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56 #include "thread_mpi/threads.h"
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)
82 /* Define a number of flags to better control the information
83 * passed to compute_globals in md.c and global_stat.
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)
112 ddnoSEL, ddnoINTERLEAVE, ddnoPP_PME, ddnoCARTESIAN, ddnoNR
124 double time_per_step;
126 gmx_large_int_t nsteps_done;
135 gmx_bool bKeepAndNumCPT;
142 /* Variables for temporary use with the deform option,
143 * used in runner.c and md.c.
144 * (These variables should be stored in the tpx file.)
146 extern gmx_large_int_t deform_init_init_step_tpx;
147 extern matrix deform_init_box_tpx;
148 #ifdef GMX_THREAD_MPI
149 extern tMPI_Thread_mutex_t deform_init_box_mutex;
151 /* The minimum number of atoms per thread. With fewer atoms than this,
152 * the number of threads will get lowered.
154 #define MIN_ATOMS_PER_THREAD 90
158 typedef double gmx_integrator_t(FILE *log,t_commrec *cr,
159 int nfile,const t_filenm fnm[],
160 const output_env_t oenv, gmx_bool bVerbose,
161 gmx_bool bCompact, int nstglobalcomm,
162 gmx_vsite_t *vsite,gmx_constr_t constr,
164 t_inputrec *inputrec,
165 gmx_mtop_t *mtop,t_fcdata *fcd,
168 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
171 int repl_ex_nst,int repl_ex_seed,
173 real cpt_period,real max_hours,
174 const char *deviceOptions,
176 gmx_runtime_t *runtime);
178 typedef struct gmx_global_stat *gmx_global_stat_t;
180 /* ROUTINES from md.c */
182 gmx_integrator_t do_md;
184 gmx_integrator_t do_md_openmm;
188 /* ROUTINES from minimize.c */
190 gmx_integrator_t do_steep;
191 /* Do steepest descents EM */
193 gmx_integrator_t do_cg;
194 /* Do conjugate gradient EM */
196 gmx_integrator_t do_lbfgs;
197 /* Do conjugate gradient L-BFGS */
199 gmx_integrator_t do_nm;
200 /* Do normal mode analysis */
202 /* ROUTINES from tpi.c */
204 gmx_integrator_t do_tpi;
205 /* Do test particle insertion */
208 /* ROUTINES from md_support.c */
210 /* return the number of steps between global communcations */
211 int check_nstglobalcomm(FILE *fplog,t_commrec *cr,
212 int nstglobalcomm,t_inputrec *ir);
214 /* check whether an 'nst'-style parameter p is a multiple of nst, and
215 set it to be one if not, with a warning. */
216 void check_nst_param(FILE *fplog,t_commrec *cr,
217 const char *desc_nst,int nst,
218 const char *desc_p,int *p);
220 /* check which of the multisim simulations has the shortest number of
221 steps and return that number of nsteps */
222 gmx_large_int_t get_multisim_nsteps(const t_commrec *cr,
223 gmx_large_int_t nsteps);
225 void rerun_parallel_comm(t_commrec *cr,t_trxframe *fr,
226 gmx_bool *bNotLastFrame);
228 /* get the conserved energy associated with the ensemble type*/
229 real compute_conserved_from_auxiliary(t_inputrec *ir, t_state *state,
232 /* reset all cycle and time counters. */
233 void reset_all_counters(FILE *fplog,t_commrec *cr,
234 gmx_large_int_t step,
235 gmx_large_int_t *step_rel,t_inputrec *ir,
236 gmx_wallcycle_t wcycle,t_nrnb *nrnb,
237 gmx_runtime_t *runtime);
241 /* ROUTINES from sim_util.c */
242 void do_pbc_first(FILE *log,matrix box,t_forcerec *fr,
243 t_graph *graph,rvec x[]);
245 void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
246 gmx_mtop_t *mtop,rvec x[]);
248 void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
249 gmx_mtop_t *mtop,rvec x[]);
253 /* ROUTINES from stat.c */
254 gmx_global_stat_t global_stat_init(t_inputrec *ir);
256 void global_stat_destroy(gmx_global_stat_t gs);
258 void global_stat(FILE *log,gmx_global_stat_t gs,
259 t_commrec *cr,gmx_enerdata_t *enerd,
260 tensor fvir,tensor svir,rvec mu_tot,
261 t_inputrec *inputrec,
262 gmx_ekindata_t *ekind,
263 gmx_constr_t constr,t_vcm *vcm,
265 gmx_mtop_t *top_global, t_state *state_local,
266 gmx_bool bSumEkinhOld, int flags);
267 /* Communicate statistics over cr->mpi_comm_mysim */
269 gmx_mdoutf_t *init_mdoutf(int nfile,const t_filenm fnm[],
271 const t_commrec *cr,const t_inputrec *ir,
272 const output_env_t oenv);
273 /* Returns a pointer to a data structure with all output file pointers
274 * and names required by mdrun.
277 void done_mdoutf(gmx_mdoutf_t *of);
278 /* Close all open output files and free the of pointer */
280 #define MDOF_X (1<<0)
281 #define MDOF_V (1<<1)
282 #define MDOF_F (1<<2)
283 #define MDOF_XTC (1<<3)
284 #define MDOF_CPT (1<<4)
286 void write_traj(FILE *fplog,t_commrec *cr,
289 gmx_mtop_t *top_global,
290 gmx_large_int_t step,double t,
291 t_state *state_local,t_state *state_global,
292 rvec *f_local,rvec *f_global,
293 int *n_xtc,rvec **x_xtc);
294 /* Routine that writes frames to trn, xtc and/or checkpoint.
295 * What is written is determined by the mdof_flags defined above.
296 * Data is collected to the master node only when necessary.
299 int do_per_step(gmx_large_int_t step,gmx_large_int_t nstep);
300 /* Return TRUE if io should be done */
302 int do_any_io(int step, t_inputrec *ir);
304 /* ROUTINES from sim_util.c */
306 double gmx_gettime();
308 void print_time(FILE *out, gmx_runtime_t *runtime,
309 gmx_large_int_t step,t_inputrec *ir, t_commrec *cr);
311 void runtime_start(gmx_runtime_t *runtime);
313 void runtime_end(gmx_runtime_t *runtime);
315 void runtime_upd_proc(gmx_runtime_t *runtime);
316 /* The processor time should be updated every once in a while,
317 * since on 32-bit manchines it loops after 72 minutes.
320 void print_date_and_time(FILE *log,int pid,const char *title,
321 const gmx_runtime_t *runtime);
323 void nstop_cm(FILE *log,t_commrec *cr,
324 int start,int nr_atoms,real mass[],rvec x[],rvec v[]);
326 void finish_run(FILE *log,t_commrec *cr,const char *confout,
327 t_inputrec *inputrec,
328 t_nrnb nrnb[],gmx_wallcycle_t wcycle,
329 gmx_runtime_t *runtime,
330 gmx_bool bWriteStat);
332 void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr);
334 void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
335 gmx_large_int_t step, int natoms,
336 matrix box,real lambda,tensor pres,tensor virial,
337 real *prescorr, real *enercorr, real *dvdlcorr);
350 void check_nnodes_top(char *fn,t_topology *top);
351 /* Reset the tpr file to work with one node if necessary */
354 /* check the version */
355 void check_ir_old_tpx_versions(t_commrec *cr,FILE *fplog,
356 t_inputrec *ir,gmx_mtop_t *mtop);
358 /* Allocate and initialize node-local state entries. */
359 void set_state_entries(t_state *state,const t_inputrec *ir,int nnodes);
361 /* Broadcast the data for a simulation, and allocate node-specific settings
362 such as rng generators. */
363 void init_parallel(FILE *log, t_commrec *cr, t_inputrec *inputrec,
367 void do_constrain_first(FILE *log,gmx_constr_t constr,
368 t_inputrec *inputrec,t_mdatoms *md,
369 t_state *state,rvec *f,
370 t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
371 t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir);
373 void dynamic_load_balancing(gmx_bool bVerbose,t_commrec *cr,real capacity[],
374 int dimension,t_mdatoms *md,t_topology *top,
375 rvec x[],rvec v[],matrix box);
376 /* Perform load balancing, i.e. split the particles over processors
377 * based on their coordinates in the "dimension" direction.
380 int multisim_min(const gmx_multisim_t *ms,int nmin,int n);
381 /* Set an appropriate value for n across the whole multi-simulation */
383 int multisim_nstsimsync(const t_commrec *cr,
384 const t_inputrec *ir,int repl_ex_nst);
385 /* Determine the interval for inter-simulation communication */
387 void init_global_signals(globsig_t *gs,const t_commrec *cr,
388 const t_inputrec *ir,int repl_ex_nst);
389 /* Constructor for globsig_t */
391 void copy_coupling_state(t_state *statea,t_state *stateb,
392 gmx_ekindata_t *ekinda,gmx_ekindata_t *ekindb, t_grpopts* opts);
393 /* Copy stuff from state A to state B */
395 void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inputrec *ir,
396 t_forcerec *fr, gmx_ekindata_t *ekind,
397 t_state *state, t_state *state_global, t_mdatoms *mdatoms,
398 t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
399 gmx_enerdata_t *enerd,tensor force_vir, tensor shake_vir, tensor total_vir,
400 tensor pres, rvec mu_tot, gmx_constr_t constr,
401 globsig_t *gs,gmx_bool bInterSimGS,
402 matrix box, gmx_mtop_t *top_global, real *pcurr,
403 int natoms, gmx_bool *bSumEkinhOld, int flags);
404 /* Compute global variables during integration */
406 int mdrunner(int nthreads_requested, FILE *fplog,t_commrec *cr,int nfile,
407 const t_filenm fnm[], const output_env_t oenv, gmx_bool bVerbose,
408 gmx_bool bCompact, int nstglobalcomm, ivec ddxyz,int dd_node_order,
409 real rdd, real rconstr, const char *dddlb_opt,real dlb_scale,
410 const char *ddcsx,const char *ddcsy,const char *ddcsz,
411 int nstepout, int resetstep, int nmultisim, int repl_ex_nst,
412 int repl_ex_seed, real pforce,real cpt_period,real max_hours,
413 const char *deviceOptions, unsigned long Flags);
414 /* Driver routine, that calls the different methods */
416 void md_print_warning(const t_commrec *cr,FILE *fplog,const char *buf);
417 /* Print a warning message to stderr on the master node
418 * and to fplog if fplog!=NULL.
421 void init_md(FILE *fplog,
422 t_commrec *cr,t_inputrec *ir, const output_env_t oenv,
423 double *t,double *t0,
424 real *lambda,double *lam0,
425 t_nrnb *nrnb,gmx_mtop_t *mtop,
427 int nfile,const t_filenm fnm[],
428 gmx_mdoutf_t **outf,t_mdebin **mdebin,
429 tensor force_vir,tensor shake_vir,
431 gmx_bool *bSimAnn,t_vcm **vcm,
432 t_state *state, unsigned long Flags);
433 /* Routine in sim_util.c */
439 #endif /* _mdrun_h */