/*
- *
- * This source code is part of
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- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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*/
#ifndef _sim_util_h
#define _sim_util_h
-#include <time.h>
-#include "typedefs.h"
-#include "enxio.h"
-#include "mdebin.h"
-#include "update.h"
-#include "vcm.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/mdoutf.h"
+#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/timing/walltime_accounting.h"
#ifdef __cplusplus
extern "C" {
#endif
-typedef struct {
- t_fileio *fp_trn;
- t_fileio *fp_xtc;
- int xtc_prec;
- ener_file_t fp_ene;
- const char *fn_cpt;
- gmx_bool bKeepAndNumCPT;
- int eIntegrator;
- gmx_bool bExpanded;
- int elamstats;
- int simulation_part;
- FILE *fp_dhdl;
- FILE *fp_field;
-} gmx_mdoutf_t;
+struct t_graph;
typedef struct gmx_global_stat *gmx_global_stat_t;
-typedef struct {
- double real;
-#ifdef GMX_CRAY_XT3
- double proc;
-#else
- clock_t proc;
-#endif
- double realtime;
- double proctime;
- double time_per_step;
- double last;
- gmx_large_int_t nsteps_done;
-} gmx_runtime_t;
-
+void do_pbc_first(FILE *log, matrix box, t_forcerec *fr,
+ struct t_graph *graph, rvec x[]);
-void do_pbc_first(FILE *log,matrix box,t_forcerec *fr,
- t_graph *graph,rvec x[]);
+void do_pbc_first_mtop(FILE *fplog, int ePBC, matrix box,
+ gmx_mtop_t *mtop, rvec x[]);
-void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
- gmx_mtop_t *mtop,rvec x[]);
+void do_pbc_mtop(FILE *fplog, int ePBC, matrix box,
+ gmx_mtop_t *mtop, rvec x[]);
-void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
- gmx_mtop_t *mtop,rvec x[]);
-
/* ROUTINES from stat.c */
gmx_global_stat_t global_stat_init(t_inputrec *ir);
void global_stat_destroy(gmx_global_stat_t gs);
-void global_stat(FILE *log,gmx_global_stat_t gs,
- t_commrec *cr,gmx_enerdata_t *enerd,
- tensor fvir,tensor svir,rvec mu_tot,
- t_inputrec *inputrec,
- gmx_ekindata_t *ekind,
- gmx_constr_t constr,t_vcm *vcm,
- int nsig,real *sig,
- gmx_mtop_t *top_global, t_state *state_local,
- gmx_bool bSumEkinhOld, int flags);
+void global_stat(FILE *log, gmx_global_stat_t gs,
+ t_commrec *cr, gmx_enerdata_t *enerd,
+ tensor fvir, tensor svir, rvec mu_tot,
+ t_inputrec *inputrec,
+ gmx_ekindata_t *ekind,
+ gmx_constr_t constr, t_vcm *vcm,
+ int nsig, real *sig,
+ gmx_mtop_t *top_global, t_state *state_local,
+ gmx_bool bSumEkinhOld, int flags);
/* Communicate statistics over cr->mpi_comm_mysim */
-gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],
- int mdrun_flags,
- const t_commrec *cr,const t_inputrec *ir,
- const output_env_t oenv);
-/* Returns a pointer to a data structure with all output file pointers
- * and names required by mdrun.
- */
-
-void done_mdoutf(gmx_mdoutf_t *of);
-/* Close all open output files and free the of pointer */
-
-#define MDOF_X (1<<0)
-#define MDOF_V (1<<1)
-#define MDOF_F (1<<2)
-#define MDOF_XTC (1<<3)
-#define MDOF_CPT (1<<4)
-
-void write_traj(FILE *fplog,t_commrec *cr,
- gmx_mdoutf_t *of,
- int mdof_flags,
- gmx_mtop_t *top_global,
- gmx_large_int_t step,double t,
- t_state *state_local,t_state *state_global,
- rvec *f_local,rvec *f_global,
- int *n_xtc,rvec **x_xtc);
-/* Routine that writes frames to trn, xtc and/or checkpoint.
- * What is written is determined by the mdof_flags defined above.
- * Data is collected to the master node only when necessary.
- */
-
-int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep);
+int do_per_step(gmx_int64_t step, gmx_int64_t nstep);
/* Return TRUE if io should be done */
/* ROUTINES from sim_util.c */
-double gmx_gettime();
+void print_time(FILE *out, gmx_walltime_accounting_t walltime_accounting,
+ gmx_int64_t step, t_inputrec *ir, t_commrec *cr);
-void print_time(FILE *out, gmx_runtime_t *runtime,
- gmx_large_int_t step,t_inputrec *ir, t_commrec *cr);
+/*! \brief Print date, time, MPI rank and a description of this point
+ * in time.
+ *
+ * \param[in] log logfile, or NULL to suppress output
+ * \param[in] rank MPI rank to include in the output
+ * \param[in] title Description to include in the output
+ * \param[in] the_time Seconds since the epoch, e.g. as reported by gmx_gettime
+ */
+void print_date_and_time(FILE *log, int rank, const char *title,
+ double the_time);
-void runtime_start(gmx_runtime_t *runtime);
+void print_start(FILE *fplog, t_commrec *cr,
+ gmx_walltime_accounting_t walltime_accounting,
+ const char *name);
-void runtime_end(gmx_runtime_t *runtime);
+void finish_run(FILE *log, t_commrec *cr,
+ t_inputrec *inputrec,
+ t_nrnb nrnb[], gmx_wallcycle_t wcycle,
+ gmx_walltime_accounting_t walltime_accounting,
+ struct nonbonded_verlet_t *nbv,
+ gmx_bool bWriteStat);
-void runtime_upd_proc(gmx_runtime_t *runtime);
-/* The processor time should be updated every once in a while,
- * since on 32-bit manchines it loops after 72 minutes.
- */
-
-void print_date_and_time(FILE *log,int pid,const char *title,
- const gmx_runtime_t *runtime);
-
-void finish_run(FILE *log,t_commrec *cr,const char *confout,
- t_inputrec *inputrec,
- t_nrnb nrnb[],gmx_wallcycle_t wcycle,
- gmx_runtime_t *runtime,
- wallclock_gpu_t *gputimes,
- int omp_nth_pp,
- gmx_bool bWriteStat);
-
-void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr);
-
-void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
- gmx_large_int_t step, int natoms,
- matrix box,real lambda,tensor pres,tensor virial,
+void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr);
+
+void calc_dispcorr(t_inputrec *ir, t_forcerec *fr,
+ int natoms,
+ matrix box, real lambda, tensor pres, tensor virial,
real *prescorr, real *enercorr, real *dvdlcorr);
-void initialize_lambdas(FILE *fplog,t_inputrec *ir,int *fep_state,real *lambda,double *lam0);
+void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, real *lambda, double *lam0);
+
+void do_constrain_first(FILE *log, gmx_constr_t constr,
+ t_inputrec *inputrec, t_mdatoms *md,
+ t_state *state, t_commrec *cr, t_nrnb *nrnb,
+ t_forcerec *fr, gmx_localtop_t *top);
-void do_constrain_first(FILE *log,gmx_constr_t constr,
- t_inputrec *inputrec,t_mdatoms *md,
- t_state *state,rvec *f,
- t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
- t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
-
void init_md(FILE *fplog,
- t_commrec *cr,t_inputrec *ir, const output_env_t oenv,
- double *t,double *t0,
- real *lambda,int *fep_state, double *lam0,
- t_nrnb *nrnb,gmx_mtop_t *mtop,
- gmx_update_t *upd,
- int nfile,const t_filenm fnm[],
- gmx_mdoutf_t **outf,t_mdebin **mdebin,
- tensor force_vir,tensor shake_vir,
- rvec mu_tot,
- gmx_bool *bSimAnn,t_vcm **vcm,
- t_state *state, unsigned long Flags);
- /* Routine in sim_util.c */
+ t_commrec *cr, t_inputrec *ir, const output_env_t oenv,
+ double *t, double *t0,
+ real *lambda, int *fep_state, double *lam0,
+ t_nrnb *nrnb, gmx_mtop_t *mtop,
+ gmx_update_t *upd,
+ int nfile, const t_filenm fnm[],
+ gmx_mdoutf_t *outf, t_mdebin **mdebin,
+ tensor force_vir, tensor shake_vir,
+ rvec mu_tot,
+ gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags,
+ gmx_wallcycle_t wcycle);
+/* Routine in sim_util.c */
+
+gmx_bool use_GPU(const struct nonbonded_verlet_t *nbv);
#ifdef __cplusplus
}
#endif
-#endif /* _sim_util_h */
+#endif /* _sim_util_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff