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37 * \brief Implements the loop for simulation reruns
39 * \author Pascal Merz <pascal.merz@colorado.edu>
40 * \ingroup module_mdrun
52 #include "gromacs/applied_forces/awh/awh.h"
53 #include "gromacs/commandline/filenm.h"
54 #include "gromacs/domdec/collect.h"
55 #include "gromacs/domdec/dlbtiming.h"
56 #include "gromacs/domdec/domdec.h"
57 #include "gromacs/domdec/domdec_network.h"
58 #include "gromacs/domdec/domdec_struct.h"
59 #include "gromacs/domdec/mdsetup.h"
60 #include "gromacs/domdec/partition.h"
61 #include "gromacs/essentialdynamics/edsam.h"
62 #include "gromacs/ewald/pme_load_balancing.h"
63 #include "gromacs/ewald/pme_pp.h"
64 #include "gromacs/fileio/trxio.h"
65 #include "gromacs/gmxlib/network.h"
66 #include "gromacs/gmxlib/nrnb.h"
67 #include "gromacs/gpu_utils/gpu_utils.h"
68 #include "gromacs/listed_forces/listed_forces.h"
69 #include "gromacs/math/functions.h"
70 #include "gromacs/math/utilities.h"
71 #include "gromacs/math/vec.h"
72 #include "gromacs/math/vectypes.h"
73 #include "gromacs/mdlib/checkpointhandler.h"
74 #include "gromacs/mdlib/compute_io.h"
75 #include "gromacs/mdlib/constr.h"
76 #include "gromacs/mdlib/ebin.h"
77 #include "gromacs/mdlib/enerdata_utils.h"
78 #include "gromacs/mdlib/energyoutput.h"
79 #include "gromacs/mdlib/expanded.h"
80 #include "gromacs/mdlib/force.h"
81 #include "gromacs/mdlib/force_flags.h"
82 #include "gromacs/mdlib/forcerec.h"
83 #include "gromacs/mdlib/freeenergyparameters.h"
84 #include "gromacs/mdlib/md_support.h"
85 #include "gromacs/mdlib/mdatoms.h"
86 #include "gromacs/mdlib/mdoutf.h"
87 #include "gromacs/mdlib/membed.h"
88 #include "gromacs/mdlib/resethandler.h"
89 #include "gromacs/mdlib/sighandler.h"
90 #include "gromacs/mdlib/simulationsignal.h"
91 #include "gromacs/mdlib/stat.h"
92 #include "gromacs/mdlib/stophandler.h"
93 #include "gromacs/mdlib/tgroup.h"
94 #include "gromacs/mdlib/trajectory_writing.h"
95 #include "gromacs/mdlib/update.h"
96 #include "gromacs/mdlib/vcm.h"
97 #include "gromacs/mdlib/vsite.h"
98 #include "gromacs/mdrunutility/handlerestart.h"
99 #include "gromacs/mdrunutility/multisim.h"
100 #include "gromacs/mdrunutility/printtime.h"
101 #include "gromacs/mdtypes/awh_history.h"
102 #include "gromacs/mdtypes/awh_params.h"
103 #include "gromacs/mdtypes/commrec.h"
104 #include "gromacs/mdtypes/df_history.h"
105 #include "gromacs/mdtypes/energyhistory.h"
106 #include "gromacs/mdtypes/forcebuffers.h"
107 #include "gromacs/mdtypes/forcerec.h"
108 #include "gromacs/mdtypes/group.h"
109 #include "gromacs/mdtypes/inputrec.h"
110 #include "gromacs/mdtypes/interaction_const.h"
111 #include "gromacs/mdtypes/md_enums.h"
112 #include "gromacs/mdtypes/mdatom.h"
113 #include "gromacs/mdtypes/mdrunoptions.h"
114 #include "gromacs/mdtypes/observableshistory.h"
115 #include "gromacs/mdtypes/simulation_workload.h"
116 #include "gromacs/mdtypes/state.h"
117 #include "gromacs/mimic/utilities.h"
118 #include "gromacs/pbcutil/pbc.h"
119 #include "gromacs/pulling/pull.h"
120 #include "gromacs/swap/swapcoords.h"
121 #include "gromacs/timing/wallcycle.h"
122 #include "gromacs/timing/walltime_accounting.h"
123 #include "gromacs/topology/atoms.h"
124 #include "gromacs/topology/idef.h"
125 #include "gromacs/topology/mtop_util.h"
126 #include "gromacs/topology/topology.h"
127 #include "gromacs/trajectory/trajectoryframe.h"
128 #include "gromacs/utility/basedefinitions.h"
129 #include "gromacs/utility/cstringutil.h"
130 #include "gromacs/utility/fatalerror.h"
131 #include "gromacs/utility/logger.h"
132 #include "gromacs/utility/real.h"
134 #include "legacysimulator.h"
135 #include "replicaexchange.h"
138 using gmx::SimulationSignaller;
139 using gmx::VirtualSitesHandler;
141 /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
143 * \param[in] rerunFrame The trajectory frame to compute energy/forces for
144 * \param[in,out] globalState The global state container
145 * \param[in] constructVsites When true, vsite coordinates are constructed
146 * \param[in] vsite Vsite setup, can be nullptr when \p constructVsites = false
147 * \param[in] timeStep Time step, used for constructing vsites
149 static void prepareRerunState(const t_trxframe& rerunFrame,
150 t_state* globalState,
151 bool constructVsites,
152 const VirtualSitesHandler* vsite,
155 auto x = makeArrayRef(globalState->x);
156 auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec*>(rerunFrame.x), globalState->natoms);
157 std::copy(rerunX.begin(), rerunX.end(), x.begin());
158 copy_mat(rerunFrame.box, globalState->box);
162 GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
164 vsite->construct(globalState->x, timeStep, globalState->v, globalState->box);
168 void gmx::LegacySimulator::do_rerun()
170 // TODO Historically, the EM and MD "integrators" used different
171 // names for the t_inputrec *parameter, but these must have the
172 // same name, now that it's a member of a struct. We use this ir
173 // alias to avoid a large ripple of nearly useless changes.
174 // t_inputrec is being replaced by IMdpOptionsProvider, so this
175 // will go away eventually.
176 const t_inputrec* ir = inputrec;
177 int64_t step, step_rel;
179 bool isLastStep = false;
180 bool doFreeEnergyPerturbation = false;
181 unsigned int force_flags;
182 tensor force_vir, shake_vir, total_vir, pres;
183 t_trxstatus* status = nullptr;
186 gmx_localtop_t top(top_global->ffparams);
188 gmx_global_stat_t gstat;
189 gmx_shellfc_t* shellfc;
193 /* Domain decomposition could incorrectly miss a bonded
194 interaction, but checking for that requires a global
195 communication stage, which does not otherwise happen in DD
196 code. So we do that alongside the first global energy reduction
197 after a new DD is made. These variables handle whether the
198 check happens, and the result it returns. */
199 bool shouldCheckNumberOfBondedInteractions = false;
200 int totalNumberOfBondedInteractions = -1;
202 SimulationSignals signals;
203 // Most global communnication stages don't propagate mdrun
204 // signals, and will use this object to achieve that.
205 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
210 "Note that it is planned that the command gmx mdrun -rerun will "
211 "be available in a different form in a future version of GROMACS, "
212 "e.g. gmx rerun -f.");
214 if (ir->efep != efepNO
215 && (mdAtoms->mdatoms()->nMassPerturbed > 0 || (constr && constr->havePerturbedConstraints())))
218 "Perturbed masses or constraints are not supported by rerun. "
219 "Either make a .tpr without mass and constraint perturbation, "
220 "or use GROMACS 2018.4, 2018.5 or later 2018 version.");
224 gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
228 gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
232 gmx_fatal(FARGS, "AWH not supported by rerun.");
234 if (replExParams.exchangeInterval > 0)
236 gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
238 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
240 gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
244 gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
248 gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
250 if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](int i) {
254 gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
257 /* Rerun can't work if an output file name is the same as the input file name.
258 * If this is the case, the user will get an error telling them what the issue is.
260 if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0
261 || strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
264 "When using mdrun -rerun, the name of the input trajectory file "
265 "%s cannot be identical to the name of an output file (whether "
266 "given explicitly with -o or -x, or by default)",
267 opt2fn("-rerun", nfile, fnm));
270 /* Settings for rerun */
272 // TODO: Avoid changing inputrec (#3854)
273 auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
274 nonConstInputrec->nstlist = 1;
275 nonConstInputrec->nstcalcenergy = 1;
276 nonConstInputrec->nstxout_compressed = 0;
278 int nstglobalcomm = 1;
279 const bool bNS = true;
281 const SimulationGroups* groups = &top_global->groups;
282 if (ir->eI == eiMimic)
284 auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
285 nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
287 int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
288 gmx::ArrayRef<real> lambda = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
289 initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
290 const bool simulationsShareState = false;
291 gmx_mdoutf* outf = init_mdoutf(fplog,
302 StartingBehavior::NewSimulation,
303 simulationsShareState,
305 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
309 mdoutf_get_fp_dhdl(outf),
311 StartingBehavior::NewSimulation,
312 simulationsShareState,
315 gstat = global_stat_init(ir);
317 /* Check for polarizable models and flexible constraints */
318 shellfc = init_shell_flexcon(fplog,
320 constr ? constr->numFlexibleConstraints() : 0,
323 runScheduleWork->simulationWork.useGpuPme);
326 double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
327 if ((io > 2000) && MASTER(cr))
329 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
333 // Local state only becomes valid now.
334 std::unique_ptr<t_state> stateInstance;
337 if (DOMAINDECOMP(cr))
339 stateInstance = std::make_unique<t_state>();
340 state = stateInstance.get();
341 dd_init_local_state(cr->dd, state_global, state);
343 /* Distribute the charge groups over the nodes from the master node */
344 dd_partition_system(fplog,
365 shouldCheckNumberOfBondedInteractions = true;
369 state_change_natoms(state_global, state_global->natoms);
370 /* Copy the pointer to the global state */
371 state = state_global;
373 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
376 auto mdatoms = mdAtoms->mdatoms();
378 // NOTE: The global state is no longer used at this point.
379 // But state_global is still used as temporary storage space for writing
380 // the global state to file and potentially for replica exchange.
381 // (Global topology should persist.)
383 update_mdatoms(mdatoms, state->lambda[efptMASS]);
385 if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
387 doFreeEnergyPerturbation = true;
393 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
394 bool bSumEkinhOld = false;
395 t_vcm* vcm = nullptr;
396 compute_globals(gstat,
401 makeConstArrayRef(state->x),
402 makeConstArrayRef(state->v),
413 gmx::ArrayRef<real>{},
416 &totalNumberOfBondedInteractions,
420 checkNumberOfBondedInteractions(mdlog,
422 totalNumberOfBondedInteractions,
425 makeConstArrayRef(state->x),
427 &shouldCheckNumberOfBondedInteractions);
432 "starting md rerun '%s', reading coordinates from"
433 " input trajectory '%s'\n\n",
435 opt2fn("-rerun", nfile, fnm));
436 if (mdrunOptions.verbose)
439 "Calculated time to finish depends on nsteps from "
440 "run input file,\nwhich may not correspond to the time "
441 "needed to process input trajectory.\n\n");
443 fprintf(fplog, "\n");
446 walltime_accounting_start_time(walltime_accounting);
447 wallcycle_start(wcycle, ewcRUN);
448 print_start(fplog, cr, walltime_accounting, "mdrun");
450 /***********************************************************
454 ************************************************************/
460 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
466 isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
467 if (rerun_fr.natoms != top_global->natoms)
470 "Number of atoms in trajectory (%d) does not match the "
471 "run input file (%d)\n",
476 if (ir->pbcType != PbcType::No)
481 "Rerun trajectory frame step %" PRId64
483 "does not contain a box, while pbc is used",
487 if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
490 "Rerun trajectory frame step %" PRId64
492 "has too small box dimensions",
502 "Rerun does not report kinetic energy, total energy, temperature, virial and "
507 rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
510 if (ir->pbcType != PbcType::No)
512 /* Set the shift vectors.
513 * Necessary here when have a static box different from the tpr box.
515 calc_shifts(rerun_fr.box, fr->shift_vec);
518 step = ir->init_step;
521 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
522 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
526 mdrunOptions.reproducible,
528 mdrunOptions.maximumHoursToRun,
533 walltime_accounting);
535 // we don't do counter resetting in rerun - finish will always be valid
536 walltime_accounting_set_valid_finish(walltime_accounting);
538 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
540 /* and stop now if we should */
541 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
544 wallcycle_start(wcycle, ewcSTEP);
548 step = rerun_fr.step;
549 step_rel = step - ir->init_step;
560 if (ir->efep != efepNO && MASTER(cr))
562 if (rerun_fr.bLambda)
564 ir->fepvals->init_lambda = rerun_fr.lambda;
568 if (rerun_fr.bFepState)
570 state->fep_state = rerun_fr.fep_state;
574 state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
579 const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
580 if (constructVsites && DOMAINDECOMP(cr))
583 "Vsite recalculation with -rerun is not implemented with domain "
585 "use a single rank");
587 prepareRerunState(rerun_fr, state_global, constructVsites, vsite, ir->delta_t);
590 isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
592 if (DOMAINDECOMP(cr))
594 /* Repartition the domain decomposition */
595 const bool bMasterState = true;
596 dd_partition_system(fplog,
616 mdrunOptions.verbose);
617 shouldCheckNumberOfBondedInteractions = true;
622 EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
625 if (ir->efep != efepNO)
627 update_mdatoms(mdatoms, state->lambda[efptMASS]);
630 force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
631 | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
632 GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
636 /* Now is the time to relax the shells */
637 relax_shell_flexcon(fplog,
640 mdrunOptions.verbose,
652 state->x.arrayRefWithPadding(),
653 state->v.arrayRefWithPadding(),
668 ddBalanceRegionHandler);
672 /* The coordinates (x) are shifted (to get whole molecules)
674 * This is parallellized as well, and does communication too.
675 * Check comments in sim_util.c
678 gmx_edsam* ed = nullptr;
692 state->x.arrayRefWithPadding(),
705 GMX_FORCE_NS | force_flags,
706 ddBalanceRegionHandler);
709 /* Now we have the energies and forces corresponding to the
710 * coordinates at time t.
713 const bool isCheckpointingStep = false;
714 const bool doRerun = true;
715 const bool bSumEkinhOld = false;
716 do_md_trajectory_writing(fplog,
736 mdrunOptions.writeConfout,
740 stopHandler->setSignal();
742 if (vsite != nullptr)
744 wallcycle_start(wcycle, ewcVSITECONSTR);
745 vsite->construct(state->x, ir->delta_t, state->v, state->box);
746 wallcycle_stop(wcycle, ewcVSITECONSTR);
750 const bool doInterSimSignal = false;
751 const bool doIntraSimSignal = true;
752 bool bSumEkinhOld = false;
753 t_vcm* vcm = nullptr;
754 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
756 compute_globals(gstat,
761 makeConstArrayRef(state->x),
762 makeConstArrayRef(state->v),
773 constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
776 &totalNumberOfBondedInteractions,
778 CGLO_GSTAT | CGLO_ENERGY
779 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
781 checkNumberOfBondedInteractions(mdlog,
783 totalNumberOfBondedInteractions,
786 makeConstArrayRef(state->x),
788 &shouldCheckNumberOfBondedInteractions);
791 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
792 the virial that should probably be addressed eventually. state->veta has better properies,
793 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
794 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
799 const bool bCalcEnerStep = true;
800 energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
808 PTCouplingArrays({ state->boxv,
809 state->nosehoover_xi,
810 state->nosehoover_vxi,
812 state->nhpres_vxi }),
822 const bool do_ene = true;
823 const bool do_log = true;
825 const bool do_dr = ir->nstdisreout != 0;
826 const bool do_or = ir->nstorireout != 0;
828 EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
829 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
833 do_log ? fplog : nullptr,
839 if (do_per_step(step, ir->nstlog))
841 if (fflush(fplog) != 0)
843 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
848 /* Print the remaining wall clock time for the run */
849 if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
853 fprintf(stderr, "\n");
855 print_time(stderr, walltime_accounting, step, ir, cr);
858 /* Ion/water position swapping.
859 * Not done in last step since trajectory writing happens before this call
860 * in the MD loop and exchanges would be lost anyway. */
861 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !isLastStep && do_per_step(step, ir->swap->nstswap))
863 const bool doRerun = true;
872 MASTER(cr) && mdrunOptions.verbose,
878 /* read next frame from input trajectory */
879 isLastStep = !read_next_frame(oenv, status, &rerun_fr);
884 rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
887 cycles = wallcycle_stop(wcycle, ewcSTEP);
888 if (DOMAINDECOMP(cr) && wcycle)
890 dd_cycles_add(cr->dd, cycles, ddCyclStep);
895 /* increase the MD step number */
900 /* End of main MD loop */
902 /* Closing TNG files can include compressing data. Therefore it is good to do that
903 * before stopping the time measurements. */
904 mdoutf_tng_close(outf);
906 /* Stop measuring walltime */
907 walltime_accounting_end_time(walltime_accounting);
914 if (!thisRankHasDuty(cr, DUTY_PME))
916 /* Tell the PME only node to finish */
917 gmx_pme_send_finish(cr);
922 done_shellfc(fplog, shellfc, step_rel);
924 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);