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
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gromacs Runs On Most of All Computer Systems
  34  */
  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 #include "membed.h"
  54
  55 #ifdef __cplusplus
  56 extern "C" {
  57 #endif
  58
  59 #define MD_POLARISE       (1<<2)
  60 #define MD_IONIZE         (1<<3)
  61 #define MD_RERUN          (1<<4)
  62 #define MD_RERUN_VSITE    (1<<5)
  63 #define MD_FFSCAN         (1<<6)
  64 #define MD_SEPPOT         (1<<7)
  65 #define MD_PARTDEC        (1<<9)
  66 #define MD_DDBONDCHECK    (1<<10)
  67 #define MD_DDBONDCOMM     (1<<11)
  68 #define MD_CONFOUT        (1<<12)
  69 #define MD_REPRODUCIBLE   (1<<13)
  70 #define MD_READ_RNG       (1<<14)
  71 #define MD_APPENDFILES    (1<<15)
  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_THREADS
 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                                 gmx_membed_t *membed,
 168                                 real cpt_period,real max_hours,
 169                                 const char *deviceOptions,
 170                                 unsigned long Flags,
 171                                 gmx_runtime_t *runtime);
 172
 173 typedef struct gmx_global_stat *gmx_global_stat_t;
 174
 175 /* ROUTINES from md.c */
 176
 177 gmx_integrator_t do_md;
 178
 179 gmx_integrator_t do_md_openmm;
 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 sim_util.c */
 202 void do_pbc_first(FILE *log,matrix box,t_forcerec *fr,
 203                          t_graph *graph,rvec x[]);
 204
 205 void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
 206                               gmx_mtop_t *mtop,rvec x[]);
 207
 208 void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
 209                         gmx_mtop_t *mtop,rvec x[]);
 210
 211
 212 /* ROUTINES from stat.c */
 213 gmx_global_stat_t global_stat_init(t_inputrec *ir);
 214
 215 void global_stat_destroy(gmx_global_stat_t gs);
 216
 217 void global_stat(FILE *log,gmx_global_stat_t gs,
 218                         t_commrec *cr,gmx_enerdata_t *enerd,
 219                         tensor fvir,tensor svir,rvec mu_tot,
 220                         t_inputrec *inputrec,
 221                         gmx_ekindata_t *ekind,
 222                         gmx_constr_t constr,t_vcm *vcm,
 223                         int nsig,real *sig,
 224                         gmx_mtop_t *top_global, t_state *state_local,
 225                         gmx_bool bSumEkinhOld, int flags);
 226 /* Communicate statistics over cr->mpi_comm_mysim */
 227
 228 gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],
 229                                  int mdrun_flags,
 230                                  const t_commrec *cr,const t_inputrec *ir,
 231                                  const output_env_t oenv);
 232 /* Returns a pointer to a data structure with all output file pointers
 233  * and names required by mdrun.
 234  */
 235
 236 void done_mdoutf(gmx_mdoutf_t *of);
 237 /* Close all open output files and free the of pointer */
 238
 239 #define MDOF_X   (1<<0)
 240 #define MDOF_V   (1<<1)
 241 #define MDOF_F   (1<<2)
 242 #define MDOF_XTC (1<<3)
 243 #define MDOF_CPT (1<<4)
 244
 245 void write_traj(FILE *fplog,t_commrec *cr,
 246                        gmx_mdoutf_t *of,
 247                        int mdof_flags,
 248                        gmx_mtop_t *top_global,
 249                        gmx_large_int_t step,double t,
 250                        t_state *state_local,t_state *state_global,
 251                        rvec *f_local,rvec *f_global,
 252                        int *n_xtc,rvec **x_xtc);
 253 /* Routine that writes frames to trn, xtc and/or checkpoint.
 254  * What is written is determined by the mdof_flags defined above.
 255  * Data is collected to the master node only when necessary.
 256  */
 257
 258 int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep);
 259 /* Return TRUE if io should be done */
 260
 261 int do_any_io(int step, t_inputrec *ir);
 262
 263 /* ROUTINES from sim_util.c */
 264
 265 double gmx_gettime();
 266
 267 void print_time(FILE *out, gmx_runtime_t *runtime,
 268                        gmx_large_int_t step,t_inputrec *ir, t_commrec *cr);
 269
 270 void runtime_start(gmx_runtime_t *runtime);
 271
 272 void runtime_end(gmx_runtime_t *runtime);
 273
 274 void runtime_upd_proc(gmx_runtime_t *runtime);
 275 /* The processor time should be updated every once in a while,
 276  * since on 32-bit manchines it loops after 72 minutes.
 277  */
 278
 279 void print_date_and_time(FILE *log,int pid,const char *title,
 280                                 const gmx_runtime_t *runtime);
 281
 282 void nstop_cm(FILE *log,t_commrec *cr,
 283                      int start,int nr_atoms,real mass[],rvec x[],rvec v[]);
 284
 285 void finish_run(FILE *log,t_commrec *cr,const char *confout,
 286                        t_inputrec *inputrec,
 287                        t_nrnb nrnb[],gmx_wallcycle_t wcycle,
 288                        gmx_runtime_t *runtime,
 289                        gmx_bool bWriteStat);
 290
 291 void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr);
 292
 293 void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
 294                           gmx_large_int_t step, int natoms,
 295                           matrix box,real lambda,tensor pres,tensor virial,
 296                           real *prescorr, real *enercorr, real *dvdlcorr);
 297
 298 typedef enum
 299 {
 300   LIST_SCALARS  =0001,
 301   LIST_INPUTREC =0002,
 302   LIST_TOP      =0004,
 303   LIST_X        =0010,
 304   LIST_V        =0020,
 305   LIST_F        =0040,
 306   LIST_LOAD     =0100
 307 } t_listitem;
 308
 309 void check_nnodes_top(char *fn,t_topology *top);
 310 /* Reset the tpr file to work with one node if necessary */
 311
 312
 313 /* check the version */
 314 void check_ir_old_tpx_versions(t_commrec *cr,FILE *fplog,
 315                                t_inputrec *ir,gmx_mtop_t *mtop);
 316
 317 /* Allocate and initialize node-local state entries. */
 318 void set_state_entries(t_state *state,const t_inputrec *ir,int nnodes);
 319
 320 /* Broadcast the data for a simulation, and allocate node-specific settings
 321    such as rng generators. */
 322 void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
 323                           gmx_mtop_t *mtop);
 324
 325
 326 void do_constrain_first(FILE *log,gmx_constr_t constr,
 327                                t_inputrec *inputrec,t_mdatoms *md,
 328                                t_state *state,rvec *f,
 329                                t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
 330                                t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
 331
 332 void dynamic_load_balancing(gmx_bool bVerbose,t_commrec *cr,real capacity[],
 333                                    int dimension,t_mdatoms *md,t_topology *top,
 334                                    rvec x[],rvec v[],matrix box);
 335 /* Perform load balancing, i.e. split the particles over processors
 336  * based on their coordinates in the "dimension" direction.
 337  */
 338
 339 int mdrunner(int nthreads_requested, FILE *fplog,t_commrec *cr,int nfile,
 340              const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
 341              gmx_bool bCompact, int nstglobalcomm, ivec ddxyz,int dd_node_order,
 342              real rdd, real rconstr, const char *dddlb_opt,real dlb_scale,
 343              const char *ddcsx,const char *ddcsy,const char *ddcsz,
 344              int nstepout, int resetstep, int nmultisim, int repl_ex_nst,
 345              int repl_ex_seed, real pforce,real cpt_period,real max_hours,
 346              const char *deviceOptions, unsigned long Flags);
 347 /* Driver routine, that calls the different methods */
 348
 349 void md_print_warning(const t_commrec *cr,FILE *fplog,const char *buf);
 350 /* Print a warning message to stderr on the master node
 351  * and to fplog if fplog!=NULL.
 352  */
 353
 354 void init_md(FILE *fplog,
 355                     t_commrec *cr,t_inputrec *ir, const output_env_t oenv,
 356                     double *t,double *t0,
 357                     real *lambda,double *lam0,
 358                     t_nrnb *nrnb,gmx_mtop_t *mtop,
 359                     gmx_update_t *upd,
 360                     int nfile,const t_filenm fnm[],
 361                     gmx_mdoutf_t **outf,t_mdebin **mdebin,
 362                     tensor force_vir,tensor shake_vir,
 363                     rvec mu_tot,
 364                     gmx_bool *bSimAnn,t_vcm **vcm,
 365                     t_state *state, unsigned long Flags);
 366   /* Routine in sim_util.c */
 367
 368 #ifdef __cplusplus
 369 }
 370 #endif
 371
 372 #endif  /* _mdrun_h */