include/sim_util.h

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
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  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
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  30  * For more info, check our website at http://www.gromacs.org
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  34  */
  35
  36 #ifndef _sim_util_h
  37 #define _sim_util_h
  38
  39 #include <time.h>
  40 #include "typedefs.h"
  41 #include "enxio.h"
  42 #include "mdebin.h"
  43 #include "update.h"
  44 #include "vcm.h"
  45
  46 #ifdef __cplusplus
  47 extern "C" {
  48 #endif
  49
  50 typedef struct {
  51   t_fileio *fp_trn;
  52   t_fileio *fp_xtc;
  53   int  xtc_prec;
  54   ener_file_t fp_ene;
  55   const char *fn_cpt;
  56   gmx_bool bKeepAndNumCPT;
  57   int  eIntegrator;
  58   gmx_bool  bExpanded;
  59   int elamstats;
  60   int  simulation_part;
  61   FILE *fp_dhdl;
  62   FILE *fp_field;
  63 } gmx_mdoutf_t;
  64
  65 typedef struct gmx_global_stat *gmx_global_stat_t;
  66
  67 typedef struct {
  68   double real;
  69 #ifdef GMX_CRAY_XT3
  70   double proc;
  71 #else
  72   clock_t proc;
  73 #endif
  74   double realtime;
  75   double proctime;
  76   double time_per_step;
  77   double last;
  78   gmx_large_int_t nsteps_done;
  79 } gmx_runtime_t;
  80
  81
  82 void do_pbc_first(FILE *log,matrix box,t_forcerec *fr,
  83                          t_graph *graph,rvec x[]);
  84
  85 void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
  86                               gmx_mtop_t *mtop,rvec x[]);
  87
  88 void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
  89                         gmx_mtop_t *mtop,rvec x[]);
  90
  91
  92
  93 /* ROUTINES from stat.c */
  94 gmx_global_stat_t global_stat_init(t_inputrec *ir);
  95
  96 void global_stat_destroy(gmx_global_stat_t gs);
  97
  98 void global_stat(FILE *log,gmx_global_stat_t gs,
  99                         t_commrec *cr,gmx_enerdata_t *enerd,
 100                         tensor fvir,tensor svir,rvec mu_tot,
 101                         t_inputrec *inputrec,
 102                         gmx_ekindata_t *ekind,
 103                         gmx_constr_t constr,t_vcm *vcm,
 104                         int nsig,real *sig,
 105                         gmx_mtop_t *top_global, t_state *state_local,
 106                         gmx_bool bSumEkinhOld, int flags);
 107 /* Communicate statistics over cr->mpi_comm_mysim */
 108
 109 gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],
 110                                  int mdrun_flags,
 111                                  const t_commrec *cr,const t_inputrec *ir,
 112                                  const output_env_t oenv);
 113 /* Returns a pointer to a data structure with all output file pointers
 114  * and names required by mdrun.
 115  */
 116
 117 void done_mdoutf(gmx_mdoutf_t *of);
 118 /* Close all open output files and free the of pointer */
 119
 120 #define MDOF_X   (1<<0)
 121 #define MDOF_V   (1<<1)
 122 #define MDOF_F   (1<<2)
 123 #define MDOF_XTC (1<<3)
 124 #define MDOF_CPT (1<<4)
 125
 126 void write_traj(FILE *fplog,t_commrec *cr,
 127                        gmx_mdoutf_t *of,
 128                        int mdof_flags,
 129                        gmx_mtop_t *top_global,
 130                        gmx_large_int_t step,double t,
 131                        t_state *state_local,t_state *state_global,
 132                        rvec *f_local,rvec *f_global,
 133                        int *n_xtc,rvec **x_xtc);
 134 /* Routine that writes frames to trn, xtc and/or checkpoint.
 135  * What is written is determined by the mdof_flags defined above.
 136  * Data is collected to the master node only when necessary.
 137  */
 138
 139 int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep);
 140 /* Return TRUE if io should be done */
 141
 142 /* ROUTINES from sim_util.c */
 143
 144 double gmx_gettime();
 145
 146 void print_time(FILE *out, gmx_runtime_t *runtime,
 147                        gmx_large_int_t step,t_inputrec *ir, t_commrec *cr);
 148
 149 void runtime_start(gmx_runtime_t *runtime);
 150
 151 void runtime_end(gmx_runtime_t *runtime);
 152
 153 void runtime_upd_proc(gmx_runtime_t *runtime);
 154 /* The processor time should be updated every once in a while,
 155  * since on 32-bit manchines it loops after 72 minutes.
 156  */
 157
 158 void print_date_and_time(FILE *log,int pid,const char *title,
 159                                 const gmx_runtime_t *runtime);
 160
 161 void finish_run(FILE *log,t_commrec *cr,const char *confout,
 162                        t_inputrec *inputrec,
 163                        t_nrnb nrnb[],gmx_wallcycle_t wcycle,
 164                        gmx_runtime_t *runtime,
 165                        wallclock_gpu_t *gputimes,
 166                        int omp_nth_pp,
 167                        gmx_bool bWriteStat);
 168
 169 void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr);
 170
 171 void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
 172                    gmx_large_int_t step, int natoms,
 173                    matrix box,real lambda,tensor pres,tensor virial,
 174                    real *prescorr, real *enercorr, real *dvdlcorr);
 175
 176 void initialize_lambdas(FILE *fplog,t_inputrec *ir,int *fep_state,real *lambda,double *lam0);
 177
 178 void do_constrain_first(FILE *log,gmx_constr_t constr,
 179                                t_inputrec *inputrec,t_mdatoms *md,
 180                                t_state *state,rvec *f,
 181                                t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
 182                                t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
 183
 184 void init_md(FILE *fplog,
 185                     t_commrec *cr,t_inputrec *ir, const output_env_t oenv,
 186                     double *t,double *t0,
 187                     real *lambda,int *fep_state, double *lam0,
 188                     t_nrnb *nrnb,gmx_mtop_t *mtop,
 189                     gmx_update_t *upd,
 190                     int nfile,const t_filenm fnm[],
 191                     gmx_mdoutf_t **outf,t_mdebin **mdebin,
 192                     tensor force_vir,tensor shake_vir,
 193                     rvec mu_tot,
 194                     gmx_bool *bSimAnn,t_vcm **vcm,
 195                     t_state *state, unsigned long Flags);
 196   /* Routine in sim_util.c */
 197
 198 #ifdef __cplusplus
 199 }
 200 #endif
 201
 202 #endif  /* _sim_util_h */