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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/output.h"
120 #include "gromacs/pulling/pull.h"
121 #include "gromacs/swap/swapcoords.h"
122 #include "gromacs/timing/wallcycle.h"
123 #include "gromacs/timing/walltime_accounting.h"
124 #include "gromacs/topology/atoms.h"
125 #include "gromacs/topology/idef.h"
126 #include "gromacs/topology/mtop_util.h"
127 #include "gromacs/topology/topology.h"
128 #include "gromacs/trajectory/trajectoryframe.h"
129 #include "gromacs/utility/basedefinitions.h"
130 #include "gromacs/utility/cstringutil.h"
131 #include "gromacs/utility/fatalerror.h"
132 #include "gromacs/utility/logger.h"
133 #include "gromacs/utility/real.h"
135 #include "legacysimulator.h"
136 #include "replicaexchange.h"
139 using gmx::SimulationSignaller;
140 using gmx::VirtualSitesHandler;
142 /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
144 * \param[in] rerunFrame The trajectory frame to compute energy/forces for
145 * \param[in,out] globalState The global state container
146 * \param[in] constructVsites When true, vsite coordinates are constructed
147 * \param[in] vsite Vsite setup, can be nullptr when \p constructVsites = false
149 static void prepareRerunState(const t_trxframe& rerunFrame,
150 t_state* globalState,
151 bool constructVsites,
152 const VirtualSitesHandler* vsite)
154 auto x = makeArrayRef(globalState->x);
155 auto rerunX = arrayRefFromArray(reinterpret_cast<gmx::RVec*>(rerunFrame.x), globalState->natoms);
156 std::copy(rerunX.begin(), rerunX.end(), x.begin());
157 copy_mat(rerunFrame.box, globalState->box);
161 GMX_ASSERT(vsite, "Need valid vsite for constructing vsites");
163 vsite->construct(globalState->x, globalState->v, globalState->box, gmx::VSiteOperation::PositionsAndVelocities);
167 void gmx::LegacySimulator::do_rerun()
169 // TODO Historically, the EM and MD "integrators" used different
170 // names for the t_inputrec *parameter, but these must have the
171 // same name, now that it's a member of a struct. We use this ir
172 // alias to avoid a large ripple of nearly useless changes.
173 // t_inputrec is being replaced by IMdpOptionsProvider, so this
174 // will go away eventually.
175 const t_inputrec* ir = inputrec;
176 int64_t step, step_rel;
178 bool isLastStep = false;
179 bool doFreeEnergyPerturbation = false;
180 unsigned int force_flags;
181 tensor force_vir, shake_vir, total_vir, pres;
182 t_trxstatus* status = nullptr;
185 gmx_localtop_t top(top_global.ffparams);
187 gmx_global_stat_t gstat;
188 gmx_shellfc_t* shellfc;
192 SimulationSignals signals;
193 // Most global communnication stages don't propagate mdrun
194 // signals, and will use this object to achieve that.
195 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
200 "Note that it is planned that the command gmx mdrun -rerun will "
201 "be available in a different form in a future version of GROMACS, "
202 "e.g. gmx rerun -f.");
204 if (ir->efep != FreeEnergyPerturbationType::No
205 && (mdAtoms->mdatoms()->nMassPerturbed > 0 || (constr && constr->havePerturbedConstraints())))
208 "Perturbed masses or constraints are not supported by rerun. "
209 "Either make a .tpr without mass and constraint perturbation, "
210 "or use GROMACS 2018.4, 2018.5 or later 2018 version.");
214 gmx_fatal(FARGS, "Expanded ensemble not supported by rerun.");
218 gmx_fatal(FARGS, "Simulated tempering not supported by rerun.");
222 gmx_fatal(FARGS, "AWH not supported by rerun.");
224 if (replExParams.exchangeInterval > 0)
226 gmx_fatal(FARGS, "Replica exchange not supported by rerun.");
228 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
230 gmx_fatal(FARGS, "Essential dynamics not supported by rerun.");
234 gmx_fatal(FARGS, "Interactive MD not supported by rerun.");
238 gmx_fatal(FARGS, "Multiple simulations not supported by rerun.");
240 if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc, [](SimulatedAnnealing i) {
241 return i != SimulatedAnnealing::No;
244 gmx_fatal(FARGS, "Simulated annealing not supported by rerun.");
247 /* Rerun can't work if an output file name is the same as the input file name.
248 * If this is the case, the user will get an error telling them what the issue is.
250 if (strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-o", nfile, fnm)) == 0
251 || strcmp(opt2fn("-rerun", nfile, fnm), opt2fn("-x", nfile, fnm)) == 0)
254 "When using mdrun -rerun, the name of the input trajectory file "
255 "%s cannot be identical to the name of an output file (whether "
256 "given explicitly with -o or -x, or by default)",
257 opt2fn("-rerun", nfile, fnm));
260 /* Settings for rerun */
262 // TODO: Avoid changing inputrec (#3854)
263 auto* nonConstInputrec = const_cast<t_inputrec*>(inputrec);
264 nonConstInputrec->nstlist = 1;
265 nonConstInputrec->nstcalcenergy = 1;
266 nonConstInputrec->nstxout_compressed = 0;
268 int nstglobalcomm = 1;
269 const bool bNS = true;
271 const SimulationGroups* groups = &top_global.groups;
272 if (ir->eI == IntegrationAlgorithm::Mimic)
274 auto* nonConstGlobalTopology = const_cast<gmx_mtop_t*>(&top_global);
275 nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(top_global);
277 int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
278 gmx::ArrayRef<real> lambda = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
279 initialize_lambdas(fplog,
283 ir->simtempvals->temperatures,
284 gmx::arrayRefFromArray(ir->opts.ref_t, ir->opts.ngtc),
288 const bool simulationsShareState = false;
289 gmx_mdoutf* outf = init_mdoutf(fplog,
300 StartingBehavior::NewSimulation,
301 simulationsShareState,
303 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf),
307 mdoutf_get_fp_dhdl(outf),
309 StartingBehavior::NewSimulation,
310 simulationsShareState,
313 gstat = global_stat_init(ir);
315 /* Check for polarizable models and flexible constraints */
316 shellfc = init_shell_flexcon(fplog,
318 constr ? constr->numFlexibleConstraints() : 0,
321 runScheduleWork->simulationWork.useGpuPme);
324 double io = compute_io(ir, top_global.natoms, *groups, energyOutput.numEnergyTerms(), 1);
325 if ((io > 2000) && MASTER(cr))
327 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
331 // Local state only becomes valid now.
332 std::unique_ptr<t_state> stateInstance;
335 if (DOMAINDECOMP(cr))
337 stateInstance = std::make_unique<t_state>();
338 state = stateInstance.get();
339 dd_init_local_state(*cr->dd, state_global, state);
341 /* Distribute the charge groups over the nodes from the master node */
342 dd_partition_system(fplog,
366 state_change_natoms(state_global, state_global->natoms);
367 /* Copy the pointer to the global state */
368 state = state_global;
370 mdAlgorithmsSetupAtomData(cr, *ir, top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
373 auto* mdatoms = mdAtoms->mdatoms();
375 // NOTE: The global state is no longer used at this point.
376 // But state_global is still used as temporary storage space for writing
377 // the global state to file and potentially for replica exchange.
378 // (Global topology should persist.)
380 update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
382 if (ir->efep != FreeEnergyPerturbationType::No && ir->fepvals->nstdhdl != 0)
384 doFreeEnergyPerturbation = true;
388 int cglo_flags = CGLO_GSTAT;
389 if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
391 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
393 bool bSumEkinhOld = false;
394 t_vcm* vcm = nullptr;
395 compute_globals(gstat,
400 makeConstArrayRef(state->x),
401 makeConstArrayRef(state->v),
412 gmx::ArrayRef<real>{},
417 if (DOMAINDECOMP(cr))
419 checkNumberOfBondedInteractions(
420 mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
427 "starting md rerun '%s', reading coordinates from"
428 " input trajectory '%s'\n\n",
430 opt2fn("-rerun", nfile, fnm));
431 if (mdrunOptions.verbose)
434 "Calculated time to finish depends on nsteps from "
435 "run input file,\nwhich may not correspond to the time "
436 "needed to process input trajectory.\n\n");
438 fprintf(fplog, "\n");
441 walltime_accounting_start_time(walltime_accounting);
442 wallcycle_start(wcycle, WallCycleCounter::Run);
443 print_start(fplog, cr, walltime_accounting, "mdrun");
445 /***********************************************************
449 ************************************************************/
455 .appendText("Simulations has constraints. Rerun does not recalculate constraints.");
461 isLastStep = !read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm), &rerun_fr, TRX_NEED_X);
462 if (rerun_fr.natoms != top_global.natoms)
465 "Number of atoms in trajectory (%d) does not match the "
466 "run input file (%d)\n",
471 if (ir->pbcType != PbcType::No)
476 "Rerun trajectory frame step %" PRId64
478 "does not contain a box, while pbc is used",
482 if (max_cutoff2(ir->pbcType, rerun_fr.box) < gmx::square(fr->rlist))
485 "Rerun trajectory frame step %" PRId64
487 "has too small box dimensions",
497 "Rerun does not report kinetic energy, total energy, temperature, virial and "
502 rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
505 if (ir->pbcType != PbcType::No)
507 /* Set the shift vectors.
508 * Necessary here when have a static box different from the tpr box.
510 calc_shifts(rerun_fr.box, fr->shift_vec);
513 step = ir->init_step;
516 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
517 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]),
521 mdrunOptions.reproducible,
523 mdrunOptions.maximumHoursToRun,
528 walltime_accounting);
530 // we don't do counter resetting in rerun - finish will always be valid
531 walltime_accounting_set_valid_finish(walltime_accounting);
533 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
535 /* and stop now if we should */
536 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
539 wallcycle_start(wcycle, WallCycleCounter::Step);
543 step = rerun_fr.step;
544 step_rel = step - ir->init_step;
555 if (ir->efep != FreeEnergyPerturbationType::No && MASTER(cr))
557 if (rerun_fr.bLambda)
559 ir->fepvals->init_lambda = rerun_fr.lambda;
563 if (rerun_fr.bFepState)
565 state->fep_state = rerun_fr.fep_state;
569 state_global->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
574 const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
575 if (constructVsites && DOMAINDECOMP(cr))
578 "Vsite recalculation with -rerun is not implemented with domain "
580 "use a single rank");
582 prepareRerunState(rerun_fr, state_global, constructVsites, vsite);
585 isLastStep = isLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
587 if (DOMAINDECOMP(cr))
589 /* Repartition the domain decomposition */
590 const bool bMasterState = true;
591 dd_partition_system(fplog,
611 mdrunOptions.verbose);
616 EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
619 if (ir->efep != FreeEnergyPerturbationType::No)
621 update_mdatoms(mdatoms, state->lambda[FreeEnergyPerturbationCouplingType::Mass]);
624 force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
625 | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 and #3400 are solved
626 GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
630 /* Now is the time to relax the shells */
631 relax_shell_flexcon(fplog,
634 mdrunOptions.verbose,
646 state->x.arrayRefWithPadding(),
647 state->v.arrayRefWithPadding(),
662 ddBalanceRegionHandler);
666 /* The coordinates (x) are shifted (to get whole molecules)
668 * This is parallellized as well, and does communication too.
669 * Check comments in sim_util.c
672 gmx_edsam* ed = nullptr;
686 state->x.arrayRefWithPadding(),
699 GMX_FORCE_NS | force_flags,
700 ddBalanceRegionHandler);
703 /* Now we have the energies and forces corresponding to the
704 * coordinates at time t.
707 const bool isCheckpointingStep = false;
708 const bool doRerun = true;
709 const bool bSumEkinhOld = false;
710 do_md_trajectory_writing(fplog,
730 mdrunOptions.writeConfout,
734 stopHandler->setSignal();
737 const bool doInterSimSignal = false;
738 const bool doIntraSimSignal = true;
739 bool bSumEkinhOld = false;
740 t_vcm* vcm = nullptr;
741 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
743 int cglo_flags = CGLO_GSTAT | CGLO_ENERGY;
744 if (DOMAINDECOMP(cr) && shouldCheckNumberOfBondedInteractions(*cr->dd))
746 cglo_flags |= CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
748 compute_globals(gstat,
753 makeConstArrayRef(state->x),
754 makeConstArrayRef(state->v),
765 constr != nullptr ? constr->rmsdData() : gmx::ArrayRef<real>{},
770 if (DOMAINDECOMP(cr))
772 checkNumberOfBondedInteractions(
773 mdlog, cr, top_global, &top, makeConstArrayRef(state->x), state->box);
777 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
778 the virial that should probably be addressed eventually. state->veta has better properies,
779 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
780 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
785 const bool bCalcEnerStep = true;
786 energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation,
792 ir->expandedvals.get(),
794 PTCouplingArrays({ state->boxv,
795 state->nosehoover_xi,
796 state->nosehoover_vxi,
798 state->nhpres_vxi }),
806 const bool do_ene = true;
807 const bool do_log = true;
809 const bool do_dr = ir->nstdisreout != 0;
810 const bool do_or = ir->nstorireout != 0;
812 EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
813 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf),
817 do_log ? fplog : nullptr,
825 pull_print_output(pull_work, step, t);
828 if (do_per_step(step, ir->nstlog))
830 if (fflush(fplog) != 0)
832 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
837 /* Print the remaining wall clock time for the run */
838 if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
842 fprintf(stderr, "\n");
844 print_time(stderr, walltime_accounting, step, ir, cr);
847 /* Ion/water position swapping.
848 * Not done in last step since trajectory writing happens before this call
849 * in the MD loop and exchanges would be lost anyway. */
850 if ((ir->eSwapCoords != SwapType::No) && (step > 0) && !isLastStep
851 && do_per_step(step, ir->swap->nstswap))
853 const bool doRerun = true;
862 MASTER(cr) && mdrunOptions.verbose,
868 /* read next frame from input trajectory */
869 isLastStep = !read_next_frame(oenv, status, &rerun_fr);
874 rerun_parallel_comm(cr, &rerun_fr, &isLastStep);
877 cycles = wallcycle_stop(wcycle, WallCycleCounter::Step);
878 if (DOMAINDECOMP(cr) && wcycle)
880 dd_cycles_add(cr->dd, cycles, ddCyclStep);
885 /* increase the MD step number */
890 /* End of main MD loop */
892 /* Closing TNG files can include compressing data. Therefore it is good to do that
893 * before stopping the time measurements. */
894 mdoutf_tng_close(outf);
896 /* Stop measuring walltime */
897 walltime_accounting_end_time(walltime_accounting);
904 if (!thisRankHasDuty(cr, DUTY_PME))
906 /* Tell the PME only node to finish */
907 gmx_pme_send_finish(cr);
912 done_shellfc(fplog, shellfc, step_rel);
914 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);