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38 * \brief Declares the loop for MiMiC QM/MM
40 * \author Viacheslav Bolnykh <v.bolnykh@hpc-leap.eu>
41 * \ingroup module_mdrun
53 #include "gromacs/applied_forces/awh/awh.h"
54 #include "gromacs/commandline/filenm.h"
55 #include "gromacs/domdec/collect.h"
56 #include "gromacs/domdec/dlbtiming.h"
57 #include "gromacs/domdec/domdec.h"
58 #include "gromacs/domdec/domdec_network.h"
59 #include "gromacs/domdec/domdec_struct.h"
60 #include "gromacs/domdec/mdsetup.h"
61 #include "gromacs/domdec/partition.h"
62 #include "gromacs/essentialdynamics/edsam.h"
63 #include "gromacs/ewald/pme_load_balancing.h"
64 #include "gromacs/ewald/pme_pp.h"
65 #include "gromacs/fileio/trxio.h"
66 #include "gromacs/gmxlib/network.h"
67 #include "gromacs/gmxlib/nrnb.h"
68 #include "gromacs/gpu_utils/gpu_utils.h"
69 #include "gromacs/listed_forces/listed_forces.h"
70 #include "gromacs/math/functions.h"
71 #include "gromacs/math/utilities.h"
72 #include "gromacs/math/vec.h"
73 #include "gromacs/math/vectypes.h"
74 #include "gromacs/mdlib/checkpointhandler.h"
75 #include "gromacs/mdlib/compute_io.h"
76 #include "gromacs/mdlib/constr.h"
77 #include "gromacs/mdlib/ebin.h"
78 #include "gromacs/mdlib/enerdata_utils.h"
79 #include "gromacs/mdlib/energyoutput.h"
80 #include "gromacs/mdlib/expanded.h"
81 #include "gromacs/mdlib/force.h"
82 #include "gromacs/mdlib/force_flags.h"
83 #include "gromacs/mdlib/forcerec.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/enerdata.h"
106 #include "gromacs/mdtypes/energyhistory.h"
107 #include "gromacs/mdtypes/forcebuffers.h"
108 #include "gromacs/mdtypes/forcerec.h"
109 #include "gromacs/mdtypes/group.h"
110 #include "gromacs/mdtypes/inputrec.h"
111 #include "gromacs/mdtypes/interaction_const.h"
112 #include "gromacs/mdtypes/md_enums.h"
113 #include "gromacs/mdtypes/mdatom.h"
114 #include "gromacs/mdtypes/mdrunoptions.h"
115 #include "gromacs/mdtypes/observableshistory.h"
116 #include "gromacs/mdtypes/state.h"
117 #include "gromacs/mimic/communicator.h"
118 #include "gromacs/mimic/utilities.h"
119 #include "gromacs/pbcutil/pbc.h"
120 #include "gromacs/pulling/pull.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"
133 #include "gromacs/utility/smalloc.h"
135 #include "legacysimulator.h"
136 #include "replicaexchange.h"
139 using gmx::SimulationSignaller;
141 void gmx::LegacySimulator::do_mimic()
143 t_inputrec* ir = inputrec;
144 int64_t step, step_rel;
145 double t, lam0[efptNR];
146 bool isLastStep = false;
147 bool doFreeEnergyPerturbation = false;
148 unsigned int force_flags;
149 tensor force_vir, shake_vir, total_vir, pres;
152 gmx_global_stat_t gstat;
153 gmx_shellfc_t* shellfc;
157 /* Domain decomposition could incorrectly miss a bonded
158 interaction, but checking for that requires a global
159 communication stage, which does not otherwise happen in DD
160 code. So we do that alongside the first global energy reduction
161 after a new DD is made. These variables handle whether the
162 check happens, and the result it returns. */
163 bool shouldCheckNumberOfBondedInteractions = false;
164 int totalNumberOfBondedInteractions = -1;
166 SimulationSignals signals;
167 // Most global communnication stages don't propagate mdrun
168 // signals, and will use this object to achieve that.
169 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
173 gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
177 gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
181 gmx_fatal(FARGS, "AWH not supported by MiMiC.");
183 if (replExParams.exchangeInterval > 0)
185 gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
187 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
189 gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
193 gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
197 gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
199 if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
200 [](int i) { return i != eannNO; }))
202 gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
205 /* Settings for rerun */
207 ir->nstcalcenergy = 1;
208 int nstglobalcomm = 1;
209 const bool bNS = true;
213 MimicCommunicator::init();
214 auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
215 MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
216 ir->nsteps = MimicCommunicator::getStepNumber();
219 ir->nstxout_compressed = 0;
220 const SimulationGroups* groups = &top_global->groups;
222 auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
223 nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
226 initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
228 const bool simulationsShareState = false;
229 gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
230 mdModulesNotifier, ir, top_global, oenv, wcycle,
231 StartingBehavior::NewSimulation, simulationsShareState, ms);
232 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
233 mdoutf_get_fp_dhdl(outf), true, StartingBehavior::NewSimulation,
236 gstat = global_stat_init(ir);
238 /* Check for polarizable models and flexible constraints */
239 shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
240 ir->nstcalcenergy, DOMAINDECOMP(cr));
243 double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
244 if ((io > 2000) && MASTER(cr))
246 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
250 // Local state only becomes valid now.
251 std::unique_ptr<t_state> stateInstance;
254 gmx_localtop_t top(top_global->ffparams);
256 if (DOMAINDECOMP(cr))
258 stateInstance = std::make_unique<t_state>();
259 state = stateInstance.get();
260 dd_init_local_state(cr->dd, state_global, state);
262 /* Distribute the charge groups over the nodes from the master node */
263 dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
264 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
265 nrnb, nullptr, FALSE);
266 shouldCheckNumberOfBondedInteractions = true;
267 gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr->mpi_comm_mygroup);
271 state_change_natoms(state_global, state_global->natoms);
272 /* Copy the pointer to the global state */
273 state = state_global;
275 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
278 auto mdatoms = mdAtoms->mdatoms();
280 // NOTE: The global state is no longer used at this point.
281 // But state_global is still used as temporary storage space for writing
282 // the global state to file and potentially for replica exchange.
283 // (Global topology should persist.)
285 update_mdatoms(mdatoms, state->lambda[efptMASS]);
287 if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
289 doFreeEnergyPerturbation = true;
295 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
296 bool bSumEkinhOld = false;
297 t_vcm* vcm = nullptr;
298 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
299 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
300 force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
301 &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
303 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
304 makeConstArrayRef(state->x), state->box,
305 &shouldCheckNumberOfBondedInteractions);
309 fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global->name));
310 if (mdrunOptions.verbose)
313 "Calculated time to finish depends on nsteps from "
314 "run input file,\nwhich may not correspond to the time "
315 "needed to process input trajectory.\n\n");
317 fprintf(fplog, "\n");
320 walltime_accounting_start_time(walltime_accounting);
321 wallcycle_start(wcycle, ewcRUN);
322 print_start(fplog, cr, walltime_accounting, "mdrun");
324 /***********************************************************
328 ************************************************************/
335 "Simulations has constraints. Constraints will "
336 "be handled by CPMD.");
342 "MiMiC does not report kinetic energy, total energy, temperature, virial and "
345 step = ir->init_step;
348 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
349 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
350 ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
351 ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
353 // we don't do counter resetting in rerun - finish will always be valid
354 walltime_accounting_set_valid_finish(walltime_accounting);
356 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
358 /* and stop now if we should */
359 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
362 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
363 wallcycle_start(wcycle, ewcSTEP);
369 MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
372 if (ir->efep != efepNO)
374 setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
379 const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
380 if (constructVsites && DOMAINDECOMP(cr))
383 "Vsite recalculation with -rerun is not implemented with domain "
385 "use a single rank");
389 if (DOMAINDECOMP(cr))
391 /* Repartition the domain decomposition */
392 const bool bMasterState = true;
393 dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
394 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
395 fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
396 shouldCheckNumberOfBondedInteractions = true;
401 EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
404 if (ir->efep != efepNO)
406 update_mdatoms(mdatoms, state->lambda[efptMASS]);
409 force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
410 | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
411 GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
415 /* Now is the time to relax the shells */
416 relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
417 imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
418 state->natoms, state->x.arrayRefWithPadding(),
419 state->v.arrayRefWithPadding(), state->box, state->lambda,
420 &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
421 fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
425 /* The coordinates (x) are shifted (to get whole molecules)
427 * This is parallellized as well, and does communication too.
428 * Check comments in sim_util.c
431 gmx_edsam* ed = nullptr;
432 do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
433 wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
434 &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
435 vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
438 /* Now we have the energies and forces corresponding to the
439 * coordinates at time t.
442 const bool isCheckpointingStep = false;
443 const bool doRerun = false;
444 const bool bSumEkinhOld = false;
445 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
446 state_global, observablesHistory, top_global, fr, outf,
447 energyOutput, ekind, f.view().force(), isCheckpointingStep,
448 doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
451 stopHandler->setSignal();
453 if (vsite != nullptr)
455 wallcycle_start(wcycle, ewcVSITECONSTR);
456 vsite->construct(state->x, ir->delta_t, state->v, state->box);
457 wallcycle_stop(wcycle, ewcVSITECONSTR);
461 const bool doInterSimSignal = false;
462 const bool doIntraSimSignal = true;
463 bool bSumEkinhOld = false;
464 t_vcm* vcm = nullptr;
465 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
467 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
468 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
469 enerd, nullptr, nullptr, nullptr, nullptr, constr, &signaller,
470 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
471 CGLO_GSTAT | CGLO_ENERGY
472 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
474 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
475 &top, makeConstArrayRef(state->x), state->box,
476 &shouldCheckNumberOfBondedInteractions);
480 gmx::HostVector<gmx::RVec> fglobal(top_global->natoms);
481 gmx::ArrayRef<gmx::RVec> ftemp;
482 gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
483 if (DOMAINDECOMP(cr))
485 ftemp = gmx::makeArrayRef(fglobal);
486 dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl,
491 ftemp = f.view().force();
496 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
497 MimicCommunicator::sendForces(ftemp, state_global->natoms);
502 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
503 the virial that should probably be addressed eventually. state->veta has better properies,
504 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
505 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
507 if (ir->efep != efepNO)
509 /* Sum up the foreign energy and dhdl terms for md and sd.
510 Currently done every step so that dhdl is correct in the .edr */
511 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
517 const bool bCalcEnerStep = true;
518 energyOutput.addDataAtEnergyStep(
519 doFreeEnergyPerturbation, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
520 ir->expandedvals, state->box,
521 PTCouplingArrays({ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
522 state->nhpres_xi, state->nhpres_vxi }),
523 state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
525 const bool do_ene = true;
526 const bool do_log = true;
528 const bool do_dr = ir->nstdisreout != 0;
529 const bool do_or = ir->nstorireout != 0;
531 EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
532 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
533 do_log ? fplog : nullptr, step, t, fr->fcdata.get(), awh);
535 if (do_per_step(step, ir->nstlog))
537 if (fflush(fplog) != 0)
539 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
544 /* Print the remaining wall clock time for the run */
545 if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
549 fprintf(stderr, "\n");
551 print_time(stderr, walltime_accounting, step, ir, cr);
554 cycles = wallcycle_stop(wcycle, ewcSTEP);
555 if (DOMAINDECOMP(cr) && wcycle)
557 dd_cycles_add(cr->dd, cycles, ddCyclStep);
560 /* increase the MD step number */
564 /* End of main MD loop */
566 /* Closing TNG files can include compressing data. Therefore it is good to do that
567 * before stopping the time measurements. */
568 mdoutf_tng_close(outf);
570 /* Stop measuring walltime */
571 walltime_accounting_end_time(walltime_accounting);
575 MimicCommunicator::finalize();
578 if (!thisRankHasDuty(cr, DUTY_PME))
580 /* Tell the PME only node to finish */
581 gmx_pme_send_finish(cr);
586 done_shellfc(fplog, shellfc, step_rel);
588 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);