Bug Summary

File:programs/mdrun/md.c
Location:line 719, column 5
Description:Value stored to 'bLastStep' is never read

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
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36 */
37#ifdef HAVE_CONFIG_H1
38#include <config.h>
39#endif
40
41#include <stdlib.h>
42
43#include "typedefs.h"
44#include "gromacs/utility/smalloc.h"
45#include "gromacs/math/vec.h"
46#include "vcm.h"
47#include "mdebin.h"
48#include "nrnb.h"
49#include "calcmu.h"
50#include "index.h"
51#include "vsite.h"
52#include "update.h"
53#include "ns.h"
54#include "mdrun.h"
55#include "md_support.h"
56#include "md_logging.h"
57#include "network.h"
58#include "physics.h"
59#include "names.h"
60#include "force.h"
61#include "disre.h"
62#include "orires.h"
63#include "pme.h"
64#include "mdatoms.h"
65#include "repl_ex.h"
66#include "deform.h"
67#include "qmmm.h"
68#include "domdec.h"
69#include "domdec_network.h"
70#include "gromacs/gmxlib/topsort.h"
71#include "coulomb.h"
72#include "constr.h"
73#include "shellfc.h"
74#include "gromacs/gmxpreprocess/compute_io.h"
75#include "checkpoint.h"
76#include "mtop_util.h"
77#include "sighandler.h"
78#include "txtdump.h"
79#include "gromacs/utility/cstringutil.h"
80#include "pme_loadbal.h"
81#include "bondf.h"
82#include "membed.h"
83#include "types/nlistheuristics.h"
84#include "types/iteratedconstraints.h"
85#include "nbnxn_cuda_data_mgmt.h"
86
87#include "gromacs/utility/gmxmpi.h"
88#include "gromacs/fileio/confio.h"
89#include "gromacs/fileio/trajectory_writing.h"
90#include "gromacs/fileio/trnio.h"
91#include "gromacs/fileio/trxio.h"
92#include "gromacs/fileio/xtcio.h"
93#include "gromacs/timing/wallcycle.h"
94#include "gromacs/timing/walltime_accounting.h"
95#include "gromacs/pulling/pull.h"
96#include "gromacs/swap/swapcoords.h"
97#include "gromacs/imd/imd.h"
98
99#ifdef GMX_FAHCORE
100#include "corewrap.h"
101#endif
102
103static void reset_all_counters(FILE *fplog, t_commrec *cr,
104 gmx_int64_t step,
105 gmx_int64_t *step_rel, t_inputrec *ir,
106 gmx_wallcycle_t wcycle, t_nrnb *nrnb,
107 gmx_walltime_accounting_t walltime_accounting,
108 nbnxn_cuda_ptr_t cu_nbv)
109{
110 char sbuf[STEPSTRSIZE22];
111
112 /* Reset all the counters related to performance over the run */
113 md_print_warn(cr, fplog, "step %s: resetting all time and cycle counters\n",
114 gmx_step_str(step, sbuf));
115
116 if (cu_nbv)
117 {
118 nbnxn_cuda_reset_timings(cu_nbv);
119 }
120
121 wallcycle_stop(wcycle, ewcRUN);
122 wallcycle_reset_all(wcycle);
123 if (DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)))
124 {
125 reset_dd_statistics_counters(cr->dd);
126 }
127 init_nrnb(nrnb);
128 ir->init_step += *step_rel;
129 ir->nsteps -= *step_rel;
130 *step_rel = 0;
131 wallcycle_start(wcycle, ewcRUN);
132 walltime_accounting_start(walltime_accounting);
133 print_date_and_time(fplog, cr->nodeid, "Restarted time", gmx_gettime());
134}
135
136double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
137 const output_env_t oenv, gmx_bool bVerbose, gmx_bool bCompact,
138 int nstglobalcomm,
139 gmx_vsite_t *vsite, gmx_constr_t constr,
140 int stepout, t_inputrec *ir,
141 gmx_mtop_t *top_global,
142 t_fcdata *fcd,
143 t_state *state_global,
144 t_mdatoms *mdatoms,
145 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
146 gmx_edsam_t ed, t_forcerec *fr,
147 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t membed,
148 real cpt_period, real max_hours,
149 const char gmx_unused__attribute__ ((unused)) *deviceOptions,
150 int imdport,
151 unsigned long Flags,
152 gmx_walltime_accounting_t walltime_accounting)
153{
154 gmx_mdoutf_t outf = NULL((void*)0);
155 gmx_int64_t step, step_rel;
156 double elapsed_time;
157 double t, t0, lam0[efptNR];
158 gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEner;
159 gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD, bNotLastFrame = FALSE0,
160 bFirstStep, bStateFromCP, bStateFromTPX, bInitStep, bLastStep,
161 bBornRadii, bStartingFromCpt;
162 gmx_bool bDoDHDL = FALSE0, bDoFEP = FALSE0, bDoExpanded = FALSE0;
163 gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE1,
164 bForceUpdate = FALSE0, bCPT;
165 gmx_bool bMasterState;
166 int force_flags, cglo_flags;
167 tensor force_vir, shake_vir, total_vir, tmp_vir, pres;
168 int i, m;
169 t_trxstatus *status;
170 rvec mu_tot;
171 t_vcm *vcm;
172 t_state *bufstate = NULL((void*)0);
173 matrix *scale_tot, pcoupl_mu, M, ebox;
174 gmx_nlheur_t nlh;
175 t_trxframe rerun_fr;
176 gmx_repl_ex_t repl_ex = NULL((void*)0);
177 int nchkpt = 1;
178 gmx_localtop_t *top;
179 t_mdebin *mdebin = NULL((void*)0);
180 t_state *state = NULL((void*)0);
181 rvec *f_global = NULL((void*)0);
182 gmx_enerdata_t *enerd;
183 rvec *f = NULL((void*)0);
184 gmx_global_stat_t gstat;
185 gmx_update_t upd = NULL((void*)0);
186 t_graph *graph = NULL((void*)0);
187 globsig_t gs;
188 gmx_groups_t *groups;
189 gmx_ekindata_t *ekind, *ekind_save;
190 gmx_shellfc_t shellfc;
191 int count, nconverged = 0;
192 real timestep = 0;
193 double tcount = 0;
194 gmx_bool bConverged = TRUE1, bOK, bSumEkinhOld, bExchanged, bNeedRepartition;
195 gmx_bool bAppend;
196 gmx_bool bResetCountersHalfMaxH = FALSE0;
197 gmx_bool bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
198 gmx_bool bUpdateDoLR;
199 real dvdl_constr;
200 rvec *cbuf = NULL((void*)0);
201 matrix lastbox;
202 real veta_save, scalevir, tracevir;
203 real vetanew = 0;
204 int lamnew = 0;
205 /* for FEP */
206 int nstfep;
207 double cycles;
208 real saved_conserved_quantity = 0;
209 real last_ekin = 0;
210 int iter_i;
211 t_extmass MassQ;
212 int **trotter_seq;
213 char sbuf[STEPSTRSIZE22], sbuf2[STEPSTRSIZE22];
214 int handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
215 gmx_iterate_t iterate;
216 gmx_int64_t multisim_nsteps = -1; /* number of steps to do before first multisim
217 simulation stops. If equal to zero, don't
218 communicate any more between multisims.*/
219 /* PME load balancing data for GPU kernels */
220 pme_load_balancing_t pme_loadbal = NULL((void*)0);
221 double cycles_pmes;
222 gmx_bool bPMETuneTry = FALSE0, bPMETuneRunning = FALSE0;
223
224 /* Interactive MD */
225 gmx_bool bIMDstep = FALSE0;
226
227#ifdef GMX_FAHCORE
228 /* Temporary addition for FAHCORE checkpointing */
229 int chkpt_ret;
230#endif
231
232 /* Check for special mdrun options */
233 bRerunMD = (Flags & MD_RERUN(1<<4));
234 bAppend = (Flags & MD_APPENDFILES(1<<15));
235 if (Flags & MD_RESETCOUNTERSHALFWAY(1<<19))
236 {
237 if (ir->nsteps > 0)
238 {
239 /* Signal to reset the counters half the simulation steps. */
240 wcycle_set_reset_counters(wcycle, ir->nsteps/2);
241 }
242 /* Signal to reset the counters halfway the simulation time. */
243 bResetCountersHalfMaxH = (max_hours > 0);
244 }
245
246 /* md-vv uses averaged full step velocities for T-control
247 md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
248 md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
249 bVV = EI_VV(ir->eI)((ir->eI) == eiVV || (ir->eI) == eiVVAK);
250 if (bVV) /* to store the initial velocities while computing virial */
251 {
252 snew(cbuf, top_global->natoms)(cbuf) = save_calloc("cbuf", "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c"
, 252, (top_global->natoms), sizeof(*(cbuf)));
253 }
254 /* all the iteratative cases - only if there are constraints */
255 bIterativeCase = ((IR_NPH_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
(((ir)->epc == epcMTTK) && (!(((ir)->etc == etcNOSEHOOVER
))))) || IR_NPT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
(((ir)->epc == epcMTTK) && ((ir)->etc == etcNOSEHOOVER
)))) && (constr) && (!bRerunMD));
256 gmx_iterate_init(&iterate, FALSE0); /* The default value of iterate->bIterationActive is set to
257 false in this step. The correct value, true or false,
258 is set at each step, as it depends on the frequency of temperature
259 and pressure control.*/
260 bTrotter = (bVV && (IR_NPT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
(((ir)->epc == epcMTTK) && ((ir)->etc == etcNOSEHOOVER
))) || IR_NPH_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
(((ir)->epc == epcMTTK) && (!(((ir)->etc == etcNOSEHOOVER
))))) || IR_NVT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
((!((ir)->epc == epcMTTK)) && ((ir)->etc == etcNOSEHOOVER
)))));
261
262 if (bRerunMD)
263 {
264 /* Since we don't know if the frames read are related in any way,
265 * rebuild the neighborlist at every step.
266 */
267 ir->nstlist = 1;
268 ir->nstcalcenergy = 1;
269 nstglobalcomm = 1;
270 }
271
272 check_ir_old_tpx_versions(cr, fplog, ir, top_global);
273
274 nstglobalcomm = check_nstglobalcomm(fplog, cr, nstglobalcomm, ir);
275 bGStatEveryStep = (nstglobalcomm == 1);
276
277 if (!bGStatEveryStep && ir->nstlist == -1 && fplog != NULL((void*)0))
278 {
279 fprintf(fplog,
280 "To reduce the energy communication with nstlist = -1\n"
281 "the neighbor list validity should not be checked at every step,\n"
282 "this means that exact integration is not guaranteed.\n"
283 "The neighbor list validity is checked after:\n"
284 " <n.list life time> - 2*std.dev.(n.list life time) steps.\n"
285 "In most cases this will result in exact integration.\n"
286 "This reduces the energy communication by a factor of 2 to 3.\n"
287 "If you want less energy communication, set nstlist > 3.\n\n");
288 }
289
290 if (bRerunMD)
291 {
292 ir->nstxout_compressed = 0;
293 }
294 groups = &top_global->groups;
295
296 /* Initial values */
297 init_md(fplog, cr, ir, oenv, &t, &t0, state_global->lambda,
298 &(state_global->fep_state), lam0,
299 nrnb, top_global, &upd,
300 nfile, fnm, &outf, &mdebin,
301 force_vir, shake_vir, mu_tot, &bSimAnn, &vcm, Flags);
302
303 clear_mat(total_vir);
304 clear_mat(pres);
305 /* Energy terms and groups */
306 snew(enerd, 1)(enerd) = save_calloc("enerd", "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c"
, 306, (1), sizeof(*(enerd)));
307 init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
308 enerd);
309 if (DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)))
310 {
311 f = NULL((void*)0);
312 }
313 else
314 {
315 snew(f, top_global->natoms)(f) = save_calloc("f", "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c"
, 315, (top_global->natoms), sizeof(*(f)));
316 }
317
318 /* Kinetic energy data */
319 snew(ekind, 1)(ekind) = save_calloc("ekind", "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c"
, 319, (1), sizeof(*(ekind)));
320 init_ekindata(fplog, top_global, &(ir->opts), ekind);
321 /* needed for iteration of constraints */
322 snew(ekind_save, 1)(ekind_save) = save_calloc("ekind_save", "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c"
, 322, (1), sizeof(*(ekind_save)));
323 init_ekindata(fplog, top_global, &(ir->opts), ekind_save);
324 /* Copy the cos acceleration to the groups struct */
325 ekind->cosacc.cos_accel = ir->cos_accel;
326
327 gstat = global_stat_init(ir);
328 debug_gmx();
329
330 /* Check for polarizable models and flexible constraints */
331 shellfc = init_shell_flexcon(fplog, fr->cutoff_scheme == ecutsVERLET,
332 top_global, n_flexible_constraints(constr),
333 (ir->bContinuation ||
334 (DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)) && !MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))) ?
335 NULL((void*)0) : state_global->x);
336
337 if (DEFORM(*ir)((*ir).deform[0][0] != 0 || (*ir).deform[1][1] != 0 || (*ir).
deform[2][2] != 0 || (*ir).deform[1][0] != 0 || (*ir).deform[
2][0] != 0 || (*ir).deform[2][1] != 0))
338 {
339 tMPI_Thread_mutex_lock(&deform_init_box_mutex);
340 set_deform_reference_box(upd,
341 deform_init_init_step_tpx,
342 deform_init_box_tpx);
343 tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
344 }
345
346 {
347 double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
348 if ((io > 2000) && MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
349 {
350 fprintf(stderrstderr,
351 "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
352 io);
353 }
354 }
355
356 if (DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)))
357 {
358 top = dd_init_local_top(top_global);
359
360 snew(state, 1)(state) = save_calloc("state", "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c"
, 360, (1), sizeof(*(state)));
361 dd_init_local_state(cr->dd, state_global, state);
362
363 if (DDMASTER(cr->dd)((cr->dd)->rank == (cr->dd)->masterrank) && ir->nstfout)
364 {
365 snew(f_global, state_global->natoms)(f_global) = save_calloc("f_global", "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c"
, 365, (state_global->natoms), sizeof(*(f_global)));
366 }
367 }
368 else
369 {
370 top = gmx_mtop_generate_local_top(top_global, ir);
371
372 forcerec_set_excl_load(fr, top);
373
374 state = serial_init_local_state(state_global);
375 f_global = f;
376
377 atoms2md(top_global, ir, 0, NULL((void*)0), top_global->natoms, mdatoms);
378
379 if (vsite)
380 {
381 set_vsite_top(vsite, top, mdatoms, cr);
382 }
383
384 if (ir->ePBC != epbcNONE && !fr->bMolPBC)
385 {
386 graph = mk_graph(fplog, &(top->idef), 0, top_global->natoms, FALSE0, FALSE0);
387 }
388
389 if (shellfc)
390 {
391 make_local_shells(cr, mdatoms, shellfc);
392 }
393
394 setup_bonded_threading(fr, &top->idef);
395 }
396
397 /* Set up interactive MD (IMD) */
398 init_IMD(ir, cr, top_global, fplog, ir->nstcalcenergy, state_global->x,
399 nfile, fnm, oenv, imdport, Flags);
400
401 if (DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)))
402 {
403 /* Distribute the charge groups over the nodes from the master node */
404 dd_partition_system(fplog, ir->init_step, cr, TRUE1, 1,
405 state_global, top_global, ir,
406 state, &f, mdatoms, top, fr,
407 vsite, shellfc, constr,
408 nrnb, wcycle, FALSE0);
409
410 }
411
412 update_mdatoms(mdatoms, state->lambda[efptMASS]);
413
414 if (opt2bSet("-cpi", nfile, fnm))
415 {
416 bStateFromCP = gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr);
417 }
418 else
419 {
420 bStateFromCP = FALSE0;
421 }
422
423 if (ir->bExpanded)
424 {
425 init_expanded_ensemble(bStateFromCP, ir, &state->dfhist);
426 }
427
428 if (MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
429 {
430 if (bStateFromCP)
431 {
432 /* Update mdebin with energy history if appending to output files */
433 if (Flags & MD_APPENDFILES(1<<15))
434 {
435 restore_energyhistory_from_state(mdebin, &state_global->enerhist);
436 }
437 else
438 {
439 /* We might have read an energy history from checkpoint,
440 * free the allocated memory and reset the counts.
441 */
442 done_energyhistory(&state_global->enerhist);
443 init_energyhistory(&state_global->enerhist);
444 }
445 }
446 /* Set the initial energy history in state by updating once */
447 update_energyhistory(&state_global->enerhist, mdebin);
448 }
449
450 /* Initialize constraints */
451 if (constr && !DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)))
452 {
453 set_constraints(constr, top, ir, mdatoms, cr);
454 }
455
456 if (repl_ex_nst > 0)
457 {
458 /* We need to be sure replica exchange can only occur
459 * when the energies are current */
460 check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
461 "repl_ex_nst", &repl_ex_nst);
462 /* This check needs to happen before inter-simulation
463 * signals are initialized, too */
464 }
465 if (repl_ex_nst > 0 && MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
466 {
467 repl_ex = init_replica_exchange(fplog, cr->ms, state_global, ir,
468 repl_ex_nst, repl_ex_nex, repl_ex_seed);
469 }
470
471 /* PME tuning is only supported with GPUs or PME nodes and not with rerun.
472 * PME tuning is not supported with PME only for LJ and not for Coulomb.
473 */
474 if ((Flags & MD_TUNEPME(1<<20)) &&
475 EEL_PME(fr->eeltype)((fr->eeltype) == eelPME || (fr->eeltype) == eelPMESWITCH
|| (fr->eeltype) == eelPMEUSER || (fr->eeltype) == eelPMEUSERSWITCH
|| (fr->eeltype) == eelP3M_AD) &&
476 ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME(1<<1))) &&
477 !bRerunMD)
478 {
479 pme_loadbal_init(&pme_loadbal, ir, state->box, fr->ic, fr->pmedata);
480 cycles_pmes = 0;
481 if (cr->duty & DUTY_PME(1<<1))
482 {
483 /* Start tuning right away, as we can't measure the load */
484 bPMETuneRunning = TRUE1;
485 }
486 else
487 {
488 /* Separate PME nodes, we can measure the PP/PME load balance */
489 bPMETuneTry = TRUE1;
490 }
491 }
492
493 if (!ir->bContinuation && !bRerunMD)
494 {
495 if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
496 {
497 /* Set the velocities of frozen particles to zero */
498 for (i = 0; i < mdatoms->homenr; i++)
499 {
500 for (m = 0; m < DIM3; m++)
501 {
502 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
503 {
504 state->v[i][m] = 0;
505 }
506 }
507 }
508 }
509
510 if (constr)
511 {
512 /* Constrain the initial coordinates and velocities */
513 do_constrain_first(fplog, constr, ir, mdatoms, state,
514 cr, nrnb, fr, top);
515 }
516 if (vsite)
517 {
518 /* Construct the virtual sites for the initial configuration */
519 construct_vsites(vsite, state->x, ir->delta_t, NULL((void*)0),
520 top->idef.iparams, top->idef.il,
521 fr->ePBC, fr->bMolPBC, cr, state->box);
522 }
523 }
524
525 debug_gmx();
526
527 /* set free energy calculation frequency as the minimum
528 greatest common denominator of nstdhdl, nstexpanded, and repl_ex_nst*/
529 nstfep = ir->fepvals->nstdhdl;
530 if (ir->bExpanded)
531 {
532 nstfep = gmx_greatest_common_divisor(ir->fepvals->nstdhdl, nstfep);
533 }
534 if (repl_ex_nst > 0)
535 {
536 nstfep = gmx_greatest_common_divisor(repl_ex_nst, nstfep);
537 }
538
539 /* I'm assuming we need global communication the first time! MRS */
540 cglo_flags = (CGLO_TEMPERATURE(1<<7) | CGLO_GSTAT(1<<4)
541 | ((ir->comm_mode != ecmNO) ? CGLO_STOPCM(1<<3) : 0)
542 | (bVV ? CGLO_PRESSURE(1<<8) : 0)
543 | (bVV ? CGLO_CONSTRAINT(1<<9) : 0)
544 | (bRerunMD ? CGLO_RERUNMD(1<<1) : 0)
545 | ((Flags & MD_READ_EKIN(1<<17)) ? CGLO_READEKIN(1<<12) : 0));
546
547 bSumEkinhOld = FALSE0;
548 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
549 NULL((void*)0), enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
550 constr, NULL((void*)0), FALSE0, state->box,
551 top_global, &bSumEkinhOld, cglo_flags);
552 if (ir->eI == eiVVAK)
553 {
554 /* a second call to get the half step temperature initialized as well */
555 /* we do the same call as above, but turn the pressure off -- internally to
556 compute_globals, this is recognized as a velocity verlet half-step
557 kinetic energy calculation. This minimized excess variables, but
558 perhaps loses some logic?*/
559
560 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
561 NULL((void*)0), enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
562 constr, NULL((void*)0), FALSE0, state->box,
563 top_global, &bSumEkinhOld,
564 cglo_flags &~(CGLO_STOPCM(1<<3) | CGLO_PRESSURE(1<<8)));
565 }
566
567 /* Calculate the initial half step temperature, and save the ekinh_old */
568 if (!(Flags & MD_STARTFROMCPT(1<<18)))
569 {
570 for (i = 0; (i < ir->opts.ngtc); i++)
571 {
572 copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
573 }
574 }
575 if (ir->eI != eiVV)
576 {
577 enerd->term[F_TEMP] *= 2; /* result of averages being done over previous and current step,
578 and there is no previous step */
579 }
580
581 /* if using an iterative algorithm, we need to create a working directory for the state. */
582 if (bIterativeCase)
583 {
584 bufstate = init_bufstate(state);
585 }
586
587 /* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
588 temperature control */
589 trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
590
591 if (MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
592 {
593 if (constr && !ir->bContinuation && ir->eConstrAlg == econtLINCS)
594 {
595 fprintf(fplog,
596 "RMS relative constraint deviation after constraining: %.2e\n",
597 constr_rmsd(constr, FALSE0));
598 }
599 if (EI_STATE_VELOCITY(ir->eI)(((ir->eI) == eiMD || ((ir->eI) == eiVV || (ir->eI) ==
eiVVAK)) || ((ir->eI) == eiSD1 || (ir->eI) == eiSD2)))
600 {
601 fprintf(fplog, "Initial temperature: %g K\n", enerd->term[F_TEMP]);
602 }
603 if (bRerunMD)
604 {
605 fprintf(stderrstderr, "starting md rerun '%s', reading coordinates from"
606 " input trajectory '%s'\n\n",
607 *(top_global->name), opt2fn("-rerun", nfile, fnm));
608 if (bVerbose)
609 {
610 fprintf(stderrstderr, "Calculated time to finish depends on nsteps from "
611 "run input file,\nwhich may not correspond to the time "
612 "needed to process input trajectory.\n\n");
613 }
614 }
615 else
616 {
617 char tbuf[20];
618 fprintf(stderrstderr, "starting mdrun '%s'\n",
619 *(top_global->name));
620 if (ir->nsteps >= 0)
621 {
622 sprintf(tbuf, "%8.1f", (ir->init_step+ir->nsteps)*ir->delta_t);
623 }
624 else
625 {
626 sprintf(tbuf, "%s", "infinite");
627 }
628 if (ir->init_step > 0)
629 {
630 fprintf(stderrstderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
631 gmx_step_str(ir->init_step+ir->nsteps, sbuf), tbuf,
632 gmx_step_str(ir->init_step, sbuf2),
633 ir->init_step*ir->delta_t);
634 }
635 else
636 {
637 fprintf(stderrstderr, "%s steps, %s ps.\n",
638 gmx_step_str(ir->nsteps, sbuf), tbuf);
639 }
640 }
641 fprintf(fplog, "\n");
642 }
643
644 walltime_accounting_start(walltime_accounting);
645 wallcycle_start(wcycle, ewcRUN);
646 print_start(fplog, cr, walltime_accounting, "mdrun");
647
648 /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
649#ifdef GMX_FAHCORE
650 chkpt_ret = fcCheckPointParallel( cr->nodeid,
651 NULL((void*)0), 0);
652 if (chkpt_ret == 0)
653 {
654 gmx_fatal( 3, __FILE__"/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c", __LINE__654, "Checkpoint error on step %d\n", 0 );
655 }
656#endif
657
658 debug_gmx();
659 /***********************************************************
660 *
661 * Loop over MD steps
662 *
663 ************************************************************/
664
665 /* if rerunMD then read coordinates and velocities from input trajectory */
666 if (bRerunMD)
667 {
668 if (getenv("GMX_FORCE_UPDATE"))
669 {
670 bForceUpdate = TRUE1;
671 }
672
673 rerun_fr.natoms = 0;
674 if (MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
675 {
676 bNotLastFrame = read_first_frame(oenv, &status,
677 opt2fn("-rerun", nfile, fnm),
678 &rerun_fr, TRX_NEED_X(1<<1) | TRX_READ_V(1<<2));
679 if (rerun_fr.natoms != top_global->natoms)
680 {
681 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c", 681,
682 "Number of atoms in trajectory (%d) does not match the "
683 "run input file (%d)\n",
684 rerun_fr.natoms, top_global->natoms);
685 }
686 if (ir->ePBC != epbcNONE)
687 {
688 if (!rerun_fr.bBox)
689 {
690 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c", 690, "Rerun trajectory frame step %d time %f does not contain a box, while pbc is used", rerun_fr.step, rerun_fr.time);
691 }
692 if (max_cutoff2(ir->ePBC, rerun_fr.box) < sqr(fr->rlistlong))
693 {
694 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c", 694, "Rerun trajectory frame step %d time %f has too small box dimensions", rerun_fr.step, rerun_fr.time);
695 }
696 }
697 }
698
699 if (PAR(cr)((cr)->nnodes > 1))
700 {
701 rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
702 }
703
704 if (ir->ePBC != epbcNONE)
705 {
706 /* Set the shift vectors.
707 * Necessary here when have a static box different from the tpr box.
708 */
709 calc_shifts(rerun_fr.box, fr->shift_vec);
710 }
711 }
712
713 /* loop over MD steps or if rerunMD to end of input trajectory */
714 bFirstStep = TRUE1;
715 /* Skip the first Nose-Hoover integration when we get the state from tpx */
716 bStateFromTPX = !bStateFromCP;
717 bInitStep = bFirstStep && (bStateFromTPX || bVV);
718 bStartingFromCpt = (Flags & MD_STARTFROMCPT(1<<18)) && bInitStep;
719 bLastStep = FALSE0;
Value stored to 'bLastStep' is never read
720 bSumEkinhOld = FALSE0;
721 bExchanged = FALSE0;
722 bNeedRepartition = FALSE0;
723
724 init_global_signals(&gs, cr, ir, repl_ex_nst);
725
726 step = ir->init_step;
727 step_rel = 0;
728
729 if (ir->nstlist == -1)
730 {
731 init_nlistheuristics(&nlh, bGStatEveryStep, step);
732 }
733
734 if (MULTISIM(cr)((cr)->ms) && (repl_ex_nst <= 0 ))
735 {
736 /* check how many steps are left in other sims */
737 multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
738 }
739
740
741 /* and stop now if we should */
742 bLastStep = (bRerunMD || (ir->nsteps >= 0 && step_rel > ir->nsteps) ||
743 ((multisim_nsteps >= 0) && (step_rel >= multisim_nsteps )));
744 while (!bLastStep || (bRerunMD && bNotLastFrame))
745 {
746
747 wallcycle_start(wcycle, ewcSTEP);
748
749 if (bRerunMD)
750 {
751 if (rerun_fr.bStep)
752 {
753 step = rerun_fr.step;
754 step_rel = step - ir->init_step;
755 }
756 if (rerun_fr.bTime)
757 {
758 t = rerun_fr.time;
759 }
760 else
761 {
762 t = step;
763 }
764 }
765 else
766 {
767 bLastStep = (step_rel == ir->nsteps);
768 t = t0 + step*ir->delta_t;
769 }
770
771 if (ir->efep != efepNO || ir->bSimTemp)
772 {
773 /* find and set the current lambdas. If rerunning, we either read in a state, or a lambda value,
774 requiring different logic. */
775
776 set_current_lambdas(step, ir->fepvals, bRerunMD, &rerun_fr, state_global, state, lam0);
777 bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
778 bDoFEP = (do_per_step(step, nstfep) && (ir->efep != efepNO));
779 bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded)
780 && (ir->bExpanded) && (step > 0) && (!bStartingFromCpt));
781 }
782
783 if (bSimAnn)
784 {
785 update_annealing_target_temp(&(ir->opts), t);
786 }
787
788 if (bRerunMD)
789 {
790 if (!DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)) || MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
791 {
792 for (i = 0; i < state_global->natoms; i++)
793 {
794 copy_rvec(rerun_fr.x[i], state_global->x[i]);
795 }
796 if (rerun_fr.bV)
797 {
798 for (i = 0; i < state_global->natoms; i++)
799 {
800 copy_rvec(rerun_fr.v[i], state_global->v[i]);
801 }
802 }
803 else
804 {
805 for (i = 0; i < state_global->natoms; i++)
806 {
807 clear_rvec(state_global->v[i]);
808 }
809 if (bRerunWarnNoV)
810 {
811 fprintf(stderrstderr, "\nWARNING: Some frames do not contain velocities.\n"
812 " Ekin, temperature and pressure are incorrect,\n"
813 " the virial will be incorrect when constraints are present.\n"
814 "\n");
815 bRerunWarnNoV = FALSE0;
816 }
817 }
818 }
819 copy_mat(rerun_fr.box, state_global->box);
820 copy_mat(state_global->box, state->box);
821
822 if (vsite && (Flags & MD_RERUN_VSITE(1<<5)))
823 {
824 if (DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)))
825 {
826 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c", 826, "Vsite recalculation with -rerun is not implemented with domain decomposition, use a single rank");
827 }
828 if (graph)
829 {
830 /* Following is necessary because the graph may get out of sync
831 * with the coordinates if we only have every N'th coordinate set
832 */
833 mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
834 shift_self(graph, state->box, state->x);
835 }
836 construct_vsites(vsite, state->x, ir->delta_t, state->v,
837 top->idef.iparams, top->idef.il,
838 fr->ePBC, fr->bMolPBC, cr, state->box);
839 if (graph)
840 {
841 unshift_self(graph, state->box, state->x);
842 }
843 }
844 }
845
846 /* Stop Center of Mass motion */
847 bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
848
849 if (bRerunMD)
850 {
851 /* for rerun MD always do Neighbour Searching */
852 bNS = (bFirstStep || ir->nstlist != 0);
853 bNStList = bNS;
854 }
855 else
856 {
857 /* Determine whether or not to do Neighbour Searching and LR */
858 bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
859
860 bNS = (bFirstStep || bExchanged || bNeedRepartition || bNStList || bDoFEP ||
861 (ir->nstlist == -1 && nlh.nabnsb > 0));
862
863 if (bNS && ir->nstlist == -1)
864 {
865 set_nlistheuristics(&nlh, bFirstStep || bExchanged || bNeedRepartition || bDoFEP, step);
866 }
867 }
868
869 /* check whether we should stop because another simulation has
870 stopped. */
871 if (MULTISIM(cr)((cr)->ms))
872 {
873 if ( (multisim_nsteps >= 0) && (step_rel >= multisim_nsteps) &&
874 (multisim_nsteps != ir->nsteps) )
875 {
876 if (bNS)
877 {
878 if (MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
879 {
880 fprintf(stderrstderr,
881 "Stopping simulation %d because another one has finished\n",
882 cr->ms->sim);
883 }
884 bLastStep = TRUE1;
885 gs.sig[eglsCHKPT] = 1;
886 }
887 }
888 }
889
890 /* < 0 means stop at next step, > 0 means stop at next NS step */
891 if ( (gs.set[eglsSTOPCOND] < 0) ||
892 ( (gs.set[eglsSTOPCOND] > 0) && (bNStList || ir->nstlist == 0) ) )
893 {
894 bLastStep = TRUE1;
895 }
896
897 /* Determine whether or not to update the Born radii if doing GB */
898 bBornRadii = bFirstStep;
899 if (ir->implicit_solvent && (step % ir->nstgbradii == 0))
900 {
901 bBornRadii = TRUE1;
902 }
903
904 do_log = do_per_step(step, ir->nstlog) || bFirstStep || bLastStep;
905 do_verbose = bVerbose &&
906 (step % stepout == 0 || bFirstStep || bLastStep);
907
908 if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
909 {
910 if (bRerunMD)
911 {
912 bMasterState = TRUE1;
913 }
914 else
915 {
916 bMasterState = FALSE0;
917 /* Correct the new box if it is too skewed */
918 if (DYNAMIC_BOX(*ir)((*ir).epc != epcNO || (*ir).eI == eiTPI || ((*ir).deform[0][
0] != 0 || (*ir).deform[1][1] != 0 || (*ir).deform[2][2] != 0
|| (*ir).deform[1][0] != 0 || (*ir).deform[2][0] != 0 || (*ir
).deform[2][1] != 0)))
919 {
920 if (correct_box(fplog, step, state->box, graph))
921 {
922 bMasterState = TRUE1;
923 }
924 }
925 if (DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)) && bMasterState)
926 {
927 dd_collect_state(cr->dd, state, state_global);
928 }
929 }
930
931 if (DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)))
932 {
933 /* Repartition the domain decomposition */
934 wallcycle_start(wcycle, ewcDOMDEC);
935 dd_partition_system(fplog, step, cr,
936 bMasterState, nstglobalcomm,
937 state_global, top_global, ir,
938 state, &f, mdatoms, top, fr,
939 vsite, shellfc, constr,
940 nrnb, wcycle,
941 do_verbose && !bPMETuneRunning);
942 wallcycle_stop(wcycle, ewcDOMDEC);
943 /* If using an iterative integrator, reallocate space to match the decomposition */
944 }
945 }
946
947 if (MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)) && do_log)
948 {
949 print_ebin_header(fplog, step, t, state->lambda[efptFEP]); /* can we improve the information printed here? */
950 }
951
952 if (ir->efep != efepNO)
953 {
954 update_mdatoms(mdatoms, state->lambda[efptMASS]);
955 }
956
957 if ((bRerunMD && rerun_fr.bV) || bExchanged)
958 {
959
960 /* We need the kinetic energy at minus the half step for determining
961 * the full step kinetic energy and possibly for T-coupling.*/
962 /* This may not be quite working correctly yet . . . . */
963 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
964 wcycle, enerd, NULL((void*)0), NULL((void*)0), NULL((void*)0), NULL((void*)0), mu_tot,
965 constr, NULL((void*)0), FALSE0, state->box,
966 top_global, &bSumEkinhOld,
967 CGLO_RERUNMD(1<<1) | CGLO_GSTAT(1<<4) | CGLO_TEMPERATURE(1<<7));
968 }
969 clear_mat(force_vir);
970
971 /* We write a checkpoint at this MD step when:
972 * either at an NS step when we signalled through gs,
973 * or at the last step (but not when we do not want confout),
974 * but never at the first step or with rerun.
975 */
976 bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
977 (bLastStep && (Flags & MD_CONFOUT(1<<12)))) &&
978 step > ir->init_step && !bRerunMD);
979 if (bCPT)
980 {
981 gs.set[eglsCHKPT] = 0;
982 }
983
984 /* Determine the energy and pressure:
985 * at nstcalcenergy steps and at energy output steps (set below).
986 */
987 if (EI_VV(ir->eI)((ir->eI) == eiVV || (ir->eI) == eiVVAK) && (!bInitStep))
988 {
989 /* for vv, the first half of the integration actually corresponds
990 to the previous step. bCalcEner is only required to be evaluated on the 'next' step,
991 but the virial needs to be calculated on both the current step and the 'next' step. Future
992 reorganization may be able to get rid of one of the bCalcVir=TRUE steps. */
993
994 bCalcEner = do_per_step(step-1, ir->nstcalcenergy);
995 bCalcVir = bCalcEner ||
996 (ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
997 }
998 else
999 {
1000 bCalcEner = do_per_step(step, ir->nstcalcenergy);
1001 bCalcVir = bCalcEner ||
1002 (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
1003 }
1004
1005 /* Do we need global communication ? */
1006 bGStat = (bCalcVir || bCalcEner || bStopCM ||
1007 do_per_step(step, nstglobalcomm) || (bVV && IR_NVT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
((!((ir)->epc == epcMTTK)) && ((ir)->etc == etcNOSEHOOVER
))) && do_per_step(step-1, nstglobalcomm)) ||
1008 (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));
1009
1010 do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
1011
1012 if (do_ene || do_log)
1013 {
1014 bCalcVir = TRUE1;
1015 bCalcEner = TRUE1;
1016 bGStat = TRUE1;
1017 }
1018
1019 /* these CGLO_ options remain the same throughout the iteration */
1020 cglo_flags = ((bRerunMD ? CGLO_RERUNMD(1<<1) : 0) |
1021 (bGStat ? CGLO_GSTAT(1<<4) : 0)
1022 );
1023
1024 force_flags = (GMX_FORCE_STATECHANGED(1<<0) |
1025 ((DYNAMIC_BOX(*ir)((*ir).epc != epcNO || (*ir).eI == eiTPI || ((*ir).deform[0][
0] != 0 || (*ir).deform[1][1] != 0 || (*ir).deform[2][2] != 0
|| (*ir).deform[1][0] != 0 || (*ir).deform[2][0] != 0 || (*ir
).deform[2][1] != 0)) || bRerunMD) ? GMX_FORCE_DYNAMICBOX(1<<1) : 0) |
1026 GMX_FORCE_ALLFORCES((1<<4) | (1<<6) | (1<<7)) |
1027 GMX_FORCE_SEPLRF(1<<5) |
1028 (bCalcVir ? GMX_FORCE_VIRIAL(1<<8) : 0) |
1029 (bCalcEner ? GMX_FORCE_ENERGY(1<<9) : 0) |
1030 (bDoFEP ? GMX_FORCE_DHDL(1<<10) : 0)
1031 );
1032
1033 if (fr->bTwinRange)
1034 {
1035 if (do_per_step(step, ir->nstcalclr))
1036 {
1037 force_flags |= GMX_FORCE_DO_LR(1<<11);
1038 }
1039 }
1040
1041 if (shellfc)
1042 {
1043 /* Now is the time to relax the shells */
1044 count = relax_shell_flexcon(fplog, cr, bVerbose, step,
1045 ir, bNS, force_flags,
1046 top,
1047 constr, enerd, fcd,
1048 state, f, force_vir, mdatoms,
1049 nrnb, wcycle, graph, groups,
1050 shellfc, fr, bBornRadii, t, mu_tot,
1051 &bConverged, vsite,
1052 mdoutf_get_fp_field(outf));
1053 tcount += count;
1054
1055 if (bConverged)
1056 {
1057 nconverged++;
1058 }
1059 }
1060 else
1061 {
1062 /* The coordinates (x) are shifted (to get whole molecules)
1063 * in do_force.
1064 * This is parallellized as well, and does communication too.
1065 * Check comments in sim_util.c
1066 */
1067 do_force(fplog, cr, ir, step, nrnb, wcycle, top, groups,
1068 state->box, state->x, &state->hist,
1069 f, force_vir, mdatoms, enerd, fcd,
1070 state->lambda, graph,
1071 fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
1072 (bNS ? GMX_FORCE_NS(1<<2) : 0) | force_flags);
1073 }
1074
1075 if (bVV && !bStartingFromCpt && !bRerunMD)
1076 /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
1077 {
1078 if (ir->eI == eiVV && bInitStep)
1079 {
1080 /* if using velocity verlet with full time step Ekin,
1081 * take the first half step only to compute the
1082 * virial for the first step. From there,
1083 * revert back to the initial coordinates
1084 * so that the input is actually the initial step.
1085 */
1086 copy_rvecn(state->v, cbuf, 0, state->natoms); /* should make this better for parallelizing? */
1087 }
1088 else
1089 {
1090 /* this is for NHC in the Ekin(t+dt/2) version of vv */
1091 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ1);
1092 }
1093
1094 /* If we are using twin-range interactions where the long-range component
1095 * is only evaluated every nstcalclr>1 steps, we should do a special update
1096 * step to combine the long-range forces on these steps.
1097 * For nstcalclr=1 this is not done, since the forces would have been added
1098 * directly to the short-range forces already.
1099 */
1100 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1101
1102 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
1103 f, bUpdateDoLR, fr->f_twin, fcd,
1104 ekind, M, upd, bInitStep, etrtVELOCITY1,
1105 cr, nrnb, constr, &top->idef);
1106
1107 if (bIterativeCase && do_per_step(step-1, ir->nstpcouple) && !bInitStep)
1108 {
1109 gmx_iterate_init(&iterate, TRUE1);
1110 }
1111 /* for iterations, we save these vectors, as we will be self-consistently iterating
1112 the calculations */
1113
1114 /*#### UPDATE EXTENDED VARIABLES IN TROTTER FORMULATION */
1115
1116 /* save the state */
1117 if (iterate.bIterationActive)
1118 {
1119 copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
1120 }
1121
1122 bFirstIterate = TRUE1;
1123 while (bFirstIterate || iterate.bIterationActive)
1124 {
1125 if (iterate.bIterationActive)
1126 {
1127 copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
1128 if (bFirstIterate && bTrotter)
1129 {
1130 /* The first time through, we need a decent first estimate
1131 of veta(t+dt) to compute the constraints. Do
1132 this by computing the box volume part of the
1133 trotter integration at this time. Nothing else
1134 should be changed by this routine here. If
1135 !(first time), we start with the previous value
1136 of veta. */
1137
1138 veta_save = state->veta;
1139 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ0);
1140 vetanew = state->veta;
1141 state->veta = veta_save;
1142 }
1143 }
1144
1145 bOK = TRUE1;
1146 if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
1147 {
1148 update_constraints(fplog, step, NULL((void*)0), ir, ekind, mdatoms,
1149 state, fr->bMolPBC, graph, f,
1150 &top->idef, shake_vir,
1151 cr, nrnb, wcycle, upd, constr,
1152 TRUE1, bCalcVir, vetanew);
1153
1154 if (!bOK)
1155 {
1156 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c", 1156, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
1157 }
1158
1159 }
1160 else if (graph)
1161 {
1162 /* Need to unshift here if a do_force has been
1163 called in the previous step */
1164 unshift_self(graph, state->box, state->x);
1165 }
1166
1167 /* if VV, compute the pressure and constraints */
1168 /* For VV2, we strictly only need this if using pressure
1169 * control, but we really would like to have accurate pressures
1170 * printed out.
1171 * Think about ways around this in the future?
1172 * For now, keep this choice in comments.
1173 */
1174 /*bPres = (ir->eI==eiVV || IR_NPT_TROTTER(ir)); */
1175 /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir)));*/
1176 bPres = TRUE1;
1177 bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
1178 if (bCalcEner && ir->eI == eiVVAK) /*MRS: 7/9/2010 -- this still doesn't fix it?*/
1179 {
1180 bSumEkinhOld = TRUE1;
1181 }
1182 /* for vv, the first half of the integration actually corresponds to the previous step.
1183 So we need information from the last step in the first half of the integration */
1184 if (bGStat || do_per_step(step-1, nstglobalcomm))
1185 {
1186 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1187 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1188 constr, NULL((void*)0), FALSE0, state->box,
1189 top_global, &bSumEkinhOld,
1190 cglo_flags
1191 | CGLO_ENERGY(1<<6)
1192 | (bTemp ? CGLO_TEMPERATURE(1<<7) : 0)
1193 | (bPres ? CGLO_PRESSURE(1<<8) : 0)
1194 | (bPres ? CGLO_CONSTRAINT(1<<9) : 0)
1195 | ((iterate.bIterationActive) ? CGLO_ITERATE(1<<10) : 0)
1196 | (bFirstIterate ? CGLO_FIRSTITERATE(1<<11) : 0)
1197 | CGLO_SCALEEKIN(1<<13)
1198 );
1199 /* explanation of above:
1200 a) We compute Ekin at the full time step
1201 if 1) we are using the AveVel Ekin, and it's not the
1202 initial step, or 2) if we are using AveEkin, but need the full
1203 time step kinetic energy for the pressure (always true now, since we want accurate statistics).
1204 b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
1205 EkinAveVel because it's needed for the pressure */
1206 }
1207 /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
1208 if (!bInitStep)
1209 {
1210 if (bTrotter)
1211 {
1212 m_add(force_vir, shake_vir, total_vir); /* we need the un-dispersion corrected total vir here */
1213 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ2);
1214 }
1215 else
1216 {
1217 if (bExchanged)
1218 {
1219
1220 /* We need the kinetic energy at minus the half step for determining
1221 * the full step kinetic energy and possibly for T-coupling.*/
1222 /* This may not be quite working correctly yet . . . . */
1223 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1224 wcycle, enerd, NULL((void*)0), NULL((void*)0), NULL((void*)0), NULL((void*)0), mu_tot,
1225 constr, NULL((void*)0), FALSE0, state->box,
1226 top_global, &bSumEkinhOld,
1227 CGLO_RERUNMD(1<<1) | CGLO_GSTAT(1<<4) | CGLO_TEMPERATURE(1<<7));
1228 }
1229 }
1230 }
1231
1232 if (iterate.bIterationActive &&
1233 done_iterating(cr, fplog, step, &iterate, bFirstIterate,
1234 state->veta, &vetanew))
1235 {
1236 break;
1237 }
1238 bFirstIterate = FALSE0;
1239 }
1240
1241 if (bTrotter && !bInitStep)
1242 {
1243 copy_mat(shake_vir, state->svir_prev);
1244 copy_mat(force_vir, state->fvir_prev);
1245 if (IR_NVT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
((!((ir)->epc == epcMTTK)) && ((ir)->etc == etcNOSEHOOVER
))) && ir->eI == eiVV)
1246 {
1247 /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
1248 enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, NULL((void*)0), (ir->eI == eiVV), FALSE0);
1249 enerd->term[F_EKIN] = trace(ekind->ekin);
1250 }
1251 }
1252 /* if it's the initial step, we performed this first step just to get the constraint virial */
1253 if (bInitStep && ir->eI == eiVV)
1254 {
1255 copy_rvecn(cbuf, state->v, 0, state->natoms);
1256 }
1257 }
1258
1259 /* MRS -- now done iterating -- compute the conserved quantity */
1260 if (bVV)
1261 {
1262 saved_conserved_quantity = compute_conserved_from_auxiliary(ir, state, &MassQ);
1263 if (ir->eI == eiVV)
1264 {
1265 last_ekin = enerd->term[F_EKIN];
1266 }
1267 if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
1268 {
1269 saved_conserved_quantity -= enerd->term[F_DISPCORR];
1270 }
1271 /* sum up the foreign energy and dhdl terms for vv. currently done every step so that dhdl is correct in the .edr */
1272 if (!bRerunMD)
1273 {
1274 sum_dhdl(enerd, state->lambda, ir->fepvals);
1275 }
1276 }
1277
1278 /* ######## END FIRST UPDATE STEP ############## */
1279 /* ######## If doing VV, we now have v(dt) ###### */
1280 if (bDoExpanded)
1281 {
1282 /* perform extended ensemble sampling in lambda - we don't
1283 actually move to the new state before outputting
1284 statistics, but if performing simulated tempering, we
1285 do update the velocities and the tau_t. */
1286
1287 lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state, &state->dfhist, step, state->v, mdatoms);
1288 /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
1289 copy_df_history(&state_global->dfhist, &state->dfhist);
1290 }
1291
1292 /* Now we have the energies and forces corresponding to the
1293 * coordinates at time t. We must output all of this before
1294 * the update.
1295 */
1296 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
1297 ir, state, state_global, top_global, fr,
1298 outf, mdebin, ekind, f, f_global,
1299 wcycle, &nchkpt,
1300 bCPT, bRerunMD, bLastStep, (Flags & MD_CONFOUT(1<<12)),
1301 bSumEkinhOld);
1302 /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
1303 bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, state->x, ir, t, wcycle);
1304
1305 /* kludge -- virial is lost with restart for NPT control. Must restart */
1306 if (bStartingFromCpt && bVV)
1307 {
1308 copy_mat(state->svir_prev, shake_vir);
1309 copy_mat(state->fvir_prev, force_vir);
1310 }
1311
1312 elapsed_time = walltime_accounting_get_current_elapsed_time(walltime_accounting);
1313
1314 /* Check whether everything is still allright */
1315 if (((int)gmx_get_stop_condition() > handled_stop_condition)
1316#ifdef GMX_THREAD_MPI
1317 && MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1))
1318#endif
1319 )
1320 {
1321 /* this is just make gs.sig compatible with the hack
1322 of sending signals around by MPI_Reduce with together with
1323 other floats */
1324 if (gmx_get_stop_condition() == gmx_stop_cond_next_ns)
1325 {
1326 gs.sig[eglsSTOPCOND] = 1;
1327 }
1328 if (gmx_get_stop_condition() == gmx_stop_cond_next)
1329 {
1330 gs.sig[eglsSTOPCOND] = -1;
1331 }
1332 /* < 0 means stop at next step, > 0 means stop at next NS step */
1333 if (fplog)
1334 {
1335 fprintf(fplog,
1336 "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
1337 gmx_get_signal_name(),
1338 gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
1339 fflush(fplog);
1340 }
1341 fprintf(stderrstderr,
1342 "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
1343 gmx_get_signal_name(),
1344 gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
1345 fflush(stderrstderr);
1346 handled_stop_condition = (int)gmx_get_stop_condition();
1347 }
1348 else if (MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)) && (bNS || ir->nstlist <= 0) &&
1349 (max_hours > 0 && elapsed_time > max_hours*60.0*60.0*0.99) &&
1350 gs.sig[eglsSTOPCOND] == 0 && gs.set[eglsSTOPCOND] == 0)
1351 {
1352 /* Signal to terminate the run */
1353 gs.sig[eglsSTOPCOND] = 1;
1354 if (fplog)
1355 {
1356 fprintf(fplog, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
1357 }
1358 fprintf(stderrstderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
1359 }
1360
1361 if (bResetCountersHalfMaxH && MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)) &&
1362 elapsed_time > max_hours*60.0*60.0*0.495)
1363 {
1364 gs.sig[eglsRESETCOUNTERS] = 1;
1365 }
1366
1367 if (ir->nstlist == -1 && !bRerunMD)
1368 {
1369 /* When bGStatEveryStep=FALSE, global_stat is only called
1370 * when we check the atom displacements, not at NS steps.
1371 * This means that also the bonded interaction count check is not
1372 * performed immediately after NS. Therefore a few MD steps could
1373 * be performed with missing interactions.
1374 * But wrong energies are never written to file,
1375 * since energies are only written after global_stat
1376 * has been called.
1377 */
1378 if (step >= nlh.step_nscheck)
1379 {
1380 nlh.nabnsb = natoms_beyond_ns_buffer(ir, fr, &top->cgs,
1381 nlh.scale_tot, state->x);
1382 }
1383 else
1384 {
1385 /* This is not necessarily true,
1386 * but step_nscheck is determined quite conservatively.
1387 */
1388 nlh.nabnsb = 0;
1389 }
1390 }
1391
1392 /* In parallel we only have to check for checkpointing in steps
1393 * where we do global communication,
1394 * otherwise the other nodes don't know.
1395 */
1396 if (MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)) && ((bGStat || !PAR(cr)((cr)->nnodes > 1)) &&
1397 cpt_period >= 0 &&
1398 (cpt_period == 0 ||
1399 elapsed_time >= nchkpt*cpt_period*60.0)) &&
1400 gs.set[eglsCHKPT] == 0)
1401 {
1402 gs.sig[eglsCHKPT] = 1;
1403 }
1404
1405 /* at the start of step, randomize or scale the velocities (trotter done elsewhere) */
1406 if (EI_VV(ir->eI)((ir->eI) == eiVV || (ir->eI) == eiVVAK))
1407 {
1408 if (!bInitStep)
1409 {
1410 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1411 }
1412 if (ETC_ANDERSEN(ir->etc)(((ir->etc) == etcANDERSENMASSIVE) || ((ir->etc) == etcANDERSEN
))) /* keep this outside of update_tcouple because of the extra info required to pass */
1413 {
1414 gmx_bool bIfRandomize;
1415 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state, upd, constr);
1416 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1417 if (constr && bIfRandomize)
1418 {
1419 update_constraints(fplog, step, NULL((void*)0), ir, ekind, mdatoms,
1420 state, fr->bMolPBC, graph, f,
1421 &top->idef, tmp_vir,
1422 cr, nrnb, wcycle, upd, constr,
1423 TRUE1, bCalcVir, vetanew);
1424 }
1425 }
1426 }
1427
1428 if (bIterativeCase && do_per_step(step, ir->nstpcouple))
1429 {
1430 gmx_iterate_init(&iterate, TRUE1);
1431 /* for iterations, we save these vectors, as we will be redoing the calculations */
1432 copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
1433 }
1434
1435 bFirstIterate = TRUE1;
1436 while (bFirstIterate || iterate.bIterationActive)
1437 {
1438 /* We now restore these vectors to redo the calculation with improved extended variables */
1439 if (iterate.bIterationActive)
1440 {
1441 copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
1442 }
1443
1444 /* We make the decision to break or not -after- the calculation of Ekin and Pressure,
1445 so scroll down for that logic */
1446
1447 /* ######### START SECOND UPDATE STEP ################# */
1448 /* Box is changed in update() when we do pressure coupling,
1449 * but we should still use the old box for energy corrections and when
1450 * writing it to the energy file, so it matches the trajectory files for
1451 * the same timestep above. Make a copy in a separate array.
1452 */
1453 copy_mat(state->box, lastbox);
1454
1455 bOK = TRUE1;
1456 dvdl_constr = 0;
1457
1458 if (!(bRerunMD && !rerun_fr.bV && !bForceUpdate))
1459 {
1460 wallcycle_start(wcycle, ewcUPDATE);
1461 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1462 if (bTrotter)
1463 {
1464 if (iterate.bIterationActive)
1465 {
1466 if (bFirstIterate)
1467 {
1468 scalevir = 1;
1469 }
1470 else
1471 {
1472 /* we use a new value of scalevir to converge the iterations faster */
1473 scalevir = tracevir/trace(shake_vir);
1474 }
1475 msmul(shake_vir, scalevir, shake_vir);
1476 m_add(force_vir, shake_vir, total_vir);
1477 clear_mat(shake_vir);
1478 }
1479 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
1480 /* We can only do Berendsen coupling after we have summed
1481 * the kinetic energy or virial. Since the happens
1482 * in global_state after update, we should only do it at
1483 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1484 */
1485 }
1486 else
1487 {
1488 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1489 update_pcouple(fplog, step, ir, state, pcoupl_mu, M, bInitStep);
1490 }
1491
1492 if (bVV)
1493 {
1494 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1495
1496 /* velocity half-step update */
1497 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
1498 bUpdateDoLR, fr->f_twin, fcd,
1499 ekind, M, upd, FALSE0, etrtVELOCITY2,
1500 cr, nrnb, constr, &top->idef);
1501 }
1502
1503 /* Above, initialize just copies ekinh into ekin,
1504 * it doesn't copy position (for VV),
1505 * and entire integrator for MD.
1506 */
1507
1508 if (ir->eI == eiVVAK)
1509 {
1510 copy_rvecn(state->x, cbuf, 0, state->natoms);
1511 }
1512 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1513
1514 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
1515 bUpdateDoLR, fr->f_twin, fcd,
1516 ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
1517 wallcycle_stop(wcycle, ewcUPDATE);
1518
1519 update_constraints(fplog, step, &dvdl_constr, ir, ekind, mdatoms, state,
1520 fr->bMolPBC, graph, f,
1521 &top->idef, shake_vir,
1522 cr, nrnb, wcycle, upd, constr,
1523 FALSE0, bCalcVir, state->veta);
1524
1525 if (ir->eI == eiVVAK)
1526 {
1527 /* erase F_EKIN and F_TEMP here? */
1528 /* just compute the kinetic energy at the half step to perform a trotter step */
1529 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1530 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1531 constr, NULL((void*)0), FALSE0, lastbox,
1532 top_global, &bSumEkinhOld,
1533 cglo_flags | CGLO_TEMPERATURE(1<<7)
1534 );
1535 wallcycle_start(wcycle, ewcUPDATE);
1536 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
1537 /* now we know the scaling, we can compute the positions again again */
1538 copy_rvecn(cbuf, state->x, 0, state->natoms);
1539
1540 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1541
1542 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
1543 bUpdateDoLR, fr->f_twin, fcd,
1544 ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
1545 wallcycle_stop(wcycle, ewcUPDATE);
1546
1547 /* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
1548 /* are the small terms in the shake_vir here due
1549 * to numerical errors, or are they important
1550 * physically? I'm thinking they are just errors, but not completely sure.
1551 * For now, will call without actually constraining, constr=NULL*/
1552 update_constraints(fplog, step, NULL((void*)0), ir, ekind, mdatoms,
1553 state, fr->bMolPBC, graph, f,
1554 &top->idef, tmp_vir,
1555 cr, nrnb, wcycle, upd, NULL((void*)0),
1556 FALSE0, bCalcVir,
1557 state->veta);
1558 }
1559 if (!bOK)
1560 {
1561 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c", 1561, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
1562 }
1563
1564 if (fr->bSepDVDL && fplog && do_log)
1565 {
1566 gmx_print_sepdvdl(fplog, "Constraint dV/dl", 0.0, dvdl_constr);
1567 }
1568 if (bVV)
1569 {
1570 /* this factor or 2 correction is necessary
1571 because half of the constraint force is removed
1572 in the vv step, so we have to double it. See
1573 the Redmine issue #1255. It is not yet clear
1574 if the factor of 2 is exact, or just a very
1575 good approximation, and this will be
1576 investigated. The next step is to see if this
1577 can be done adding a dhdl contribution from the
1578 rattle step, but this is somewhat more
1579 complicated with the current code. Will be
1580 investigated, hopefully for 4.6.3. However,
1581 this current solution is much better than
1582 having it completely wrong.
1583 */
1584 enerd->term[F_DVDL_CONSTR] += 2*dvdl_constr;
1585 }
1586 else
1587 {
1588 enerd->term[F_DVDL_CONSTR] += dvdl_constr;
1589 }
1590 }
1591 else if (graph)
1592 {
1593 /* Need to unshift here */
1594 unshift_self(graph, state->box, state->x);
1595 }
1596
1597 if (vsite != NULL((void*)0))
1598 {
1599 wallcycle_start(wcycle, ewcVSITECONSTR);
1600 if (graph != NULL((void*)0))
1601 {
1602 shift_self(graph, state->box, state->x);
1603 }
1604 construct_vsites(vsite, state->x, ir->delta_t, state->v,
1605 top->idef.iparams, top->idef.il,
1606 fr->ePBC, fr->bMolPBC, cr, state->box);
1607
1608 if (graph != NULL((void*)0))
1609 {
1610 unshift_self(graph, state->box, state->x);
1611 }
1612 wallcycle_stop(wcycle, ewcVSITECONSTR);
1613 }
1614
1615 /* ############## IF NOT VV, Calculate globals HERE, also iterate constraints ############ */
1616 /* With Leap-Frog we can skip compute_globals at
1617 * non-communication steps, but we need to calculate
1618 * the kinetic energy one step before communication.
1619 */
1620 if (bGStat || (!EI_VV(ir->eI)((ir->eI) == eiVV || (ir->eI) == eiVVAK) && do_per_step(step+1, nstglobalcomm)))
1621 {
1622 if (ir->nstlist == -1 && bFirstIterate)
1623 {
1624 gs.sig[eglsNABNSB] = nlh.nabnsb;
1625 }
1626 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1627 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1628 constr,
1629 bFirstIterate ? &gs : NULL((void*)0),
1630 (step_rel % gs.nstms == 0) &&
1631 (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
1632 lastbox,
1633 top_global, &bSumEkinhOld,
1634 cglo_flags
1635 | (!EI_VV(ir->eI)((ir->eI) == eiVV || (ir->eI) == eiVVAK) || bRerunMD ? CGLO_ENERGY(1<<6) : 0)
1636 | (!EI_VV(ir->eI)((ir->eI) == eiVV || (ir->eI) == eiVVAK) && bStopCM ? CGLO_STOPCM(1<<3) : 0)
1637 | (!EI_VV(ir->eI)((ir->eI) == eiVV || (ir->eI) == eiVVAK) ? CGLO_TEMPERATURE(1<<7) : 0)
1638 | (!EI_VV(ir->eI)((ir->eI) == eiVV || (ir->eI) == eiVVAK) || bRerunMD ? CGLO_PRESSURE(1<<8) : 0)
1639 | (iterate.bIterationActive ? CGLO_ITERATE(1<<10) : 0)
1640 | (bFirstIterate ? CGLO_FIRSTITERATE(1<<11) : 0)
1641 | CGLO_CONSTRAINT(1<<9)
1642 );
1643 if (ir->nstlist == -1 && bFirstIterate)
1644 {
1645 nlh.nabnsb = gs.set[eglsNABNSB];
1646 gs.set[eglsNABNSB] = 0;
1647 }
1648 }
1649 /* bIterate is set to keep it from eliminating the old ekin kinetic energy terms */
1650 /* ############# END CALC EKIN AND PRESSURE ################# */
1651
1652 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
1653 the virial that should probably be addressed eventually. state->veta has better properies,
1654 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
1655 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
1656
1657 if (iterate.bIterationActive &&
1658 done_iterating(cr, fplog, step, &iterate, bFirstIterate,
1659 trace(shake_vir), &tracevir))
1660 {
1661 break;
1662 }
1663 bFirstIterate = FALSE0;
1664 }
1665
1666 if (!bVV || bRerunMD)
1667 {
1668 /* sum up the foreign energy and dhdl terms for md and sd. currently done every step so that dhdl is correct in the .edr */
1669 sum_dhdl(enerd, state->lambda, ir->fepvals);
1670 }
1671 update_box(fplog, step, ir, mdatoms, state, f,
1672 ir->nstlist == -1 ? &nlh.scale_tot : NULL((void*)0), pcoupl_mu, nrnb, upd);
1673
1674 /* ################# END UPDATE STEP 2 ################# */
1675 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1676
1677 /* The coordinates (x) were unshifted in update */
1678 if (!bGStat)
1679 {
1680 /* We will not sum ekinh_old,
1681 * so signal that we still have to do it.
1682 */
1683 bSumEkinhOld = TRUE1;
1684 }
1685
1686 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1687
1688 /* use the directly determined last velocity, not actually the averaged half steps */
1689 if (bTrotter && ir->eI == eiVV)
1690 {
1691 enerd->term[F_EKIN] = last_ekin;
1692 }
1693 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1694
1695 if (bVV)
1696 {
1697 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1698 }
1699 else
1700 {
1701 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + compute_conserved_from_auxiliary(ir, state, &MassQ);
1702 }
1703 /* ######### END PREPARING EDR OUTPUT ########### */
1704
1705 /* Output stuff */
1706 if (MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
1707 {
1708 gmx_bool do_dr, do_or;
1709
1710 if (fplog && do_log && bDoExpanded)
1711 {
1712 /* only needed if doing expanded ensemble */
1713 PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL((void*)0),
1714 &state_global->dfhist, state->fep_state, ir->nstlog, step);
1715 }
1716 if (!(bStartingFromCpt && (EI_VV(ir->eI)((ir->eI) == eiVV || (ir->eI) == eiVVAK))))
1717 {
1718 if (bCalcEner)
1719 {
1720 upd_mdebin(mdebin, bDoDHDL, TRUE1,
1721 t, mdatoms->tmass, enerd, state,
1722 ir->fepvals, ir->expandedvals, lastbox,
1723 shake_vir, force_vir, total_vir, pres,
1724 ekind, mu_tot, constr);
1725 }
1726 else
1727 {
1728 upd_mdebin_step(mdebin);
1729 }
1730
1731 do_dr = do_per_step(step, ir->nstdisreout);
1732 do_or = do_per_step(step, ir->nstorireout);
1733
1734 print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL((void*)0),
1735 step, t,
1736 eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
1737 }
1738 if (ir->ePull != epullNO)
1739 {
1740 pull_print_output(ir->pull, step, t);
1741 }
1742
1743 if (do_per_step(step, ir->nstlog))
1744 {
1745 if (fflush(fplog) != 0)
1746 {
1747 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/programs/mdrun/md.c", 1747, "Cannot flush logfile - maybe you are out of disk space?");
1748 }
1749 }
1750 }
1751 if (bDoExpanded)
1752 {
1753 /* Have to do this part _after_ outputting the logfile and the edr file */
1754 /* Gets written into the state at the beginning of next loop*/
1755 state->fep_state = lamnew;
1756 }
1757 /* Print the remaining wall clock time for the run */
1758 if (MULTIMASTER(cr)((((((cr)->nodeid == 0) || !((cr)->nnodes > 1)) &&
((cr)->duty & (1<<0))) || !((cr)->nnodes >
1)) && (!((cr)->ms) || (((cr)->ms)->sim == 0
))) && (do_verbose || gmx_got_usr_signal()) && !bPMETuneRunning)
1759 {
1760 if (shellfc)
1761 {
1762 fprintf(stderrstderr, "\n");
1763 }
1764 print_time(stderrstderr, walltime_accounting, step, ir, cr);
1765 }
1766
1767 /* Ion/water position swapping.
1768 * Not done in last step since trajectory writing happens before this call
1769 * in the MD loop and exchanges would be lost anyway. */
1770 bNeedRepartition = FALSE0;
1771 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep &&
1772 do_per_step(step, ir->swap->nstswap))
1773 {
1774 bNeedRepartition = do_swapcoords(cr, step, t, ir, wcycle,
1775 bRerunMD ? rerun_fr.x : state->x,
1776 bRerunMD ? rerun_fr.box : state->box,
1777 top_global, MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)) && bVerbose, bRerunMD);
1778
1779 if (bNeedRepartition && DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)))
1780 {
1781 dd_collect_state(cr->dd, state, state_global);
1782 }
1783 }
1784
1785 /* Replica exchange */
1786 bExchanged = FALSE0;
1787 if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
1788 do_per_step(step, repl_ex_nst))
1789 {
1790 bExchanged = replica_exchange(fplog, cr, repl_ex,
1791 state_global, enerd,
1792 state, step, t);
1793 }
1794
1795 if ( (bExchanged || bNeedRepartition) && DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)) )
1796 {
1797 dd_partition_system(fplog, step, cr, TRUE1, 1,
1798 state_global, top_global, ir,
1799 state, &f, mdatoms, top, fr,
1800 vsite, shellfc, constr,
1801 nrnb, wcycle, FALSE0);
1802 }
1803
1804 bFirstStep = FALSE0;
1805 bInitStep = FALSE0;
1806 bStartingFromCpt = FALSE0;
1807
1808 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
1809 /* With all integrators, except VV, we need to retain the pressure
1810 * at the current step for coupling at the next step.
1811 */
1812 if ((state->flags & (1<<estPRES_PREV)) &&
1813 (bGStatEveryStep ||
1814 (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
1815 {
1816 /* Store the pressure in t_state for pressure coupling
1817 * at the next MD step.
1818 */
1819 copy_mat(pres, state->pres_prev);
1820 }
1821
1822 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
1823
1824 if ( (membed != NULL((void*)0)) && (!bLastStep) )
1825 {
1826 rescale_membed(step_rel, membed, state_global->x);
1827 }
1828
1829 if (bRerunMD)
1830 {
1831 if (MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
1832 {
1833 /* read next frame from input trajectory */
1834 bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
1835 }
1836
1837 if (PAR(cr)((cr)->nnodes > 1))
1838 {
1839 rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
1840 }
1841 }
1842
1843 if (!bRerunMD || !rerun_fr.bStep)
1844 {
1845 /* increase the MD step number */
1846 step++;
1847 step_rel++;
1848 }
1849
1850 cycles = wallcycle_stop(wcycle, ewcSTEP);
1851 if (DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes >
1)) && wcycle)
1852 {
1853 dd_cycles_add(cr->dd, cycles, ddCyclStep);
1854 }
1855
1856 if (bPMETuneRunning || bPMETuneTry)
1857 {
1858 /* PME grid + cut-off optimization with GPUs or PME nodes */
1859
1860 /* Count the total cycles over the last steps */
1861 cycles_pmes += cycles;
1862
1863 /* We can only switch cut-off at NS steps */
1864 if (step % ir->nstlist == 0)
1865 {
1866 /* PME grid + cut-off optimization with GPUs or PME nodes */
1867 if (bPMETuneTry)
1868 {
1869 if (DDMASTER(cr->dd)((cr->dd)->rank == (cr->dd)->masterrank))
1870 {
1871 /* PME node load is too high, start tuning */
1872 bPMETuneRunning = (dd_pme_f_ratio(cr->dd) >= 1.05);
1873 }
1874 dd_bcast(cr->dd, sizeof(gmx_bool), &bPMETuneRunning);
1875
1876 if (bPMETuneRunning || step_rel > ir->nstlist*50)
1877 {
1878 bPMETuneTry = FALSE0;
1879 }
1880 }
1881 if (bPMETuneRunning)
1882 {
1883 /* init_step might not be a multiple of nstlist,
1884 * but the first cycle is always skipped anyhow.
1885 */
1886 bPMETuneRunning =
1887 pme_load_balance(pme_loadbal, cr,
1888 (bVerbose && MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1))) ? stderrstderr : NULL((void*)0),
1889 fplog,
1890 ir, state, cycles_pmes,
1891 fr->ic, fr->nbv, &fr->pmedata,
1892 step);
1893
1894 /* Update constants in forcerec/inputrec to keep them in sync with fr->ic */
1895 fr->ewaldcoeff_q = fr->ic->ewaldcoeff_q;
1896 fr->ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
1897 fr->rlist = fr->ic->rlist;
1898 fr->rlistlong = fr->ic->rlistlong;
1899 fr->rcoulomb = fr->ic->rcoulomb;
1900 fr->rvdw = fr->ic->rvdw;
1901
1902 if (ir->eDispCorr != edispcNO)
1903 {
1904 calc_enervirdiff(NULL((void*)0), ir->eDispCorr, fr);
1905 }
1906 }
1907 cycles_pmes = 0;
1908 }
1909 }
1910
1911 if (step_rel == wcycle_get_reset_counters(wcycle) ||
1912 gs.set[eglsRESETCOUNTERS] != 0)
1913 {
1914 /* Reset all the counters related to performance over the run */
1915 reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
1916 fr->nbv != NULL((void*)0) && fr->nbv->bUseGPU ? fr->nbv->cu_nbv : NULL((void*)0));
1917 wcycle_set_reset_counters(wcycle, -1);
1918 if (!(cr->duty & DUTY_PME(1<<1)))
1919 {
1920 /* Tell our PME node to reset its counters */
1921 gmx_pme_send_resetcounters(cr, step);
1922 }
1923 /* Correct max_hours for the elapsed time */
1924 max_hours -= elapsed_time/(60.0*60.0);
1925 bResetCountersHalfMaxH = FALSE0;
1926 gs.set[eglsRESETCOUNTERS] = 0;
1927 }
1928
1929 /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
1930 IMD_prep_energies_send_positions(ir->bIMD && MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)), bIMDstep, ir->imd, enerd, step, bCalcEner, wcycle);
1931
1932 }
1933 /* End of main MD loop */
1934 debug_gmx();
1935
1936 /* Stop measuring walltime */
1937 walltime_accounting_end(walltime_accounting);
1938
1939 if (bRerunMD && MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
1940 {
1941 close_trj(status);
1942 }
1943
1944 if (!(cr->duty & DUTY_PME(1<<1)))
1945 {
1946 /* Tell the PME only node to finish */
1947 gmx_pme_send_finish(cr);
1948 }
1949
1950 if (MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
1951 {
1952 if (ir->nstcalcenergy > 0 && !bRerunMD)
1953 {
1954 print_ebin(mdoutf_get_fp_ene(outf), FALSE0, FALSE0, FALSE0, fplog, step, t,
1955 eprAVER, FALSE0, mdebin, fcd, groups, &(ir->opts));
1956 }
1957 }
1958
1959 done_mdoutf(outf);
1960 debug_gmx();
1961
1962 if (ir->nstlist == -1 && nlh.nns > 0 && fplog)
1963 {
1964 fprintf(fplog, "Average neighborlist lifetime: %.1f steps, std.dev.: %.1f steps\n", nlh.s1/nlh.nns, sqrt(nlh.s2/nlh.nns - sqr(nlh.s1/nlh.nns)));
1965 fprintf(fplog, "Average number of atoms that crossed the half buffer length: %.1f\n\n", nlh.ab/nlh.nns);
1966 }
1967
1968 if (pme_loadbal != NULL((void*)0))
1969 {
1970 pme_loadbal_done(pme_loadbal, cr, fplog,
1971 fr->nbv != NULL((void*)0) && fr->nbv->bUseGPU);
1972 }
1973
1974 if (shellfc && fplog)
1975 {
1976 fprintf(fplog, "Fraction of iterations that converged: %.2f %%\n",
1977 (nconverged*100.0)/step_rel);
1978 fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
1979 tcount/step_rel);
1980 }
1981
1982 if (repl_ex_nst > 0 && MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1)))
1983 {
1984 print_replica_exchange_statistics(fplog, repl_ex);
1985 }
1986
1987 /* IMD cleanup, if bIMD is TRUE. */
1988 IMD_finalize(ir->bIMD, ir->imd);
1989
1990 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
1991
1992 return 0;
1993}