This file defines integrators for energy minimization.
- Author
- Berk Hess hess@.nosp@m.kth..nosp@m.se
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Erik Lindahl erik@.nosp@m.kth..nosp@m.se
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static void | print_em_start (FILE *fplog, const t_commrec *cr, gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle *wcycle, const char *name) |
| | Print the EM starting conditions.
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static void | em_time_end (gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle *wcycle) |
| | Stop counting time for EM.
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static void | sp_header (FILE *out, const char *minimizer, real ftol, int nsteps) |
| | Printing a log file and console header.
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static void | warn_step (FILE *fp, real ftol, real fmax, gmx_bool bLastStep, gmx_bool bConstrain) |
| | Print warning message.
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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.
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static void | get_f_norm_max (const t_commrec *cr, const t_grpopts *opts, t_mdatoms *mdatoms, gmx::ArrayRef< const gmx::RVec > f, real *fnorm, real *fmax, int *a_fmax) |
| | Compute the norm and max of the force array in parallel.
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static void | get_state_f_norm_max (const t_commrec *cr, const t_grpopts *opts, t_mdatoms *mdatoms, em_state_t *ems) |
| | Compute the norm of the force.
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static void | init_em (FILE *fplog, const gmx::MDLogger &mdlog, const char *title, const t_commrec *cr, const t_inputrec *ir, const MDModulesNotifiers &mdModulesNotifiers, gmx::ImdSession *imdSession, pull_t *pull_work, t_state *state_global, const gmx_mtop_t &top_global, em_state_t *ems, gmx_localtop_t *top, t_nrnb *nrnb, t_forcerec *fr, gmx::MDAtoms *mdAtoms, gmx_global_stat_t *gstat, VirtualSitesHandler *vsite, gmx::Constraints *constr, gmx_shellfc_t **shellfc) |
| | Initialize the energy minimization.
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static void | finish_em (const t_commrec *cr, gmx_mdoutf_t outf, gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle *wcycle) |
| | Finalize the minimization.
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static void | swap_em_state (em_state_t **ems1, em_state_t **ems2) |
| | Swap two different EM states during minimization.
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static void | write_em_traj (FILE *fplog, const t_commrec *cr, gmx_mdoutf_t outf, gmx_bool bX, gmx_bool bF, const char *confout, const gmx_mtop_t &top_global, const t_inputrec *ir, int64_t step, em_state_t *state, t_state *state_global, ObservablesHistory *observablesHistory) |
| | Save the EM trajectory.
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static bool | do_em_step (const t_commrec *cr, const t_inputrec *ir, t_mdatoms *md, em_state_t *ems1, real a, gmx::ArrayRefWithPadding< const gmx::RVec > force, em_state_t *ems2, gmx::Constraints *constr, int64_t count) |
| | Do one minimization step.
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static void | em_dd_partition_system (FILE *fplog, const gmx::MDLogger &mdlog, int step, const t_commrec *cr, const gmx_mtop_t &top_global, const t_inputrec *ir, const MDModulesNotifiers &mdModulesNotifiers, gmx::ImdSession *imdSession, pull_t *pull_work, em_state_t *ems, gmx_localtop_t *top, gmx::MDAtoms *mdAtoms, t_forcerec *fr, VirtualSitesHandler *vsite, gmx::Constraints *constr, t_nrnb *nrnb, gmx_wallcycle *wcycle) |
| | Prepare EM for using domain decomposition parallellization.
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void | anonymous_namespace{minimize.cpp}::setCoordinates (std::vector< RVec > *coords, ArrayRef< const RVec > refCoords) |
| | Copy coordinates, OpenMP parallelized, from refCoords to coords.
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real | anonymous_namespace{minimize.cpp}::maxCoordinateDifference (ArrayRef< const RVec > coords1, ArrayRef< const RVec > coords2, MPI_Comm mpiCommMyGroup) |
| | Returns the maximum difference an atom moved between two coordinate sets, over all ranks.
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static double | reorder_partsum (const t_commrec *cr, const t_grpopts *opts, const gmx_mtop_t &top_global, const em_state_t *s_min, const em_state_t *s_b) |
| | Parallel utility summing energies and forces.
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static real | pr_beta (const t_commrec *cr, const t_grpopts *opts, t_mdatoms *mdatoms, const gmx_mtop_t &top_global, const em_state_t *s_min, const em_state_t *s_b) |
| | Print some stuff, like beta, whatever that means.
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Include dependency graph for minimize.cpp:
1.8.5