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static em_state_t * | init_em_state () |
| Initiate em_state_t structure and return pointer to it.
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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.
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static void | em_time_end (gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle_t 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, gmx_bool bLastStep, gmx_bool bConstrain) |
| Print warning message.
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static void | print_converged (FILE *fp, const char *alg, real ftol, gmx_int64_t count, gmx_bool bDone, gmx_int64_t nsteps, real epot, real fmax, int nfmax, real fnorm) |
| Print message about convergence of the EM.
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static void | get_f_norm_max (t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms, 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 (t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms, em_state_t *ems) |
| Compute the norm of the force.
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void | init_em (FILE *fplog, const char *title, t_commrec *cr, t_inputrec *ir, t_state *state_global, gmx_mtop_t *top_global, em_state_t *ems, gmx_localtop_t **top, rvec **f, t_nrnb *nrnb, rvec mu_tot, t_forcerec *fr, gmx_enerdata_t **enerd, t_graph **graph, t_mdatoms *mdatoms, gmx_global_stat_t *gstat, gmx_vsite_t *vsite, gmx_constr_t constr, int nfile, const t_filenm fnm[], gmx_mdoutf_t *outf, t_mdebin **mdebin, int imdport, unsigned long Flags, gmx_wallcycle_t wcycle) |
| Initialize the energy minimization.
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static void | finish_em (t_commrec *cr, gmx_mdoutf_t outf, gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle_t 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 | copy_em_coords (em_state_t *ems, t_state *state) |
| Copy coordinate from an EM state to a "normal" state structure.
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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) |
| Save the EM trajectory.
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static bool | do_em_step (t_commrec *cr, t_inputrec *ir, t_mdatoms *md, gmx_bool bMolPBC, em_state_t *ems1, real a, rvec *f, 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.
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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, t_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.
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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, t_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.
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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.
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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.
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double | gmx::do_cg (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| Do conjugate gradients minimization. More...
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double | gmx::do_lbfgs (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| Do L-BFGS conjugate gradients minimization. More...
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double | gmx::do_steep (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| Do steepest descents minimization. More...
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double | gmx::do_nm (FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose, int nstglobalcomm, gmx_vsite_t *vsite, gmx_constr_t constr, int stepout, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, t_mdatoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t *membed, real cpt_period, real max_hours, int imdport, unsigned long Flags, gmx_walltime_accounting_t walltime_accounting) |
| Do normal modes analysis. More...
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