include/sim_util.h

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  38
  39 #ifndef _sim_util_h
  40 #define _sim_util_h
  41
  42 #include <time.h>
  43 #include "visibility.h"
  44 #include "typedefs.h"
  45 #include "enxio.h"
  46 #include "mdebin.h"
  47 #include "update.h"
  48 #include "vcm.h"
  49
  50 #ifdef __cplusplus
  51 extern "C" {
  52 #endif
  53
  54 typedef struct {
  55     t_fileio   *fp_trn;
  56     t_fileio   *fp_xtc;
  57     int         xtc_prec;
  58     ener_file_t fp_ene;
  59     const char *fn_cpt;
  60     gmx_bool    bKeepAndNumCPT;
  61     int         eIntegrator;
  62     gmx_bool    bExpanded;
  63     int         elamstats;
  64     int         simulation_part;
  65     FILE       *fp_dhdl;
  66     FILE       *fp_field;
  67 } gmx_mdoutf_t;
  68
  69 typedef struct gmx_global_stat *gmx_global_stat_t;
  70
  71 typedef struct {
  72     double          real;
  73 #ifdef GMX_CRAY_XT3
  74     double          proc;
  75 #else
  76     clock_t         proc;
  77 #endif
  78     double          realtime;
  79     double          proctime;
  80     double          time_per_step;
  81     double          last;
  82     gmx_large_int_t nsteps_done;
  83 } gmx_runtime_t;
  84
  85
  86 GMX_LIBMD_EXPORT
  87 void do_pbc_first(FILE *log, matrix box, t_forcerec *fr,
  88                   t_graph *graph, rvec x[]);
  89
  90 GMX_LIBMD_EXPORT
  91 void do_pbc_first_mtop(FILE *fplog, int ePBC, matrix box,
  92                        gmx_mtop_t *mtop, rvec x[]);
  93
  94 GMX_LIBMD_EXPORT
  95 void do_pbc_mtop(FILE *fplog, int ePBC, matrix box,
  96                  gmx_mtop_t *mtop, rvec x[]);
  97
  98
  99
 100 /* ROUTINES from stat.c */
 101 GMX_LIBMD_EXPORT
 102 gmx_global_stat_t global_stat_init(t_inputrec *ir);
 103
 104 void global_stat_destroy(gmx_global_stat_t gs);
 105
 106 void global_stat(FILE *log, gmx_global_stat_t gs,
 107                  t_commrec *cr, gmx_enerdata_t *enerd,
 108                  tensor fvir, tensor svir, rvec mu_tot,
 109                  t_inputrec *inputrec,
 110                  gmx_ekindata_t *ekind,
 111                  gmx_constr_t constr, t_vcm *vcm,
 112                  int nsig, real *sig,
 113                  gmx_mtop_t *top_global, t_state *state_local,
 114                  gmx_bool bSumEkinhOld, int flags);
 115 /* Communicate statistics over cr->mpi_comm_mysim */
 116
 117 gmx_mdoutf_t *init_mdoutf(int nfile, const t_filenm fnm[],
 118                           int mdrun_flags,
 119                           const t_commrec *cr, const t_inputrec *ir,
 120                           const output_env_t oenv);
 121 /* Returns a pointer to a data structure with all output file pointers
 122  * and names required by mdrun.
 123  */
 124
 125 GMX_LIBMD_EXPORT
 126 void done_mdoutf(gmx_mdoutf_t *of);
 127 /* Close all open output files and free the of pointer */
 128
 129 #define MDOF_X   (1<<0)
 130 #define MDOF_V   (1<<1)
 131 #define MDOF_F   (1<<2)
 132 #define MDOF_XTC (1<<3)
 133 #define MDOF_CPT (1<<4)
 134
 135 GMX_LIBMD_EXPORT
 136 void write_traj(FILE *fplog, t_commrec *cr,
 137                 gmx_mdoutf_t *of,
 138                 int mdof_flags,
 139                 gmx_mtop_t *top_global,
 140                 gmx_large_int_t step, double t,
 141                 t_state *state_local, t_state *state_global,
 142                 rvec *f_local, rvec *f_global,
 143                 int *n_xtc, rvec **x_xtc);
 144 /* Routine that writes frames to trn, xtc and/or checkpoint.
 145  * What is written is determined by the mdof_flags defined above.
 146  * Data is collected to the master node only when necessary.
 147  */
 148
 149 GMX_LIBMD_EXPORT
 150 int do_per_step(gmx_large_int_t step, gmx_large_int_t nstep);
 151 /* Return TRUE if io should be done */
 152
 153 /* ROUTINES from sim_util.c */
 154
 155 GMX_LIBMD_EXPORT
 156 double gmx_gettime();
 157
 158 GMX_LIBMD_EXPORT
 159 void print_time(FILE *out, gmx_runtime_t *runtime,
 160                 gmx_large_int_t step, t_inputrec *ir, t_commrec *cr);
 161
 162 GMX_LIBMD_EXPORT
 163 void runtime_start(gmx_runtime_t *runtime);
 164
 165 GMX_LIBMD_EXPORT
 166 void runtime_end(gmx_runtime_t *runtime);
 167
 168 GMX_LIBMD_EXPORT
 169 void runtime_upd_proc(gmx_runtime_t *runtime);
 170 /* The processor time should be updated every once in a while,
 171  * since on 32-bit manchines it loops after 72 minutes.
 172  */
 173
 174 GMX_LIBMD_EXPORT
 175 void print_date_and_time(FILE *log, int pid, const char *title,
 176                          const gmx_runtime_t *runtime);
 177
 178 GMX_LIBMD_EXPORT
 179 void finish_run(FILE *log, t_commrec *cr, const char *confout,
 180                 t_inputrec *inputrec,
 181                 t_nrnb nrnb[], gmx_wallcycle_t wcycle,
 182                 gmx_runtime_t *runtime,
 183                 wallclock_gpu_t *gputimes,
 184                 int omp_nth_pp,
 185                 gmx_bool bWriteStat);
 186
 187 void calc_enervirdiff(FILE *fplog, int eDispCorr, t_forcerec *fr);
 188
 189 void calc_dispcorr(FILE *fplog, t_inputrec *ir, t_forcerec *fr,
 190                    gmx_large_int_t step, int natoms,
 191                    matrix box, real lambda, tensor pres, tensor virial,
 192                    real *prescorr, real *enercorr, real *dvdlcorr);
 193
 194 void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, real *lambda, double *lam0);
 195
 196 GMX_LIBMD_EXPORT
 197 void do_constrain_first(FILE *log, gmx_constr_t constr,
 198                         t_inputrec *inputrec, t_mdatoms *md,
 199                         t_state *state, rvec *f,
 200                         t_graph *graph, t_commrec *cr, t_nrnb *nrnb,
 201                         t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
 202
 203 GMX_LIBMD_EXPORT
 204 void init_md(FILE *fplog,
 205              t_commrec *cr, t_inputrec *ir, const output_env_t oenv,
 206              double *t, double *t0,
 207              real *lambda, int *fep_state, double *lam0,
 208              t_nrnb *nrnb, gmx_mtop_t *mtop,
 209              gmx_update_t *upd,
 210              int nfile, const t_filenm fnm[],
 211              gmx_mdoutf_t **outf, t_mdebin **mdebin,
 212              tensor force_vir, tensor shake_vir,
 213              rvec mu_tot,
 214              gmx_bool *bSimAnn, t_vcm **vcm,
 215              t_state *state, unsigned long Flags);
 216 /* Routine in sim_util.c */
 217
 218 #ifdef __cplusplus
 219 }
 220 #endif
 221
 222 #endif  /* _sim_util_h */