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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/partition.h"
61 #include "gromacs/essentialdynamics/edsam.h"
62 #include "gromacs/ewald/pme.h"
63 #include "gromacs/ewald/pme_load_balancing.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/imd/imd.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/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/md_support.h"
84 #include "gromacs/mdlib/mdatoms.h"
85 #include "gromacs/mdlib/mdoutf.h"
86 #include "gromacs/mdlib/mdrun.h"
87 #include "gromacs/mdlib/mdsetup.h"
88 #include "gromacs/mdlib/membed.h"
89 #include "gromacs/mdlib/ns.h"
90 #include "gromacs/mdlib/resethandler.h"
91 #include "gromacs/mdlib/shellfc.h"
92 #include "gromacs/mdlib/sighandler.h"
93 #include "gromacs/mdlib/sim_util.h"
94 #include "gromacs/mdlib/simulationsignal.h"
95 #include "gromacs/mdlib/stophandler.h"
96 #include "gromacs/mdlib/tgroup.h"
97 #include "gromacs/mdlib/trajectory_writing.h"
98 #include "gromacs/mdlib/update.h"
99 #include "gromacs/mdlib/vcm.h"
100 #include "gromacs/mdlib/vsite.h"
101 #include "gromacs/mdrunutility/printtime.h"
102 #include "gromacs/mdtypes/awh_history.h"
103 #include "gromacs/mdtypes/awh_params.h"
104 #include "gromacs/mdtypes/commrec.h"
105 #include "gromacs/mdtypes/df_history.h"
106 #include "gromacs/mdtypes/enerdata.h"
107 #include "gromacs/mdtypes/energyhistory.h"
108 #include "gromacs/mdtypes/fcdata.h"
109 #include "gromacs/mdtypes/forcerec.h"
110 #include "gromacs/mdtypes/group.h"
111 #include "gromacs/mdtypes/inputrec.h"
112 #include "gromacs/mdtypes/interaction_const.h"
113 #include "gromacs/mdtypes/md_enums.h"
114 #include "gromacs/mdtypes/mdatom.h"
115 #include "gromacs/mdtypes/observableshistory.h"
116 #include "gromacs/mdtypes/state.h"
117 #include "gromacs/mimic/MimicCommunicator.h"
118 #include "gromacs/mimic/MimicUtils.h"
119 #include "gromacs/pbcutil/mshift.h"
120 #include "gromacs/pbcutil/pbc.h"
121 #include "gromacs/pulling/pull.h"
122 #include "gromacs/swap/swapcoords.h"
123 #include "gromacs/timing/wallcycle.h"
124 #include "gromacs/timing/walltime_accounting.h"
125 #include "gromacs/topology/atoms.h"
126 #include "gromacs/topology/idef.h"
127 #include "gromacs/topology/mtop_util.h"
128 #include "gromacs/topology/topology.h"
129 #include "gromacs/trajectory/trajectoryframe.h"
130 #include "gromacs/utility/basedefinitions.h"
131 #include "gromacs/utility/cstringutil.h"
132 #include "gromacs/utility/fatalerror.h"
133 #include "gromacs/utility/logger.h"
134 #include "gromacs/utility/real.h"
135 #include "gromacs/utility/smalloc.h"
137 #include "integrator.h"
138 #include "replicaexchange.h"
140 using gmx::SimulationSignaller;
142 void gmx::Integrator::do_mimic()
144 t_inputrec *ir = inputrec;
145 int64_t step, step_rel;
146 double t, lam0[efptNR];
147 bool isLastStep = false;
148 bool doFreeEnergyPerturbation = false;
150 tensor force_vir, shake_vir, total_vir, pres;
153 gmx_enerdata_t *enerd;
154 PaddedVector<gmx::RVec> f {};
155 gmx_global_stat_t gstat;
156 t_graph *graph = nullptr;
157 gmx_groups_t *groups;
158 gmx_shellfc_t *shellfc;
162 /* Domain decomposition could incorrectly miss a bonded
163 interaction, but checking for that requires a global
164 communication stage, which does not otherwise happen in DD
165 code. So we do that alongside the first global energy reduction
166 after a new DD is made. These variables handle whether the
167 check happens, and the result it returns. */
168 bool shouldCheckNumberOfBondedInteractions = false;
169 int totalNumberOfBondedInteractions = -1;
171 SimulationSignals signals;
172 // Most global communnication stages don't propagate mdrun
173 // signals, and will use this object to achieve that.
174 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
178 gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
182 gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
186 gmx_fatal(FARGS, "AWH not supported by MiMiC.");
188 if (replExParams.exchangeInterval > 0)
190 gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
192 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
194 gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
198 gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
202 gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
204 if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
205 [](int i){return i != eannNO; }))
207 gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
210 /* Settings for rerun */
212 ir->nstcalcenergy = 1;
213 int nstglobalcomm = 1;
214 const bool bNS = true;
216 // Communicator to interact with MiMiC
217 MimicCommunicator mimicCommunicator {};
220 mimicCommunicator.init();
221 mimicCommunicator.sendInitData(top_global, state_global->x);
222 ir->nsteps = mimicCommunicator.getStepNumber();
225 ir->nstxout_compressed = 0;
226 groups = &top_global->groups;
227 top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
229 initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
232 gmx_mdoutf *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, oenv, wcycle);
233 gmx::EnergyOutput energyOutput;
234 energyOutput.prepare(mdoutf_get_fp_ene(outf), top_global, ir, mdoutf_get_fp_dhdl(outf), true);
236 /* Energy terms and groups */
238 init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
241 /* Kinetic energy data */
242 std::unique_ptr<gmx_ekindata_t> eKinData = std::make_unique<gmx_ekindata_t>();
243 gmx_ekindata_t *ekind = eKinData.get();
244 init_ekindata(fplog, top_global, &(ir->opts), ekind);
245 /* Copy the cos acceleration to the groups struct */
246 ekind->cosacc.cos_accel = ir->cos_accel;
248 gstat = global_stat_init(ir);
250 /* Check for polarizable models and flexible constraints */
251 shellfc = init_shell_flexcon(fplog,
252 top_global, constr ? constr->numFlexibleConstraints() : 0,
253 ir->nstcalcenergy, DOMAINDECOMP(cr));
256 double io = compute_io(ir, top_global->natoms, groups, energyOutput.numEnergyTerms(), 1);
257 if ((io > 2000) && MASTER(cr))
260 "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
265 // Local state only becomes valid now.
266 std::unique_ptr<t_state> stateInstance;
269 if (DOMAINDECOMP(cr))
271 dd_init_local_top(*top_global, &top);
273 stateInstance = std::make_unique<t_state>();
274 state = stateInstance.get();
275 dd_init_local_state(cr->dd, state_global, state);
277 /* Distribute the charge groups over the nodes from the master node */
278 dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1,
279 state_global, *top_global, ir,
280 state, &f, mdAtoms, &top, fr,
282 nrnb, nullptr, FALSE);
283 shouldCheckNumberOfBondedInteractions = true;
284 gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr);
288 state_change_natoms(state_global, state_global->natoms);
289 /* We need to allocate one element extra, since we might use
290 * (unaligned) 4-wide SIMD loads to access rvec entries.
292 f.resizeWithPadding(state_global->natoms);
293 /* Copy the pointer to the global state */
294 state = state_global;
296 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr,
297 &graph, mdAtoms, constr, vsite, shellfc);
300 auto mdatoms = mdAtoms->mdatoms();
302 // NOTE: The global state is no longer used at this point.
303 // But state_global is still used as temporary storage space for writing
304 // the global state to file and potentially for replica exchange.
305 // (Global topology should persist.)
307 update_mdatoms(mdatoms, state->lambda[efptMASS]);
309 if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
311 doFreeEnergyPerturbation = true;
315 int cglo_flags = (CGLO_INITIALIZATION | CGLO_GSTAT |
316 (shouldCheckNumberOfBondedInteractions ?
317 CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
318 bool bSumEkinhOld = false;
319 t_vcm *vcm = nullptr;
320 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
321 nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
322 constr, &nullSignaller, state->box,
323 &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
325 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
326 top_global, &top, state,
327 &shouldCheckNumberOfBondedInteractions);
331 fprintf(stderr, "starting MiMiC MD run '%s'\n\n",
332 *(top_global->name));
333 if (mdrunOptions.verbose)
335 fprintf(stderr, "Calculated time to finish depends on nsteps from "
336 "run input file,\nwhich may not correspond to the time "
337 "needed to process input trajectory.\n\n");
339 fprintf(fplog, "\n");
342 walltime_accounting_start_time(walltime_accounting);
343 wallcycle_start(wcycle, ewcRUN);
344 print_start(fplog, cr, walltime_accounting, "mdrun");
346 /***********************************************************
350 ************************************************************/
354 GMX_LOG(mdlog.info).asParagraph().
355 appendText("Simulations has constraints. Constraints will "
356 "be handled by CPMD.");
359 GMX_LOG(mdlog.info).asParagraph().
360 appendText("MiMiC does not report kinetic energy, total energy, temperature, virial and pressure.");
362 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
363 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false,
364 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstglobalcomm,
365 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
367 // we don't do counter resetting in rerun - finish will always be valid
368 walltime_accounting_set_valid_finish(walltime_accounting);
370 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
372 step = ir->init_step;
375 /* and stop now if we should */
376 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
379 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
380 wallcycle_start(wcycle, ewcSTEP);
386 mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
389 if (ir->efep != efepNO)
391 setCurrentLambdasLocal(step, ir->fepvals, lam0, state);
396 const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
397 if (constructVsites && DOMAINDECOMP(cr))
399 gmx_fatal(FARGS, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
400 "use a single rank");
404 if (DOMAINDECOMP(cr))
406 /* Repartition the domain decomposition */
407 const bool bMasterState = true;
408 dd_partition_system(fplog, mdlog, step, cr,
409 bMasterState, nstglobalcomm,
410 state_global, *top_global, ir,
411 state, &f, mdAtoms, &top, fr,
414 mdrunOptions.verbose);
415 shouldCheckNumberOfBondedInteractions = true;
420 print_ebin_header(fplog, step, t); /* can we improve the information printed here? */
423 if (ir->efep != efepNO)
425 update_mdatoms(mdatoms, state->lambda[efptMASS]);
428 force_flags = (GMX_FORCE_STATECHANGED |
429 GMX_FORCE_DYNAMICBOX |
430 GMX_FORCE_ALLFORCES |
431 GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
433 (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
437 /* Now is the time to relax the shells */
438 relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose,
439 enforcedRotation, step,
440 ir, bNS, force_flags, &top,
442 state, f.arrayRefWithPadding(), force_vir, mdatoms,
443 nrnb, wcycle, graph, groups,
444 shellfc, fr, ppForceWorkload, t, mu_tot,
446 ddBalanceRegionHandler);
450 /* The coordinates (x) are shifted (to get whole molecules)
452 * This is parallellized as well, and does communication too.
453 * Check comments in sim_util.c
456 gmx_edsam *ed = nullptr;
457 do_force(fplog, cr, ms, ir, awh, enforcedRotation,
458 step, nrnb, wcycle, &top, groups,
459 state->box, state->x.arrayRefWithPadding(), &state->hist,
460 f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
461 state->lambda, graph,
462 fr, ppForceWorkload, vsite, mu_tot, t, ed,
463 GMX_FORCE_NS | force_flags,
464 ddBalanceRegionHandler);
467 /* Now we have the energies and forces corresponding to the
468 * coordinates at time t.
471 const bool isCheckpointingStep = false;
472 const bool doRerun = false;
473 const bool bSumEkinhOld = false;
474 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
475 ir, state, state_global, observablesHistory,
477 outf, energyOutput, ekind, f,
478 isCheckpointingStep, doRerun, isLastStep,
479 mdrunOptions.writeConfout,
483 stopHandler->setSignal();
487 /* Need to unshift here */
488 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
491 if (vsite != nullptr)
493 wallcycle_start(wcycle, ewcVSITECONSTR);
494 if (graph != nullptr)
496 shift_self(graph, state->box, as_rvec_array(state->x.data()));
498 construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
499 top.idef.iparams, top.idef.il,
500 fr->ePBC, fr->bMolPBC, cr, state->box);
502 if (graph != nullptr)
504 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
506 wallcycle_stop(wcycle, ewcVSITECONSTR);
510 const bool doInterSimSignal = false;
511 const bool doIntraSimSignal = true;
512 bool bSumEkinhOld = false;
513 t_vcm *vcm = nullptr;
514 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
516 compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
517 wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
520 &totalNumberOfBondedInteractions, &bSumEkinhOld,
521 CGLO_GSTAT | CGLO_ENERGY
522 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
524 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
525 top_global, &top, state,
526 &shouldCheckNumberOfBondedInteractions);
530 gmx::HostVector<gmx::RVec> fglobal(top_global->natoms);
531 gmx::ArrayRef<gmx::RVec> ftemp;
532 gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
533 if (DOMAINDECOMP(cr))
535 ftemp = gmx::makeArrayRef(fglobal);
536 dd_collect_vec(cr->dd, state, flocal, ftemp);
540 ftemp = gmx::makeArrayRef(f);
545 mimicCommunicator.sendEnergies(enerd->term[F_EPOT]);
546 mimicCommunicator.sendForces(ftemp, state_global->natoms);
552 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
553 the virial that should probably be addressed eventually. state->veta has better properies,
554 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
555 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
557 if (ir->efep != efepNO)
559 /* Sum up the foreign energy and dhdl terms for md and sd.
560 Currently done every step so that dhdl is correct in the .edr */
561 sum_dhdl(enerd, state->lambda, ir->fepvals);
567 const bool bCalcEnerStep = true;
568 energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep,
569 t, mdatoms->tmass, enerd, state,
570 ir->fepvals, ir->expandedvals, state->box,
571 shake_vir, force_vir, total_vir, pres,
572 ekind, mu_tot, constr);
574 const bool do_ene = true;
575 const bool do_log = true;
577 const bool do_dr = ir->nstdisreout != 0;
578 const bool do_or = ir->nstorireout != 0;
580 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
581 do_log ? fplog : nullptr,
583 eprNORMAL, fcd, groups, &(ir->opts), awh);
585 if (do_per_step(step, ir->nstlog))
587 if (fflush(fplog) != 0)
589 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
594 /* Print the remaining wall clock time for the run */
595 if (isMasterSimMasterRank(ms, cr) &&
596 (mdrunOptions.verbose || gmx_got_usr_signal()))
600 fprintf(stderr, "\n");
602 print_time(stderr, walltime_accounting, step, ir, cr);
605 cycles = wallcycle_stop(wcycle, ewcSTEP);
606 if (DOMAINDECOMP(cr) && wcycle)
608 dd_cycles_add(cr->dd, cycles, ddCyclStep);
611 /* increase the MD step number */
615 /* End of main MD loop */
617 /* Closing TNG files can include compressing data. Therefore it is good to do that
618 * before stopping the time measurements. */
619 mdoutf_tng_close(outf);
621 /* Stop measuring walltime */
622 walltime_accounting_end_time(walltime_accounting);
626 mimicCommunicator.finalize();
629 if (!thisRankHasDuty(cr, DUTY_PME))
631 /* Tell the PME only node to finish */
632 gmx_pme_send_finish(cr);
637 done_shellfc(fplog, shellfc, step_rel);
639 // Clean up swapcoords
640 if (ir->eSwapCoords != eswapNO)
642 finish_swapcoords(ir->swap);
645 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
647 destroy_enerdata(enerd);