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Gromacs
2018.8
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Gromacs
2018.8
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#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"
Include dependency graph for minimize.cpp:This file defines integrators for energy minimization.
Classes | |
| struct | em_state_t |
| Utility structure for manipulating states during EM. More... | |
Functions | |
| static void | print_em_start (FILE *fplog, 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, gmx_bool bLastStep, gmx_bool bConstrain) |
| Print warning message. | |
| 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) |
| Print message about convergence of the EM. | |
| static void | get_f_norm_max (t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms, const rvec *f, real *fnorm, real *fmax, int *a_fmax) |
| Compute the norm and max of the force array in parallel. | |
| static void | get_state_f_norm_max (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 char *title, t_commrec *cr, gmx::IMDOutputProvider *outputProvider, t_inputrec *ir, const MdrunOptions &mdrunOptions, t_state *state_global, gmx_mtop_t *top_global, em_state_t *ems, gmx_localtop_t **top, t_nrnb *nrnb, rvec mu_tot, t_forcerec *fr, gmx_enerdata_t **enerd, t_graph **graph, gmx::MDAtoms *mdAtoms, gmx_global_stat_t *gstat, gmx_vsite_t *vsite, gmx_constr_t constr, gmx_shellfc_t **shellfc, int nfile, const t_filenm fnm[], gmx_mdoutf_t *outf, t_mdebin **mdebin, gmx_wallcycle_t wcycle) |
| Initialize the energy minimization. | |
| static void | finish_em (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, t_commrec *cr, gmx_mdoutf_t outf, gmx_bool bX, gmx_bool bF, const char *confout, gmx_mtop_t *top_global, t_inputrec *ir, gmx_int64_t step, em_state_t *state, t_state *state_global, ObservablesHistory *observablesHistory) |
| Save the EM trajectory. | |
| static bool | do_em_step (t_commrec *cr, t_inputrec *ir, t_mdatoms *md, gmx_bool bMolPBC, em_state_t *ems1, real a, const PaddedRVecVector *force, em_state_t *ems2, gmx_constr_t constr, gmx_localtop_t *top, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_int64_t count) |
| Do one minimization step. | |
| static void | em_dd_partition_system (FILE *fplog, int step, t_commrec *cr, gmx_mtop_t *top_global, t_inputrec *ir, em_state_t *ems, gmx_localtop_t *top, gmx::MDAtoms *mdAtoms, t_forcerec *fr, gmx_vsite_t *vsite, gmx_constr_t constr, t_nrnb *nrnb, gmx_wallcycle_t wcycle) |
| Prepare EM for using domain decomposition parallellization. | |
| static void | evaluate_energy (FILE *fplog, t_commrec *cr, gmx_mtop_t *top_global, em_state_t *ems, gmx_localtop_t *top, t_inputrec *inputrec, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_global_stat_t gstat, gmx_vsite_t *vsite, gmx_constr_t constr, t_fcdata *fcd, t_graph *graph, gmx::MDAtoms *mdAtoms, t_forcerec *fr, rvec mu_tot, gmx_enerdata_t *enerd, tensor vir, tensor pres, gmx_int64_t count, gmx_bool bFirst) |
| De one energy evaluation. | |
| static double | reorder_partsum (t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms, gmx_mtop_t *top_global, em_state_t *s_min, em_state_t *s_b) |
| Parallel utility summing energies and forces. | |
| static real | pr_beta (t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms, gmx_mtop_t *top_global, em_state_t *s_min, em_state_t *s_b) |
| Print some stuff, like beta, whatever that means. | |
| double | gmx::do_cg (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, ObservablesHistory *observablesHistory, gmx::MDAtoms *mdAtoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t *membed, gmx_walltime_accounting_t walltime_accounting) |
| Do conjugate gradients minimization. More... | |
| double | gmx::do_lbfgs (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, ObservablesHistory *observablesHistory, gmx::MDAtoms *mdAtoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t *membed, gmx_walltime_accounting_t walltime_accounting) |
| Do L-BFGS conjugate gradients minimization. More... | |
| double | gmx::do_steep (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, ObservablesHistory *observablesHistory, gmx::MDAtoms *mdAtoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t *membed, gmx_walltime_accounting_t walltime_accounting) |
| Do steepest descents minimization. More... | |
| double | gmx::do_nm (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, ObservablesHistory *observablesHistory, gmx::MDAtoms *mdAtoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t *membed, gmx_walltime_accounting_t walltime_accounting) |
| Do normal modes analysis. More... | |
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