minimize.cpp File Reference

#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/dlbtiming.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/mdsetup.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/dispersioncorrection.h"
#include "gromacs/mdlib/ebin.h"
#include "gromacs/mdlib/enerdata_utils.h"
#include "gromacs/mdlib/energyoutput.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/stat.h"
#include "gromacs/mdlib/tgroup.h"
#include "gromacs/mdlib/trajectory_writing.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/mdrunutility/printtime.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdrunoptions.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 "legacysimulator.h"
#include "shellfc.h"

Include dependency graph for minimize.cpp:

Description

This file defines integrators for energy minimization.

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Erik Lindahl erik@.nosp@m.kth..nosp@m.se

Classes
struct	em_state_t
	Utility structure for manipulating states during EM. More...
class	anonymous_namespace{minimize.cpp}::EnergyEvaluator
	Class to handle the work of setting and doing an energy evaluation. More...

Functions
static void	print_em_start (FILE *fplog, const t_commrec *cr, gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle_t wcycle, const char *name)
	Print the EM starting conditions.
static void	em_time_end (gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle_t wcycle)
	Stop counting time for EM.
static void	sp_header (FILE *out, const char *minimizer, real ftol, int nsteps)
	Printing a log file and console header.
static void	warn_step (FILE *fp, real ftol, real fmax, gmx_bool bLastStep, gmx_bool bConstrain)
	Print warning message.
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)
	Print message about convergence of the EM.
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)
	Compute the norm and max of the force array in parallel.
static void	get_state_f_norm_max (const t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms, em_state_t *ems)
	Compute the norm of the force.
static void	init_em (FILE *fplog, const gmx::MDLogger &mdlog, const char *title, const t_commrec *cr, t_inputrec *ir, gmx::ImdSession *imdSession, pull_t *pull_work, t_state *state_global, gmx_mtop_t *top_global, em_state_t *ems, gmx_localtop_t *top, t_nrnb *nrnb, t_forcerec *fr, t_graph **graph, gmx::MDAtoms *mdAtoms, gmx_global_stat_t *gstat, gmx_vsite_t *vsite, gmx::Constraints *constr, gmx_shellfc_t **shellfc)
	Initialize the energy minimization.
static void	finish_em (const t_commrec *cr, gmx_mdoutf_t outf, gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle_t wcycle)
	Finalize the minimization.
static void	swap_em_state (em_state_t **ems1, em_state_t **ems2)
	Swap two different EM states during minimization.
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)
	Save the EM trajectory.
static bool	do_em_step (const t_commrec *cr, t_inputrec *ir, t_mdatoms *md, em_state_t *ems1, real a, const PaddedHostVector< gmx::RVec > *force, em_state_t *ems2, gmx::Constraints *constr, int64_t count)
	Do one minimization step.
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, gmx::ImdSession *imdSession, pull_t *pull_work, 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)
	Prepare EM for using domain decomposition parallellization.
static double	reorder_partsum (const t_commrec *cr, t_grpopts *opts, gmx_mtop_t *top_global, em_state_t *s_min, em_state_t *s_b)
	Parallel utility summing energies and forces.
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)
	Print some stuff, like beta, whatever that means.