minimize.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
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/*! \internal \file
 *
 * \brief This file defines integrators for energy minimization
 *
 * \author Berk Hess <hess@kth.se>
 * \author Erik Lindahl <erik@kth.se>
 * \ingroup module_mdlib
 */
#include "gmxpre.h"

#include "minimize.h"

#include "config.h"

#include <cmath>
#include <cstring>
#include <ctime>

#include <algorithm>
#include <vector>

#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/mtxio.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/imd/imd.h"
#include "gromacs/linearalgebra/sparsematrix.h"
#include "gromacs/listed-forces/manage-threading.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/mdsetup.h"
#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/shellfc.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdlib/trajectory_writing.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"

/* PLUMED */
#include "../../../Plumed.h"
extern int    plumedswitch;
extern plumed plumedmain;
extern void(*plumedcmd)(plumed,const char*,const void*);
/* END PLUMED */

//! Utility structure for manipulating states during EM
typedef struct {
    //! Copy of the global state
    t_state          s;
    //! Force array
    PaddedRVecVector f;
    //! Potential energy
    real             epot;
    //! Norm of the force
    real             fnorm;
    //! Maximum force
    real             fmax;
    //! Direction
    int              a_fmax;
} em_state_t;

//! Print the EM starting conditions
static void print_em_start(FILE                     *fplog,
                           t_commrec                *cr,
                           gmx_walltime_accounting_t walltime_accounting,
                           gmx_wallcycle_t           wcycle,
                           const char               *name)
{
    walltime_accounting_start(walltime_accounting);
    wallcycle_start(wcycle, ewcRUN);
    print_start(fplog, cr, walltime_accounting, name);
}

//! Stop counting time for EM
static void em_time_end(gmx_walltime_accounting_t walltime_accounting,
                        gmx_wallcycle_t           wcycle)
{
    wallcycle_stop(wcycle, ewcRUN);

    walltime_accounting_end(walltime_accounting);
}

//! Printing a log file and console header
static void sp_header(FILE *out, const char *minimizer, real ftol, int nsteps)
{
    fprintf(out, "\n");
    fprintf(out, "%s:\n", minimizer);
    fprintf(out, "   Tolerance (Fmax)   = %12.5e\n", ftol);
    fprintf(out, "   Number of steps    = %12d\n", nsteps);
}

//! Print warning message
static void warn_step(FILE *fp, real ftol, gmx_bool bLastStep, gmx_bool bConstrain)
{
    char buffer[2048];
    if (bLastStep)
    {
        sprintf(buffer,
                "\nEnergy minimization reached the maximum number "
                "of steps before the forces reached the requested "
                "precision Fmax < %g.\n", ftol);
    }
    else
    {
        sprintf(buffer,
                "\nEnergy minimization has stopped, but the forces have "
                "not converged to the requested precision Fmax < %g (which "
                "may not be possible for your system). It stopped "
                "because the algorithm tried to make a new step whose size "
                "was too small, or there was no change in the energy since "
                "last step. Either way, we regard the minimization as "
                "converged to within the available machine precision, "
                "given your starting configuration and EM parameters.\n%s%s",
                ftol,
                sizeof(real) < sizeof(double) ?
                "\nDouble precision normally gives you higher accuracy, but "
                "this is often not needed for preparing to run molecular "
                "dynamics.\n" :
                "",
                bConstrain ?
                "You might need to increase your constraint accuracy, or turn\n"
                "off constraints altogether (set constraints = none in mdp file)\n" :
                "");
    }
    fputs(wrap_lines(buffer, 78, 0, FALSE), fp);
}

//! Print message about convergence of the EM
static void print_converged(FILE *fp, const char *alg, real ftol,
                            gmx_int64_t count, gmx_bool bDone, gmx_int64_t nsteps,
                            const em_state_t *ems, double sqrtNumAtoms)
{
    char buf[STEPSTRSIZE];

    if (bDone)
    {