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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/mshift.h"
120 #include "gromacs/pbcutil/pbc.h"
121 #include "gromacs/pulling/pull.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"
134 #include "gromacs/utility/smalloc.h"
136 #include "legacysimulator.h"
137 #include "replicaexchange.h"
140 using gmx::SimulationSignaller;
142 void gmx::LegacySimulator::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;
149 unsigned int force_flags;
150 tensor force_vir, shake_vir, total_vir, pres;
153 PaddedHostVector<gmx::RVec> f{};
154 gmx_global_stat_t gstat;
155 t_graph* graph = nullptr;
156 gmx_shellfc_t* shellfc;
160 /* Domain decomposition could incorrectly miss a bonded
161 interaction, but checking for that requires a global
162 communication stage, which does not otherwise happen in DD
163 code. So we do that alongside the first global energy reduction
164 after a new DD is made. These variables handle whether the
165 check happens, and the result it returns. */
166 bool shouldCheckNumberOfBondedInteractions = false;
167 int totalNumberOfBondedInteractions = -1;
169 SimulationSignals signals;
170 // Most global communnication stages don't propagate mdrun
171 // signals, and will use this object to achieve that.
172 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
176 gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
180 gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
184 gmx_fatal(FARGS, "AWH not supported by MiMiC.");
186 if (replExParams.exchangeInterval > 0)
188 gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
190 if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
192 gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
196 gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
200 gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
202 if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
203 [](int i) { return i != eannNO; }))
205 gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
208 /* Settings for rerun */
210 ir->nstcalcenergy = 1;
211 int nstglobalcomm = 1;
212 const bool bNS = true;
214 // Communicator to interact with MiMiC
215 MimicCommunicator mimicCommunicator{};
218 mimicCommunicator.init();
219 mimicCommunicator.sendInitData(top_global, state_global->x);
220 ir->nsteps = mimicCommunicator.getStepNumber();
223 ir->nstxout_compressed = 0;
224 SimulationGroups* groups = &top_global->groups;
225 top_global->intermolecularExclusionGroup = genQmmmIndices(*top_global);
227 initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
229 gmx_mdoutf* outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier,
230 ir, top_global, oenv, wcycle, StartingBehavior::NewSimulation);
231 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
232 mdoutf_get_fp_dhdl(outf), true, StartingBehavior::NewSimulation,
235 gstat = global_stat_init(ir);
237 /* Check for polarizable models and flexible constraints */
238 shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
239 ir->nstcalcenergy, DOMAINDECOMP(cr));
242 double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
243 if ((io > 2000) && MASTER(cr))
245 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
249 // Local state only becomes valid now.
250 std::unique_ptr<t_state> stateInstance;
253 if (DOMAINDECOMP(cr))
255 dd_init_local_top(*top_global, &top);
257 stateInstance = std::make_unique<t_state>();
258 state = stateInstance.get();
259 dd_init_local_state(cr->dd, state_global, state);
261 /* Distribute the charge groups over the nodes from the master node */
262 dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
263 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
264 nrnb, nullptr, FALSE);
265 shouldCheckNumberOfBondedInteractions = true;
266 gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr);
270 state_change_natoms(state_global, state_global->natoms);
271 /* We need to allocate one element extra, since we might use
272 * (unaligned) 4-wide SIMD loads to access rvec entries.
274 f.resizeWithPadding(state_global->natoms);
275 /* Copy the pointer to the global state */
276 state = state_global;
278 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &graph, mdAtoms, constr, vsite, shellfc);
281 auto mdatoms = mdAtoms->mdatoms();
283 // NOTE: The global state is no longer used at this point.
284 // But state_global is still used as temporary storage space for writing
285 // the global state to file and potentially for replica exchange.
286 // (Global topology should persist.)
288 update_mdatoms(mdatoms, state->lambda[efptMASS]);
290 if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
292 doFreeEnergyPerturbation = true;
298 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
299 bool bSumEkinhOld = false;
300 t_vcm* vcm = nullptr;
301 compute_globals(gstat, cr, ir, fr, ekind, state->x.rvec_array(), state->v.rvec_array(),
302 state->box, state->lambda[efptVDW], mdatoms, nrnb, vcm, nullptr, enerd,
303 force_vir, shake_vir, total_vir, pres, mu_tot, constr, &nullSignaller,
304 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
306 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
307 state->x.rvec_array(), state->box,
308 &shouldCheckNumberOfBondedInteractions);
312 fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global->name));
313 if (mdrunOptions.verbose)
316 "Calculated time to finish depends on nsteps from "
317 "run input file,\nwhich may not correspond to the time "
318 "needed to process input trajectory.\n\n");
320 fprintf(fplog, "\n");
323 walltime_accounting_start_time(walltime_accounting);
324 wallcycle_start(wcycle, ewcRUN);
325 print_start(fplog, cr, walltime_accounting, "mdrun");
327 /***********************************************************
331 ************************************************************/
338 "Simulations has constraints. Constraints will "
339 "be handled by CPMD.");
345 "MiMiC does not report kinetic energy, total energy, temperature, virial and "
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 step = ir->init_step;
361 /* and stop now if we should */
362 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
365 isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
366 wallcycle_start(wcycle, ewcSTEP);
372 mimicCommunicator.getCoords(&state_global->x, state_global->natoms);
375 if (ir->efep != efepNO)
377 setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
382 const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
383 if (constructVsites && DOMAINDECOMP(cr))
386 "Vsite recalculation with -rerun is not implemented with domain "
388 "use a single rank");
392 if (DOMAINDECOMP(cr))
394 /* Repartition the domain decomposition */
395 const bool bMasterState = true;
396 dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
397 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
398 fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
399 shouldCheckNumberOfBondedInteractions = true;
404 energyOutput.printHeader(fplog, step, t); /* can we improve the information printed here? */
407 if (ir->efep != efepNO)
409 update_mdatoms(mdatoms, state->lambda[efptMASS]);
412 force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
413 | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
414 GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
418 /* Now is the time to relax the shells */
419 relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
420 imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
421 state->natoms, state->x.arrayRefWithPadding(),
422 state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
423 f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
424 shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
428 /* The coordinates (x) are shifted (to get whole molecules)
430 * This is parallellized as well, and does communication too.
431 * Check comments in sim_util.c
434 gmx_edsam* ed = nullptr;
435 do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
436 wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
437 f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
438 fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
439 ddBalanceRegionHandler);
442 /* Now we have the energies and forces corresponding to the
443 * coordinates at time t.
446 const bool isCheckpointingStep = false;
447 const bool doRerun = false;
448 const bool bSumEkinhOld = false;
449 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
450 state_global, observablesHistory, top_global, fr, outf,
451 energyOutput, ekind, f, isCheckpointingStep, doRerun,
452 isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
455 stopHandler->setSignal();
459 /* Need to unshift here */
460 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
463 if (vsite != nullptr)
465 wallcycle_start(wcycle, ewcVSITECONSTR);
466 if (graph != nullptr)
468 shift_self(graph, state->box, as_rvec_array(state->x.data()));
470 construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t,
471 as_rvec_array(state->v.data()), top.idef.iparams, top.idef.il,
472 fr->pbcType, fr->bMolPBC, cr, state->box);
474 if (graph != nullptr)
476 unshift_self(graph, state->box, as_rvec_array(state->x.data()));
478 wallcycle_stop(wcycle, ewcVSITECONSTR);
482 const bool doInterSimSignal = false;
483 const bool doIntraSimSignal = true;
484 bool bSumEkinhOld = false;
485 t_vcm* vcm = nullptr;
486 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
488 compute_globals(gstat, cr, ir, fr, ekind, state->x.rvec_array(), state->v.rvec_array(),
489 state->box, state->lambda[efptVDW], mdatoms, nrnb, vcm, wcycle, enerd,
490 nullptr, nullptr, nullptr, nullptr, mu_tot, constr, &signaller,
491 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
492 CGLO_GSTAT | CGLO_ENERGY
493 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
495 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
496 &top, state->x.rvec_array(), state->box,
497 &shouldCheckNumberOfBondedInteractions);
501 gmx::HostVector<gmx::RVec> fglobal(top_global->natoms);
502 gmx::ArrayRef<gmx::RVec> ftemp;
503 gmx::ArrayRef<const gmx::RVec> flocal = gmx::makeArrayRef(f);
504 if (DOMAINDECOMP(cr))
506 ftemp = gmx::makeArrayRef(fglobal);
507 dd_collect_vec(cr->dd, state, flocal, ftemp);
511 ftemp = gmx::makeArrayRef(f);
516 mimicCommunicator.sendEnergies(enerd->term[F_EPOT]);
517 mimicCommunicator.sendForces(ftemp, state_global->natoms);
522 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
523 the virial that should probably be addressed eventually. state->veta has better properies,
524 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
525 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
527 if (ir->efep != efepNO)
529 /* Sum up the foreign energy and dhdl terms for md and sd.
530 Currently done every step so that dhdl is correct in the .edr */
531 sum_dhdl(enerd, state->lambda, *ir->fepvals);
537 const bool bCalcEnerStep = true;
538 energyOutput.addDataAtEnergyStep(doFreeEnergyPerturbation, bCalcEnerStep, t,
539 mdatoms->tmass, enerd, state, ir->fepvals,
540 ir->expandedvals, state->box, shake_vir, force_vir,
541 total_vir, pres, ekind, mu_tot, constr);
543 const bool do_ene = true;
544 const bool do_log = true;
546 const bool do_dr = ir->nstdisreout != 0;
547 const bool do_or = ir->nstorireout != 0;
549 energyOutput.printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
550 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
551 do_log ? fplog : nullptr, step, t, fcd, awh);
553 if (do_per_step(step, ir->nstlog))
555 if (fflush(fplog) != 0)
557 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
562 /* Print the remaining wall clock time for the run */
563 if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
567 fprintf(stderr, "\n");
569 print_time(stderr, walltime_accounting, step, ir, cr);
572 cycles = wallcycle_stop(wcycle, ewcSTEP);
573 if (DOMAINDECOMP(cr) && wcycle)
575 dd_cycles_add(cr->dd, cycles, ddCyclStep);
578 /* increase the MD step number */
582 /* End of main MD loop */
584 /* Closing TNG files can include compressing data. Therefore it is good to do that
585 * before stopping the time measurements. */
586 mdoutf_tng_close(outf);
588 /* Stop measuring walltime */
589 walltime_accounting_end_time(walltime_accounting);
593 mimicCommunicator.finalize();
596 if (!thisRankHasDuty(cr, DUTY_PME))
598 /* Tell the PME only node to finish */
599 gmx_pme_send_finish(cr);
604 done_shellfc(fplog, shellfc, step_rel);
606 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);