
+ }
+
+ walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
+
+ destroy_enerdata(enerd);
+ sfree(enerd);
+ sfree(top);
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff