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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  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 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include <stdio.h>
  44 #include "typedefs.h"
  45 #include "network.h"
  46 #include "tgroup.h"
  47 #include "filenm.h"
  48 #include "mshift.h"
  49 #include "force.h"
  50 #include "time.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<<14)
  73 #define MD_READ_RNG     (1<<15)
  74 #define MD_APPENDFILES  (1<<16)
  75 #define MD_READ_EKIN    (1<<17)
  76 #define MD_STARTFROMCPT (1<<18)
  77 #define MD_RESETCOUNTERSHALFWAY (1<<19)
  78
  79 /* Define a number of flags to better control the information
  80  * passed to compute_globals in md.c and global_stat.
  81  */
  82
  83 /* We are rerunning the simulation */
  84 #define CGLO_RERUNMD        (1<<1)
  85 /* we are computing the kinetic energy from average velocities */
  86 #define CGLO_EKINAVEVEL     (1<<2)
  87 /* we are removing the center of mass momenta */
  88 #define CGLO_STOPCM         (1<<3)
  89 /* bGStat is defined in do_md */
  90 #define CGLO_GSTAT          (1<<4)
  91 /* bNEMD is defined in do_md */
  92 #define CGLO_NEMD           (1<<5)
  93 /* Sum the energy terms in global computation */
  94 #define CGLO_ENERGY         (1<<6)
  95 /* Sum the kinetic energy terms in global computation */
  96 #define CGLO_TEMPERATURE    (1<<7)
  97 /* Sum the kinetic energy terms in global computation */
  98 #define CGLO_PRESSURE       (1<<8)
  99 /* Sum the constraint term in global computation */
 100 #define CGLO_CONSTRAINT     (1<<9)
 101 /* we are using an integrator that requires iteration over some steps - currently not used*/
 102 #define CGLO_ITERATE        (1<<10)
 103 /* it is the first time we are iterating (or, only once through is required */
 104 #define CGLO_FIRSTITERATE   (1<<11)
 105 /* Reading ekin from the trajectory */
 106 #define CGLO_READEKIN       (1<<12)
 107 /* we need to reset the ekin rescaling factor here */
 108 #define CGLO_SCALEEKIN      (1<<13)
 109
 110 enum {
 111   ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
 112 };
 113
 114 typedef struct {
 115   double real;
 116 #ifdef GMX_CRAY_XT3
 117   double proc;
 118 #else
 119   clock_t proc;
 120 #endif
 121   double realtime;
 122   double proctime;
 123   double time_per_step;
 124   double last;
 125   gmx_large_int_t nsteps_done;
 126 } gmx_runtime_t;
 127
 128 typedef struct {
 129   int  fp_trn;
 130   int  fp_xtc;
 131   int  xtc_prec;
 132   ener_file_t fp_ene;
 133   const char *fn_cpt;
 134   int  eIntegrator;
 135   int  simulation_part;
 136   FILE *fp_dhdl;
 137   FILE *fp_field;
 138 } gmx_mdoutf_t;
 139
 140 /* Variables for temporary use with the deform option,
 141  * used in runner.c and md.c.
 142  * (These variables should be stored in the tpx file.)
 143  */
 144 extern gmx_large_int_t     deform_init_init_step_tpx;
 145 extern matrix              deform_init_box_tpx;
 146 #ifdef GMX_THREADS
 147 extern tMPI_Thread_mutex_t deform_init_box_mutex;
 148 #endif
 149
 150
 151 typedef double gmx_integrator_t(FILE *log,t_commrec *cr,
 152                                 int nfile,const t_filenm fnm[],
 153                                 const output_env_t oenv, bool bVerbose,
 154                                 bool bCompact, int nstglobalcomm,
 155                                 gmx_vsite_t *vsite,gmx_constr_t constr,
 156                                 int stepout,
 157                                 t_inputrec *inputrec,
 158                                 gmx_mtop_t *mtop,t_fcdata *fcd,
 159                                 t_state *state,
 160                                 t_mdatoms *mdatoms,
 161                                 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 162                                 gmx_edsam_t ed,
 163                                 t_forcerec *fr,
 164                                 int repl_ex_nst,int repl_ex_seed,
 165                                 real cpt_period,real max_hours,
 166                                 const char *deviceOptions,
 167                                 unsigned long Flags,
 168                                 gmx_runtime_t *runtime);
 169
 170 typedef struct gmx_global_stat *gmx_global_stat_t;
 171
 172 /* ROUTINES from md.c */
 173
 174 extern gmx_integrator_t do_md;
 175
 176 extern gmx_integrator_t do_md_openmm;
 177
 178 /* ROUTINES from minimize.c */
 179
 180 extern gmx_integrator_t do_steep;
 181 /* Do steepest descents EM */
 182
 183 extern gmx_integrator_t do_cg;
 184 /* Do conjugate gradient EM */
 185
 186 extern gmx_integrator_t do_lbfgs;
 187 /* Do conjugate gradient L-BFGS */
 188
 189 extern gmx_integrator_t do_nm;
 190 /* Do normal mode analysis */
 191
 192 /* ROUTINES from tpi.c */
 193
 194 extern gmx_integrator_t do_tpi;
 195 /* Do test particle insertion */
 196
 197
 198 /* ROUTINES from sim_util.c */
 199 extern void do_pbc_first(FILE *log,matrix box,t_forcerec *fr,
 200                          t_graph *graph,rvec x[]);
 201
 202 extern void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
 203                               gmx_mtop_t *mtop,rvec x[]);
 204
 205 extern void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
 206                         gmx_mtop_t *mtop,rvec x[]);
 207
 208
 209 /* ROUTINES from stat.c */
 210 extern gmx_global_stat_t global_stat_init(t_inputrec *ir);
 211
 212 extern void global_stat_destroy(gmx_global_stat_t gs);
 213
 214 extern void global_stat(FILE *log,gmx_global_stat_t gs,
 215                         t_commrec *cr,gmx_enerdata_t *enerd,
 216                         tensor fvir,tensor svir,rvec mu_tot,
 217                         t_inputrec *inputrec,
 218                         gmx_ekindata_t *ekind,
 219                         gmx_constr_t constr,t_vcm *vcm,
 220                         int nsig,real *sig,
 221                         gmx_mtop_t *top_global, t_state *state_local,
 222                         bool bSumEkinhOld, int flags);
 223 /* Communicate statistics over cr->mpi_comm_mysim */
 224
 225 extern gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],
 226                                  bool bAppendFiles,
 227                                  const t_commrec *cr,const t_inputrec *ir,
 228                                  const output_env_t oenv);
 229 /* Returns a pointer to a data structure with all output file pointers
 230  * and names required by mdrun.
 231  */
 232
 233 extern void done_mdoutf(gmx_mdoutf_t *of);
 234 /* Close all open output files and free the of pointer */
 235
 236 #define MDOF_X   (1<<0)
 237 #define MDOF_V   (1<<1)
 238 #define MDOF_F   (1<<2)
 239 #define MDOF_XTC (1<<3)
 240 #define MDOF_CPT (1<<4)
 241
 242 extern void write_traj(FILE *fplog,t_commrec *cr,
 243                        gmx_mdoutf_t *of,
 244                        int mdof_flags,
 245                        gmx_mtop_t *top_global,
 246                        gmx_large_int_t step,double t,
 247                        t_state *state_local,t_state *state_global,
 248                        rvec *f_local,rvec *f_global,
 249                        int *n_xtc,rvec **x_xtc);
 250 /* Routine that writes frames to trn, xtc and/or checkpoint.
 251  * What is written is determined by the mdof_flags defined above.
 252  * Data is collected to the master node only when necessary.
 253  */
 254
 255 extern int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep);
 256 /* Return TRUE if io should be done */
 257
 258 extern int do_any_io(int step, t_inputrec *ir);
 259
 260 /* ROUTINES from sim_util.c */
 261
 262 extern double gmx_gettime();
 263
 264 extern void print_time(FILE *out, gmx_runtime_t *runtime,
 265                        gmx_large_int_t step,t_inputrec *ir, t_commrec *cr);
 266
 267 extern void runtime_start(gmx_runtime_t *runtime);
 268
 269 extern void runtime_end(gmx_runtime_t *runtime);
 270
 271 extern void runtime_upd_proc(gmx_runtime_t *runtime);
 272 /* The processor time should be updated every once in a while,
 273  * since on 32-bit manchines it loops after 72 minutes.
 274  */
 275
 276 extern void print_date_and_time(FILE *log,int pid,const char *title,
 277                                 const gmx_runtime_t *runtime);
 278
 279 extern void nstop_cm(FILE *log,t_commrec *cr,
 280                      int start,int nr_atoms,real mass[],rvec x[],rvec v[]);
 281
 282 extern void finish_run(FILE *log,t_commrec *cr,const char *confout,
 283                        t_inputrec *inputrec,
 284                        t_nrnb nrnb[],gmx_wallcycle_t wcycle,
 285                        gmx_runtime_t *runtime,
 286                        bool bWriteStat);
 287
 288 extern void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr);
 289
 290 extern void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
 291                           gmx_large_int_t step, int natoms,
 292                           matrix box,real lambda,tensor pres,tensor virial,
 293                           real *prescorr, real *enercorr, real *dvdlcorr);
 294
 295 typedef enum
 296 {
 297   LIST_SCALARS  =0001,
 298   LIST_INPUTREC =0002,
 299   LIST_TOP      =0004,
 300   LIST_X        =0010,
 301   LIST_V        =0020,
 302   LIST_F        =0040,
 303   LIST_LOAD     =0100
 304 } t_listitem;
 305
 306 extern void check_nnodes_top(char *fn,t_topology *top);
 307 /* Reset the tpr file to work with one node if necessary */
 308
 309 extern void init_single(FILE *log, t_inputrec *inputrec, const char *tpbfile,
 310                         gmx_mtop_t *mtop, t_state *state);
 311      /*
 312       * Allocates space for the topology (top), the coordinates x, the
 313       * velocities v, masses mass. Reads the parameters, topology,
 314       * coordinates and velocities from the file specified in tpbfile
 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
 322 extern void init_parallel(FILE *log,const char *tpxfile, t_commrec *cr,
 323                           t_inputrec *inputrec,gmx_mtop_t *mtop,
 324                           t_state *state, int list);
 325      /*
 326       * Loads the data for a simulation from the ring. Parameters, topology
 327       * coordinates, velocities, and masses are initialised equal to using
 328       * init_single() in the single processor version. The extra argument
 329       * f_add is allocated to use for the update of the forces, the load
 330       * array specifies in which part of the x and f array the subsystems
 331       * of the other processors are located. Homenr0, homenr1, nparts0 and
 332       * nparts1 are necessary to calculate the non bonded interaction using
 333       * the symmetry and thus calculating every force only once. List is a
 334       * facility for logging (and debugging). One can decide to print none or a
 335       * set of * selected parameters to the file specified by log. Parameters
 336       * are printed by or-ing the corresponding items from t_listitem. A 0
 337       * (zero) specifies that nothing is to be printed on the file. The function
 338       * returns the number of shifts over the ring to perform to calculate
 339       * all interactions.
 340       *
 341       * NOTE: for threaded simulations that don't support parallel runs (at
 342       * the moment that's only the LBGFS integrator), this function may
 343       * cancel them and re-write the commrec.
 344       */
 345
 346 extern void do_constrain_first(FILE *log,gmx_constr_t constr,
 347                                t_inputrec *inputrec,t_mdatoms *md,
 348                                t_state *state,rvec *f,
 349                                t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
 350                                t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
 351
 352 extern void dynamic_load_balancing(bool bVerbose,t_commrec *cr,real capacity[],
 353                                    int dimension,t_mdatoms *md,t_topology *top,
 354                                    rvec x[],rvec v[],matrix box);
 355 /* Perform load balancing, i.e. split the particles over processors
 356  * based on their coordinates in the "dimension" direction.
 357  */
 358
 359 int mdrunner(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
 360              const output_env_t oenv, bool bVerbose,bool bCompact,
 361              int nstglobalcomm, ivec ddxyz,int dd_node_order,real rdd,
 362              real rconstr, const char *dddlb_opt,real dlb_scale,
 363              const char *ddcsx,const char *ddcsy,const char *ddcsz,
 364              int nstepout, int resetstep, int nmultisim, int repl_ex_nst,int repl_ex_seed,
 365              real pforce,real cpt_period,real max_hours,
 366              const char *deviceOptions, unsigned long Flags);
 367 /* Driver routine, that calls the different methods */
 368
 369 int mdrunner_threads(int nthreads,
 370                      FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
 371                      const output_env_t oenv, bool bVerbose,bool bCompact,
 372                      int nstglobalcomm,
 373                      ivec ddxyz,int dd_node_order,real rdd,real rconstr,
 374                      const char *dddlb_opt,real dlb_scale,
 375                      const char *ddcsx,const char *ddcsy,const char *ddcsz,
 376                      int nstepout,int resetstep,int nmultisim, int repl_ex_nst,
 377                      int repl_ex_seed, real pforce,real cpt_period,
 378                      real max_hours, const char *deviceOptions, unsigned long Flags);
 379 /* initializes nthread threads before running mdrunner: is the preferred
 380    way to start a simulation (even if nthreads=1 and no threads are started) */
 381
 382 extern void md_print_warning(const t_commrec *cr,FILE *fplog,const char *buf);
 383 /* Print a warning message to stderr on the master node
 384  * and to fplog if fplog!=NULL.
 385  */
 386
 387 extern void init_md(FILE *fplog,
 388                     t_commrec *cr,t_inputrec *ir, const output_env_t oenv,
 389                     double *t,double *t0,
 390                     real *lambda,double *lam0,
 391                     t_nrnb *nrnb,gmx_mtop_t *mtop,
 392                     gmx_update_t *upd,
 393                     int nfile,const t_filenm fnm[],
 394                     gmx_mdoutf_t **outf,t_mdebin **mdebin,
 395                     tensor force_vir,tensor shake_vir,
 396                     rvec mu_tot,
 397                     bool *bNEMD,bool *bSimAnn,t_vcm **vcm,
 398                     t_state *state, unsigned long Flags);
 399   /* Routine in sim_util.c */
 400
 401 #ifdef __cplusplus
 402 }
 403 #endif
 404
 405 #endif  /* _mdrun_h */