/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Gromacs Runs On Most of All Computer Systems
*/
#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;
+ 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;
typedef struct gmx_global_stat *gmx_global_stat_t;
typedef struct {
- double real;
+ double real;
#ifdef GMX_CRAY_XT3
- double proc;
+ double proc;
#else
- clock_t proc;
+ clock_t proc;
#endif
- double realtime;
- double proctime;
- double time_per_step;
- double last;
- gmx_large_int_t nsteps_done;
+ 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,
- 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);
+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.
*/
#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);
+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_large_int_t step, gmx_large_int_t nstep);
/* Return TRUE if io should be done */
/* ROUTINES from sim_util.c */
double gmx_gettime();
void print_time(FILE *out, gmx_runtime_t *runtime,
- gmx_large_int_t step,t_inputrec *ir, t_commrec *cr);
+ gmx_large_int_t step, t_inputrec *ir, t_commrec *cr);
void runtime_start(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,
+
+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,
+ 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, rvec *f,
+ t_graph *graph, t_commrec *cr, t_nrnb *nrnb,
+ t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
-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,
+ t_state *state, unsigned long Flags);
+/* Routine in sim_util.c */
#ifdef __cplusplus
}
#endif
-#endif /* _sim_util_h */
+#endif /* _sim_util_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff