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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/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/manage_threading.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/fcdata.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;
151 PaddedHostVector<gmx::RVec> f{};
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;
211 // Communicator to interact with MiMiC
212 MimicCommunicator mimicCommunicator{};
215 mimicCommunicator.init();
216 mimicCommunicator.sendInitData(top_global, state_global->x);
217 ir->nsteps = mimicCommunicator.getStepNumber();
220 ir->nstxout_compressed = 0;
221 SimulationGroups* groups = &top_global->groups;
222 top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
224 initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
226 const bool simulationsShareState = false;
227 gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
228 mdModulesNotifier, ir, top_global, oenv, wcycle,
229 StartingBehavior::NewSimulation, simulationsShareState, ms);
230 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
231 mdoutf_get_fp_dhdl(outf), true, StartingBehavior::NewSimulation,
234 gstat = global_stat_init(ir);
236 /* Check for polarizable models and flexible constraints */
237 shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
238 ir->nstcalcenergy, DOMAINDECOMP(cr));
241 double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
242 if ((io > 2000) && MASTER(cr))
244 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
248 // Local state only becomes valid now.
249 std::unique_ptr<t_state> stateInstance;
252 gmx_localtop_t top(top_global->ffparams);
254 if (DOMAINDECOMP(cr))
256 stateInstance = std::make_unique<t_state>();
257 state = stateInstance.get();
258 dd_init_local_state(cr->dd, state_global, state);
260 /* Distribute the charge groups over the nodes from the master node */
261 dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
262 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
263 nrnb, nullptr, FALSE);
264 shouldCheckNumberOfBondedInteractions = true;
265 gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr);
269 state_change_natoms(state_global, state_global->natoms);
270 /* Copy the pointer to the global state */
271 state = state_global;
273 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
276 auto mdatoms = mdAtoms->mdatoms();
278 // NOTE: The global state is no longer used at this point.
279 // But state_global is still used as temporary storage space for writing
280 // the global state to file and potentially for replica exchange.
281 // (Global topology should persist.)
283 update_mdatoms(mdatoms, state->lambda[efptMASS]);
285 if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
287 doFreeEnergyPerturbation = true;
293 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
294 bool bSumEkinhOld = false;
295 t_vcm* vcm = nullptr;
296 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
297 makeConstArrayRef(state->v), state->box, state->lambda[efptVDW], mdatoms, nrnb,
298 vcm, nullptr, enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
299 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
301 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
302 makeConstArrayRef(state->x), state->box,
303 &shouldCheckNumberOfBondedInteractions);
307 fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global->name));
308 if (mdrunOptions.verbose)
311 "Calculated time to finish depends on nsteps from "
312 "run input file,\nwhich may not correspond to the time "
313 "needed to process input trajectory.\n\n");
315 fprintf(fplog, "\n");
318 walltime_accounting_start_time(walltime_accounting);
319 wallcycle_start(wcycle, ewcRUN);
320 print_start(fplog, cr, walltime_accounting, "mdrun");
322 /***********************************************************
326 ************************************************************/
333 "Simulations has constraints. Constraints will "
334 "be handled by CPMD.");
340 "MiMiC does not report kinetic energy, total energy, temperature, virial and "
343 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
344 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
345 ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
346 ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
348 // we don't do counter resetting in rerun - finish will always be valid
349 walltime_accounting_set_valid_finish(walltime_accounting);
351 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
353 step = ir->init_step;
356 /* and stop now if we should */
357 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
360 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
361 wallcycle_start(wcycle, ewcSTEP);
367 mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
370 if (ir->efep != efepNO)
372 setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
377 const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
378 if (constructVsites && DOMAINDECOMP(cr))
381 "Vsite recalculation with -rerun is not implemented with domain "
383 "use a single rank");
387 if (DOMAINDECOMP(cr))
389 /* Repartition the domain decomposition */
390 const bool bMasterState = true;
391 dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
392 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
393 fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
394 shouldCheckNumberOfBondedInteractions = true;
399 energyOutput.printHeader(fplog, step, t); /* can we improve the information printed here? */
402 if (ir->efep != efepNO)
404 update_mdatoms(mdatoms, state->lambda[efptMASS]);
407 force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
408 | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
409 GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
413 /* Now is the time to relax the shells */
414 relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
415 imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
416 state->natoms, state->x.arrayRefWithPadding(),
417 state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
418 f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, shellfc,
419 fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
423 /* The coordinates (x) are shifted (to get whole molecules)
425 * This is parallellized as well, and does communication too.
426 * Check comments in sim_util.c
429 gmx_edsam* ed = nullptr;
430 do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
431 wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
432 f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, fr,
433 runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
434 ddBalanceRegionHandler);
437 /* Now we have the energies and forces corresponding to the
438 * coordinates at time t.
441 const bool isCheckpointingStep = false;
442 const bool doRerun = false;
443 const bool bSumEkinhOld = false;
444 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
445 state_global, observablesHistory, top_global, fr, outf,
446 energyOutput, ekind, f, isCheckpointingStep, doRerun,
447 isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
450 stopHandler->setSignal();
452 if (vsite != nullptr)
454 wallcycle_start(wcycle, ewcVSITECONSTR);
455 construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t,
456 as_rvec_array(state->v.data()), top.idef.iparams, top.idef.il,
457 fr->pbcType, fr->bMolPBC, cr, state->box);
458 wallcycle_stop(wcycle, ewcVSITECONSTR);
462 const bool doInterSimSignal = false;
463 const bool doIntraSimSignal = true;
464 bool bSumEkinhOld = false;
465 t_vcm* vcm = nullptr;
466 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
468 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
469 makeConstArrayRef(state->v), state->box, state->lambda[efptVDW], mdatoms,
470 nrnb, vcm, wcycle, enerd, nullptr, nullptr, nullptr, nullptr, constr,
471 &signaller, state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
472 CGLO_GSTAT | CGLO_ENERGY
473 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
475 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
476 &top, makeConstArrayRef(state->x), state->box,
477 &shouldCheckNumberOfBondedInteractions);
481 gmx::HostVector<gmx::RVec> fglobal(top_global->natoms);
482 gmx::ArrayRef<gmx::RVec> ftemp;
483 gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
484 if (DOMAINDECOMP(cr))
486 ftemp = gmx::makeArrayRef(fglobal);
487 dd_collect_vec(cr->dd, state, flocal, ftemp);
491 ftemp = gmx::makeArrayRef(f);
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 sum_dhdl(enerd, state->lambda, *ir->fepvals);
517 const bool bCalcEnerStep = true;
518 energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep, t,
519 mdatoms->tmass, enerd, state, ir->fepvals,
520 ir->expandedvals, state->box, shake_vir, force_vir,
521 total_vir, pres, ekind, mu_tot, constr);
523 const bool do_ene = true;
524 const bool do_log = true;
526 const bool do_dr = ir->nstdisreout != 0;
527 const bool do_or = ir->nstorireout != 0;
529 energyOutput.printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
530 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
531 do_log ? fplog : nullptr, step, t, fcd, awh);
533 if (do_per_step(step, ir->nstlog))
535 if (fflush(fplog) != 0)
537 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
542 /* Print the remaining wall clock time for the run */
543 if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
547 fprintf(stderr, "\n");
549 print_time(stderr, walltime_accounting, step, ir, cr);
552 cycles = wallcycle_stop(wcycle, ewcSTEP);
553 if (DOMAINDECOMP(cr) && wcycle)
555 dd_cycles_add(cr->dd, cycles, ddCyclStep);
558 /* increase the MD step number */
562 /* End of main MD loop */
564 /* Closing TNG files can include compressing data. Therefore it is good to do that
565 * before stopping the time measurements. */
566 mdoutf_tng_close(outf);
568 /* Stop measuring walltime */
569 walltime_accounting_end_time(walltime_accounting);
573 mimicCommunicator.finalize();
576 if (!thisRankHasDuty(cr, DUTY_PME))
578 /* Tell the PME only node to finish */
579 gmx_pme_send_finish(cr);
584 done_shellfc(fplog, shellfc, step_rel);
586 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);