2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team,
6 * check out http://www.gromacs.org for more information.
7 * Copyright (c) 2012,2013, by the GROMACS development team, led by
8 * David van der Spoel, Berk Hess, Erik Lindahl, and including many
9 * others, as listed in the AUTHORS file in the top-level source
10 * directory and at http://www.gromacs.org.
12 * GROMACS is free software; you can redistribute it and/or
13 * modify it under the terms of the GNU Lesser General Public License
14 * as published by the Free Software Foundation; either version 2.1
15 * of the License, or (at your option) any later version.
17 * GROMACS is distributed in the hope that it will be useful,
18 * but WITHOUT ANY WARRANTY; without even the implied warranty of
19 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
20 * Lesser General Public License for more details.
22 * You should have received a copy of the GNU Lesser General Public
23 * License along with GROMACS; if not, see
24 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
25 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
27 * If you want to redistribute modifications to GROMACS, please
28 * consider that scientific software is very special. Version
29 * control is crucial - bugs must be traceable. We will be happy to
30 * consider code for inclusion in the official distribution, but
31 * derived work must not be called official GROMACS. Details are found
32 * in the README & COPYING files - if they are missing, get the
33 * official version at http://www.gromacs.org.
35 * To help us fund GROMACS development, we humbly ask that you cite
36 * the research papers on the package. Check out http://www.gromacs.org.
58 #include "md_support.h"
59 #include "md_logging.h"
74 #include "mpelogging.h"
76 #include "domdec_network.h"
82 #include "compute_io.h"
84 #include "checkpoint.h"
85 #include "mtop_util.h"
86 #include "sighandler.h"
89 #include "pme_loadbal.h"
92 #include "types/nlistheuristics.h"
93 #include "types/iteratedconstraints.h"
94 #include "nbnxn_cuda_data_mgmt.h"
104 #include "corewrap.h"
107 static void reset_all_counters(FILE *fplog, t_commrec *cr,
108 gmx_large_int_t step,
109 gmx_large_int_t *step_rel, t_inputrec *ir,
110 gmx_wallcycle_t wcycle, t_nrnb *nrnb,
111 gmx_runtime_t *runtime,
112 nbnxn_cuda_ptr_t cu_nbv)
114 char sbuf[STEPSTRSIZE];
116 /* Reset all the counters related to performance over the run */
117 md_print_warn(cr, fplog, "step %s: resetting all time and cycle counters\n",
118 gmx_step_str(step, sbuf));
122 nbnxn_cuda_reset_timings(cu_nbv);
125 wallcycle_stop(wcycle, ewcRUN);
126 wallcycle_reset_all(wcycle);
127 if (DOMAINDECOMP(cr))
129 reset_dd_statistics_counters(cr->dd);
132 ir->init_step += *step_rel;
133 ir->nsteps -= *step_rel;
135 wallcycle_start(wcycle, ewcRUN);
136 runtime_start(runtime);
137 print_date_and_time(fplog, cr->nodeid, "Restarted time", runtime);
140 double do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
141 const output_env_t oenv, gmx_bool bVerbose, gmx_bool bCompact,
143 gmx_vsite_t *vsite, gmx_constr_t constr,
144 int stepout, t_inputrec *ir,
145 gmx_mtop_t *top_global,
147 t_state *state_global,
149 t_nrnb *nrnb, gmx_wallcycle_t wcycle,
150 gmx_edsam_t ed, t_forcerec *fr,
151 int repl_ex_nst, int repl_ex_nex, int repl_ex_seed, gmx_membed_t membed,
152 real cpt_period, real max_hours,
153 const char *deviceOptions,
155 gmx_runtime_t *runtime)
158 gmx_large_int_t step, step_rel;
160 double t, t0, lam0[efptNR];
161 gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEner;
162 gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD, bNotLastFrame = FALSE,
163 bFirstStep, bStateFromCP, bStateFromTPX, bInitStep, bLastStep,
164 bBornRadii, bStartingFromCpt;
165 gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
166 gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
167 bForceUpdate = FALSE, bCPT;
169 gmx_bool bMasterState;
170 int force_flags, cglo_flags;
171 tensor force_vir, shake_vir, total_vir, tmp_vir, pres;
176 t_state *bufstate = NULL;
177 matrix *scale_tot, pcoupl_mu, M, ebox;
180 gmx_repl_ex_t repl_ex = NULL;
183 t_mdebin *mdebin = NULL;
184 t_state *state = NULL;
185 rvec *f_global = NULL;
188 gmx_enerdata_t *enerd;
190 gmx_global_stat_t gstat;
191 gmx_update_t upd = NULL;
192 t_graph *graph = NULL;
194 gmx_rng_t mcrng = NULL;
196 gmx_groups_t *groups;
197 gmx_ekindata_t *ekind, *ekind_save;
198 gmx_shellfc_t shellfc;
199 int count, nconverged = 0;
202 gmx_bool bIonize = FALSE;
203 gmx_bool bTCR = FALSE, bConverged = TRUE, bOK, bSumEkinhOld, bExchanged;
205 gmx_bool bResetCountersHalfMaxH = FALSE;
206 gmx_bool bVV, bIterativeCase, bFirstIterate, bTemp, bPres, bTrotter;
207 gmx_bool bUpdateDoLR;
208 real mu_aver = 0, dvdl_constr;
209 int a0, a1, gnx = 0, ii;
210 atom_id *grpindex = NULL;
212 t_coupl_rec *tcr = NULL;
213 rvec *xcopy = NULL, *vcopy = NULL, *cbuf = NULL;
214 matrix boxcopy = {{0}}, lastbox;
216 real fom, oldfom, veta_save, pcurr, scalevir, tracevir;
223 real saved_conserved_quantity = 0;
228 char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
229 int handled_stop_condition = gmx_stop_cond_none; /* compare to get_stop_condition*/
230 gmx_iterate_t iterate;
231 gmx_large_int_t multisim_nsteps = -1; /* number of steps to do before first multisim
232 simulation stops. If equal to zero, don't
233 communicate any more between multisims.*/
234 /* PME load balancing data for GPU kernels */
235 pme_load_balancing_t pme_loadbal = NULL;
237 gmx_bool bPMETuneTry = FALSE, bPMETuneRunning = FALSE;
240 /* Temporary addition for FAHCORE checkpointing */
244 /* Check for special mdrun options */
245 bRerunMD = (Flags & MD_RERUN);
246 bIonize = (Flags & MD_IONIZE);
247 bFFscan = (Flags & MD_FFSCAN);
248 bAppend = (Flags & MD_APPENDFILES);
249 if (Flags & MD_RESETCOUNTERSHALFWAY)
253 /* Signal to reset the counters half the simulation steps. */
254 wcycle_set_reset_counters(wcycle, ir->nsteps/2);
256 /* Signal to reset the counters halfway the simulation time. */
257 bResetCountersHalfMaxH = (max_hours > 0);
260 /* md-vv uses averaged full step velocities for T-control
261 md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
262 md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
264 if (bVV) /* to store the initial velocities while computing virial */
266 snew(cbuf, top_global->natoms);
268 /* all the iteratative cases - only if there are constraints */
269 bIterativeCase = ((IR_NPH_TROTTER(ir) || IR_NPT_TROTTER(ir)) && (constr) && (!bRerunMD));
270 gmx_iterate_init(&iterate, FALSE); /* The default value of iterate->bIterationActive is set to
271 false in this step. The correct value, true or false,
272 is set at each step, as it depends on the frequency of temperature
273 and pressure control.*/
274 bTrotter = (bVV && (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir) || IR_NVT_TROTTER(ir)));
278 /* Since we don't know if the frames read are related in any way,
279 * rebuild the neighborlist at every step.
282 ir->nstcalcenergy = 1;
286 check_ir_old_tpx_versions(cr, fplog, ir, top_global);
288 nstglobalcomm = check_nstglobalcomm(fplog, cr, nstglobalcomm, ir);
289 bGStatEveryStep = (nstglobalcomm == 1);
291 if (!bGStatEveryStep && ir->nstlist == -1 && fplog != NULL)
294 "To reduce the energy communication with nstlist = -1\n"
295 "the neighbor list validity should not be checked at every step,\n"
296 "this means that exact integration is not guaranteed.\n"
297 "The neighbor list validity is checked after:\n"
298 " <n.list life time> - 2*std.dev.(n.list life time) steps.\n"
299 "In most cases this will result in exact integration.\n"
300 "This reduces the energy communication by a factor of 2 to 3.\n"
301 "If you want less energy communication, set nstlist > 3.\n\n");
304 if (bRerunMD || bFFscan)
308 groups = &top_global->groups;
311 init_md(fplog, cr, ir, oenv, &t, &t0, state_global->lambda,
312 &(state_global->fep_state), lam0,
313 nrnb, top_global, &upd,
314 nfile, fnm, &outf, &mdebin,
315 force_vir, shake_vir, mu_tot, &bSimAnn, &vcm, state_global, Flags);
317 clear_mat(total_vir);
319 /* Energy terms and groups */
321 init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
323 if (DOMAINDECOMP(cr))
329 snew(f, top_global->natoms);
332 /* Kinetic energy data */
334 init_ekindata(fplog, top_global, &(ir->opts), ekind);
335 /* needed for iteration of constraints */
337 init_ekindata(fplog, top_global, &(ir->opts), ekind_save);
338 /* Copy the cos acceleration to the groups struct */
339 ekind->cosacc.cos_accel = ir->cos_accel;
341 gstat = global_stat_init(ir);
344 /* Check for polarizable models and flexible constraints */
345 shellfc = init_shell_flexcon(fplog, fr->cutoff_scheme == ecutsVERLET,
346 top_global, n_flexible_constraints(constr),
347 (ir->bContinuation ||
348 (DOMAINDECOMP(cr) && !MASTER(cr))) ?
349 NULL : state_global->x);
351 if (shellfc && ir->eI == eiNM)
353 /* Currently shells don't work with Normal Modes */
354 gmx_fatal(FARGS, "Normal Mode analysis is not supported with shells.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
357 if (vsite && ir->eI == eiNM)
359 /* Currently virtual sites don't work with Normal Modes */
360 gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
365 #ifdef GMX_THREAD_MPI
366 tMPI_Thread_mutex_lock(&deform_init_box_mutex);
368 set_deform_reference_box(upd,
369 deform_init_init_step_tpx,
370 deform_init_box_tpx);
371 #ifdef GMX_THREAD_MPI
372 tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
377 double io = compute_io(ir, top_global->natoms, groups, mdebin->ebin->nener, 1);
378 if ((io > 2000) && MASTER(cr))
381 "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
386 if (DOMAINDECOMP(cr))
388 top = dd_init_local_top(top_global);
391 dd_init_local_state(cr->dd, state_global, state);
393 if (DDMASTER(cr->dd) && ir->nstfout)
395 snew(f_global, state_global->natoms);
402 /* Initialize the particle decomposition and split the topology */
403 top = split_system(fplog, top_global, ir, cr);
405 pd_cg_range(cr, &fr->cg0, &fr->hcg);
406 pd_at_range(cr, &a0, &a1);
410 top = gmx_mtop_generate_local_top(top_global, ir);
413 a1 = top_global->natoms;
416 forcerec_set_excl_load(fr, top, cr);
418 state = partdec_init_local_state(cr, state_global);
421 atoms2md(top_global, ir, 0, NULL, a0, a1-a0, mdatoms);
425 set_vsite_top(vsite, top, mdatoms, cr);
428 if (ir->ePBC != epbcNONE && !fr->bMolPBC)
430 graph = mk_graph(fplog, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
435 make_local_shells(cr, mdatoms, shellfc);
438 setup_bonded_threading(fr, &top->idef);
440 if (ir->pull && PAR(cr))
442 dd_make_local_pull_groups(NULL, ir->pull, mdatoms);
446 if (DOMAINDECOMP(cr))
448 /* Distribute the charge groups over the nodes from the master node */
449 dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
450 state_global, top_global, ir,
451 state, &f, mdatoms, top, fr,
452 vsite, shellfc, constr,
453 nrnb, wcycle, FALSE);
457 update_mdatoms(mdatoms, state->lambda[efptMASS]);
459 if (opt2bSet("-cpi", nfile, fnm))
461 bStateFromCP = gmx_fexist_master(opt2fn_master("-cpi", nfile, fnm, cr), cr);
465 bStateFromCP = FALSE;
470 init_expanded_ensemble(bStateFromCP,ir,&mcrng,&state->dfhist);
477 /* Update mdebin with energy history if appending to output files */
478 if (Flags & MD_APPENDFILES)
480 restore_energyhistory_from_state(mdebin, &state_global->enerhist);
484 /* We might have read an energy history from checkpoint,
485 * free the allocated memory and reset the counts.
487 done_energyhistory(&state_global->enerhist);
488 init_energyhistory(&state_global->enerhist);
491 /* Set the initial energy history in state by updating once */
492 update_energyhistory(&state_global->enerhist, mdebin);
495 if ((state->flags & (1<<estLD_RNG)) && (Flags & MD_READ_RNG))
497 /* Set the random state if we read a checkpoint file */
498 set_stochd_state(upd, state);
501 if (state->flags & (1<<estMC_RNG))
503 set_mc_state(mcrng, state);
506 /* Initialize constraints */
509 if (!DOMAINDECOMP(cr))
511 set_constraints(constr, top, ir, mdatoms, cr);
515 /* Check whether we have to GCT stuff */
516 bTCR = ftp2bSet(efGCT, nfile, fnm);
521 fprintf(stderr, "Will do General Coupling Theory!\n");
523 gnx = top_global->mols.nr;
525 for (i = 0; (i < gnx); i++)
533 /* We need to be sure replica exchange can only occur
534 * when the energies are current */
535 check_nst_param(fplog, cr, "nstcalcenergy", ir->nstcalcenergy,
536 "repl_ex_nst", &repl_ex_nst);
537 /* This check needs to happen before inter-simulation
538 * signals are initialized, too */
540 if (repl_ex_nst > 0 && MASTER(cr))
542 repl_ex = init_replica_exchange(fplog, cr->ms, state_global, ir,
543 repl_ex_nst, repl_ex_nex, repl_ex_seed);
546 /* PME tuning is only supported with GPUs or PME nodes and not with rerun.
547 * With perturbed charges with soft-core we should not change the cut-off.
549 if ((Flags & MD_TUNEPME) &&
550 EEL_PME(fr->eeltype) &&
551 ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME)) &&
552 !(ir->efep != efepNO && mdatoms->nChargePerturbed > 0 && ir->fepvals->bScCoul) &&
555 pme_loadbal_init(&pme_loadbal, ir, state->box, fr->ic, fr->pmedata);
557 if (cr->duty & DUTY_PME)
559 /* Start tuning right away, as we can't measure the load */
560 bPMETuneRunning = TRUE;
564 /* Separate PME nodes, we can measure the PP/PME load balance */
569 if (!ir->bContinuation && !bRerunMD)
571 if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
573 /* Set the velocities of frozen particles to zero */
574 for (i = mdatoms->start; i < mdatoms->start+mdatoms->homenr; i++)
576 for (m = 0; m < DIM; m++)
578 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
588 /* Constrain the initial coordinates and velocities */
589 do_constrain_first(fplog, constr, ir, mdatoms, state, f,
590 graph, cr, nrnb, fr, top, shake_vir);
594 /* Construct the virtual sites for the initial configuration */
595 construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, NULL,
596 top->idef.iparams, top->idef.il,
597 fr->ePBC, fr->bMolPBC, graph, cr, state->box);
603 /* set free energy calculation frequency as the minimum
604 greatest common denominator of nstdhdl, nstexpanded, and repl_ex_nst*/
605 nstfep = ir->fepvals->nstdhdl;
608 nstfep = gmx_greatest_common_divisor(ir->fepvals->nstdhdl,nstfep);
612 nstfep = gmx_greatest_common_divisor(repl_ex_nst,nstfep);
615 /* I'm assuming we need global communication the first time! MRS */
616 cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
617 | ((ir->comm_mode != ecmNO) ? CGLO_STOPCM : 0)
618 | (bVV ? CGLO_PRESSURE : 0)
619 | (bVV ? CGLO_CONSTRAINT : 0)
620 | (bRerunMD ? CGLO_RERUNMD : 0)
621 | ((Flags & MD_READ_EKIN) ? CGLO_READEKIN : 0));
623 bSumEkinhOld = FALSE;
624 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
625 NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
626 constr, NULL, FALSE, state->box,
627 top_global, &pcurr, top_global->natoms, &bSumEkinhOld, cglo_flags);
628 if (ir->eI == eiVVAK)
630 /* a second call to get the half step temperature initialized as well */
631 /* we do the same call as above, but turn the pressure off -- internally to
632 compute_globals, this is recognized as a velocity verlet half-step
633 kinetic energy calculation. This minimized excess variables, but
634 perhaps loses some logic?*/
636 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
637 NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
638 constr, NULL, FALSE, state->box,
639 top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
640 cglo_flags &~(CGLO_STOPCM | CGLO_PRESSURE));
643 /* Calculate the initial half step temperature, and save the ekinh_old */
644 if (!(Flags & MD_STARTFROMCPT))
646 for (i = 0; (i < ir->opts.ngtc); i++)
648 copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
653 enerd->term[F_TEMP] *= 2; /* result of averages being done over previous and current step,
654 and there is no previous step */
657 /* if using an iterative algorithm, we need to create a working directory for the state. */
660 bufstate = init_bufstate(state);
664 snew(xcopy, state->natoms);
665 snew(vcopy, state->natoms);
666 copy_rvecn(state->x, xcopy, 0, state->natoms);
667 copy_rvecn(state->v, vcopy, 0, state->natoms);
668 copy_mat(state->box, boxcopy);
671 /* need to make an initiation call to get the Trotter variables set, as well as other constants for non-trotter
672 temperature control */
673 trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
677 if (constr && !ir->bContinuation && ir->eConstrAlg == econtLINCS)
680 "RMS relative constraint deviation after constraining: %.2e\n",
681 constr_rmsd(constr, FALSE));
683 if (EI_STATE_VELOCITY(ir->eI))
685 fprintf(fplog, "Initial temperature: %g K\n", enerd->term[F_TEMP]);
689 fprintf(stderr, "starting md rerun '%s', reading coordinates from"
690 " input trajectory '%s'\n\n",
691 *(top_global->name), opt2fn("-rerun", nfile, fnm));
694 fprintf(stderr, "Calculated time to finish depends on nsteps from "
695 "run input file,\nwhich may not correspond to the time "
696 "needed to process input trajectory.\n\n");
702 fprintf(stderr, "starting mdrun '%s'\n",
703 *(top_global->name));
706 sprintf(tbuf, "%8.1f", (ir->init_step+ir->nsteps)*ir->delta_t);
710 sprintf(tbuf, "%s", "infinite");
712 if (ir->init_step > 0)
714 fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
715 gmx_step_str(ir->init_step+ir->nsteps, sbuf), tbuf,
716 gmx_step_str(ir->init_step, sbuf2),
717 ir->init_step*ir->delta_t);
721 fprintf(stderr, "%s steps, %s ps.\n",
722 gmx_step_str(ir->nsteps, sbuf), tbuf);
725 fprintf(fplog, "\n");
728 print_start(fplog, cr, runtime, "mdrun");
729 runtime_start(runtime);
730 wallcycle_start(wcycle, ewcRUN);
732 /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
734 chkpt_ret = fcCheckPointParallel( cr->nodeid,
738 gmx_fatal( 3, __FILE__, __LINE__, "Checkpoint error on step %d\n", 0 );
743 /***********************************************************
747 ************************************************************/
749 /* if rerunMD then read coordinates and velocities from input trajectory */
752 if (getenv("GMX_FORCE_UPDATE"))
760 bNotLastFrame = read_first_frame(oenv, &status,
761 opt2fn("-rerun", nfile, fnm),
762 &rerun_fr, TRX_NEED_X | TRX_READ_V);
763 if (rerun_fr.natoms != top_global->natoms)
766 "Number of atoms in trajectory (%d) does not match the "
767 "run input file (%d)\n",
768 rerun_fr.natoms, top_global->natoms);
770 if (ir->ePBC != epbcNONE)
774 gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f does not contain a box, while pbc is used", rerun_fr.step, rerun_fr.time);
776 if (max_cutoff2(ir->ePBC, rerun_fr.box) < sqr(fr->rlistlong))
778 gmx_fatal(FARGS, "Rerun trajectory frame step %d time %f has too small box dimensions", rerun_fr.step, rerun_fr.time);
785 rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
788 if (ir->ePBC != epbcNONE)
790 /* Set the shift vectors.
791 * Necessary here when have a static box different from the tpr box.
793 calc_shifts(rerun_fr.box, fr->shift_vec);
797 /* loop over MD steps or if rerunMD to end of input trajectory */
799 /* Skip the first Nose-Hoover integration when we get the state from tpx */
800 bStateFromTPX = !bStateFromCP;
801 bInitStep = bFirstStep && (bStateFromTPX || bVV);
802 bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
804 bSumEkinhOld = FALSE;
807 init_global_signals(&gs, cr, ir, repl_ex_nst);
809 step = ir->init_step;
812 if (ir->nstlist == -1)
814 init_nlistheuristics(&nlh, bGStatEveryStep, step);
817 if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
819 /* check how many steps are left in other sims */
820 multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
824 /* and stop now if we should */
825 bLastStep = (bRerunMD || (ir->nsteps >= 0 && step_rel > ir->nsteps) ||
826 ((multisim_nsteps >= 0) && (step_rel >= multisim_nsteps )));
827 while (!bLastStep || (bRerunMD && bNotLastFrame))
830 wallcycle_start(wcycle, ewcSTEP);
832 GMX_MPE_LOG(ev_timestep1);
838 step = rerun_fr.step;
839 step_rel = step - ir->init_step;
852 bLastStep = (step_rel == ir->nsteps);
853 t = t0 + step*ir->delta_t;
856 if (ir->efep != efepNO || ir->bSimTemp)
858 /* find and set the current lambdas. If rerunning, we either read in a state, or a lambda value,
859 requiring different logic. */
861 set_current_lambdas(step, ir->fepvals, bRerunMD, &rerun_fr, state_global, state, lam0);
862 bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
863 bDoFEP = (do_per_step(step, nstfep) && (ir->efep != efepNO));
864 bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded)
865 && (ir->bExpanded) && (step > 0) && (!bStartingFromCpt));
870 update_annealing_target_temp(&(ir->opts), t);
875 if (!(DOMAINDECOMP(cr) && !MASTER(cr)))
877 for (i = 0; i < state_global->natoms; i++)
879 copy_rvec(rerun_fr.x[i], state_global->x[i]);
883 for (i = 0; i < state_global->natoms; i++)
885 copy_rvec(rerun_fr.v[i], state_global->v[i]);
890 for (i = 0; i < state_global->natoms; i++)
892 clear_rvec(state_global->v[i]);
896 fprintf(stderr, "\nWARNING: Some frames do not contain velocities.\n"
897 " Ekin, temperature and pressure are incorrect,\n"
898 " the virial will be incorrect when constraints are present.\n"
900 bRerunWarnNoV = FALSE;
904 copy_mat(rerun_fr.box, state_global->box);
905 copy_mat(state_global->box, state->box);
907 if (vsite && (Flags & MD_RERUN_VSITE))
909 if (DOMAINDECOMP(cr))
911 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented for domain decomposition, use particle decomposition");
915 /* Following is necessary because the graph may get out of sync
916 * with the coordinates if we only have every N'th coordinate set
918 mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
919 shift_self(graph, state->box, state->x);
921 construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, state->v,
922 top->idef.iparams, top->idef.il,
923 fr->ePBC, fr->bMolPBC, graph, cr, state->box);
926 unshift_self(graph, state->box, state->x);
931 /* Stop Center of Mass motion */
932 bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
934 /* Copy back starting coordinates in case we're doing a forcefield scan */
937 for (ii = 0; (ii < state->natoms); ii++)
939 copy_rvec(xcopy[ii], state->x[ii]);
940 copy_rvec(vcopy[ii], state->v[ii]);
942 copy_mat(boxcopy, state->box);
947 /* for rerun MD always do Neighbour Searching */
948 bNS = (bFirstStep || ir->nstlist != 0);
953 /* Determine whether or not to do Neighbour Searching and LR */
954 bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
956 bNS = (bFirstStep || bExchanged || bNStList || bDoFEP ||
957 (ir->nstlist == -1 && nlh.nabnsb > 0));
959 if (bNS && ir->nstlist == -1)
961 set_nlistheuristics(&nlh, bFirstStep || bExchanged || bDoFEP, step);
965 /* check whether we should stop because another simulation has
969 if ( (multisim_nsteps >= 0) && (step_rel >= multisim_nsteps) &&
970 (multisim_nsteps != ir->nsteps) )
977 "Stopping simulation %d because another one has finished\n",
981 gs.sig[eglsCHKPT] = 1;
986 /* < 0 means stop at next step, > 0 means stop at next NS step */
987 if ( (gs.set[eglsSTOPCOND] < 0) ||
988 ( (gs.set[eglsSTOPCOND] > 0) && (bNStList || ir->nstlist == 0) ) )
993 /* Determine whether or not to update the Born radii if doing GB */
994 bBornRadii = bFirstStep;
995 if (ir->implicit_solvent && (step % ir->nstgbradii == 0))
1000 do_log = do_per_step(step, ir->nstlog) || bFirstStep || bLastStep;
1001 do_verbose = bVerbose &&
1002 (step % stepout == 0 || bFirstStep || bLastStep);
1004 if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
1008 bMasterState = TRUE;
1012 bMasterState = FALSE;
1013 /* Correct the new box if it is too skewed */
1014 if (DYNAMIC_BOX(*ir))
1016 if (correct_box(fplog, step, state->box, graph))
1018 bMasterState = TRUE;
1021 if (DOMAINDECOMP(cr) && bMasterState)
1023 dd_collect_state(cr->dd, state, state_global);
1027 if (DOMAINDECOMP(cr))
1029 /* Repartition the domain decomposition */
1030 wallcycle_start(wcycle, ewcDOMDEC);
1031 dd_partition_system(fplog, step, cr,
1032 bMasterState, nstglobalcomm,
1033 state_global, top_global, ir,
1034 state, &f, mdatoms, top, fr,
1035 vsite, shellfc, constr,
1037 do_verbose && !bPMETuneRunning);
1038 wallcycle_stop(wcycle, ewcDOMDEC);
1039 /* If using an iterative integrator, reallocate space to match the decomposition */
1043 if (MASTER(cr) && do_log && !bFFscan)
1045 print_ebin_header(fplog, step, t, state->lambda[efptFEP]); /* can we improve the information printed here? */
1048 if (ir->efep != efepNO)
1050 update_mdatoms(mdatoms, state->lambda[efptMASS]);
1053 if ((bRerunMD && rerun_fr.bV) || bExchanged)
1056 /* We need the kinetic energy at minus the half step for determining
1057 * the full step kinetic energy and possibly for T-coupling.*/
1058 /* This may not be quite working correctly yet . . . . */
1059 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1060 wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
1061 constr, NULL, FALSE, state->box,
1062 top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
1063 CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
1065 clear_mat(force_vir);
1067 /* Ionize the atoms if necessary */
1070 ionize(fplog, oenv, mdatoms, top_global, t, ir, state->x, state->v,
1071 mdatoms->start, mdatoms->start+mdatoms->homenr, state->box, cr);
1074 /* Update force field in ffscan program */
1077 if (update_forcefield(fplog,
1079 mdatoms->nr, state->x, state->box))
1087 GMX_MPE_LOG(ev_timestep2);
1089 /* We write a checkpoint at this MD step when:
1090 * either at an NS step when we signalled through gs,
1091 * or at the last step (but not when we do not want confout),
1092 * but never at the first step or with rerun.
1094 bCPT = (((gs.set[eglsCHKPT] && (bNS || ir->nstlist == 0)) ||
1095 (bLastStep && (Flags & MD_CONFOUT))) &&
1096 step > ir->init_step && !bRerunMD);
1099 gs.set[eglsCHKPT] = 0;
1102 /* Determine the energy and pressure:
1103 * at nstcalcenergy steps and at energy output steps (set below).
1105 if (EI_VV(ir->eI) && (!bInitStep))
1107 /* for vv, the first half of the integration actually corresponds
1108 to the previous step. bCalcEner is only required to be evaluated on the 'next' step,
1109 but the virial needs to be calculated on both the current step and the 'next' step. Future
1110 reorganization may be able to get rid of one of the bCalcVir=TRUE steps. */
1112 bCalcEner = do_per_step(step-1, ir->nstcalcenergy);
1113 bCalcVir = bCalcEner ||
1114 (ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
1118 bCalcEner = do_per_step(step, ir->nstcalcenergy);
1119 bCalcVir = bCalcEner ||
1120 (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
1123 /* Do we need global communication ? */
1124 bGStat = (bCalcVir || bCalcEner || bStopCM ||
1125 do_per_step(step, nstglobalcomm) || (bVV && IR_NVT_TROTTER(ir) && do_per_step(step-1, nstglobalcomm)) ||
1126 (ir->nstlist == -1 && !bRerunMD && step >= nlh.step_nscheck));
1128 do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
1130 if (do_ene || do_log)
1137 /* these CGLO_ options remain the same throughout the iteration */
1138 cglo_flags = ((bRerunMD ? CGLO_RERUNMD : 0) |
1139 (bGStat ? CGLO_GSTAT : 0)
1142 force_flags = (GMX_FORCE_STATECHANGED |
1143 ((DYNAMIC_BOX(*ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
1144 GMX_FORCE_ALLFORCES |
1146 (bCalcVir ? GMX_FORCE_VIRIAL : 0) |
1147 (bCalcEner ? GMX_FORCE_ENERGY : 0) |
1148 (bDoFEP ? GMX_FORCE_DHDL : 0)
1153 if (do_per_step(step, ir->nstcalclr))
1155 force_flags |= GMX_FORCE_DO_LR;
1161 /* Now is the time to relax the shells */
1162 count = relax_shell_flexcon(fplog, cr, bVerbose, bFFscan ? step+1 : step,
1163 ir, bNS, force_flags,
1164 bStopCM, top, top_global,
1166 state, f, force_vir, mdatoms,
1167 nrnb, wcycle, graph, groups,
1168 shellfc, fr, bBornRadii, t, mu_tot,
1169 state->natoms, &bConverged, vsite,
1180 /* The coordinates (x) are shifted (to get whole molecules)
1182 * This is parallellized as well, and does communication too.
1183 * Check comments in sim_util.c
1185 do_force(fplog, cr, ir, step, nrnb, wcycle, top, top_global, groups,
1186 state->box, state->x, &state->hist,
1187 f, force_vir, mdatoms, enerd, fcd,
1188 state->lambda, graph,
1189 fr, vsite, mu_tot, t, outf->fp_field, ed, bBornRadii,
1190 (bNS ? GMX_FORCE_NS : 0) | force_flags);
1193 GMX_BARRIER(cr->mpi_comm_mygroup);
1197 mu_aver = calc_mu_aver(cr, state->x, mdatoms->chargeA,
1198 mu_tot, &top_global->mols, mdatoms, gnx, grpindex);
1201 if (bTCR && bFirstStep)
1203 tcr = init_coupling(fplog, nfile, fnm, cr, fr, mdatoms, &(top->idef));
1204 fprintf(fplog, "Done init_coupling\n");
1208 if (bVV && !bStartingFromCpt && !bRerunMD)
1209 /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
1211 if (ir->eI == eiVV && bInitStep)
1213 /* if using velocity verlet with full time step Ekin,
1214 * take the first half step only to compute the
1215 * virial for the first step. From there,
1216 * revert back to the initial coordinates
1217 * so that the input is actually the initial step.
1219 copy_rvecn(state->v, cbuf, 0, state->natoms); /* should make this better for parallelizing? */
1223 /* this is for NHC in the Ekin(t+dt/2) version of vv */
1224 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ1);
1227 /* If we are using twin-range interactions where the long-range component
1228 * is only evaluated every nstcalclr>1 steps, we should do a special update
1229 * step to combine the long-range forces on these steps.
1230 * For nstcalclr=1 this is not done, since the forces would have been added
1231 * directly to the short-range forces already.
1233 * TODO Remove various aspects of VV+twin-range in master
1234 * branch, because VV integrators did not ever support
1235 * twin-range multiple time stepping with constraints.
1237 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1239 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
1240 f, bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
1241 ekind, M, wcycle, upd, bInitStep, etrtVELOCITY1,
1242 cr, nrnb, constr, &top->idef);
1244 if (bIterativeCase && do_per_step(step-1, ir->nstpcouple) && !bInitStep)
1246 gmx_iterate_init(&iterate, TRUE);
1248 /* for iterations, we save these vectors, as we will be self-consistently iterating
1251 /*#### UPDATE EXTENDED VARIABLES IN TROTTER FORMULATION */
1253 /* save the state */
1254 if (iterate.bIterationActive)
1256 copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
1259 bFirstIterate = TRUE;
1260 while (bFirstIterate || iterate.bIterationActive)
1262 if (iterate.bIterationActive)
1264 copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
1265 if (bFirstIterate && bTrotter)
1267 /* The first time through, we need a decent first estimate
1268 of veta(t+dt) to compute the constraints. Do
1269 this by computing the box volume part of the
1270 trotter integration at this time. Nothing else
1271 should be changed by this routine here. If
1272 !(first time), we start with the previous value
1275 veta_save = state->veta;
1276 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ0);
1277 vetanew = state->veta;
1278 state->veta = veta_save;
1283 if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
1285 update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
1286 state, fr->bMolPBC, graph, f,
1287 &top->idef, shake_vir, NULL,
1288 cr, nrnb, wcycle, upd, constr,
1289 bInitStep, TRUE, bCalcVir, vetanew);
1291 if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
1293 /* Correct the virial for multiple time stepping */
1294 m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
1297 if (!bOK && !bFFscan)
1299 gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
1305 /* Need to unshift here if a do_force has been
1306 called in the previous step */
1307 unshift_self(graph, state->box, state->x);
1310 /* if VV, compute the pressure and constraints */
1311 /* For VV2, we strictly only need this if using pressure
1312 * control, but we really would like to have accurate pressures
1314 * Think about ways around this in the future?
1315 * For now, keep this choice in comments.
1317 /*bPres = (ir->eI==eiVV || IR_NPT_TROTTER(ir)); */
1318 /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && IR_NPT_TROTTER(ir)));*/
1320 bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
1321 if (bCalcEner && ir->eI == eiVVAK) /*MRS: 7/9/2010 -- this still doesn't fix it?*/
1323 bSumEkinhOld = TRUE;
1325 /* for vv, the first half of the integration actually corresponds to the previous step.
1326 So we need information from the last step in the first half of the integration */
1327 if (bGStat || do_per_step(step-1, nstglobalcomm))
1329 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1330 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1331 constr, NULL, FALSE, state->box,
1332 top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
1335 | (bTemp ? CGLO_TEMPERATURE : 0)
1336 | (bPres ? CGLO_PRESSURE : 0)
1337 | (bPres ? CGLO_CONSTRAINT : 0)
1338 | ((iterate.bIterationActive) ? CGLO_ITERATE : 0)
1339 | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
1342 /* explanation of above:
1343 a) We compute Ekin at the full time step
1344 if 1) we are using the AveVel Ekin, and it's not the
1345 initial step, or 2) if we are using AveEkin, but need the full
1346 time step kinetic energy for the pressure (always true now, since we want accurate statistics).
1347 b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
1348 EkinAveVel because it's needed for the pressure */
1350 /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
1355 m_add(force_vir, shake_vir, total_vir); /* we need the un-dispersion corrected total vir here */
1356 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ2);
1363 /* We need the kinetic energy at minus the half step for determining
1364 * the full step kinetic energy and possibly for T-coupling.*/
1365 /* This may not be quite working correctly yet . . . . */
1366 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1367 wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
1368 constr, NULL, FALSE, state->box,
1369 top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
1370 CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
1375 if (iterate.bIterationActive &&
1376 done_iterating(cr, fplog, step, &iterate, bFirstIterate,
1377 state->veta, &vetanew))
1381 bFirstIterate = FALSE;
1384 if (bTrotter && !bInitStep)
1386 copy_mat(shake_vir, state->svir_prev);
1387 copy_mat(force_vir, state->fvir_prev);
1388 if (IR_NVT_TROTTER(ir) && ir->eI == eiVV)
1390 /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
1391 enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, NULL, (ir->eI == eiVV), FALSE, FALSE);
1392 enerd->term[F_EKIN] = trace(ekind->ekin);
1395 /* if it's the initial step, we performed this first step just to get the constraint virial */
1396 if (bInitStep && ir->eI == eiVV)
1398 copy_rvecn(cbuf, state->v, 0, state->natoms);
1401 GMX_MPE_LOG(ev_timestep1);
1404 /* MRS -- now done iterating -- compute the conserved quantity */
1407 saved_conserved_quantity = compute_conserved_from_auxiliary(ir, state, &MassQ);
1410 last_ekin = enerd->term[F_EKIN];
1412 if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
1414 saved_conserved_quantity -= enerd->term[F_DISPCORR];
1416 /* sum up the foreign energy and dhdl terms for vv. currently done every step so that dhdl is correct in the .edr */
1419 sum_dhdl(enerd, state->lambda, ir->fepvals);
1423 /* ######## END FIRST UPDATE STEP ############## */
1424 /* ######## If doing VV, we now have v(dt) ###### */
1427 /* perform extended ensemble sampling in lambda - we don't
1428 actually move to the new state before outputting
1429 statistics, but if performing simulated tempering, we
1430 do update the velocities and the tau_t. */
1432 lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state, &state->dfhist, step, mcrng, state->v, mdatoms);
1433 /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
1434 copy_df_history(&state_global->dfhist,&state->dfhist);
1436 /* ################## START TRAJECTORY OUTPUT ################# */
1438 /* Now we have the energies and forces corresponding to the
1439 * coordinates at time t. We must output all of this before
1441 * for RerunMD t is read from input trajectory
1443 GMX_MPE_LOG(ev_output_start);
1446 if (do_per_step(step, ir->nstxout))
1448 mdof_flags |= MDOF_X;
1450 if (do_per_step(step, ir->nstvout))
1452 mdof_flags |= MDOF_V;
1454 if (do_per_step(step, ir->nstfout))
1456 mdof_flags |= MDOF_F;
1458 if (do_per_step(step, ir->nstxtcout))
1460 mdof_flags |= MDOF_XTC;
1464 mdof_flags |= MDOF_CPT;
1468 #if defined(GMX_FAHCORE) || defined(GMX_WRITELASTSTEP)
1471 /* Enforce writing positions and velocities at end of run */
1472 mdof_flags |= (MDOF_X | MDOF_V);
1478 fcReportProgress( ir->nsteps, step );
1481 #if defined(__native_client__)
1482 fcCheckin(MASTER(cr));
1485 /* sync bCPT and fc record-keeping */
1486 if (bCPT && MASTER(cr))
1488 fcRequestCheckPoint();
1492 if (mdof_flags != 0)
1494 wallcycle_start(wcycle, ewcTRAJ);
1497 if (state->flags & (1<<estLD_RNG))
1499 get_stochd_state(upd, state);
1501 if (state->flags & (1<<estMC_RNG))
1503 get_mc_state(mcrng, state);
1509 state_global->ekinstate.bUpToDate = FALSE;
1513 update_ekinstate(&state_global->ekinstate, ekind);
1514 state_global->ekinstate.bUpToDate = TRUE;
1516 update_energyhistory(&state_global->enerhist, mdebin);
1519 write_traj(fplog, cr, outf, mdof_flags, top_global,
1520 step, t, state, state_global, f, f_global, &n_xtc, &x_xtc);
1527 if (bLastStep && step_rel == ir->nsteps &&
1528 (Flags & MD_CONFOUT) && MASTER(cr) &&
1529 !bRerunMD && !bFFscan)
1531 /* x and v have been collected in write_traj,
1532 * because a checkpoint file will always be written
1535 fprintf(stderr, "\nWriting final coordinates.\n");
1538 /* Make molecules whole only for confout writing */
1539 do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, state_global->x);
1541 write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
1542 *top_global->name, top_global,
1543 state_global->x, state_global->v,
1544 ir->ePBC, state->box);
1547 wallcycle_stop(wcycle, ewcTRAJ);
1549 GMX_MPE_LOG(ev_output_finish);
1551 /* kludge -- virial is lost with restart for NPT control. Must restart */
1552 if (bStartingFromCpt && bVV)
1554 copy_mat(state->svir_prev, shake_vir);
1555 copy_mat(state->fvir_prev, force_vir);
1557 /* ################## END TRAJECTORY OUTPUT ################ */
1559 /* Determine the wallclock run time up till now */
1560 run_time = gmx_gettime() - (double)runtime->real;
1562 /* Check whether everything is still allright */
1563 if (((int)gmx_get_stop_condition() > handled_stop_condition)
1564 #ifdef GMX_THREAD_MPI
1569 /* this is just make gs.sig compatible with the hack
1570 of sending signals around by MPI_Reduce with together with
1572 if (gmx_get_stop_condition() == gmx_stop_cond_next_ns)
1574 gs.sig[eglsSTOPCOND] = 1;
1576 if (gmx_get_stop_condition() == gmx_stop_cond_next)
1578 gs.sig[eglsSTOPCOND] = -1;
1580 /* < 0 means stop at next step, > 0 means stop at next NS step */
1584 "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
1585 gmx_get_signal_name(),
1586 gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
1590 "\n\nReceived the %s signal, stopping at the next %sstep\n\n",
1591 gmx_get_signal_name(),
1592 gs.sig[eglsSTOPCOND] == 1 ? "NS " : "");
1594 handled_stop_condition = (int)gmx_get_stop_condition();
1596 else if (MASTER(cr) && (bNS || ir->nstlist <= 0) &&
1597 (max_hours > 0 && run_time > max_hours*60.0*60.0*0.99) &&
1598 gs.sig[eglsSTOPCOND] == 0 && gs.set[eglsSTOPCOND] == 0)
1600 /* Signal to terminate the run */
1601 gs.sig[eglsSTOPCOND] = 1;
1604 fprintf(fplog, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
1606 fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n", gmx_step_str(step, sbuf), max_hours*0.99);
1609 if (bResetCountersHalfMaxH && MASTER(cr) &&
1610 run_time > max_hours*60.0*60.0*0.495)
1612 gs.sig[eglsRESETCOUNTERS] = 1;
1615 if (ir->nstlist == -1 && !bRerunMD)
1617 /* When bGStatEveryStep=FALSE, global_stat is only called
1618 * when we check the atom displacements, not at NS steps.
1619 * This means that also the bonded interaction count check is not
1620 * performed immediately after NS. Therefore a few MD steps could
1621 * be performed with missing interactions.
1622 * But wrong energies are never written to file,
1623 * since energies are only written after global_stat
1626 if (step >= nlh.step_nscheck)
1628 nlh.nabnsb = natoms_beyond_ns_buffer(ir, fr, &top->cgs,
1629 nlh.scale_tot, state->x);
1633 /* This is not necessarily true,
1634 * but step_nscheck is determined quite conservatively.
1640 /* In parallel we only have to check for checkpointing in steps
1641 * where we do global communication,
1642 * otherwise the other nodes don't know.
1644 if (MASTER(cr) && ((bGStat || !PAR(cr)) &&
1647 run_time >= nchkpt*cpt_period*60.0)) &&
1648 gs.set[eglsCHKPT] == 0)
1650 gs.sig[eglsCHKPT] = 1;
1653 /* at the start of step, randomize or scale the velocities (trotter done elsewhere) */
1658 update_tcouple(fplog, step, ir, state, ekind, wcycle, upd, &MassQ, mdatoms);
1660 if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
1662 gmx_bool bIfRandomize;
1663 bIfRandomize = update_randomize_velocities(ir, step, mdatoms, state, upd, &top->idef, constr, DOMAINDECOMP(cr));
1664 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1665 if (constr && bIfRandomize)
1667 update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
1668 state, fr->bMolPBC, graph, f,
1669 &top->idef, tmp_vir, NULL,
1670 cr, nrnb, wcycle, upd, constr,
1671 bInitStep, TRUE, bCalcVir, vetanew);
1676 if (bIterativeCase && do_per_step(step, ir->nstpcouple))
1678 gmx_iterate_init(&iterate, TRUE);
1679 /* for iterations, we save these vectors, as we will be redoing the calculations */
1680 copy_coupling_state(state, bufstate, ekind, ekind_save, &(ir->opts));
1683 bFirstIterate = TRUE;
1684 while (bFirstIterate || iterate.bIterationActive)
1686 /* We now restore these vectors to redo the calculation with improved extended variables */
1687 if (iterate.bIterationActive)
1689 copy_coupling_state(bufstate, state, ekind_save, ekind, &(ir->opts));
1692 /* We make the decision to break or not -after- the calculation of Ekin and Pressure,
1693 so scroll down for that logic */
1695 /* ######### START SECOND UPDATE STEP ################# */
1696 GMX_MPE_LOG(ev_update_start);
1697 /* Box is changed in update() when we do pressure coupling,
1698 * but we should still use the old box for energy corrections and when
1699 * writing it to the energy file, so it matches the trajectory files for
1700 * the same timestep above. Make a copy in a separate array.
1702 copy_mat(state->box, lastbox);
1707 if (!(bRerunMD && !rerun_fr.bV && !bForceUpdate))
1709 wallcycle_start(wcycle, ewcUPDATE);
1710 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1713 if (iterate.bIterationActive)
1721 /* we use a new value of scalevir to converge the iterations faster */
1722 scalevir = tracevir/trace(shake_vir);
1724 msmul(shake_vir, scalevir, shake_vir);
1725 m_add(force_vir, shake_vir, total_vir);
1726 clear_mat(shake_vir);
1728 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
1729 /* We can only do Berendsen coupling after we have summed
1730 * the kinetic energy or virial. Since the happens
1731 * in global_state after update, we should only do it at
1732 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1737 update_tcouple(fplog, step, ir, state, ekind, wcycle, upd, &MassQ, mdatoms);
1738 update_pcouple(fplog, step, ir, state, pcoupl_mu, M, wcycle,
1744 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1746 /* velocity half-step update */
1747 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
1748 bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
1749 ekind, M, wcycle, upd, FALSE, etrtVELOCITY2,
1750 cr, nrnb, constr, &top->idef);
1753 /* Above, initialize just copies ekinh into ekin,
1754 * it doesn't copy position (for VV),
1755 * and entire integrator for MD.
1758 if (ir->eI == eiVVAK)
1760 copy_rvecn(state->x, cbuf, 0, state->natoms);
1762 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1764 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
1765 bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
1766 ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
1767 wallcycle_stop(wcycle, ewcUPDATE);
1769 update_constraints(fplog, step, &dvdl_constr, ir, ekind, mdatoms, state,
1770 fr->bMolPBC, graph, f,
1771 &top->idef, shake_vir, force_vir,
1772 cr, nrnb, wcycle, upd, constr,
1773 bInitStep, FALSE, bCalcVir, state->veta);
1775 if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
1777 /* Correct the virial for multiple time stepping */
1778 m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
1781 if (ir->eI == eiVVAK)
1783 /* erase F_EKIN and F_TEMP here? */
1784 /* just compute the kinetic energy at the half step to perform a trotter step */
1785 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1786 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1787 constr, NULL, FALSE, lastbox,
1788 top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
1789 cglo_flags | CGLO_TEMPERATURE
1791 wallcycle_start(wcycle, ewcUPDATE);
1792 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
1793 /* now we know the scaling, we can compute the positions again again */
1794 copy_rvecn(cbuf, state->x, 0, state->natoms);
1796 bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
1798 update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
1799 bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
1800 ekind, M, wcycle, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
1801 wallcycle_stop(wcycle, ewcUPDATE);
1803 /* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
1804 /* are the small terms in the shake_vir here due
1805 * to numerical errors, or are they important
1806 * physically? I'm thinking they are just errors, but not completely sure.
1807 * For now, will call without actually constraining, constr=NULL*/
1808 update_constraints(fplog, step, NULL, ir, ekind, mdatoms,
1809 state, fr->bMolPBC, graph, f,
1810 &top->idef, tmp_vir, force_vir,
1811 cr, nrnb, wcycle, upd, NULL,
1812 bInitStep, FALSE, bCalcVir,
1815 if (!bOK && !bFFscan)
1817 gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
1820 if (fr->bSepDVDL && fplog && do_log)
1822 fprintf(fplog, sepdvdlformat, "Constraint dV/dl", 0.0, dvdl_constr);
1826 /* this factor or 2 correction is necessary
1827 because half of the constraint force is removed
1828 in the vv step, so we have to double it. See
1829 the Redmine issue #1255. It is not yet clear
1830 if the factor of 2 is exact, or just a very
1831 good approximation, and this will be
1832 investigated. The next step is to see if this
1833 can be done adding a dhdl contribution from the
1834 rattle step, but this is somewhat more
1835 complicated with the current code. Will be
1836 investigated, hopefully for 4.6.3. However,
1837 this current solution is much better than
1838 having it completely wrong.
1840 enerd->term[F_DVDL_CONSTR] += 2*dvdl_constr;
1844 enerd->term[F_DVDL_CONSTR] += dvdl_constr;
1849 /* Need to unshift here */
1850 unshift_self(graph, state->box, state->x);
1853 GMX_BARRIER(cr->mpi_comm_mygroup);
1854 GMX_MPE_LOG(ev_update_finish);
1858 wallcycle_start(wcycle, ewcVSITECONSTR);
1861 shift_self(graph, state->box, state->x);
1863 construct_vsites(fplog, vsite, state->x, nrnb, ir->delta_t, state->v,
1864 top->idef.iparams, top->idef.il,
1865 fr->ePBC, fr->bMolPBC, graph, cr, state->box);
1869 unshift_self(graph, state->box, state->x);
1871 wallcycle_stop(wcycle, ewcVSITECONSTR);
1874 /* ############## IF NOT VV, Calculate globals HERE, also iterate constraints ############ */
1875 /* With Leap-Frog we can skip compute_globals at
1876 * non-communication steps, but we need to calculate
1877 * the kinetic energy one step before communication.
1879 if (bGStat || (!EI_VV(ir->eI) && do_per_step(step+1, nstglobalcomm)))
1881 if (ir->nstlist == -1 && bFirstIterate)
1883 gs.sig[eglsNABNSB] = nlh.nabnsb;
1885 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, state_global, mdatoms, nrnb, vcm,
1886 wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
1888 bFirstIterate ? &gs : NULL,
1889 (step_rel % gs.nstms == 0) &&
1890 (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
1892 top_global, &pcurr, top_global->natoms, &bSumEkinhOld,
1894 | (!EI_VV(ir->eI) || bRerunMD ? CGLO_ENERGY : 0)
1895 | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
1896 | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
1897 | (!EI_VV(ir->eI) || bRerunMD ? CGLO_PRESSURE : 0)
1898 | (iterate.bIterationActive ? CGLO_ITERATE : 0)
1899 | (bFirstIterate ? CGLO_FIRSTITERATE : 0)
1902 if (ir->nstlist == -1 && bFirstIterate)
1904 nlh.nabnsb = gs.set[eglsNABNSB];
1905 gs.set[eglsNABNSB] = 0;
1908 /* bIterate is set to keep it from eliminating the old ekin kinetic energy terms */
1909 /* ############# END CALC EKIN AND PRESSURE ################# */
1911 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
1912 the virial that should probably be addressed eventually. state->veta has better properies,
1913 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
1914 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
1916 if (iterate.bIterationActive &&
1917 done_iterating(cr, fplog, step, &iterate, bFirstIterate,
1918 trace(shake_vir), &tracevir))
1922 bFirstIterate = FALSE;
1925 if (!bVV || bRerunMD)
1927 /* sum up the foreign energy and dhdl terms for md and sd. currently done every step so that dhdl is correct in the .edr */
1928 sum_dhdl(enerd, state->lambda, ir->fepvals);
1930 update_box(fplog, step, ir, mdatoms, state, graph, f,
1931 ir->nstlist == -1 ? &nlh.scale_tot : NULL, pcoupl_mu, nrnb, wcycle, upd, bInitStep, FALSE);
1933 /* ################# END UPDATE STEP 2 ################# */
1934 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1936 /* The coordinates (x) were unshifted in update */
1937 if (bFFscan && (shellfc == NULL || bConverged))
1939 if (print_forcefield(fplog, enerd->term, mdatoms->homenr,
1941 &(top_global->mols), mdatoms->massT, pres))
1945 fprintf(stderr, "\n");
1951 /* We will not sum ekinh_old,
1952 * so signal that we still have to do it.
1954 bSumEkinhOld = TRUE;
1959 /* Only do GCT when the relaxation of shells (minimization) has converged,
1960 * otherwise we might be coupling to bogus energies.
1961 * In parallel we must always do this, because the other sims might
1965 /* Since this is called with the new coordinates state->x, I assume
1966 * we want the new box state->box too. / EL 20040121
1968 do_coupling(fplog, oenv, nfile, fnm, tcr, t, step, enerd->term, fr,
1970 mdatoms, &(top->idef), mu_aver,
1971 top_global->mols.nr, cr,
1972 state->box, total_vir, pres,
1973 mu_tot, state->x, f, bConverged);
1977 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1979 /* use the directly determined last velocity, not actually the averaged half steps */
1980 if (bTrotter && ir->eI == eiVV)
1982 enerd->term[F_EKIN] = last_ekin;
1984 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1988 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1992 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + compute_conserved_from_auxiliary(ir, state, &MassQ);
1994 /* Check for excessively large energies */
1998 real etot_max = 1e200;
2000 real etot_max = 1e30;
2002 if (fabs(enerd->term[F_ETOT]) > etot_max)
2004 fprintf(stderr, "Energy too large (%g), giving up\n",
2005 enerd->term[F_ETOT]);
2008 /* ######### END PREPARING EDR OUTPUT ########### */
2010 /* Time for performance */
2011 if (((step % stepout) == 0) || bLastStep)
2013 runtime_upd_proc(runtime);
2019 gmx_bool do_dr, do_or;
2021 if (fplog && do_log && bDoExpanded)
2023 /* only needed if doing expanded ensemble */
2024 PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
2025 &state_global->dfhist, state->fep_state, ir->nstlog, step);
2027 if (!(bStartingFromCpt && (EI_VV(ir->eI))))
2031 upd_mdebin(mdebin, bDoDHDL, TRUE,
2032 t, mdatoms->tmass, enerd, state,
2033 ir->fepvals, ir->expandedvals, lastbox,
2034 shake_vir, force_vir, total_vir, pres,
2035 ekind, mu_tot, constr);
2039 upd_mdebin_step(mdebin);
2042 do_dr = do_per_step(step, ir->nstdisreout);
2043 do_or = do_per_step(step, ir->nstorireout);
2045 print_ebin(outf->fp_ene, do_ene, do_dr, do_or, do_log ? fplog : NULL,
2047 eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
2049 if (ir->ePull != epullNO)
2051 pull_print_output(ir->pull, step, t);
2054 if (do_per_step(step, ir->nstlog))
2056 if (fflush(fplog) != 0)
2058 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
2064 /* Have to do this part _after_ outputting the logfile and the edr file */
2065 /* Gets written into the state at the beginning of next loop*/
2066 state->fep_state = lamnew;
2069 /* Remaining runtime */
2070 if (MULTIMASTER(cr) && (do_verbose || gmx_got_usr_signal()) && !bPMETuneRunning)
2074 fprintf(stderr, "\n");
2076 print_time(stderr, runtime, step, ir, cr);
2079 /* Replica exchange */
2081 if ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
2082 do_per_step(step, repl_ex_nst))
2084 bExchanged = replica_exchange(fplog, cr, repl_ex,
2085 state_global, enerd,
2088 if (bExchanged && DOMAINDECOMP(cr))
2090 dd_partition_system(fplog, step, cr, TRUE, 1,
2091 state_global, top_global, ir,
2092 state, &f, mdatoms, top, fr,
2093 vsite, shellfc, constr,
2094 nrnb, wcycle, FALSE);
2100 bStartingFromCpt = FALSE;
2102 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
2103 /* With all integrators, except VV, we need to retain the pressure
2104 * at the current step for coupling at the next step.
2106 if ((state->flags & (1<<estPRES_PREV)) &&
2108 (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
2110 /* Store the pressure in t_state for pressure coupling
2111 * at the next MD step.
2113 copy_mat(pres, state->pres_prev);
2116 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
2118 if ( (membed != NULL) && (!bLastStep) )
2120 rescale_membed(step_rel, membed, state_global->x);
2127 /* read next frame from input trajectory */
2128 bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
2133 rerun_parallel_comm(cr, &rerun_fr, &bNotLastFrame);
2137 if (!bRerunMD || !rerun_fr.bStep)
2139 /* increase the MD step number */
2144 cycles = wallcycle_stop(wcycle, ewcSTEP);
2145 if (DOMAINDECOMP(cr) && wcycle)
2147 dd_cycles_add(cr->dd, cycles, ddCyclStep);
2150 if (bPMETuneRunning || bPMETuneTry)
2152 /* PME grid + cut-off optimization with GPUs or PME nodes */
2154 /* Count the total cycles over the last steps */
2155 cycles_pmes += cycles;
2157 /* We can only switch cut-off at NS steps */
2158 if (step % ir->nstlist == 0)
2160 /* PME grid + cut-off optimization with GPUs or PME nodes */
2163 if (DDMASTER(cr->dd))
2165 /* PME node load is too high, start tuning */
2166 bPMETuneRunning = (dd_pme_f_ratio(cr->dd) >= 1.05);
2168 dd_bcast(cr->dd, sizeof(gmx_bool), &bPMETuneRunning);
2170 if (bPMETuneRunning || step_rel > ir->nstlist*50)
2172 bPMETuneTry = FALSE;
2175 if (bPMETuneRunning)
2177 /* init_step might not be a multiple of nstlist,
2178 * but the first cycle is always skipped anyhow.
2181 pme_load_balance(pme_loadbal, cr,
2182 (bVerbose && MASTER(cr)) ? stderr : NULL,
2184 ir, state, cycles_pmes,
2185 fr->ic, fr->nbv, &fr->pmedata,
2188 /* Update constants in forcerec/inputrec to keep them in sync with fr->ic */
2189 fr->ewaldcoeff = fr->ic->ewaldcoeff;
2190 fr->rlist = fr->ic->rlist;
2191 fr->rlistlong = fr->ic->rlistlong;
2192 fr->rcoulomb = fr->ic->rcoulomb;
2193 fr->rvdw = fr->ic->rvdw;
2199 if (step_rel == wcycle_get_reset_counters(wcycle) ||
2200 gs.set[eglsRESETCOUNTERS] != 0)
2202 /* Reset all the counters related to performance over the run */
2203 reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, runtime,
2204 fr->nbv != NULL && fr->nbv->bUseGPU ? fr->nbv->cu_nbv : NULL);
2205 wcycle_set_reset_counters(wcycle, -1);
2206 if (!(cr->duty & DUTY_PME))
2208 /* Tell our PME node to reset its counters */
2209 gmx_pme_send_resetcounters(cr, step);
2211 /* Correct max_hours for the elapsed time */
2212 max_hours -= run_time/(60.0*60.0);
2213 bResetCountersHalfMaxH = FALSE;
2214 gs.set[eglsRESETCOUNTERS] = 0;
2218 /* End of main MD loop */
2222 runtime_end(runtime);
2224 if (bRerunMD && MASTER(cr))
2229 if (!(cr->duty & DUTY_PME))
2231 /* Tell the PME only node to finish */
2232 gmx_pme_send_finish(cr);
2237 if (ir->nstcalcenergy > 0 && !bRerunMD)
2239 print_ebin(outf->fp_ene, FALSE, FALSE, FALSE, fplog, step, t,
2240 eprAVER, FALSE, mdebin, fcd, groups, &(ir->opts));
2248 if (ir->nstlist == -1 && nlh.nns > 0 && fplog)
2250 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)));
2251 fprintf(fplog, "Average number of atoms that crossed the half buffer length: %.1f\n\n", nlh.ab/nlh.nns);
2254 if (pme_loadbal != NULL)
2256 pme_loadbal_done(pme_loadbal, cr, fplog,
2257 fr->nbv != NULL && fr->nbv->bUseGPU);
2260 if (shellfc && fplog)
2262 fprintf(fplog, "Fraction of iterations that converged: %.2f %%\n",
2263 (nconverged*100.0)/step_rel);
2264 fprintf(fplog, "Average number of force evaluations per MD step: %.2f\n\n",
2268 if (repl_ex_nst > 0 && MASTER(cr))
2270 print_replica_exchange_statistics(fplog, repl_ex);
2273 runtime->nsteps_done = step_rel;