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 #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_APPENDFILESSET (1<<21)
  72 #define MD_KEEPANDNUMCPT  (1<<16)
  73 #define MD_READ_EKIN      (1<<17)
  74 #define MD_STARTFROMCPT   (1<<18)
  75 #define MD_RESETCOUNTERSHALFWAY (1<<19)
  76
  77 /* Define a number of flags to better control the information
  78  * passed to compute_globals in md.c and global_stat.
  79  */
  80
  81 /* We are rerunning the simulation */
  82 #define CGLO_RERUNMD        (1<<1)
  83 /* we are computing the kinetic energy from average velocities */
  84 #define CGLO_EKINAVEVEL     (1<<2)
  85 /* we are removing the center of mass momenta */
  86 #define CGLO_STOPCM         (1<<3)
  87 /* bGStat is defined in do_md */
  88 #define CGLO_GSTAT          (1<<4)
  89 /* Sum the energy terms in global computation */
  90 #define CGLO_ENERGY         (1<<6)
  91 /* Sum the kinetic energy terms in global computation */
  92 #define CGLO_TEMPERATURE    (1<<7)
  93 /* Sum the kinetic energy terms in global computation */
  94 #define CGLO_PRESSURE       (1<<8)
  95 /* Sum the constraint term in global computation */
  96 #define CGLO_CONSTRAINT     (1<<9)
  97 /* we are using an integrator that requires iteration over some steps - currently not used*/
  98 #define CGLO_ITERATE        (1<<10)
  99 /* it is the first time we are iterating (or, only once through is required */
 100 #define CGLO_FIRSTITERATE   (1<<11)
 101 /* Reading ekin from the trajectory */
 102 #define CGLO_READEKIN       (1<<12)
 103 /* we need to reset the ekin rescaling factor here */
 104 #define CGLO_SCALEEKIN      (1<<13)
 105
 106 enum {
 107   ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
 108 };
 109
 110 typedef struct {
 111   double real;
 112 #ifdef GMX_CRAY_XT3
 113   double proc;
 114 #else
 115   clock_t proc;
 116 #endif
 117   double realtime;
 118   double proctime;
 119   double time_per_step;
 120   double last;
 121   gmx_large_int_t nsteps_done;
 122 } gmx_runtime_t;
 123
 124 typedef struct {
 125   t_fileio *fp_trn;
 126   t_fileio *fp_xtc;
 127   int  xtc_prec;
 128   ener_file_t fp_ene;
 129   const char *fn_cpt;
 130   gmx_bool bKeepAndNumCPT;
 131   int  eIntegrator;
 132   int  simulation_part;
 133   FILE *fp_dhdl;
 134   FILE *fp_field;
 135 } gmx_mdoutf_t;
 136
 137 /* Variables for temporary use with the deform option,
 138  * used in runner.c and md.c.
 139  * (These variables should be stored in the tpx file.)
 140  */
 141 extern gmx_large_int_t     deform_init_init_step_tpx;
 142 extern matrix              deform_init_box_tpx;
 143 #ifdef GMX_THREAD_MPI
 144 extern tMPI_Thread_mutex_t deform_init_box_mutex;
 145
 146 /* The minimum number of atoms per thread. With fewer atoms than this,
 147  * the number of threads will get lowered.
 148  */
 149 #define MIN_ATOMS_PER_THREAD    90
 150 #endif
 151
 152
 153 typedef double gmx_integrator_t(FILE *log,t_commrec *cr,
 154                                 int nfile,const t_filenm fnm[],
 155                                 const output_env_t oenv, gmx_bool bVerbose,
 156                                 gmx_bool bCompact, int nstglobalcomm,
 157                                 gmx_vsite_t *vsite,gmx_constr_t constr,
 158                                 int stepout,
 159                                 t_inputrec *inputrec,
 160                                 gmx_mtop_t *mtop,t_fcdata *fcd,
 161                                 t_state *state,
 162                                 t_mdatoms *mdatoms,
 163                                 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 164                                 gmx_edsam_t ed,
 165                                 t_forcerec *fr,
 166                                 int repl_ex_nst,int repl_ex_seed,
 167                                 real cpt_period,real max_hours,
 168                                 const char *deviceOptions,
 169                                 unsigned long Flags,
 170                                 gmx_runtime_t *runtime);
 171
 172 typedef struct gmx_global_stat *gmx_global_stat_t;
 173
 174 /* ROUTINES from md.c */
 175
 176 gmx_integrator_t do_md;
 177
 178 gmx_integrator_t do_md_openmm;
 179
 180
 181
 182 /* ROUTINES from minimize.c */
 183
 184 gmx_integrator_t do_steep;
 185 /* Do steepest descents EM */
 186
 187 gmx_integrator_t do_cg;
 188 /* Do conjugate gradient EM */
 189
 190 gmx_integrator_t do_lbfgs;
 191 /* Do conjugate gradient L-BFGS */
 192
 193 gmx_integrator_t do_nm;
 194 /* Do normal mode analysis */
 195
 196 /* ROUTINES from tpi.c */
 197
 198 gmx_integrator_t do_tpi;
 199 /* Do test particle insertion */
 200
 201
 202 /* ROUTINES from md_support.c */
 203
 204 /* return the number of steps between global communcations */
 205 int check_nstglobalcomm(FILE *fplog,t_commrec *cr,
 206                         int nstglobalcomm,t_inputrec *ir);
 207
 208 /* check whether an 'nst'-style parameter p is a multiple of nst, and
 209    set it to be one if not, with a warning. */
 210 void check_nst_param(FILE *fplog,t_commrec *cr,
 211                      const char *desc_nst,int nst,
 212                      const char *desc_p,int *p);
 213
 214 /* check which of the multisim simulations has the shortest number of
 215    steps and return that number of nsteps */
 216 gmx_large_int_t get_multisim_nsteps(const t_commrec *cr,
 217                                     gmx_large_int_t nsteps);
 218
 219 void rerun_parallel_comm(t_commrec *cr,t_trxframe *fr,
 220                          gmx_bool *bNotLastFrame);
 221
 222 /* get the conserved energy associated with the ensemble type*/
 223 real compute_conserved_from_auxiliary(t_inputrec *ir, t_state *state,
 224                                       t_extmass *MassQ);
 225
 226 /* reset all cycle and time counters. */
 227 void reset_all_counters(FILE *fplog,t_commrec *cr,
 228                         gmx_large_int_t step,
 229                         gmx_large_int_t *step_rel,t_inputrec *ir,
 230                         gmx_wallcycle_t wcycle,t_nrnb *nrnb,
 231                         gmx_runtime_t *runtime);
 232
 233
 234
 235 /* ROUTINES from sim_util.c */
 236 void do_pbc_first(FILE *log,matrix box,t_forcerec *fr,
 237                          t_graph *graph,rvec x[]);
 238
 239 void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
 240                               gmx_mtop_t *mtop,rvec x[]);
 241
 242 void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
 243                         gmx_mtop_t *mtop,rvec x[]);
 244
 245
 246
 247 /* ROUTINES from stat.c */
 248 gmx_global_stat_t global_stat_init(t_inputrec *ir);
 249
 250 void global_stat_destroy(gmx_global_stat_t gs);
 251
 252 void global_stat(FILE *log,gmx_global_stat_t gs,
 253                         t_commrec *cr,gmx_enerdata_t *enerd,
 254                         tensor fvir,tensor svir,rvec mu_tot,
 255                         t_inputrec *inputrec,
 256                         gmx_ekindata_t *ekind,
 257                         gmx_constr_t constr,t_vcm *vcm,
 258                         int nsig,real *sig,
 259                         gmx_mtop_t *top_global, t_state *state_local,
 260                         gmx_bool bSumEkinhOld, int flags);
 261 /* Communicate statistics over cr->mpi_comm_mysim */
 262
 263 gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],
 264                                  int mdrun_flags,
 265                                  const t_commrec *cr,const t_inputrec *ir,
 266                                  const output_env_t oenv);
 267 /* Returns a pointer to a data structure with all output file pointers
 268  * and names required by mdrun.
 269  */
 270
 271 void done_mdoutf(gmx_mdoutf_t *of);
 272 /* Close all open output files and free the of pointer */
 273
 274 #define MDOF_X   (1<<0)
 275 #define MDOF_V   (1<<1)
 276 #define MDOF_F   (1<<2)
 277 #define MDOF_XTC (1<<3)
 278 #define MDOF_CPT (1<<4)
 279
 280 void write_traj(FILE *fplog,t_commrec *cr,
 281                        gmx_mdoutf_t *of,
 282                        int mdof_flags,
 283                        gmx_mtop_t *top_global,
 284                        gmx_large_int_t step,double t,
 285                        t_state *state_local,t_state *state_global,
 286                        rvec *f_local,rvec *f_global,
 287                        int *n_xtc,rvec **x_xtc);
 288 /* Routine that writes frames to trn, xtc and/or checkpoint.
 289  * What is written is determined by the mdof_flags defined above.
 290  * Data is collected to the master node only when necessary.
 291  */
 292
 293 int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep);
 294 /* Return TRUE if io should be done */
 295
 296 int do_any_io(int step, t_inputrec *ir);
 297
 298 /* ROUTINES from sim_util.c */
 299
 300 double gmx_gettime();
 301
 302 void print_time(FILE *out, gmx_runtime_t *runtime,
 303                        gmx_large_int_t step,t_inputrec *ir, t_commrec *cr);
 304
 305 void runtime_start(gmx_runtime_t *runtime);
 306
 307 void runtime_end(gmx_runtime_t *runtime);
 308
 309 void runtime_upd_proc(gmx_runtime_t *runtime);
 310 /* The processor time should be updated every once in a while,
 311  * since on 32-bit manchines it loops after 72 minutes.
 312  */
 313
 314 void print_date_and_time(FILE *log,int pid,const char *title,
 315                                 const gmx_runtime_t *runtime);
 316
 317 void nstop_cm(FILE *log,t_commrec *cr,
 318                      int start,int nr_atoms,real mass[],rvec x[],rvec v[]);
 319
 320 void finish_run(FILE *log,t_commrec *cr,const char *confout,
 321                        t_inputrec *inputrec,
 322                        t_nrnb nrnb[],gmx_wallcycle_t wcycle,
 323                        gmx_runtime_t *runtime,
 324                        gmx_bool bWriteStat);
 325
 326 void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr);
 327
 328 void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
 329                           gmx_large_int_t step, int natoms,
 330                           matrix box,real lambda,tensor pres,tensor virial,
 331                           real *prescorr, real *enercorr, real *dvdlcorr);
 332
 333 typedef enum
 334 {
 335   LIST_SCALARS  =0001,
 336   LIST_INPUTREC =0002,
 337   LIST_TOP      =0004,
 338   LIST_X        =0010,
 339   LIST_V        =0020,
 340   LIST_F        =0040,
 341   LIST_LOAD     =0100
 342 } t_listitem;
 343
 344 void check_nnodes_top(char *fn,t_topology *top);
 345 /* Reset the tpr file to work with one node if necessary */
 346
 347
 348 /* check the version */
 349 void check_ir_old_tpx_versions(t_commrec *cr,FILE *fplog,
 350                                t_inputrec *ir,gmx_mtop_t *mtop);
 351
 352 /* Allocate and initialize node-local state entries. */
 353 void set_state_entries(t_state *state,const t_inputrec *ir,int nnodes);
 354
 355 /* Broadcast the data for a simulation, and allocate node-specific settings
 356    such as rng generators. */
 357 void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
 358                           gmx_mtop_t *mtop);
 359
 360
 361 void do_constrain_first(FILE *log,gmx_constr_t constr,
 362                                t_inputrec *inputrec,t_mdatoms *md,
 363                                t_state *state,rvec *f,
 364                                t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
 365                                t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
 366
 367 void dynamic_load_balancing(gmx_bool bVerbose,t_commrec *cr,real capacity[],
 368                                    int dimension,t_mdatoms *md,t_topology *top,
 369                                    rvec x[],rvec v[],matrix box);
 370 /* Perform load balancing, i.e. split the particles over processors
 371  * based on their coordinates in the "dimension" direction.
 372  */
 373
 374 int multisim_min(const gmx_multisim_t *ms,int nmin,int n);
 375 /* Set an appropriate value for n across the whole multi-simulation */
 376
 377 int multisim_nstsimsync(const t_commrec *cr,
 378                         const t_inputrec *ir,int repl_ex_nst);
 379 /* Determine the interval for inter-simulation communication */
 380
 381 void init_global_signals(globsig_t *gs,const t_commrec *cr,
 382                          const t_inputrec *ir,int repl_ex_nst);
 383 /* Constructor for globsig_t */
 384
 385 void copy_coupling_state(t_state *statea,t_state *stateb,
 386                          gmx_ekindata_t *ekinda,gmx_ekindata_t *ekindb, t_grpopts* opts);
 387 /* Copy stuff from state A to state B */
 388
 389 void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inputrec *ir,
 390                      t_forcerec *fr, gmx_ekindata_t *ekind,
 391                      t_state *state, t_state *state_global, t_mdatoms *mdatoms,
 392                      t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
 393                      gmx_enerdata_t *enerd,tensor force_vir, tensor shake_vir, tensor total_vir,
 394                      tensor pres, rvec mu_tot, gmx_constr_t constr,
 395                      globsig_t *gs,gmx_bool bInterSimGS,
 396                      matrix box, gmx_mtop_t *top_global, real *pcurr,
 397                      int natoms, gmx_bool *bSumEkinhOld, int flags);
 398 /* Compute global variables during integration */
 399
 400 int mdrunner(int nthreads_requested, FILE *fplog,t_commrec *cr,int nfile,
 401              const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
 402              gmx_bool bCompact, int nstglobalcomm, ivec ddxyz,int dd_node_order,
 403              real rdd, real rconstr, const char *dddlb_opt,real dlb_scale,
 404              const char *ddcsx,const char *ddcsy,const char *ddcsz,
 405              int nstepout, int resetstep, int nmultisim, int repl_ex_nst,
 406              int repl_ex_seed, real pforce,real cpt_period,real max_hours,
 407              const char *deviceOptions, unsigned long Flags);
 408 /* Driver routine, that calls the different methods */
 409
 410 void md_print_warning(const t_commrec *cr,FILE *fplog,const char *buf);
 411 /* Print a warning message to stderr on the master node
 412  * and to fplog if fplog!=NULL.
 413  */
 414
 415 void init_md(FILE *fplog,
 416                     t_commrec *cr,t_inputrec *ir, const output_env_t oenv,
 417                     double *t,double *t0,
 418                     real *lambda,double *lam0,
 419                     t_nrnb *nrnb,gmx_mtop_t *mtop,
 420                     gmx_update_t *upd,
 421                     int nfile,const t_filenm fnm[],
 422                     gmx_mdoutf_t **outf,t_mdebin **mdebin,
 423                     tensor force_vir,tensor shake_vir,
 424                     rvec mu_tot,
 425                     gmx_bool *bSimAnn,t_vcm **vcm,
 426                     t_state *state, unsigned long Flags);
 427   /* Routine in sim_util.c */
 428
 429 #ifdef __cplusplus
 430 }
 431 #endif
 432
 433 #endif  /* _mdrun_h */