include/mdrun.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
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  35
  36 #ifndef _mdrun_h
  37 #define _mdrun_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include <stdio.h>
  44 #include <time.h>
  45 #include "typedefs.h"
  46 #include "network.h"
  47 #include "tgroup.h"
  48 #include "filenm.h"
  49 #include "mshift.h"
  50 #include "force.h"
  51 #include "edsam.h"
  52 #include "mdebin.h"
  53 #include "vcm.h"
  54 #include "vsite.h"
  55 #include "pull.h"
  56 #include "update.h"
  57
  58 #ifdef __cplusplus
  59 extern "C" {
  60 #endif
  61
  62 #define MD_POLARISE       (1<<2)
  63 #define MD_IONIZE         (1<<3)
  64 #define MD_RERUN          (1<<4)
  65 #define MD_RERUN_VSITE    (1<<5)
  66 #define MD_FFSCAN         (1<<6)
  67 #define MD_SEPPOT         (1<<7)
  68 #define MD_PARTDEC        (1<<9)
  69 #define MD_DDBONDCHECK    (1<<10)
  70 #define MD_DDBONDCOMM     (1<<11)
  71 #define MD_CONFOUT        (1<<12)
  72 #define MD_REPRODUCIBLE   (1<<13)
  73 #define MD_READ_RNG       (1<<14)
  74 #define MD_APPENDFILES    (1<<15)
  75 #define MD_KEEPANDNUMCPT  (1<<16)
  76 #define MD_READ_EKIN      (1<<17)
  77 #define MD_STARTFROMCPT   (1<<18)
  78 #define MD_RESETCOUNTERSHALFWAY (1<<19)
  79
  80 /* Define a number of flags to better control the information
  81  * passed to compute_globals in md.c and global_stat.
  82  */
  83
  84 /* We are rerunning the simulation */
  85 #define CGLO_RERUNMD        (1<<1)
  86 /* we are computing the kinetic energy from average velocities */
  87 #define CGLO_EKINAVEVEL     (1<<2)
  88 /* we are removing the center of mass momenta */
  89 #define CGLO_STOPCM         (1<<3)
  90 /* bGStat is defined in do_md */
  91 #define CGLO_GSTAT          (1<<4)
  92 /* bNEMD is defined in do_md */
  93 #define CGLO_NEMD           (1<<5)
  94 /* Sum the energy terms in global computation */
  95 #define CGLO_ENERGY         (1<<6)
  96 /* Sum the kinetic energy terms in global computation */
  97 #define CGLO_TEMPERATURE    (1<<7)
  98 /* Sum the kinetic energy terms in global computation */
  99 #define CGLO_PRESSURE       (1<<8)
 100 /* Sum the constraint term in global computation */
 101 #define CGLO_CONSTRAINT     (1<<9)
 102 /* we are using an integrator that requires iteration over some steps - currently not used*/
 103 #define CGLO_ITERATE        (1<<10)
 104 /* it is the first time we are iterating (or, only once through is required */
 105 #define CGLO_FIRSTITERATE   (1<<11)
 106 /* Reading ekin from the trajectory */
 107 #define CGLO_READEKIN       (1<<12)
 108 /* we need to reset the ekin rescaling factor here */
 109 #define CGLO_SCALEEKIN      (1<<13)
 110
 111 enum {
 112   ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
 113 };
 114
 115 typedef struct {
 116   double real;
 117 #ifdef GMX_CRAY_XT3
 118   double proc;
 119 #else
 120   clock_t proc;
 121 #endif
 122   double realtime;
 123   double proctime;
 124   double time_per_step;
 125   double last;
 126   gmx_large_int_t nsteps_done;
 127 } gmx_runtime_t;
 128
 129 typedef struct {
 130   t_fileio *fp_trn;
 131   t_fileio *fp_xtc;
 132   int  xtc_prec;
 133   ener_file_t fp_ene;
 134   const char *fn_cpt;
 135   bool bKeepAndNumCPT;
 136   int  eIntegrator;
 137   int  simulation_part;
 138   FILE *fp_dhdl;
 139   FILE *fp_field;
 140 } gmx_mdoutf_t;
 141
 142 /* Variables for temporary use with the deform option,
 143  * used in runner.c and md.c.
 144  * (These variables should be stored in the tpx file.)
 145  */
 146 extern gmx_large_int_t     deform_init_init_step_tpx;
 147 extern matrix              deform_init_box_tpx;
 148 #ifdef GMX_THREADS
 149 extern tMPI_Thread_mutex_t deform_init_box_mutex;
 150
 151 /* The minimum number of atoms per thread. With fewer atoms than this,
 152  * the number of threads will get lowered.
 153  */
 154 #define MIN_ATOMS_PER_THREAD    90
 155 #endif
 156
 157
 158 typedef double gmx_integrator_t(FILE *log,t_commrec *cr,
 159                                 int nfile,const t_filenm fnm[],
 160                                 const output_env_t oenv, bool bVerbose,
 161                                 bool bCompact, int nstglobalcomm,
 162                                 gmx_vsite_t *vsite,gmx_constr_t constr,
 163                                 int stepout,
 164                                 t_inputrec *inputrec,
 165                                 gmx_mtop_t *mtop,t_fcdata *fcd,
 166                                 t_state *state,
 167                                 t_mdatoms *mdatoms,
 168                                 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 169                                 gmx_edsam_t ed,
 170                                 t_forcerec *fr,
 171                                 int repl_ex_nst,int repl_ex_seed,
 172                                 real cpt_period,real max_hours,
 173                                 const char *deviceOptions,
 174                                 unsigned long Flags,
 175                                 gmx_runtime_t *runtime);
 176
 177 typedef struct gmx_global_stat *gmx_global_stat_t;
 178
 179 /* ROUTINES from md.c */
 180
 181 extern gmx_integrator_t do_md;
 182
 183 extern gmx_integrator_t do_md_openmm;
 184
 185 /* ROUTINES from minimize.c */
 186
 187 extern gmx_integrator_t do_steep;
 188 /* Do steepest descents EM */
 189
 190 extern gmx_integrator_t do_cg;
 191 /* Do conjugate gradient EM */
 192
 193 extern gmx_integrator_t do_lbfgs;
 194 /* Do conjugate gradient L-BFGS */
 195
 196 extern gmx_integrator_t do_nm;
 197 /* Do normal mode analysis */
 198
 199 /* ROUTINES from tpi.c */
 200
 201 extern gmx_integrator_t do_tpi;
 202 /* Do test particle insertion */
 203
 204
 205 /* ROUTINES from sim_util.c */
 206 extern void do_pbc_first(FILE *log,matrix box,t_forcerec *fr,
 207                          t_graph *graph,rvec x[]);
 208
 209 extern void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
 210                               gmx_mtop_t *mtop,rvec x[]);
 211
 212 extern void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
 213                         gmx_mtop_t *mtop,rvec x[]);
 214
 215
 216 /* ROUTINES from stat.c */
 217 extern gmx_global_stat_t global_stat_init(t_inputrec *ir);
 218
 219 extern void global_stat_destroy(gmx_global_stat_t gs);
 220
 221 extern void global_stat(FILE *log,gmx_global_stat_t gs,
 222                         t_commrec *cr,gmx_enerdata_t *enerd,
 223                         tensor fvir,tensor svir,rvec mu_tot,
 224                         t_inputrec *inputrec,
 225                         gmx_ekindata_t *ekind,
 226                         gmx_constr_t constr,t_vcm *vcm,
 227                         int nsig,real *sig,
 228                         gmx_mtop_t *top_global, t_state *state_local,
 229                         bool bSumEkinhOld, int flags);
 230 /* Communicate statistics over cr->mpi_comm_mysim */
 231
 232 extern gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],
 233                                  int mdrun_flags,
 234                                  const t_commrec *cr,const t_inputrec *ir,
 235                                  const output_env_t oenv);
 236 /* Returns a pointer to a data structure with all output file pointers
 237  * and names required by mdrun.
 238  */
 239
 240 extern void done_mdoutf(gmx_mdoutf_t *of);
 241 /* Close all open output files and free the of pointer */
 242
 243 #define MDOF_X   (1<<0)
 244 #define MDOF_V   (1<<1)
 245 #define MDOF_F   (1<<2)
 246 #define MDOF_XTC (1<<3)
 247 #define MDOF_CPT (1<<4)
 248
 249 extern void write_traj(FILE *fplog,t_commrec *cr,
 250                        gmx_mdoutf_t *of,
 251                        int mdof_flags,
 252                        gmx_mtop_t *top_global,
 253                        gmx_large_int_t step,double t,
 254                        t_state *state_local,t_state *state_global,
 255                        rvec *f_local,rvec *f_global,
 256                        int *n_xtc,rvec **x_xtc);
 257 /* Routine that writes frames to trn, xtc and/or checkpoint.
 258  * What is written is determined by the mdof_flags defined above.
 259  * Data is collected to the master node only when necessary.
 260  */
 261
 262 extern int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep);
 263 /* Return TRUE if io should be done */
 264
 265 extern int do_any_io(int step, t_inputrec *ir);
 266
 267 /* ROUTINES from sim_util.c */
 268
 269 extern double gmx_gettime();
 270
 271 extern void print_time(FILE *out, gmx_runtime_t *runtime,
 272                        gmx_large_int_t step,t_inputrec *ir, t_commrec *cr);
 273
 274 extern void runtime_start(gmx_runtime_t *runtime);
 275
 276 extern void runtime_end(gmx_runtime_t *runtime);
 277
 278 extern void runtime_upd_proc(gmx_runtime_t *runtime);
 279 /* The processor time should be updated every once in a while,
 280  * since on 32-bit manchines it loops after 72 minutes.
 281  */
 282
 283 extern void print_date_and_time(FILE *log,int pid,const char *title,
 284                                 const gmx_runtime_t *runtime);
 285
 286 extern void nstop_cm(FILE *log,t_commrec *cr,
 287                      int start,int nr_atoms,real mass[],rvec x[],rvec v[]);
 288
 289 extern void finish_run(FILE *log,t_commrec *cr,const char *confout,
 290                        t_inputrec *inputrec,
 291                        t_nrnb nrnb[],gmx_wallcycle_t wcycle,
 292                        gmx_runtime_t *runtime,
 293                        bool bWriteStat);
 294
 295 extern void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr);
 296
 297 extern void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
 298                           gmx_large_int_t step, int natoms,
 299                           matrix box,real lambda,tensor pres,tensor virial,
 300                           real *prescorr, real *enercorr, real *dvdlcorr);
 301
 302 typedef enum
 303 {
 304   LIST_SCALARS  =0001,
 305   LIST_INPUTREC =0002,
 306   LIST_TOP      =0004,
 307   LIST_X        =0010,
 308   LIST_V        =0020,
 309   LIST_F        =0040,
 310   LIST_LOAD     =0100
 311 } t_listitem;
 312
 313 extern void check_nnodes_top(char *fn,t_topology *top);
 314 /* Reset the tpr file to work with one node if necessary */
 315
 316
 317 /* check the version */
 318 void check_ir_old_tpx_versions(t_commrec *cr,FILE *fplog,
 319                                t_inputrec *ir,gmx_mtop_t *mtop);
 320
 321 /* Allocate and initialize node-local state entries. */
 322 void set_state_entries(t_state *state,t_inputrec *ir,int nnodes);
 323
 324 /* Broadcast the data for a simulation, and allocate node-specific settings
 325    such as rng generators. */
 326 extern void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
 327                           gmx_mtop_t *mtop, t_state *state);
 328
 329
 330 extern void do_constrain_first(FILE *log,gmx_constr_t constr,
 331                                t_inputrec *inputrec,t_mdatoms *md,
 332                                t_state *state,rvec *f,
 333                                t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
 334                                t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
 335
 336 extern void dynamic_load_balancing(bool bVerbose,t_commrec *cr,real capacity[],
 337                                    int dimension,t_mdatoms *md,t_topology *top,
 338                                    rvec x[],rvec v[],matrix box);
 339 /* Perform load balancing, i.e. split the particles over processors
 340  * based on their coordinates in the "dimension" direction.
 341  */
 342
 343 int mdrunner(int nthreads_requested, FILE *fplog,t_commrec *cr,int nfile,
 344              const t_filenm fnm[], const output_env_t oenv, bool bVerbose,
 345              bool bCompact, int nstglobalcomm, ivec ddxyz,int dd_node_order,
 346              real rdd, real rconstr, const char *dddlb_opt,real dlb_scale,
 347              const char *ddcsx,const char *ddcsy,const char *ddcsz,
 348              int nstepout, int resetstep, int nmultisim, int repl_ex_nst,
 349              int repl_ex_seed, real pforce,real cpt_period,real max_hours,
 350              const char *deviceOptions, unsigned long Flags);
 351 /* Driver routine, that calls the different methods */
 352
 353 extern void md_print_warning(const t_commrec *cr,FILE *fplog,const char *buf);
 354 /* Print a warning message to stderr on the master node
 355  * and to fplog if fplog!=NULL.
 356  */
 357
 358 extern void init_md(FILE *fplog,
 359                     t_commrec *cr,t_inputrec *ir, const output_env_t oenv,
 360                     double *t,double *t0,
 361                     real *lambda,double *lam0,
 362                     t_nrnb *nrnb,gmx_mtop_t *mtop,
 363                     gmx_update_t *upd,
 364                     int nfile,const t_filenm fnm[],
 365                     gmx_mdoutf_t **outf,t_mdebin **mdebin,
 366                     tensor force_vir,tensor shake_vir,
 367                     rvec mu_tot,
 368                     bool *bNEMD,bool *bSimAnn,t_vcm **vcm,
 369                     t_state *state, unsigned long Flags);
 370   /* Routine in sim_util.c */
 371
 372 #ifdef __cplusplus
 373 }
 374 #endif
 375
 376 #endif  /* _mdrun_h */