include/mdrun.h

   1 /*
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   4  *
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   6  *
   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
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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
  55 #ifdef GMX_THREAD_MPI
  56 #include "thread_mpi/threads.h"
  57 #endif
  58
  59 #ifdef __cplusplus
  60 extern "C" {
  61 #endif
  62
  63 #define MD_POLARISE       (1<<2)
  64 #define MD_IONIZE         (1<<3)
  65 #define MD_RERUN          (1<<4)
  66 #define MD_RERUN_VSITE    (1<<5)
  67 #define MD_FFSCAN         (1<<6)
  68 #define MD_SEPPOT         (1<<7)
  69 #define MD_PARTDEC        (1<<9)
  70 #define MD_DDBONDCHECK    (1<<10)
  71 #define MD_DDBONDCOMM     (1<<11)
  72 #define MD_CONFOUT        (1<<12)
  73 #define MD_REPRODUCIBLE   (1<<13)
  74 #define MD_READ_RNG       (1<<14)
  75 #define MD_APPENDFILES    (1<<15)
  76 #define MD_APPENDFILESSET (1<<21)
  77 #define MD_KEEPANDNUMCPT  (1<<16)
  78 #define MD_READ_EKIN      (1<<17)
  79 #define MD_STARTFROMCPT   (1<<18)
  80 #define MD_RESETCOUNTERSHALFWAY (1<<19)
  81
  82 /* Define a number of flags to better control the information
  83  * passed to compute_globals in md.c and global_stat.
  84  */
  85
  86 /* We are rerunning the simulation */
  87 #define CGLO_RERUNMD        (1<<1)
  88 /* we are computing the kinetic energy from average velocities */
  89 #define CGLO_EKINAVEVEL     (1<<2)
  90 /* we are removing the center of mass momenta */
  91 #define CGLO_STOPCM         (1<<3)
  92 /* bGStat is defined in do_md */
  93 #define CGLO_GSTAT          (1<<4)
  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   gmx_bool bKeepAndNumCPT;
 136   int  eIntegrator;
 137   gmx_bool  bExpanded;
 138   int elamstats;
 139   int  simulation_part;
 140   FILE *fp_dhdl;
 141   FILE *fp_field;
 142 } gmx_mdoutf_t;
 143
 144 /* Variables for temporary use with the deform option,
 145  * used in runner.c and md.c.
 146  * (These variables should be stored in the tpx file.)
 147  */
 148 extern gmx_large_int_t     deform_init_init_step_tpx;
 149 extern matrix              deform_init_box_tpx;
 150 #ifdef GMX_THREAD_MPI
 151 extern tMPI_Thread_mutex_t deform_init_box_mutex;
 152
 153 /* The minimum number of atoms per thread. With fewer atoms than this,
 154  * the number of threads will get lowered.
 155  */
 156 #define MIN_ATOMS_PER_THREAD    90
 157 #endif
 158
 159
 160 typedef double gmx_integrator_t(FILE *log,t_commrec *cr,
 161                                 int nfile,const t_filenm fnm[],
 162                                 const output_env_t oenv, gmx_bool bVerbose,
 163                                 gmx_bool bCompact, int nstglobalcomm,
 164                                 gmx_vsite_t *vsite,gmx_constr_t constr,
 165                                 int stepout,
 166                                 t_inputrec *inputrec,
 167                                 gmx_mtop_t *mtop,t_fcdata *fcd,
 168                                 t_state *state,
 169                                 t_mdatoms *mdatoms,
 170                                 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 171                                 gmx_edsam_t ed,
 172                                 t_forcerec *fr,
 173                                 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
 174                                 gmx_membed_t membed,
 175                                 real cpt_period,real max_hours,
 176                                 const char *deviceOptions,
 177                                 unsigned long Flags,
 178                                 gmx_runtime_t *runtime);
 179
 180 typedef struct gmx_global_stat *gmx_global_stat_t;
 181
 182 /* ROUTINES from md.c */
 183
 184 gmx_integrator_t do_md;
 185
 186 gmx_integrator_t do_md_openmm;
 187
 188
 189
 190 /* ROUTINES from minimize.c */
 191
 192 gmx_integrator_t do_steep;
 193 /* Do steepest descents EM */
 194
 195 gmx_integrator_t do_cg;
 196 /* Do conjugate gradient EM */
 197
 198 gmx_integrator_t do_lbfgs;
 199 /* Do conjugate gradient L-BFGS */
 200
 201 gmx_integrator_t do_nm;
 202 /* Do normal mode analysis */
 203
 204 /* ROUTINES from tpi.c */
 205
 206 gmx_integrator_t do_tpi;
 207 /* Do test particle insertion */
 208
 209
 210 /* ROUTINES from md_support.c */
 211
 212 /* return the number of steps between global communcations */
 213 int check_nstglobalcomm(FILE *fplog,t_commrec *cr,
 214                         int nstglobalcomm,t_inputrec *ir);
 215
 216 /* check whether an 'nst'-style parameter p is a multiple of nst, and
 217    set it to be one if not, with a warning. */
 218 void check_nst_param(FILE *fplog,t_commrec *cr,
 219                      const char *desc_nst,int nst,
 220                      const char *desc_p,int *p);
 221
 222 /* check which of the multisim simulations has the shortest number of
 223    steps and return that number of nsteps */
 224 gmx_large_int_t get_multisim_nsteps(const t_commrec *cr,
 225                                     gmx_large_int_t nsteps);
 226
 227 void rerun_parallel_comm(t_commrec *cr,t_trxframe *fr,
 228                          gmx_bool *bNotLastFrame);
 229
 230 /* get the conserved energy associated with the ensemble type*/
 231 real compute_conserved_from_auxiliary(t_inputrec *ir, t_state *state,
 232                                       t_extmass *MassQ);
 233
 234 /* set the lambda values at each step of mdrun when they change */
 235 void set_current_lambdas(gmx_large_int_t step, t_lambda *fepvals, gmx_bool bRerunMD,
 236                          t_trxframe *rerun_fr, t_state *state_global, t_state *state, double lam0[]);
 237
 238 /* reset all cycle and time counters. */
 239 void reset_all_counters(FILE *fplog,t_commrec *cr,
 240                         gmx_large_int_t step,
 241                         gmx_large_int_t *step_rel,t_inputrec *ir,
 242                         gmx_wallcycle_t wcycle,t_nrnb *nrnb,
 243                         gmx_runtime_t *runtime);
 244
 245
 246
 247 /* ROUTINES from sim_util.c */
 248 void do_pbc_first(FILE *log,matrix box,t_forcerec *fr,
 249                          t_graph *graph,rvec x[]);
 250
 251 void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
 252                               gmx_mtop_t *mtop,rvec x[]);
 253
 254 void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
 255                         gmx_mtop_t *mtop,rvec x[]);
 256
 257
 258
 259 /* ROUTINES from stat.c */
 260 gmx_global_stat_t global_stat_init(t_inputrec *ir);
 261
 262 void global_stat_destroy(gmx_global_stat_t gs);
 263
 264 void global_stat(FILE *log,gmx_global_stat_t gs,
 265                         t_commrec *cr,gmx_enerdata_t *enerd,
 266                         tensor fvir,tensor svir,rvec mu_tot,
 267                         t_inputrec *inputrec,
 268                         gmx_ekindata_t *ekind,
 269                         gmx_constr_t constr,t_vcm *vcm,
 270                         int nsig,real *sig,
 271                         gmx_mtop_t *top_global, t_state *state_local,
 272                         gmx_bool bSumEkinhOld, int flags);
 273 /* Communicate statistics over cr->mpi_comm_mysim */
 274
 275 gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],
 276                                  int mdrun_flags,
 277                                  const t_commrec *cr,const t_inputrec *ir,
 278                                  const output_env_t oenv);
 279 /* Returns a pointer to a data structure with all output file pointers
 280  * and names required by mdrun.
 281  */
 282
 283 void done_mdoutf(gmx_mdoutf_t *of);
 284 /* Close all open output files and free the of pointer */
 285
 286 #define MDOF_X   (1<<0)
 287 #define MDOF_V   (1<<1)
 288 #define MDOF_F   (1<<2)
 289 #define MDOF_XTC (1<<3)
 290 #define MDOF_CPT (1<<4)
 291
 292 void write_traj(FILE *fplog,t_commrec *cr,
 293                        gmx_mdoutf_t *of,
 294                        int mdof_flags,
 295                        gmx_mtop_t *top_global,
 296                        gmx_large_int_t step,double t,
 297                        t_state *state_local,t_state *state_global,
 298                        rvec *f_local,rvec *f_global,
 299                        int *n_xtc,rvec **x_xtc);
 300 /* Routine that writes frames to trn, xtc and/or checkpoint.
 301  * What is written is determined by the mdof_flags defined above.
 302  * Data is collected to the master node only when necessary.
 303  */
 304
 305 int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep);
 306 /* Return TRUE if io should be done */
 307
 308 int do_any_io(int step, t_inputrec *ir);
 309
 310 /* ROUTINES from sim_util.c */
 311
 312 double gmx_gettime();
 313
 314 void print_time(FILE *out, gmx_runtime_t *runtime,
 315                        gmx_large_int_t step,t_inputrec *ir, t_commrec *cr);
 316
 317 void runtime_start(gmx_runtime_t *runtime);
 318
 319 void runtime_end(gmx_runtime_t *runtime);
 320
 321 void runtime_upd_proc(gmx_runtime_t *runtime);
 322 /* The processor time should be updated every once in a while,
 323  * since on 32-bit manchines it loops after 72 minutes.
 324  */
 325
 326 void print_date_and_time(FILE *log,int pid,const char *title,
 327                                 const gmx_runtime_t *runtime);
 328
 329 void nstop_cm(FILE *log,t_commrec *cr,
 330                      int start,int nr_atoms,real mass[],rvec x[],rvec v[]);
 331
 332 void finish_run(FILE *log,t_commrec *cr,const char *confout,
 333                        t_inputrec *inputrec,
 334                        t_nrnb nrnb[],gmx_wallcycle_t wcycle,
 335                        gmx_runtime_t *runtime,
 336                        gmx_bool bWriteStat);
 337
 338 void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr);
 339
 340 void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
 341                    gmx_large_int_t step, int natoms,
 342                    matrix box,real lambda,tensor pres,tensor virial,
 343                    real *prescorr, real *enercorr, real *dvdlcorr);
 344
 345 void initialize_lambdas(FILE *fplog,t_inputrec *ir,int *fep_state,real *lambda,double *lam0);
 346
 347 void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit);
 348
 349 int ExpandedEnsembleDynamics(FILE *log,t_inputrec *ir, gmx_enerdata_t *enerd,
 350                              t_state *state, t_extmass *MassQ, df_history_t *dfhist,
 351                              gmx_large_int_t step, gmx_rng_t mcrng,
 352                              rvec *v, t_mdatoms *mdatoms);
 353
 354 void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
 355                                int nlam, int frequency, gmx_large_int_t step);
 356
 357 void get_mc_state(gmx_rng_t rng,t_state *state);
 358
 359 void set_mc_state(gmx_rng_t rng,t_state *state);
 360
 361
 362 typedef enum
 363 {
 364   LIST_SCALARS  =0001,
 365   LIST_INPUTREC =0002,
 366   LIST_TOP      =0004,
 367   LIST_X        =0010,
 368   LIST_V        =0020,
 369   LIST_F        =0040,
 370   LIST_LOAD     =0100
 371 } t_listitem;
 372
 373 void check_nnodes_top(char *fn,t_topology *top);
 374 /* Reset the tpr file to work with one node if necessary */
 375
 376
 377 /* check the version */
 378 void check_ir_old_tpx_versions(t_commrec *cr,FILE *fplog,
 379                                t_inputrec *ir,gmx_mtop_t *mtop);
 380
 381 /* Allocate and initialize node-local state entries. */
 382 void set_state_entries(t_state *state,const t_inputrec *ir,int nnodes);
 383
 384 /* Broadcast the data for a simulation, and allocate node-specific settings
 385    such as rng generators. */
 386 void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
 387                           gmx_mtop_t *mtop);
 388
 389
 390 void do_constrain_first(FILE *log,gmx_constr_t constr,
 391                                t_inputrec *inputrec,t_mdatoms *md,
 392                                t_state *state,rvec *f,
 393                                t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
 394                                t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
 395
 396 void dynamic_load_balancing(gmx_bool bVerbose,t_commrec *cr,real capacity[],
 397                                    int dimension,t_mdatoms *md,t_topology *top,
 398                                    rvec x[],rvec v[],matrix box);
 399 /* Perform load balancing, i.e. split the particles over processors
 400  * based on their coordinates in the "dimension" direction.
 401  */
 402
 403 int multisim_min(const gmx_multisim_t *ms,int nmin,int n);
 404 /* Set an appropriate value for n across the whole multi-simulation */
 405
 406 int multisim_nstsimsync(const t_commrec *cr,
 407                         const t_inputrec *ir,int repl_ex_nst);
 408 /* Determine the interval for inter-simulation communication */
 409
 410 void init_global_signals(globsig_t *gs,const t_commrec *cr,
 411                          const t_inputrec *ir,int repl_ex_nst);
 412 /* Constructor for globsig_t */
 413
 414 void copy_coupling_state(t_state *statea,t_state *stateb,
 415                          gmx_ekindata_t *ekinda,gmx_ekindata_t *ekindb, t_grpopts* opts);
 416 /* Copy stuff from state A to state B */
 417
 418 void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inputrec *ir,
 419                      t_forcerec *fr, gmx_ekindata_t *ekind,
 420                      t_state *state, t_state *state_global, t_mdatoms *mdatoms,
 421                      t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
 422                      gmx_enerdata_t *enerd,tensor force_vir, tensor shake_vir, tensor total_vir,
 423                      tensor pres, rvec mu_tot, gmx_constr_t constr,
 424                      globsig_t *gs,gmx_bool bInterSimGS,
 425                      matrix box, gmx_mtop_t *top_global, real *pcurr,
 426                      int natoms, gmx_bool *bSumEkinhOld, int flags);
 427 /* Compute global variables during integration */
 428
 429 int mdrunner(int nthreads_requested, FILE *fplog,t_commrec *cr,int nfile,
 430              const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
 431              gmx_bool bCompact, int nstglobalcomm, ivec ddxyz,int dd_node_order,
 432              real rdd, real rconstr, const char *dddlb_opt,real dlb_scale,
 433              const char *ddcsx,const char *ddcsy,const char *ddcsz,
 434              int nstepout, int resetstep, int nmultisim, int repl_ex_nst, int repl_ex_nex,
 435              int repl_ex_seed, real pforce,real cpt_period,real max_hours,
 436              const char *deviceOptions, unsigned long Flags);
 437 /* Driver routine, that calls the different methods */
 438
 439 void md_print_warning(const t_commrec *cr,FILE *fplog,const char *buf);
 440 /* Print a warning message to stderr on the master node
 441  * and to fplog if fplog!=NULL.
 442  */
 443
 444 void init_md(FILE *fplog,
 445                     t_commrec *cr,t_inputrec *ir, const output_env_t oenv,
 446                     double *t,double *t0,
 447                     real *lambda,int *fep_state, double *lam0,
 448                     t_nrnb *nrnb,gmx_mtop_t *mtop,
 449                     gmx_update_t *upd,
 450                     int nfile,const t_filenm fnm[],
 451                     gmx_mdoutf_t **outf,t_mdebin **mdebin,
 452                     tensor force_vir,tensor shake_vir,
 453                     rvec mu_tot,
 454                     gmx_bool *bSimAnn,t_vcm **vcm,
 455                     t_state *state, unsigned long Flags);
 456   /* Routine in sim_util.c */
 457
 458 #ifdef __cplusplus
 459 }
 460 #endif
 461
 462 #endif  /* _mdrun_h */