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
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  35
  36 #ifndef _mdrun_h
  37 #define _mdrun_h
  38
  39 #include <stdio.h>
  40 #include <time.h>
  41 #include "typedefs.h"
  42 #include "network.h"
  43 #include "tgroup.h"
  44 #include "filenm.h"
  45 #include "mshift.h"
  46 #include "force.h"
  47 #include "edsam.h"
  48 #include "mdebin.h"
  49 #include "vcm.h"
  50 #include "vsite.h"
  51 #include "pull.h"
  52 #include "update.h"
  53
  54 #ifdef __cplusplus
  55 extern "C" {
  56 #endif
  57
  58 #define MD_POLARISE       (1<<2)
  59 #define MD_IONIZE         (1<<3)
  60 #define MD_RERUN          (1<<4)
  61 #define MD_RERUN_VSITE    (1<<5)
  62 #define MD_FFSCAN         (1<<6)
  63 #define MD_SEPPOT         (1<<7)
  64 #define MD_PARTDEC        (1<<9)
  65 #define MD_DDBONDCHECK    (1<<10)
  66 #define MD_DDBONDCOMM     (1<<11)
  67 #define MD_CONFOUT        (1<<12)
  68 #define MD_REPRODUCIBLE   (1<<13)
  69 #define MD_READ_RNG       (1<<14)
  70 #define MD_APPENDFILES    (1<<15)
  71 #define MD_KEEPANDNUMCPT  (1<<16)
  72 #define MD_READ_EKIN      (1<<17)
  73 #define MD_STARTFROMCPT   (1<<18)
  74 #define MD_RESETCOUNTERSHALFWAY (1<<19)
  75
  76 /* Define a number of flags to better control the information
  77  * passed to compute_globals in md.c and global_stat.
  78  */
  79
  80 /* We are rerunning the simulation */
  81 #define CGLO_RERUNMD        (1<<1)
  82 /* we are computing the kinetic energy from average velocities */
  83 #define CGLO_EKINAVEVEL     (1<<2)
  84 /* we are removing the center of mass momenta */
  85 #define CGLO_STOPCM         (1<<3)
  86 /* bGStat is defined in do_md */
  87 #define CGLO_GSTAT          (1<<4)
  88 /* Sum the energy terms in global computation */
  89 #define CGLO_ENERGY         (1<<6)
  90 /* Sum the kinetic energy terms in global computation */
  91 #define CGLO_TEMPERATURE    (1<<7)
  92 /* Sum the kinetic energy terms in global computation */
  93 #define CGLO_PRESSURE       (1<<8)
  94 /* Sum the constraint term in global computation */
  95 #define CGLO_CONSTRAINT     (1<<9)
  96 /* we are using an integrator that requires iteration over some steps - currently not used*/
  97 #define CGLO_ITERATE        (1<<10)
  98 /* it is the first time we are iterating (or, only once through is required */
  99 #define CGLO_FIRSTITERATE   (1<<11)
 100 /* Reading ekin from the trajectory */
 101 #define CGLO_READEKIN       (1<<12)
 102 /* we need to reset the ekin rescaling factor here */
 103 #define CGLO_SCALEEKIN      (1<<13)
 104
 105 enum {
 106   ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
 107 };
 108
 109 typedef struct {
 110   double real;
 111 #ifdef GMX_CRAY_XT3
 112   double proc;
 113 #else
 114   clock_t proc;
 115 #endif
 116   double realtime;
 117   double proctime;
 118   double time_per_step;
 119   double last;
 120   gmx_large_int_t nsteps_done;
 121 } gmx_runtime_t;
 122
 123 typedef struct {
 124   t_fileio *fp_trn;
 125   t_fileio *fp_xtc;
 126   int  xtc_prec;
 127   ener_file_t fp_ene;
 128   const char *fn_cpt;
 129   gmx_bool bKeepAndNumCPT;
 130   int  eIntegrator;
 131   int  simulation_part;
 132   FILE *fp_dhdl;
 133   FILE *fp_field;
 134 } gmx_mdoutf_t;
 135
 136 /* Variables for temporary use with the deform option,
 137  * used in runner.c and md.c.
 138  * (These variables should be stored in the tpx file.)
 139  */
 140 extern gmx_large_int_t     deform_init_init_step_tpx;
 141 extern matrix              deform_init_box_tpx;
 142 #ifdef GMX_THREAD_MPI
 143 extern tMPI_Thread_mutex_t deform_init_box_mutex;
 144
 145 /* The minimum number of atoms per thread. With fewer atoms than this,
 146  * the number of threads will get lowered.
 147  */
 148 #define MIN_ATOMS_PER_THREAD    90
 149 #endif
 150
 151
 152 typedef double gmx_integrator_t(FILE *log,t_commrec *cr,
 153                                 int nfile,const t_filenm fnm[],
 154                                 const output_env_t oenv, gmx_bool bVerbose,
 155                                 gmx_bool bCompact, int nstglobalcomm,
 156                                 gmx_vsite_t *vsite,gmx_constr_t constr,
 157                                 int stepout,
 158                                 t_inputrec *inputrec,
 159                                 gmx_mtop_t *mtop,t_fcdata *fcd,
 160                                 t_state *state,
 161                                 t_mdatoms *mdatoms,
 162                                 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 163                                 gmx_edsam_t ed,
 164                                 t_forcerec *fr,
 165                                 int repl_ex_nst,int repl_ex_seed,
 166                                 real cpt_period,real max_hours,
 167                                 const char *deviceOptions,
 168                                 unsigned long Flags,
 169                                 gmx_runtime_t *runtime);
 170
 171 typedef struct gmx_global_stat *gmx_global_stat_t;
 172
 173 /* ROUTINES from md.c */
 174
 175 gmx_integrator_t do_md;
 176
 177 gmx_integrator_t do_md_openmm;
 178
 179
 180
 181 /* ROUTINES from minimize.c */
 182
 183 gmx_integrator_t do_steep;
 184 /* Do steepest descents EM */
 185
 186 gmx_integrator_t do_cg;
 187 /* Do conjugate gradient EM */
 188
 189 gmx_integrator_t do_lbfgs;
 190 /* Do conjugate gradient L-BFGS */
 191
 192 gmx_integrator_t do_nm;
 193 /* Do normal mode analysis */
 194
 195 /* ROUTINES from tpi.c */
 196
 197 gmx_integrator_t do_tpi;
 198 /* Do test particle insertion */
 199
 200
 201 /* ROUTINES from md_support.c */
 202
 203 /* return the number of steps between global communcations */
 204 int check_nstglobalcomm(FILE *fplog,t_commrec *cr,
 205                         int nstglobalcomm,t_inputrec *ir);
 206
 207 /* check whether an 'nst'-style parameter p is a multiple of nst, and
 208    set it to be one if not, with a warning. */
 209 void check_nst_param(FILE *fplog,t_commrec *cr,
 210                      const char *desc_nst,int nst,
 211                      const char *desc_p,int *p);
 212
 213 /* check which of the multisim simulations has the shortest number of
 214    steps and return that number of nsteps */
 215 gmx_large_int_t get_multisim_nsteps(const t_commrec *cr,
 216                                     gmx_large_int_t nsteps);
 217
 218 void rerun_parallel_comm(t_commrec *cr,t_trxframe *fr,
 219                          gmx_bool *bNotLastFrame);
 220
 221 /* get the conserved energy associated with the ensemble type*/
 222 real compute_conserved_from_auxiliary(t_inputrec *ir, t_state *state,
 223                                       t_extmass *MassQ);
 224
 225 /* reset all cycle and time counters. */
 226 void reset_all_counters(FILE *fplog,t_commrec *cr,
 227                         gmx_large_int_t step,
 228                         gmx_large_int_t *step_rel,t_inputrec *ir,
 229                         gmx_wallcycle_t wcycle,t_nrnb *nrnb,
 230                         gmx_runtime_t *runtime);
 231
 232
 233
 234 /* ROUTINES from sim_util.c */
 235 void do_pbc_first(FILE *log,matrix box,t_forcerec *fr,
 236                          t_graph *graph,rvec x[]);
 237
 238 void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
 239                               gmx_mtop_t *mtop,rvec x[]);
 240
 241 void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
 242                         gmx_mtop_t *mtop,rvec x[]);
 243
 244
 245
 246 /* ROUTINES from stat.c */
 247 gmx_global_stat_t global_stat_init(t_inputrec *ir);
 248
 249 void global_stat_destroy(gmx_global_stat_t gs);
 250
 251 void global_stat(FILE *log,gmx_global_stat_t gs,
 252                         t_commrec *cr,gmx_enerdata_t *enerd,
 253                         tensor fvir,tensor svir,rvec mu_tot,
 254                         t_inputrec *inputrec,
 255                         gmx_ekindata_t *ekind,
 256                         gmx_constr_t constr,t_vcm *vcm,
 257                         int nsig,real *sig,
 258                         gmx_mtop_t *top_global, t_state *state_local,
 259                         gmx_bool bSumEkinhOld, int flags);
 260 /* Communicate statistics over cr->mpi_comm_mysim */
 261
 262 gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],
 263                                  int mdrun_flags,
 264                                  const t_commrec *cr,const t_inputrec *ir,
 265                                  const output_env_t oenv);
 266 /* Returns a pointer to a data structure with all output file pointers
 267  * and names required by mdrun.
 268  */
 269
 270 void done_mdoutf(gmx_mdoutf_t *of);
 271 /* Close all open output files and free the of pointer */
 272
 273 #define MDOF_X   (1<<0)
 274 #define MDOF_V   (1<<1)
 275 #define MDOF_F   (1<<2)
 276 #define MDOF_XTC (1<<3)
 277 #define MDOF_CPT (1<<4)
 278
 279 void write_traj(FILE *fplog,t_commrec *cr,
 280                        gmx_mdoutf_t *of,
 281                        int mdof_flags,
 282                        gmx_mtop_t *top_global,
 283                        gmx_large_int_t step,double t,
 284                        t_state *state_local,t_state *state_global,
 285                        rvec *f_local,rvec *f_global,
 286                        int *n_xtc,rvec **x_xtc);
 287 /* Routine that writes frames to trn, xtc and/or checkpoint.
 288  * What is written is determined by the mdof_flags defined above.
 289  * Data is collected to the master node only when necessary.
 290  */
 291
 292 int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep);
 293 /* Return TRUE if io should be done */
 294
 295 int do_any_io(int step, t_inputrec *ir);
 296
 297 /* ROUTINES from sim_util.c */
 298
 299 double gmx_gettime();
 300
 301 void print_time(FILE *out, gmx_runtime_t *runtime,
 302                        gmx_large_int_t step,t_inputrec *ir, t_commrec *cr);
 303
 304 void runtime_start(gmx_runtime_t *runtime);
 305
 306 void runtime_end(gmx_runtime_t *runtime);
 307
 308 void runtime_upd_proc(gmx_runtime_t *runtime);
 309 /* The processor time should be updated every once in a while,
 310  * since on 32-bit manchines it loops after 72 minutes.
 311  */
 312
 313 void print_date_and_time(FILE *log,int pid,const char *title,
 314                                 const gmx_runtime_t *runtime);
 315
 316 void nstop_cm(FILE *log,t_commrec *cr,
 317                      int start,int nr_atoms,real mass[],rvec x[],rvec v[]);
 318
 319 void finish_run(FILE *log,t_commrec *cr,const char *confout,
 320                        t_inputrec *inputrec,
 321                        t_nrnb nrnb[],gmx_wallcycle_t wcycle,
 322                        gmx_runtime_t *runtime,
 323                        gmx_bool bWriteStat);
 324
 325 void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr);
 326
 327 void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
 328                           gmx_large_int_t step, int natoms,
 329                           matrix box,real lambda,tensor pres,tensor virial,
 330                           real *prescorr, real *enercorr, real *dvdlcorr);
 331
 332 typedef enum
 333 {
 334   LIST_SCALARS  =0001,
 335   LIST_INPUTREC =0002,
 336   LIST_TOP      =0004,
 337   LIST_X        =0010,
 338   LIST_V        =0020,
 339   LIST_F        =0040,
 340   LIST_LOAD     =0100
 341 } t_listitem;
 342
 343 void check_nnodes_top(char *fn,t_topology *top);
 344 /* Reset the tpr file to work with one node if necessary */
 345
 346
 347 /* check the version */
 348 void check_ir_old_tpx_versions(t_commrec *cr,FILE *fplog,
 349                                t_inputrec *ir,gmx_mtop_t *mtop);
 350
 351 /* Allocate and initialize node-local state entries. */
 352 void set_state_entries(t_state *state,const t_inputrec *ir,int nnodes);
 353
 354 /* Broadcast the data for a simulation, and allocate node-specific settings
 355    such as rng generators. */
 356 void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
 357                           gmx_mtop_t *mtop);
 358
 359
 360 void do_constrain_first(FILE *log,gmx_constr_t constr,
 361                                t_inputrec *inputrec,t_mdatoms *md,
 362                                t_state *state,rvec *f,
 363                                t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
 364                                t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
 365
 366 void dynamic_load_balancing(gmx_bool bVerbose,t_commrec *cr,real capacity[],
 367                                    int dimension,t_mdatoms *md,t_topology *top,
 368                                    rvec x[],rvec v[],matrix box);
 369 /* Perform load balancing, i.e. split the particles over processors
 370  * based on their coordinates in the "dimension" direction.
 371  */
 372
 373 int multisim_min(const gmx_multisim_t *ms,int nmin,int n);
 374 /* Set an appropriate value for n across the whole multi-simulation */
 375
 376 int multisim_nstsimsync(const t_commrec *cr,
 377                         const t_inputrec *ir,int repl_ex_nst);
 378 /* Determine the interval for inter-simulation communication */
 379
 380 void init_global_signals(globsig_t *gs,const t_commrec *cr,
 381                          const t_inputrec *ir,int repl_ex_nst);
 382 /* Constructor for globsig_t */
 383
 384 void copy_coupling_state(t_state *statea,t_state *stateb,
 385                          gmx_ekindata_t *ekinda,gmx_ekindata_t *ekindb, t_grpopts* opts);
 386 /* Copy stuff from state A to state B */
 387
 388 void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inputrec *ir,
 389                      t_forcerec *fr, gmx_ekindata_t *ekind,
 390                      t_state *state, t_state *state_global, t_mdatoms *mdatoms,
 391                      t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
 392                      gmx_enerdata_t *enerd,tensor force_vir, tensor shake_vir, tensor total_vir,
 393                      tensor pres, rvec mu_tot, gmx_constr_t constr,
 394                      globsig_t *gs,gmx_bool bInterSimGS,
 395                      matrix box, gmx_mtop_t *top_global, real *pcurr,
 396                      int natoms, gmx_bool *bSumEkinhOld, int flags);
 397 /* Compute global variables during integration */
 398
 399 int mdrunner(int nthreads_requested, FILE *fplog,t_commrec *cr,int nfile,
 400              const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
 401              gmx_bool bCompact, int nstglobalcomm, ivec ddxyz,int dd_node_order,
 402              real rdd, real rconstr, const char *dddlb_opt,real dlb_scale,
 403              const char *ddcsx,const char *ddcsy,const char *ddcsz,
 404              int nstepout, int resetstep, int nmultisim, int repl_ex_nst,
 405              int repl_ex_seed, real pforce,real cpt_period,real max_hours,
 406              const char *deviceOptions, unsigned long Flags);
 407 /* Driver routine, that calls the different methods */
 408
 409 void md_print_warning(const t_commrec *cr,FILE *fplog,const char *buf);
 410 /* Print a warning message to stderr on the master node
 411  * and to fplog if fplog!=NULL.
 412  */
 413
 414 void init_md(FILE *fplog,
 415                     t_commrec *cr,t_inputrec *ir, const output_env_t oenv,
 416                     double *t,double *t0,
 417                     real *lambda,double *lam0,
 418                     t_nrnb *nrnb,gmx_mtop_t *mtop,
 419                     gmx_update_t *upd,
 420                     int nfile,const t_filenm fnm[],
 421                     gmx_mdoutf_t **outf,t_mdebin **mdebin,
 422                     tensor force_vir,tensor shake_vir,
 423                     rvec mu_tot,
 424                     gmx_bool *bSimAnn,t_vcm **vcm,
 425                     t_state *state, unsigned long Flags);
 426   /* Routine in sim_util.c */
 427
 428 #ifdef __cplusplus
 429 }
 430 #endif
 431
 432 #endif  /* _mdrun_h */