2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2011-2019,2020, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
39 * \brief Implements the integrator for normal molecular dynamics simulations
41 * \author David van der Spoel <david.vanderspoel@icm.uu.se>
42 * \ingroup module_mdrun
55 #include "gromacs/applied_forces/awh/awh.h"
56 #include "gromacs/commandline/filenm.h"
57 #include "gromacs/domdec/collect.h"
58 #include "gromacs/domdec/dlbtiming.h"
59 #include "gromacs/domdec/domdec.h"
60 #include "gromacs/domdec/domdec_network.h"
61 #include "gromacs/domdec/domdec_struct.h"
62 #include "gromacs/domdec/gpuhaloexchange.h"
63 #include "gromacs/domdec/mdsetup.h"
64 #include "gromacs/domdec/partition.h"
65 #include "gromacs/essentialdynamics/edsam.h"
66 #include "gromacs/ewald/pme_load_balancing.h"
67 #include "gromacs/ewald/pme_pp.h"
68 #include "gromacs/fileio/trxio.h"
69 #include "gromacs/gmxlib/network.h"
70 #include "gromacs/gmxlib/nrnb.h"
71 #include "gromacs/gpu_utils/device_stream_manager.h"
72 #include "gromacs/gpu_utils/gpu_utils.h"
73 #include "gromacs/imd/imd.h"
74 #include "gromacs/listed_forces/listed_forces.h"
75 #include "gromacs/math/functions.h"
76 #include "gromacs/math/invertmatrix.h"
77 #include "gromacs/math/vec.h"
78 #include "gromacs/math/vectypes.h"
79 #include "gromacs/mdlib/checkpointhandler.h"
80 #include "gromacs/mdlib/compute_io.h"
81 #include "gromacs/mdlib/constr.h"
82 #include "gromacs/mdlib/coupling.h"
83 #include "gromacs/mdlib/ebin.h"
84 #include "gromacs/mdlib/enerdata_utils.h"
85 #include "gromacs/mdlib/energyoutput.h"
86 #include "gromacs/mdlib/expanded.h"
87 #include "gromacs/mdlib/force.h"
88 #include "gromacs/mdlib/force_flags.h"
89 #include "gromacs/mdlib/forcerec.h"
90 #include "gromacs/mdlib/freeenergyparameters.h"
91 #include "gromacs/mdlib/md_support.h"
92 #include "gromacs/mdlib/mdatoms.h"
93 #include "gromacs/mdlib/mdoutf.h"
94 #include "gromacs/mdlib/membed.h"
95 #include "gromacs/mdlib/resethandler.h"
96 #include "gromacs/mdlib/sighandler.h"
97 #include "gromacs/mdlib/simulationsignal.h"
98 #include "gromacs/mdlib/stat.h"
99 #include "gromacs/mdlib/stophandler.h"
100 #include "gromacs/mdlib/tgroup.h"
101 #include "gromacs/mdlib/trajectory_writing.h"
102 #include "gromacs/mdlib/update.h"
103 #include "gromacs/mdlib/update_constrain_gpu.h"
104 #include "gromacs/mdlib/vcm.h"
105 #include "gromacs/mdlib/vsite.h"
106 #include "gromacs/mdrunutility/handlerestart.h"
107 #include "gromacs/mdrunutility/multisim.h"
108 #include "gromacs/mdrunutility/printtime.h"
109 #include "gromacs/mdtypes/awh_history.h"
110 #include "gromacs/mdtypes/awh_params.h"
111 #include "gromacs/mdtypes/commrec.h"
112 #include "gromacs/mdtypes/df_history.h"
113 #include "gromacs/mdtypes/energyhistory.h"
114 #include "gromacs/mdtypes/fcdata.h"
115 #include "gromacs/mdtypes/forcebuffers.h"
116 #include "gromacs/mdtypes/forcerec.h"
117 #include "gromacs/mdtypes/group.h"
118 #include "gromacs/mdtypes/inputrec.h"
119 #include "gromacs/mdtypes/interaction_const.h"
120 #include "gromacs/mdtypes/md_enums.h"
121 #include "gromacs/mdtypes/mdatom.h"
122 #include "gromacs/mdtypes/mdrunoptions.h"
123 #include "gromacs/mdtypes/observableshistory.h"
124 #include "gromacs/mdtypes/pullhistory.h"
125 #include "gromacs/mdtypes/simulation_workload.h"
126 #include "gromacs/mdtypes/state.h"
127 #include "gromacs/mdtypes/state_propagator_data_gpu.h"
128 #include "gromacs/modularsimulator/energydata.h"
129 #include "gromacs/nbnxm/gpu_data_mgmt.h"
130 #include "gromacs/nbnxm/nbnxm.h"
131 #include "gromacs/pbcutil/pbc.h"
132 #include "gromacs/pulling/output.h"
133 #include "gromacs/pulling/pull.h"
134 #include "gromacs/swap/swapcoords.h"
135 #include "gromacs/timing/wallcycle.h"
136 #include "gromacs/timing/walltime_accounting.h"
137 #include "gromacs/topology/atoms.h"
138 #include "gromacs/topology/idef.h"
139 #include "gromacs/topology/mtop_util.h"
140 #include "gromacs/topology/topology.h"
141 #include "gromacs/trajectory/trajectoryframe.h"
142 #include "gromacs/utility/basedefinitions.h"
143 #include "gromacs/utility/cstringutil.h"
144 #include "gromacs/utility/fatalerror.h"
145 #include "gromacs/utility/logger.h"
146 #include "gromacs/utility/real.h"
147 #include "gromacs/utility/smalloc.h"
149 #include "legacysimulator.h"
150 #include "replicaexchange.h"
154 # include "corewrap.h"
157 using gmx::SimulationSignaller;
159 void gmx::LegacySimulator::do_md()
161 // TODO Historically, the EM and MD "integrators" used different
162 // names for the t_inputrec *parameter, but these must have the
163 // same name, now that it's a member of a struct. We use this ir
164 // alias to avoid a large ripple of nearly useless changes.
165 // t_inputrec is being replaced by IMdpOptionsProvider, so this
166 // will go away eventually.
167 t_inputrec* ir = inputrec;
168 int64_t step, step_rel;
169 double t, t0 = ir->init_t;
170 gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
171 gmx_bool bNS = FALSE, bNStList, bStopCM, bFirstStep, bInitStep, bLastStep = FALSE;
172 gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
173 gmx_bool do_ene, do_log, do_verbose;
174 gmx_bool bMasterState;
175 unsigned int force_flags;
176 tensor force_vir = { { 0 } }, shake_vir = { { 0 } }, total_vir = { { 0 } }, pres = { { 0 } };
179 matrix pressureCouplingMu, M;
180 gmx_repl_ex_t repl_ex = nullptr;
181 gmx_global_stat_t gstat;
182 gmx_shellfc_t* shellfc;
183 gmx_bool bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
184 gmx_bool bTemp, bPres, bTrotter;
186 std::vector<RVec> cbuf;
192 real saved_conserved_quantity = 0;
195 char sbuf[STEPSTRSIZE], sbuf2[STEPSTRSIZE];
197 /* PME load balancing data for GPU kernels */
198 gmx_bool bPMETune = FALSE;
199 gmx_bool bPMETunePrinting = FALSE;
201 bool bInteractiveMDstep = false;
203 /* Domain decomposition could incorrectly miss a bonded
204 interaction, but checking for that requires a global
205 communication stage, which does not otherwise happen in DD
206 code. So we do that alongside the first global energy reduction
207 after a new DD is made. These variables handle whether the
208 check happens, and the result it returns. */
209 bool shouldCheckNumberOfBondedInteractions = false;
210 int totalNumberOfBondedInteractions = -1;
212 SimulationSignals signals;
213 // Most global communnication stages don't propagate mdrun
214 // signals, and will use this object to achieve that.
215 SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
217 if (!mdrunOptions.writeConfout)
219 // This is on by default, and the main known use case for
220 // turning it off is for convenience in benchmarking, which is
221 // something that should not show up in the general user
226 "The -noconfout functionality is deprecated, and may be removed in a "
230 /* md-vv uses averaged full step velocities for T-control
231 md-vv-avek uses averaged half step velocities for T-control (but full step ekin for P control)
232 md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
233 bTrotter = (EI_VV(ir->eI)
234 && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir) || inputrecNvtTrotter(ir)));
236 const bool bRerunMD = false;
238 int nstglobalcomm = computeGlobalCommunicationPeriod(mdlog, ir, cr);
239 bGStatEveryStep = (nstglobalcomm == 1);
241 const SimulationGroups* groups = &top_global->groups;
243 std::unique_ptr<EssentialDynamics> ed = nullptr;
244 if (opt2bSet("-ei", nfile, fnm))
246 /* Initialize essential dynamics sampling */
247 ed = init_edsam(mdlog, opt2fn_null("-ei", nfile, fnm), opt2fn("-eo", nfile, fnm), top_global,
248 ir, cr, constr, state_global, observablesHistory, oenv, startingBehavior);
250 else if (observablesHistory->edsamHistory)
253 "The checkpoint is from a run with essential dynamics sampling, "
254 "but the current run did not specify the -ei option. "
255 "Either specify the -ei option to mdrun, or do not use this checkpoint file.");
258 int* fep_state = MASTER(cr) ? &state_global->fep_state : nullptr;
259 gmx::ArrayRef<real> lambda = MASTER(cr) ? state_global->lambda : gmx::ArrayRef<real>();
260 initialize_lambdas(fplog, *ir, MASTER(cr), fep_state, lambda);
261 Update upd(*ir, deform);
262 const bool doSimulatedAnnealing = initSimulatedAnnealing(ir, &upd);
263 const bool useReplicaExchange = (replExParams.exchangeInterval > 0);
265 const t_fcdata& fcdata = *fr->fcdata;
267 bool simulationsShareState = false;
268 int nstSignalComm = nstglobalcomm;
270 // TODO This implementation of ensemble orientation restraints is nasty because
271 // a user can't just do multi-sim with single-sim orientation restraints.
272 bool usingEnsembleRestraints =
273 (fcdata.disres->nsystems > 1) || ((ms != nullptr) && (fcdata.orires->nr != 0));
274 bool awhUsesMultiSim = (ir->bDoAwh && ir->awhParams->shareBiasMultisim && (ms != nullptr));
276 // Replica exchange, ensemble restraints and AWH need all
277 // simulations to remain synchronized, so they need
278 // checkpoints and stop conditions to act on the same step, so
279 // the propagation of such signals must take place between
280 // simulations, not just within simulations.
281 // TODO: Make algorithm initializers set these flags.
282 simulationsShareState = useReplicaExchange || usingEnsembleRestraints || awhUsesMultiSim;
284 if (simulationsShareState)
286 // Inter-simulation signal communication does not need to happen
287 // often, so we use a minimum of 200 steps to reduce overhead.
288 const int c_minimumInterSimulationSignallingInterval = 200;
289 nstSignalComm = ((c_minimumInterSimulationSignallingInterval + nstglobalcomm - 1) / nstglobalcomm)
294 if (startingBehavior != StartingBehavior::RestartWithAppending)
296 pleaseCiteCouplingAlgorithms(fplog, *ir);
299 init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, mdModulesNotifier, ir,
300 top_global, oenv, wcycle, startingBehavior, simulationsShareState, ms);
301 gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
302 mdoutf_get_fp_dhdl(outf), false, startingBehavior, mdModulesNotifier);
304 gstat = global_stat_init(ir);
306 /* Check for polarizable models and flexible constraints */
307 shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
308 ir->nstcalcenergy, DOMAINDECOMP(cr));
311 double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
312 if ((io > 2000) && MASTER(cr))
314 fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
318 // Local state only becomes valid now.
319 std::unique_ptr<t_state> stateInstance;
323 gmx_localtop_t top(top_global->ffparams);
325 auto mdatoms = mdAtoms->mdatoms();
327 const auto& simulationWork = runScheduleWork->simulationWork;
328 const bool useGpuForPme = simulationWork.useGpuPme;
329 const bool useGpuForNonbonded = simulationWork.useGpuNonbonded;
330 const bool useGpuForBufferOps = simulationWork.useGpuBufferOps;
331 const bool useGpuForUpdate = simulationWork.useGpuUpdate;
333 ForceBuffers f(((useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
334 ? PinningPolicy::PinnedIfSupported
335 : PinningPolicy::CannotBePinned);
336 if (DOMAINDECOMP(cr))
338 stateInstance = std::make_unique<t_state>();
339 state = stateInstance.get();
340 dd_init_local_state(cr->dd, state_global, state);
342 /* Distribute the charge groups over the nodes from the master node */
343 dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
344 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
345 nrnb, nullptr, FALSE);
346 shouldCheckNumberOfBondedInteractions = true;
347 upd.setNumAtoms(state->natoms);
351 state_change_natoms(state_global, state_global->natoms);
352 /* Copy the pointer to the global state */
353 state = state_global;
355 /* Generate and initialize new topology */
356 mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
358 upd.setNumAtoms(state->natoms);
361 std::unique_ptr<UpdateConstrainGpu> integrator;
363 StatePropagatorDataGpu* stateGpu = fr->stateGpu;
365 // TODO: the assertions below should be handled by UpdateConstraintsBuilder.
368 GMX_RELEASE_ASSERT(!DOMAINDECOMP(cr) || ddUsesUpdateGroups(*cr->dd) || constr == nullptr
369 || constr->numConstraintsTotal() == 0,
370 "Constraints in domain decomposition are only supported with update "
371 "groups if using GPU update.\n");
372 GMX_RELEASE_ASSERT(ir->eConstrAlg != econtSHAKE || constr == nullptr
373 || constr->numConstraintsTotal() == 0,
374 "SHAKE is not supported with GPU update.");
375 GMX_RELEASE_ASSERT(useGpuForPme || (useGpuForNonbonded && simulationWork.useGpuBufferOps),
376 "Either PME or short-ranged non-bonded interaction tasks must run on "
377 "the GPU to use GPU update.\n");
378 GMX_RELEASE_ASSERT(ir->eI == eiMD,
379 "Only the md integrator is supported with the GPU update.\n");
381 ir->etc != etcNOSEHOOVER,
382 "Nose-Hoover temperature coupling is not supported with the GPU update.\n");
384 ir->epc == epcNO || ir->epc == epcPARRINELLORAHMAN || ir->epc == epcBERENDSEN
385 || ir->epc == epcCRESCALE,
386 "Only Parrinello-Rahman, Berendsen, and C-rescale pressure coupling are supported "
387 "with the GPU update.\n");
388 GMX_RELEASE_ASSERT(!mdatoms->haveVsites,
389 "Virtual sites are not supported with the GPU update.\n");
390 GMX_RELEASE_ASSERT(ed == nullptr,
391 "Essential dynamics is not supported with the GPU update.\n");
392 GMX_RELEASE_ASSERT(!ir->bPull || !pull_have_constraint(ir->pull),
393 "Constraints pulling is not supported with the GPU update.\n");
394 GMX_RELEASE_ASSERT(fcdata.orires->nr == 0,
395 "Orientation restraints are not supported with the GPU update.\n");
398 || (!haveFreeEnergyType(*ir, efptBONDED) && !haveFreeEnergyType(*ir, efptMASS)),
399 "Free energy perturbation of masses and constraints are not supported with the GPU "
402 if (constr != nullptr && constr->numConstraintsTotal() > 0)
406 .appendText("Updating coordinates and applying constraints on the GPU.");
410 GMX_LOG(mdlog.info).asParagraph().appendText("Updating coordinates on the GPU.");
412 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
413 "Device stream manager should be initialized in order to use GPU "
414 "update-constraints.");
416 fr->deviceStreamManager->streamIsValid(gmx::DeviceStreamType::UpdateAndConstraints),
417 "Update stream should be initialized in order to use GPU "
418 "update-constraints.");
419 integrator = std::make_unique<UpdateConstrainGpu>(
420 *ir, *top_global, fr->deviceStreamManager->context(),
421 fr->deviceStreamManager->stream(gmx::DeviceStreamType::UpdateAndConstraints),
422 stateGpu->xUpdatedOnDevice());
424 integrator->setPbc(PbcType::Xyz, state->box);
427 if (useGpuForPme || (useGpuForNonbonded && useGpuForBufferOps) || useGpuForUpdate)
429 changePinningPolicy(&state->x, PinningPolicy::PinnedIfSupported);
433 changePinningPolicy(&state->v, PinningPolicy::PinnedIfSupported);
436 // NOTE: The global state is no longer used at this point.
437 // But state_global is still used as temporary storage space for writing
438 // the global state to file and potentially for replica exchange.
439 // (Global topology should persist.)
441 update_mdatoms(mdatoms, state->lambda[efptMASS]);
445 /* Check nstexpanded here, because the grompp check was broken */
446 if (ir->expandedvals->nstexpanded % ir->nstcalcenergy != 0)
449 "With expanded ensemble, nstexpanded should be a multiple of nstcalcenergy");
451 init_expanded_ensemble(startingBehavior != StartingBehavior::NewSimulation, ir, state->dfhist);
456 EnergyData::initializeEnergyHistory(startingBehavior, observablesHistory, &energyOutput);
459 preparePrevStepPullCom(ir, pull_work, mdatoms->massT, state, state_global, cr,
460 startingBehavior != StartingBehavior::NewSimulation);
462 // TODO: Remove this by converting AWH into a ForceProvider
463 auto awh = prepareAwhModule(fplog, *ir, state_global, cr, ms,
464 startingBehavior != StartingBehavior::NewSimulation,
465 shellfc != nullptr, opt2fn("-awh", nfile, fnm), pull_work);
467 if (useReplicaExchange && MASTER(cr))
469 repl_ex = init_replica_exchange(fplog, ms, top_global->natoms, ir, replExParams);
471 /* PME tuning is only supported in the Verlet scheme, with PME for
472 * Coulomb. It is not supported with only LJ PME. */
473 bPMETune = (mdrunOptions.tunePme && EEL_PME(fr->ic->eeltype) && !mdrunOptions.reproducible
474 && ir->cutoff_scheme != ecutsGROUP);
476 pme_load_balancing_t* pme_loadbal = nullptr;
479 pme_loadbal_init(&pme_loadbal, cr, mdlog, *ir, state->box, *fr->ic, *fr->nbv, fr->pmedata,
483 if (!ir->bContinuation)
485 if (state->flags & (1U << estV))
487 auto v = makeArrayRef(state->v);
488 /* Set the velocities of vsites, shells and frozen atoms to zero */
489 for (i = 0; i < mdatoms->homenr; i++)
491 if (mdatoms->ptype[i] == eptVSite || mdatoms->ptype[i] == eptShell)
495 else if (mdatoms->cFREEZE)
497 for (m = 0; m < DIM; m++)
499 if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
510 /* Constrain the initial coordinates and velocities */
511 do_constrain_first(fplog, constr, ir, mdatoms->nr, mdatoms->homenr,
512 state->x.arrayRefWithPadding(), state->v.arrayRefWithPadding(),
513 state->box, state->lambda[efptBONDED]);
517 /* Construct the virtual sites for the initial configuration */
518 vsite->construct(state->x, ir->delta_t, {}, state->box);
522 if (ir->efep != efepNO)
524 /* Set free energy calculation frequency as the greatest common
525 * denominator of nstdhdl and repl_ex_nst. */
526 nstfep = ir->fepvals->nstdhdl;
529 nstfep = std::gcd(ir->expandedvals->nstexpanded, nstfep);
531 if (useReplicaExchange)
533 nstfep = std::gcd(replExParams.exchangeInterval, nstfep);
537 nstfep = std::gcd(ir->awhParams->nstSampleCoord, nstfep);
541 /* Be REALLY careful about what flags you set here. You CANNOT assume
542 * this is the first step, since we might be restarting from a checkpoint,
543 * and in that case we should not do any modifications to the state.
545 bStopCM = (ir->comm_mode != ecmNO && !ir->bContinuation);
547 // When restarting from a checkpoint, it can be appropriate to
548 // initialize ekind from quantities in the checkpoint. Otherwise,
549 // compute_globals must initialize ekind before the simulation
550 // starts/restarts. However, only the master rank knows what was
551 // found in the checkpoint file, so we have to communicate in
552 // order to coordinate the restart.
554 // TODO Consider removing this communication if/when checkpoint
555 // reading directly follows .tpr reading, because all ranks can
556 // agree on hasReadEkinState at that time.
557 bool hasReadEkinState = MASTER(cr) ? state_global->ekinstate.hasReadEkinState : false;
560 gmx_bcast(sizeof(hasReadEkinState), &hasReadEkinState, cr->mpi_comm_mygroup);
562 if (hasReadEkinState)
564 restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
567 unsigned int cglo_flags =
568 (CGLO_TEMPERATURE | CGLO_GSTAT | (EI_VV(ir->eI) ? CGLO_PRESSURE : 0)
569 | (EI_VV(ir->eI) ? CGLO_CONSTRAINT : 0) | (hasReadEkinState ? CGLO_READEKIN : 0));
571 bSumEkinhOld = FALSE;
573 t_vcm vcm(top_global->groups, *ir);
574 reportComRemovalInfo(fplog, vcm);
576 /* To minimize communication, compute_globals computes the COM velocity
577 * and the kinetic energy for the velocities without COM motion removed.
578 * Thus to get the kinetic energy without the COM contribution, we need
579 * to call compute_globals twice.
581 for (int cgloIteration = 0; cgloIteration < (bStopCM ? 2 : 1); cgloIteration++)
583 unsigned int cglo_flags_iteration = cglo_flags;
584 if (bStopCM && cgloIteration == 0)
586 cglo_flags_iteration |= CGLO_STOPCM;
587 cglo_flags_iteration &= ~CGLO_TEMPERATURE;
589 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
590 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
591 enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
592 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
594 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
596 if (cglo_flags_iteration & CGLO_STOPCM)
598 /* At initialization, do not pass x with acceleration-correction mode
599 * to avoid (incorrect) correction of the initial coordinates.
601 auto x = (vcm.mode == ecmLINEAR_ACCELERATION_CORRECTION) ? ArrayRef<RVec>()
602 : makeArrayRef(state->x);
603 process_and_stopcm_grp(fplog, &vcm, *mdatoms, x, makeArrayRef(state->v));
604 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
607 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
608 makeConstArrayRef(state->x), state->box,
609 &shouldCheckNumberOfBondedInteractions);
610 if (ir->eI == eiVVAK)
612 /* a second call to get the half step temperature initialized as well */
613 /* we do the same call as above, but turn the pressure off -- internally to
614 compute_globals, this is recognized as a velocity verlet half-step
615 kinetic energy calculation. This minimized excess variables, but
616 perhaps loses some logic?*/
618 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
619 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, nullptr,
620 enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
621 state->box, nullptr, &bSumEkinhOld, cglo_flags & ~CGLO_PRESSURE);
624 /* Calculate the initial half step temperature, and save the ekinh_old */
625 if (startingBehavior == StartingBehavior::NewSimulation)
627 for (i = 0; (i < ir->opts.ngtc); i++)
629 copy_mat(ekind->tcstat[i].ekinh, ekind->tcstat[i].ekinh_old);
633 /* need to make an initiation call to get the Trotter variables set, as well as other constants
634 for non-trotter temperature control */
635 auto trotter_seq = init_npt_vars(ir, state, &MassQ, bTrotter);
639 if (!ir->bContinuation)
641 if (constr && ir->eConstrAlg == econtLINCS)
643 fprintf(fplog, "RMS relative constraint deviation after constraining: %.2e\n",
646 if (EI_STATE_VELOCITY(ir->eI))
648 real temp = enerd->term[F_TEMP];
651 /* Result of Ekin averaged over velocities of -half
652 * and +half step, while we only have -half step here.
656 fprintf(fplog, "Initial temperature: %g K\n", temp);
661 fprintf(stderr, "starting mdrun '%s'\n", *(top_global->name));
664 sprintf(tbuf, "%8.1f", (ir->init_step + ir->nsteps) * ir->delta_t);
668 sprintf(tbuf, "%s", "infinite");
670 if (ir->init_step > 0)
672 fprintf(stderr, "%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
673 gmx_step_str(ir->init_step + ir->nsteps, sbuf), tbuf,
674 gmx_step_str(ir->init_step, sbuf2), ir->init_step * ir->delta_t);
678 fprintf(stderr, "%s steps, %s ps.\n", gmx_step_str(ir->nsteps, sbuf), tbuf);
680 fprintf(fplog, "\n");
683 walltime_accounting_start_time(walltime_accounting);
684 wallcycle_start(wcycle, ewcRUN);
685 print_start(fplog, cr, walltime_accounting, "mdrun");
688 /* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
689 int chkpt_ret = fcCheckPointParallel(cr->nodeid, NULL, 0);
692 gmx_fatal(3, __FILE__, __LINE__, "Checkpoint error on step %d\n", 0);
696 /***********************************************************
700 ************************************************************/
703 /* Skip the first Nose-Hoover integration when we get the state from tpx */
704 bInitStep = startingBehavior == StartingBehavior::NewSimulation || EI_VV(ir->eI);
705 bSumEkinhOld = FALSE;
707 bNeedRepartition = FALSE;
709 step = ir->init_step;
712 auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
713 compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), simulationsShareState,
714 MASTER(cr), ir->nstlist, mdrunOptions.reproducible, nstSignalComm,
715 mdrunOptions.maximumHoursToRun, ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
717 auto checkpointHandler = std::make_unique<CheckpointHandler>(
718 compat::make_not_null<SimulationSignal*>(&signals[eglsCHKPT]), simulationsShareState,
719 ir->nstlist == 0, MASTER(cr), mdrunOptions.writeConfout,
720 mdrunOptions.checkpointOptions.period);
722 const bool resetCountersIsLocal = true;
723 auto resetHandler = std::make_unique<ResetHandler>(
724 compat::make_not_null<SimulationSignal*>(&signals[eglsRESETCOUNTERS]),
725 !resetCountersIsLocal, ir->nsteps, MASTER(cr), mdrunOptions.timingOptions.resetHalfway,
726 mdrunOptions.maximumHoursToRun, mdlog, wcycle, walltime_accounting);
728 const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
730 if (MASTER(cr) && isMultiSim(ms) && !useReplicaExchange)
732 logInitialMultisimStatus(ms, cr, mdlog, simulationsShareState, ir->nsteps, ir->init_step);
735 /* and stop now if we should */
736 bLastStep = (bLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
740 /* Determine if this is a neighbor search step */
741 bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
743 if (bPMETune && bNStList)
745 // This has to be here because PME load balancing is called so early.
746 // TODO: Move to after all booleans are defined.
747 if (useGpuForUpdate && !bFirstStep)
749 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
750 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
752 /* PME grid + cut-off optimization with GPUs or PME nodes */
753 pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
754 fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
755 &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
758 wallcycle_start(wcycle, ewcSTEP);
760 bLastStep = (step_rel == ir->nsteps);
761 t = t0 + step * ir->delta_t;
763 // TODO Refactor this, so that nstfep does not need a default value of zero
764 if (ir->efep != efepNO || ir->bSimTemp)
766 /* find and set the current lambdas */
767 state->lambda = currentLambdas(step, *(ir->fepvals), state->fep_state);
769 bDoDHDL = do_per_step(step, ir->fepvals->nstdhdl);
770 bDoFEP = ((ir->efep != efepNO) && do_per_step(step, nstfep));
771 bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded) && (ir->bExpanded)
775 bDoReplEx = (useReplicaExchange && (step > 0) && !bLastStep
776 && do_per_step(step, replExParams.exchangeInterval));
778 if (doSimulatedAnnealing)
780 update_annealing_target_temp(ir, t, &upd);
783 /* Stop Center of Mass motion */
784 bStopCM = (ir->comm_mode != ecmNO && do_per_step(step, ir->nstcomm));
786 /* Determine whether or not to do Neighbour Searching */
787 bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
789 /* Note that the stopHandler will cause termination at nstglobalcomm
790 * steps. Since this concides with nstcalcenergy, nsttcouple and/or
791 * nstpcouple steps, we have computed the half-step kinetic energy
792 * of the previous step and can always output energies at the last step.
794 bLastStep = bLastStep || stopHandler->stoppingAfterCurrentStep(bNS);
796 /* do_log triggers energy and virial calculation. Because this leads
797 * to different code paths, forces can be different. Thus for exact
798 * continuation we should avoid extra log output.
799 * Note that the || bLastStep can result in non-exact continuation
800 * beyond the last step. But we don't consider that to be an issue.
802 do_log = (do_per_step(step, ir->nstlog)
803 || (bFirstStep && startingBehavior == StartingBehavior::NewSimulation) || bLastStep);
804 do_verbose = mdrunOptions.verbose
805 && (step % mdrunOptions.verboseStepPrintInterval == 0 || bFirstStep || bLastStep);
807 if (useGpuForUpdate && !bFirstStep && bNS)
809 // Copy velocities from the GPU on search steps to keep a copy on host (device buffers are reinitialized).
810 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
811 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
812 // Copy coordinate from the GPU when needed at the search step.
813 // NOTE: The cases when coordinates needed on CPU for force evaluation are handled in sim_utils.
814 // NOTE: If the coordinates are to be written into output file they are also copied separately before the output.
815 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
816 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
819 if (bNS && !(bFirstStep && ir->bContinuation))
821 bMasterState = FALSE;
822 /* Correct the new box if it is too skewed */
823 if (inputrecDynamicBox(ir))
825 if (correct_box(fplog, step, state->box))
828 // If update is offloaded, it should be informed about the box size change
831 integrator->setPbc(PbcType::Xyz, state->box);
835 if (DOMAINDECOMP(cr) && bMasterState)
837 dd_collect_state(cr->dd, state, state_global);
840 if (DOMAINDECOMP(cr))
842 /* Repartition the domain decomposition */
843 dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
844 *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
845 fr, vsite, constr, nrnb, wcycle, do_verbose && !bPMETunePrinting);
846 shouldCheckNumberOfBondedInteractions = true;
847 upd.setNumAtoms(state->natoms);
851 // Allocate or re-size GPU halo exchange object, if necessary
852 if (bNS && havePPDomainDecomposition(cr) && simulationWork.useGpuHaloExchange
853 && useGpuForNonbonded && is1D(*cr->dd))
855 GMX_RELEASE_ASSERT(fr->deviceStreamManager != nullptr,
856 "GPU device manager has to be initialized to use GPU "
857 "version of halo exchange.");
858 // TODO remove need to pass local stream into GPU halo exchange - Issue #3093
859 constructGpuHaloExchange(mdlog, *cr, *fr->deviceStreamManager, wcycle);
862 if (MASTER(cr) && do_log)
864 gmx::EnergyOutput::printHeader(fplog, step,
865 t); /* can we improve the information printed here? */
868 if (ir->efep != efepNO)
870 update_mdatoms(mdatoms, state->lambda[efptMASS]);
876 /* We need the kinetic energy at minus the half step for determining
877 * the full step kinetic energy and possibly for T-coupling.*/
878 /* This may not be quite working correctly yet . . . . */
879 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
880 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
881 enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
882 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
883 CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
884 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
885 &top, makeConstArrayRef(state->x), state->box,
886 &shouldCheckNumberOfBondedInteractions);
888 clear_mat(force_vir);
890 checkpointHandler->decideIfCheckpointingThisStep(bNS, bFirstStep, bLastStep);
892 /* Determine the energy and pressure:
893 * at nstcalcenergy steps and at energy output steps (set below).
895 if (EI_VV(ir->eI) && (!bInitStep))
897 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
898 bCalcVir = bCalcEnerStep
900 && (do_per_step(step, ir->nstpcouple) || do_per_step(step - 1, ir->nstpcouple)));
904 bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
905 bCalcVir = bCalcEnerStep || (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
907 bCalcEner = bCalcEnerStep;
909 do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
911 if (do_ene || do_log || bDoReplEx)
917 /* Do we need global communication ? */
918 bGStat = (bCalcVir || bCalcEner || bStopCM || do_per_step(step, nstglobalcomm)
919 || (EI_VV(ir->eI) && inputrecNvtTrotter(ir) && do_per_step(step - 1, nstglobalcomm)));
921 force_flags = (GMX_FORCE_STATECHANGED | ((inputrecDynamicBox(ir)) ? GMX_FORCE_DYNAMICBOX : 0)
922 | GMX_FORCE_ALLFORCES | (bCalcVir ? GMX_FORCE_VIRIAL : 0)
923 | (bCalcEner ? GMX_FORCE_ENERGY : 0) | (bDoFEP ? GMX_FORCE_DHDL : 0));
927 /* Now is the time to relax the shells */
928 relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
929 imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
930 state->natoms, state->x.arrayRefWithPadding(),
931 state->v.arrayRefWithPadding(), state->box, state->lambda,
932 &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
933 fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
937 /* The AWH history need to be saved _before_ doing force calculations where the AWH bias
938 is updated (or the AWH update will be performed twice for one step when continuing).
939 It would be best to call this update function from do_md_trajectory_writing but that
940 would occur after do_force. One would have to divide the update_awh function into one
941 function applying the AWH force and one doing the AWH bias update. The update AWH
942 bias function could then be called after do_md_trajectory_writing (then containing
943 update_awh_history). The checkpointing will in the future probably moved to the start
944 of the md loop which will rid of this issue. */
945 if (awh && checkpointHandler->isCheckpointingStep() && MASTER(cr))
947 awh->updateHistory(state_global->awhHistory.get());
950 /* The coordinates (x) are shifted (to get whole molecules)
952 * This is parallellized as well, and does communication too.
953 * Check comments in sim_util.c
955 do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
956 nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
957 &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
958 vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
959 (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
962 // VV integrators do not need the following velocity half step
963 // if it is the first step after starting from a checkpoint.
964 // That is, the half step is needed on all other steps, and
965 // also the first step when starting from a .tpr file.
966 if (EI_VV(ir->eI) && (!bFirstStep || startingBehavior == StartingBehavior::NewSimulation))
967 /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
969 rvec* vbuf = nullptr;
971 wallcycle_start(wcycle, ewcUPDATE);
972 if (ir->eI == eiVV && bInitStep)
974 /* if using velocity verlet with full time step Ekin,
975 * take the first half step only to compute the
976 * virial for the first step. From there,
977 * revert back to the initial coordinates
978 * so that the input is actually the initial step.
980 snew(vbuf, state->natoms);
981 copy_rvecn(state->v.rvec_array(), vbuf, 0,
982 state->natoms); /* should make this better for parallelizing? */
986 /* this is for NHC in the Ekin(t+dt/2) version of vv */
987 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ,
988 trotter_seq, ettTSEQ1);
991 upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
992 M, etrtVELOCITY1, cr, constr != nullptr);
994 wallcycle_stop(wcycle, ewcUPDATE);
995 constrain_velocities(constr, do_log, do_ene, step, state, nullptr, bCalcVir, shake_vir);
996 wallcycle_start(wcycle, ewcUPDATE);
997 /* if VV, compute the pressure and constraints */
998 /* For VV2, we strictly only need this if using pressure
999 * control, but we really would like to have accurate pressures
1001 * Think about ways around this in the future?
1002 * For now, keep this choice in comments.
1004 /*bPres = (ir->eI==eiVV || inputrecNptTrotter(ir)); */
1005 /*bTemp = ((ir->eI==eiVV &&(!bInitStep)) || (ir->eI==eiVVAK && inputrecNptTrotter(ir)));*/
1007 bTemp = ((ir->eI == eiVV && (!bInitStep)) || (ir->eI == eiVVAK));
1008 if (bCalcEner && ir->eI == eiVVAK)
1010 bSumEkinhOld = TRUE;
1012 /* for vv, the first half of the integration actually corresponds to the previous step.
1013 So we need information from the last step in the first half of the integration */
1014 if (bGStat || do_per_step(step - 1, nstglobalcomm))
1016 wallcycle_stop(wcycle, ewcUPDATE);
1017 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
1018 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
1019 enerd, force_vir, shake_vir, total_vir, pres, constr, &nullSignaller,
1020 state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
1021 (bGStat ? CGLO_GSTAT : 0) | (bCalcEner ? CGLO_ENERGY : 0)
1022 | (bTemp ? CGLO_TEMPERATURE : 0) | (bPres ? CGLO_PRESSURE : 0)
1023 | (bPres ? CGLO_CONSTRAINT : 0) | (bStopCM ? CGLO_STOPCM : 0)
1024 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
1027 /* explanation of above:
1028 a) We compute Ekin at the full time step
1029 if 1) we are using the AveVel Ekin, and it's not the
1030 initial step, or 2) if we are using AveEkin, but need the full
1031 time step kinetic energy for the pressure (always true now, since we want accurate statistics).
1032 b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
1033 EkinAveVel because it's needed for the pressure */
1034 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
1035 top_global, &top, makeConstArrayRef(state->x),
1036 state->box, &shouldCheckNumberOfBondedInteractions);
1039 process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
1040 makeArrayRef(state->v));
1041 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
1043 wallcycle_start(wcycle, ewcUPDATE);
1045 /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
1050 m_add(force_vir, shake_vir,
1051 total_vir); /* we need the un-dispersion corrected total vir here */
1052 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ,
1053 trotter_seq, ettTSEQ2);
1055 /* TODO This is only needed when we're about to write
1056 * a checkpoint, because we use it after the restart
1057 * (in a kludge?). But what should we be doing if
1058 * the startingBehavior is NewSimulation or bInitStep are true? */
1059 if (inputrecNptTrotter(ir) || inputrecNphTrotter(ir))
1061 copy_mat(shake_vir, state->svir_prev);
1062 copy_mat(force_vir, state->fvir_prev);
1064 if (inputrecNvtTrotter(ir) && ir->eI == eiVV)
1066 /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
1067 enerd->term[F_TEMP] =
1068 sum_ekin(&(ir->opts), ekind, nullptr, (ir->eI == eiVV), FALSE);
1069 enerd->term[F_EKIN] = trace(ekind->ekin);
1072 else if (bExchanged)
1074 wallcycle_stop(wcycle, ewcUPDATE);
1075 /* We need the kinetic energy at minus the half step for determining
1076 * the full step kinetic energy and possibly for T-coupling.*/
1077 /* This may not be quite working correctly yet . . . . */
1078 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
1079 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle,
1080 enerd, nullptr, nullptr, nullptr, nullptr, constr, &nullSignaller,
1081 state->box, nullptr, &bSumEkinhOld, CGLO_GSTAT | CGLO_TEMPERATURE);
1082 wallcycle_start(wcycle, ewcUPDATE);
1085 /* if it's the initial step, we performed this first step just to get the constraint virial */
1086 if (ir->eI == eiVV && bInitStep)
1088 copy_rvecn(vbuf, state->v.rvec_array(), 0, state->natoms);
1091 wallcycle_stop(wcycle, ewcUPDATE);
1094 /* compute the conserved quantity */
1097 saved_conserved_quantity = NPT_energy(ir, state, &MassQ);
1100 last_ekin = enerd->term[F_EKIN];
1102 if ((ir->eDispCorr != edispcEnerPres) && (ir->eDispCorr != edispcAllEnerPres))
1104 saved_conserved_quantity -= enerd->term[F_DISPCORR];
1106 /* sum up the foreign kinetic energy and dK/dl terms for vv. currently done every step so that dhdl is correct in the .edr */
1107 if (ir->efep != efepNO)
1109 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
1113 /* ######## END FIRST UPDATE STEP ############## */
1114 /* ######## If doing VV, we now have v(dt) ###### */
1117 /* perform extended ensemble sampling in lambda - we don't
1118 actually move to the new state before outputting
1119 statistics, but if performing simulated tempering, we
1120 do update the velocities and the tau_t. */
1122 lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state,
1123 state->dfhist, step, state->v.rvec_array(), mdatoms);
1124 /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
1127 copy_df_history(state_global->dfhist, state->dfhist);
1131 // Copy coordinate from the GPU for the output/checkpointing if the update is offloaded and
1132 // coordinates have not already been copied for i) search or ii) CPU force tasks.
1133 if (useGpuForUpdate && !bNS && !runScheduleWork->domainWork.haveCpuLocalForceWork
1134 && (do_per_step(step, ir->nstxout) || do_per_step(step, ir->nstxout_compressed)
1135 || checkpointHandler->isCheckpointingStep()))
1137 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1138 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1140 // Copy velocities if needed for the output/checkpointing.
1141 // NOTE: Copy on the search steps is done at the beginning of the step.
1142 if (useGpuForUpdate && !bNS
1143 && (do_per_step(step, ir->nstvout) || checkpointHandler->isCheckpointingStep()))
1145 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1146 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1148 // Copy forces for the output if the forces were reduced on the GPU (not the case on virial steps)
1149 // and update is offloaded hence forces are kept on the GPU for update and have not been
1150 // already transferred in do_force().
1151 // TODO: There should be an improved, explicit mechanism that ensures this copy is only executed
1152 // when the forces are ready on the GPU -- the same synchronizer should be used as the one
1153 // prior to GPU update.
1154 // TODO: When the output flags will be included in step workload, this copy can be combined with the
1155 // copy call in do_force(...).
1156 // NOTE: The forces should not be copied here if the vsites are present, since they were modified
1157 // on host after the D2H copy in do_force(...).
1158 if (runScheduleWork->stepWork.useGpuFBufferOps && (simulationWork.useGpuUpdate && !vsite)
1159 && do_per_step(step, ir->nstfout))
1161 stateGpu->copyForcesFromGpu(f.view().force(), AtomLocality::Local);
1162 stateGpu->waitForcesReadyOnHost(AtomLocality::Local);
1164 /* Now we have the energies and forces corresponding to the
1165 * coordinates at time t. We must output all of this before
1168 do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
1169 observablesHistory, top_global, fr, outf, energyOutput, ekind,
1170 f.view().force(), checkpointHandler->isCheckpointingStep(),
1171 bRerunMD, bLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
1172 /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
1173 bInteractiveMDstep = imdSession->run(step, bNS, state->box, state->x.rvec_array(), t);
1175 /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
1176 if (startingBehavior != StartingBehavior::NewSimulation && bFirstStep
1177 && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)))
1179 copy_mat(state->svir_prev, shake_vir);
1180 copy_mat(state->fvir_prev, force_vir);
1183 stopHandler->setSignal();
1184 resetHandler->setSignal(walltime_accounting);
1186 if (bGStat || !PAR(cr))
1188 /* In parallel we only have to check for checkpointing in steps
1189 * where we do global communication,
1190 * otherwise the other nodes don't know.
1192 checkpointHandler->setSignal(walltime_accounting);
1195 /* ######### START SECOND UPDATE STEP ################# */
1197 /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen
1198 controlled in preprocessing */
1200 if (ETC_ANDERSEN(ir->etc)) /* keep this outside of update_tcouple because of the extra info required to pass */
1202 gmx_bool bIfRandomize;
1203 bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
1204 /* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
1205 if (constr && bIfRandomize)
1207 constrain_velocities(constr, do_log, do_ene, step, state, nullptr, false, nullptr);
1210 /* Box is changed in update() when we do pressure coupling,
1211 * but we should still use the old box for energy corrections and when
1212 * writing it to the energy file, so it matches the trajectory files for
1213 * the same timestep above. Make a copy in a separate array.
1215 copy_mat(state->box, lastbox);
1219 wallcycle_start(wcycle, ewcUPDATE);
1220 /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
1223 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ3);
1224 /* We can only do Berendsen coupling after we have summed
1225 * the kinetic energy or virial. Since the happens
1226 * in global_state after update, we should only do it at
1227 * step % nstlist = 1 with bGStatEveryStep=FALSE.
1232 update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
1233 update_pcouple_before_coordinates(fplog, step, ir, state, pressureCouplingMu, M, bInitStep);
1238 /* velocity half-step update */
1239 upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
1240 M, etrtVELOCITY2, cr, constr != nullptr);
1243 /* Above, initialize just copies ekinh into ekin,
1244 * it doesn't copy position (for VV),
1245 * and entire integrator for MD.
1248 if (ir->eI == eiVVAK)
1250 cbuf.resize(state->x.size());
1251 std::copy(state->x.begin(), state->x.end(), cbuf.begin());
1254 /* With leap-frog type integrators we compute the kinetic energy
1255 * at a whole time step as the average of the half-time step kinetic
1256 * energies of two subsequent steps. Therefore we need to compute the
1257 * half step kinetic energy also if we need energies at the next step.
1259 const bool needHalfStepKineticEnergy =
1260 (!EI_VV(ir->eI) && (do_per_step(step + 1, nstglobalcomm) || step_rel + 1 == ir->nsteps));
1262 // Parrinello-Rahman requires the pressure to be availible before the update to compute
1263 // the velocity scaling matrix. Hence, it runs one step after the nstpcouple step.
1264 const bool doParrinelloRahman = (ir->epc == epcPARRINELLORAHMAN
1265 && do_per_step(step + ir->nstpcouple - 1, ir->nstpcouple));
1267 if (useGpuForUpdate)
1269 if (bNS && (bFirstStep || DOMAINDECOMP(cr)))
1271 integrator->set(stateGpu->getCoordinates(), stateGpu->getVelocities(),
1272 stateGpu->getForces(), top.idef, *mdatoms, ekind->ngtc);
1274 // Copy data to the GPU after buffers might have being reinitialized
1275 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1276 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1279 // If the buffer ops were not offloaded this step, the forces are on the host and have to be copied
1280 if (!runScheduleWork->stepWork.useGpuFBufferOps)
1282 stateGpu->copyForcesToGpu(f.view().force(), AtomLocality::Local);
1285 const bool doTemperatureScaling =
1286 (ir->etc != etcNO && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
1288 // This applies Leap-Frog, LINCS and SETTLE in succession
1289 integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
1290 AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
1291 ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
1292 ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
1294 // Copy velocities D2H after update if:
1295 // - Globals are computed this step (includes the energy output steps).
1296 // - Temperature is needed for the next step.
1297 if (bGStat || needHalfStepKineticEnergy)
1299 stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
1300 stateGpu->waitVelocitiesReadyOnHost(AtomLocality::Local);
1305 upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
1306 M, etrtPOSITION, cr, constr != nullptr);
1308 wallcycle_stop(wcycle, ewcUPDATE);
1310 constrain_coordinates(constr, do_log, do_ene, step, state,
1311 upd.xp()->arrayRefWithPadding(), &dvdl_constr, bCalcVir, shake_vir);
1313 upd.update_sd_second_half(*ir, step, &dvdl_constr, mdatoms, state, cr, nrnb, wcycle,
1314 constr, do_log, do_ene);
1315 upd.finish_update(*ir, mdatoms, state, wcycle, constr != nullptr);
1318 if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
1320 updatePrevStepPullCom(pull_work, state);
1323 if (ir->eI == eiVVAK)
1325 /* erase F_EKIN and F_TEMP here? */
1326 /* just compute the kinetic energy at the half step to perform a trotter step */
1327 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
1328 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm, wcycle, enerd,
1329 force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, lastbox,
1330 nullptr, &bSumEkinhOld, (bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE);
1331 wallcycle_start(wcycle, ewcUPDATE);
1332 trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
1333 /* now we know the scaling, we can compute the positions again */
1334 std::copy(cbuf.begin(), cbuf.end(), state->x.begin());
1336 upd.update_coords(*ir, step, mdatoms, state, f.view().forceWithPadding(), fcdata, ekind,
1337 M, etrtPOSITION, cr, constr != nullptr);
1338 wallcycle_stop(wcycle, ewcUPDATE);
1340 /* do we need an extra constraint here? just need to copy out of as_rvec_array(state->v.data()) to upd->xp? */
1341 /* are the small terms in the shake_vir here due
1342 * to numerical errors, or are they important
1343 * physically? I'm thinking they are just errors, but not completely sure.
1344 * For now, will call without actually constraining, constr=NULL*/
1345 upd.finish_update(*ir, mdatoms, state, wcycle, false);
1349 /* this factor or 2 correction is necessary
1350 because half of the constraint force is removed
1351 in the vv step, so we have to double it. See
1352 the Issue #1255. It is not yet clear
1353 if the factor of 2 is exact, or just a very
1354 good approximation, and this will be
1355 investigated. The next step is to see if this
1356 can be done adding a dhdl contribution from the
1357 rattle step, but this is somewhat more
1358 complicated with the current code. Will be
1359 investigated, hopefully for 4.6.3. However,
1360 this current solution is much better than
1361 having it completely wrong.
1363 enerd->term[F_DVDL_CONSTR] += 2 * dvdl_constr;
1367 enerd->term[F_DVDL_CONSTR] += dvdl_constr;
1370 if (vsite != nullptr)
1372 wallcycle_start(wcycle, ewcVSITECONSTR);
1373 vsite->construct(state->x, ir->delta_t, state->v, state->box);
1374 wallcycle_stop(wcycle, ewcVSITECONSTR);
1377 /* ############## IF NOT VV, Calculate globals HERE ############ */
1378 /* With Leap-Frog we can skip compute_globals at
1379 * non-communication steps, but we need to calculate
1380 * the kinetic energy one step before communication.
1383 // Organize to do inter-simulation signalling on steps if
1384 // and when algorithms require it.
1385 const bool doInterSimSignal = (simulationsShareState && do_per_step(step, nstSignalComm));
1387 if (bGStat || needHalfStepKineticEnergy || doInterSimSignal)
1389 // Copy coordinates when needed to stop the CM motion.
1390 if (useGpuForUpdate && !EI_VV(ir->eI) && bStopCM)
1392 stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
1393 stateGpu->waitCoordinatesReadyOnHost(AtomLocality::Local);
1395 // Since we're already communicating at this step, we
1396 // can propagate intra-simulation signals. Note that
1397 // check_nstglobalcomm has the responsibility for
1398 // choosing the value of nstglobalcomm that is one way
1399 // bGStat becomes true, so we can't get into a
1400 // situation where e.g. checkpointing can't be
1402 bool doIntraSimSignal = true;
1403 SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
1405 compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
1406 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, &vcm,
1407 wcycle, enerd, force_vir, shake_vir, total_vir, pres, constr,
1408 &signaller, lastbox, &totalNumberOfBondedInteractions, &bSumEkinhOld,
1409 (bGStat ? CGLO_GSTAT : 0) | (!EI_VV(ir->eI) && bCalcEner ? CGLO_ENERGY : 0)
1410 | (!EI_VV(ir->eI) && bStopCM ? CGLO_STOPCM : 0)
1411 | (!EI_VV(ir->eI) ? CGLO_TEMPERATURE : 0)
1412 | (!EI_VV(ir->eI) ? CGLO_PRESSURE : 0) | CGLO_CONSTRAINT
1413 | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
1415 checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions,
1416 top_global, &top, makeConstArrayRef(state->x),
1417 state->box, &shouldCheckNumberOfBondedInteractions);
1418 if (!EI_VV(ir->eI) && bStopCM)
1420 process_and_stopcm_grp(fplog, &vcm, *mdatoms, makeArrayRef(state->x),
1421 makeArrayRef(state->v));
1422 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
1424 // TODO: The special case of removing CM motion should be dealt more gracefully
1425 if (useGpuForUpdate)
1427 stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
1428 // Here we block until the H2D copy completes because event sync with the
1429 // force kernels that use the coordinates on the next steps is not implemented
1430 // (not because of a race on state->x being modified on the CPU while H2D is in progress).
1431 stateGpu->waitCoordinatesCopiedToDevice(AtomLocality::Local);
1432 // If the COM removal changed the velocities on the CPU, this has to be accounted for.
1433 if (vcm.mode != ecmNO)
1435 stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
1442 /* ############# END CALC EKIN AND PRESSURE ################# */
1444 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
1445 the virial that should probably be addressed eventually. state->veta has better properies,
1446 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
1447 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
1449 if (ir->efep != efepNO && !EI_VV(ir->eI))
1451 /* Sum up the foreign energy and dK/dl terms for md and sd.
1452 Currently done every step so that dH/dl is correct in the .edr */
1453 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
1456 update_pcouple_after_coordinates(fplog, step, ir, mdatoms, pres, force_vir, shake_vir,
1457 pressureCouplingMu, state, nrnb, upd.deform(), !useGpuForUpdate);
1459 const bool doBerendsenPressureCoupling =
1460 (inputrec->epc == epcBERENDSEN && do_per_step(step, inputrec->nstpcouple));
1461 const bool doCRescalePressureCoupling =
1462 (inputrec->epc == epcCRESCALE && do_per_step(step, inputrec->nstpcouple));
1464 && (doBerendsenPressureCoupling || doCRescalePressureCoupling || doParrinelloRahman))
1466 integrator->scaleCoordinates(pressureCouplingMu);
1467 if (doCRescalePressureCoupling)
1469 matrix pressureCouplingInvMu;
1470 gmx::invertBoxMatrix(pressureCouplingMu, pressureCouplingInvMu);
1471 integrator->scaleVelocities(pressureCouplingInvMu);
1473 integrator->setPbc(PbcType::Xyz, state->box);
1476 /* ################# END UPDATE STEP 2 ################# */
1477 /* #### We now have r(t+dt) and v(t+dt/2) ############# */
1479 /* The coordinates (x) were unshifted in update */
1482 /* We will not sum ekinh_old,
1483 * so signal that we still have to do it.
1485 bSumEkinhOld = TRUE;
1490 /* ######### BEGIN PREPARING EDR OUTPUT ########### */
1492 /* use the directly determined last velocity, not actually the averaged half steps */
1493 if (bTrotter && ir->eI == eiVV)
1495 enerd->term[F_EKIN] = last_ekin;
1497 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1499 if (integratorHasConservedEnergyQuantity(ir))
1503 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1507 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + NPT_energy(ir, state, &MassQ);
1510 /* ######### END PREPARING EDR OUTPUT ########### */
1516 if (fplog && do_log && bDoExpanded)
1518 /* only needed if doing expanded ensemble */
1519 PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals,
1520 ir->bSimTemp ? ir->simtempvals : nullptr,
1521 state_global->dfhist, state->fep_state, ir->nstlog, step);
1525 energyOutput.addDataAtEnergyStep(
1526 bDoDHDL, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
1527 ir->expandedvals, lastbox,
1528 PTCouplingArrays{ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
1529 state->nhpres_xi, state->nhpres_vxi },
1530 state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
1534 energyOutput.recordNonEnergyStep();
1537 gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
1538 gmx_bool do_or = do_per_step(step, ir->nstorireout);
1540 if (doSimulatedAnnealing)
1542 gmx::EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups,
1545 if (do_log || do_ene || do_dr || do_or)
1547 energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
1548 do_log ? fplog : nullptr, step, t,
1549 fr->fcdata.get(), awh.get());
1551 if (do_log && ir->bDoAwh && awh->hasFepLambdaDimension())
1553 const bool isInitialOutput = false;
1554 printLambdaStateToLog(fplog, state->lambda, isInitialOutput);
1559 pull_print_output(pull_work, step, t);
1562 if (do_per_step(step, ir->nstlog))
1564 if (fflush(fplog) != 0)
1566 gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
1572 /* Have to do this part _after_ outputting the logfile and the edr file */
1573 /* Gets written into the state at the beginning of next loop*/
1574 state->fep_state = lamnew;
1576 else if (ir->bDoAwh && awh->needForeignEnergyDifferences(step))
1578 state->fep_state = awh->fepLambdaState();
1580 /* Print the remaining wall clock time for the run */
1581 if (isMasterSimMasterRank(ms, MASTER(cr)) && (do_verbose || gmx_got_usr_signal()) && !bPMETunePrinting)
1585 fprintf(stderr, "\n");
1587 print_time(stderr, walltime_accounting, step, ir, cr);
1590 /* Ion/water position swapping.
1591 * Not done in last step since trajectory writing happens before this call
1592 * in the MD loop and exchanges would be lost anyway. */
1593 bNeedRepartition = FALSE;
1594 if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep && do_per_step(step, ir->swap->nstswap))
1597 do_swapcoords(cr, step, t, ir, swap, wcycle, as_rvec_array(state->x.data()),
1598 state->box, MASTER(cr) && mdrunOptions.verbose, bRerunMD);
1600 if (bNeedRepartition && DOMAINDECOMP(cr))
1602 dd_collect_state(cr->dd, state, state_global);
1606 /* Replica exchange */
1610 bExchanged = replica_exchange(fplog, cr, ms, repl_ex, state_global, enerd, state, step, t);
1613 if ((bExchanged || bNeedRepartition) && DOMAINDECOMP(cr))
1615 dd_partition_system(fplog, mdlog, step, cr, TRUE, 1, state_global, *top_global, ir,
1616 imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
1617 nrnb, wcycle, FALSE);
1618 shouldCheckNumberOfBondedInteractions = true;
1619 upd.setNumAtoms(state->natoms);
1625 /* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
1626 /* With all integrators, except VV, we need to retain the pressure
1627 * at the current step for coupling at the next step.
1629 if ((state->flags & (1U << estPRES_PREV))
1630 && (bGStatEveryStep || (ir->nstpcouple > 0 && step % ir->nstpcouple == 0)))
1632 /* Store the pressure in t_state for pressure coupling
1633 * at the next MD step.
1635 copy_mat(pres, state->pres_prev);
1638 /* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
1640 if ((membed != nullptr) && (!bLastStep))
1642 rescale_membed(step_rel, membed, as_rvec_array(state_global->x.data()));
1645 cycles = wallcycle_stop(wcycle, ewcSTEP);
1646 if (DOMAINDECOMP(cr) && wcycle)
1648 dd_cycles_add(cr->dd, cycles, ddCyclStep);
1651 /* increase the MD step number */
1655 resetHandler->resetCounters(step, step_rel, mdlog, fplog, cr, fr->nbv.get(), nrnb,
1656 fr->pmedata, pme_loadbal, wcycle, walltime_accounting);
1658 /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
1659 imdSession->updateEnergyRecordAndSendPositionsAndEnergies(bInteractiveMDstep, step, bCalcEner);
1661 /* End of main MD loop */
1663 /* Closing TNG files can include compressing data. Therefore it is good to do that
1664 * before stopping the time measurements. */
1665 mdoutf_tng_close(outf);
1667 /* Stop measuring walltime */
1668 walltime_accounting_end_time(walltime_accounting);
1670 if (!thisRankHasDuty(cr, DUTY_PME))
1672 /* Tell the PME only node to finish */
1673 gmx_pme_send_finish(cr);
1678 if (ir->nstcalcenergy > 0)
1680 gmx::EnergyOutput::printAnnealingTemperatures(fplog, groups, &(ir->opts));
1681 energyOutput.printAverages(fplog, groups);
1688 pme_loadbal_done(pme_loadbal, fplog, mdlog, fr->nbv->useGpu());
1691 done_shellfc(fplog, shellfc, step_rel);
1693 if (useReplicaExchange && MASTER(cr))
1695 print_replica_exchange_statistics(fplog, repl_ex);
1698 walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
1700 global_stat_destroy(gstat);