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37 * \brief Implements the loop for simulation reruns
39 * \author Pascal Merz <pascal.merz@colorado.edu>
40 * \ingroup module_mdrun
54 #include "gromacs/awh/awh.h"
55 #include "gromacs/commandline/filenm.h"
56 #include "gromacs/domdec/collect.h"
57 #include "gromacs/domdec/dlbtiming.h"
58 #include "gromacs/domdec/domdec.h"
59 #include "gromacs/domdec/domdec_network.h"
60 #include "gromacs/domdec/domdec_struct.h"
61 #include "gromacs/domdec/partition.h"
62 #include "gromacs/essentialdynamics/edsam.h"
63 #include "gromacs/ewald/pme.h"
64 #include "gromacs/ewald/pme_load_balancing.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/imd/imd.h"
70 #include "gromacs/listed_forces/manage_threading.h"
71 #include "gromacs/math/functions.h"
72 #include "gromacs/math/utilities.h"
73 #include "gromacs/math/vec.h"
74 #include "gromacs/math/vectypes.h"
75 #include "gromacs/mdlib/checkpointhandler.h"
76 #include "gromacs/mdlib/compute_io.h"
77 #include "gromacs/mdlib/constr.h"
78 #include "gromacs/mdlib/ebin.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/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/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/utilities.h"
118 #include "gromacs/pbcutil/mshift.h"
119 #include "gromacs/pbcutil/pbc.h"
120 #include "gromacs/pulling/pull.h"
121 #include "gromacs/swap/swapcoords.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 "integrator.h"
137 #include "replicaexchange.h"
139 using gmx::SimulationSignaller
;
141 /*! \brief Copy the state from \p rerunFrame to \p globalState and, if requested, construct vsites
143 * \param[in] rerunFrame The trajectory frame to compute energy/forces for
144 * \param[in,out] globalState The global state container
145 * \param[in] constructVsites When true, vsite coordinates are constructed
146 * \param[in] vsite Vsite setup, can be nullptr when \p constructVsites = false
147 * \param[in] idef Topology parameters, used for constructing vsites
148 * \param[in] timeStep Time step, used for constructing vsites
149 * \param[in] forceRec Force record, used for constructing vsites
150 * \param[in,out] graph The molecular graph, used for constructing vsites when != nullptr
152 static void prepareRerunState(const t_trxframe
&rerunFrame
,
153 t_state
*globalState
,
154 bool constructVsites
,
155 const gmx_vsite_t
*vsite
,
158 const t_forcerec
&forceRec
,
161 auto x
= makeArrayRef(globalState
->x
);
162 auto rerunX
= arrayRefFromArray(reinterpret_cast<gmx::RVec
*>(rerunFrame
.x
), globalState
->natoms
);
163 std::copy(rerunX
.begin(), rerunX
.end(), x
.begin());
164 copy_mat(rerunFrame
.box
, globalState
->box
);
168 GMX_ASSERT(vsite
, "Need valid vsite for constructing vsites");
172 /* Following is necessary because the graph may get out of sync
173 * with the coordinates if we only have every N'th coordinate set
175 mk_mshift(nullptr, graph
, forceRec
.ePBC
, globalState
->box
, globalState
->x
.rvec_array());
176 shift_self(graph
, globalState
->box
, as_rvec_array(globalState
->x
.data()));
178 construct_vsites(vsite
, globalState
->x
.rvec_array(), timeStep
, globalState
->v
.rvec_array(),
179 idef
.iparams
, idef
.il
,
180 forceRec
.ePBC
, forceRec
.bMolPBC
, nullptr, globalState
->box
);
183 unshift_self(graph
, globalState
->box
, globalState
->x
.rvec_array());
188 void gmx::Integrator::do_rerun()
190 // TODO Historically, the EM and MD "integrators" used different
191 // names for the t_inputrec *parameter, but these must have the
192 // same name, now that it's a member of a struct. We use this ir
193 // alias to avoid a large ripple of nearly useless changes.
194 // t_inputrec is being replaced by IMdpOptionsProvider, so this
195 // will go away eventually.
196 t_inputrec
*ir
= inputrec
;
197 int64_t step
, step_rel
;
198 double t
, lam0
[efptNR
];
199 bool isLastStep
= false;
200 bool doFreeEnergyPerturbation
= false;
202 tensor force_vir
, shake_vir
, total_vir
, pres
;
207 gmx_enerdata_t
*enerd
;
208 PaddedVector
<gmx::RVec
> f
{};
209 gmx_global_stat_t gstat
;
210 t_graph
*graph
= nullptr;
211 gmx_groups_t
*groups
;
212 gmx_shellfc_t
*shellfc
;
216 /* Domain decomposition could incorrectly miss a bonded
217 interaction, but checking for that requires a global
218 communication stage, which does not otherwise happen in DD
219 code. So we do that alongside the first global energy reduction
220 after a new DD is made. These variables handle whether the
221 check happens, and the result it returns. */
222 bool shouldCheckNumberOfBondedInteractions
= false;
223 int totalNumberOfBondedInteractions
= -1;
225 SimulationSignals signals
;
226 // Most global communnication stages don't propagate mdrun
227 // signals, and will use this object to achieve that.
228 SimulationSignaller
nullSignaller(nullptr, nullptr, nullptr, false, false);
230 GMX_LOG(mdlog
.info
).asParagraph().
231 appendText("Note that it is planned that the command gmx mdrun -rerun will "
232 "be available in a different form in a future version of GROMACS, "
233 "e.g. gmx rerun -f.");
235 if (ir
->efep
!= efepNO
&& (mdAtoms
->mdatoms()->nMassPerturbed
> 0 ||
236 (constr
&& constr
->havePerturbedConstraints())))
238 gmx_fatal(FARGS
, "Perturbed masses or constraints are not supported by rerun. "
239 "Either make a .tpr without mass and constraint perturbation, "
240 "or use GROMACS 2018.4, 2018.5 or later 2018 version.");
244 gmx_fatal(FARGS
, "Expanded ensemble not supported by rerun.");
248 gmx_fatal(FARGS
, "Simulated tempering not supported by rerun.");
252 gmx_fatal(FARGS
, "AWH not supported by rerun.");
254 if (replExParams
.exchangeInterval
> 0)
256 gmx_fatal(FARGS
, "Replica exchange not supported by rerun.");
258 if (opt2bSet("-ei", nfile
, fnm
) || observablesHistory
->edsamHistory
!= nullptr)
260 gmx_fatal(FARGS
, "Essential dynamics not supported by rerun.");
264 gmx_fatal(FARGS
, "Interactive MD not supported by rerun.");
268 gmx_fatal(FARGS
, "Multiple simulations not supported by rerun.");
270 if (std::any_of(ir
->opts
.annealing
, ir
->opts
.annealing
+ ir
->opts
.ngtc
,
271 [](int i
){return i
!= eannNO
; }))
273 gmx_fatal(FARGS
, "Simulated annealing not supported by rerun.");
276 /* Rerun can't work if an output file name is the same as the input file name.
277 * If this is the case, the user will get an error telling them what the issue is.
279 if (strcmp(opt2fn("-rerun", nfile
, fnm
), opt2fn("-o", nfile
, fnm
)) == 0 ||
280 strcmp(opt2fn("-rerun", nfile
, fnm
), opt2fn("-x", nfile
, fnm
)) == 0)
282 gmx_fatal(FARGS
, "When using mdrun -rerun, the name of the input trajectory file "
283 "%s cannot be identical to the name of an output file (whether "
284 "given explicitly with -o or -x, or by default)",
285 opt2fn("-rerun", nfile
, fnm
));
288 /* Settings for rerun */
290 ir
->nstcalcenergy
= 1;
291 int nstglobalcomm
= 1;
292 const bool bNS
= true;
294 ir
->nstxout_compressed
= 0;
295 groups
= &top_global
->groups
;
296 if (ir
->eI
== eiMimic
)
298 top_global
->intermolecularExclusionGroup
= genQmmmIndices(*top_global
);
301 initialize_lambdas(fplog
, *ir
, MASTER(cr
), &state_global
->fep_state
, state_global
->lambda
, lam0
);
303 gmx_mdoutf
*outf
= init_mdoutf(fplog
, nfile
, fnm
, mdrunOptions
, cr
, outputProvider
, ir
, top_global
, oenv
, wcycle
);
304 gmx::EnergyOutput energyOutput
;
305 energyOutput
.prepare(mdoutf_get_fp_ene(outf
), top_global
, ir
, mdoutf_get_fp_dhdl(outf
), true);
307 /* Energy terms and groups */
309 init_enerdata(top_global
->groups
.grps
[egcENER
].nr
, ir
->fepvals
->n_lambda
,
312 /* Kinetic energy data */
313 std::unique_ptr
<gmx_ekindata_t
> eKinData
= std::make_unique
<gmx_ekindata_t
>();
314 gmx_ekindata_t
*ekind
= eKinData
.get();
315 init_ekindata(fplog
, top_global
, &(ir
->opts
), ekind
);
316 /* Copy the cos acceleration to the groups struct */
317 ekind
->cosacc
.cos_accel
= ir
->cos_accel
;
319 gstat
= global_stat_init(ir
);
321 /* Check for polarizable models and flexible constraints */
322 shellfc
= init_shell_flexcon(fplog
,
323 top_global
, constr
? constr
->numFlexibleConstraints() : 0,
324 ir
->nstcalcenergy
, DOMAINDECOMP(cr
));
327 double io
= compute_io(ir
, top_global
->natoms
, groups
, energyOutput
.numEnergyTerms(), 1);
328 if ((io
> 2000) && MASTER(cr
))
331 "\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
336 // Local state only becomes valid now.
337 std::unique_ptr
<t_state
> stateInstance
;
340 if (DOMAINDECOMP(cr
))
342 dd_init_local_top(*top_global
, &top
);
344 stateInstance
= std::make_unique
<t_state
>();
345 state
= stateInstance
.get();
346 dd_init_local_state(cr
->dd
, state_global
, state
);
348 /* Distribute the charge groups over the nodes from the master node */
349 dd_partition_system(fplog
, mdlog
, ir
->init_step
, cr
, TRUE
, 1,
350 state_global
, *top_global
, ir
,
351 state
, &f
, mdAtoms
, &top
, fr
,
353 nrnb
, nullptr, FALSE
);
354 shouldCheckNumberOfBondedInteractions
= true;
358 state_change_natoms(state_global
, state_global
->natoms
);
359 /* We need to allocate one element extra, since we might use
360 * (unaligned) 4-wide SIMD loads to access rvec entries.
362 f
.resizeWithPadding(state_global
->natoms
);
363 /* Copy the pointer to the global state */
364 state
= state_global
;
366 mdAlgorithmsSetupAtomData(cr
, ir
, *top_global
, &top
, fr
,
367 &graph
, mdAtoms
, constr
, vsite
, shellfc
);
370 auto mdatoms
= mdAtoms
->mdatoms();
372 // NOTE: The global state is no longer used at this point.
373 // But state_global is still used as temporary storage space for writing
374 // the global state to file and potentially for replica exchange.
375 // (Global topology should persist.)
377 update_mdatoms(mdatoms
, state
->lambda
[efptMASS
]);
379 if (ir
->efep
!= efepNO
&& ir
->fepvals
->nstdhdl
!= 0)
381 doFreeEnergyPerturbation
= true;
385 int cglo_flags
= (CGLO_INITIALIZATION
| CGLO_GSTAT
|
386 (shouldCheckNumberOfBondedInteractions
? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
: 0));
387 bool bSumEkinhOld
= false;
388 t_vcm
*vcm
= nullptr;
389 compute_globals(fplog
, gstat
, cr
, ir
, fr
, ekind
, state
, mdatoms
, nrnb
, vcm
,
390 nullptr, enerd
, force_vir
, shake_vir
, total_vir
, pres
, mu_tot
,
391 constr
, &nullSignaller
, state
->box
,
392 &totalNumberOfBondedInteractions
, &bSumEkinhOld
, cglo_flags
);
394 checkNumberOfBondedInteractions(mdlog
, cr
, totalNumberOfBondedInteractions
,
395 top_global
, &top
, state
,
396 &shouldCheckNumberOfBondedInteractions
);
400 fprintf(stderr
, "starting md rerun '%s', reading coordinates from"
401 " input trajectory '%s'\n\n",
402 *(top_global
->name
), opt2fn("-rerun", nfile
, fnm
));
403 if (mdrunOptions
.verbose
)
405 fprintf(stderr
, "Calculated time to finish depends on nsteps from "
406 "run input file,\nwhich may not correspond to the time "
407 "needed to process input trajectory.\n\n");
409 fprintf(fplog
, "\n");
412 walltime_accounting_start_time(walltime_accounting
);
413 wallcycle_start(wcycle
, ewcRUN
);
414 print_start(fplog
, cr
, walltime_accounting
, "mdrun");
416 /***********************************************************
420 ************************************************************/
424 GMX_LOG(mdlog
.info
).asParagraph().
425 appendText("Simulations has constraints. Rerun does not recalculate constraints.");
431 isLastStep
= !read_first_frame(oenv
, &status
,
432 opt2fn("-rerun", nfile
, fnm
),
433 &rerun_fr
, TRX_NEED_X
);
434 if (rerun_fr
.natoms
!= top_global
->natoms
)
437 "Number of atoms in trajectory (%d) does not match the "
438 "run input file (%d)\n",
439 rerun_fr
.natoms
, top_global
->natoms
);
442 if (ir
->ePBC
!= epbcNONE
)
446 gmx_fatal(FARGS
, "Rerun trajectory frame step %" PRId64
" time %f "
447 "does not contain a box, while pbc is used",
448 rerun_fr
.step
, rerun_fr
.time
);
450 if (max_cutoff2(ir
->ePBC
, rerun_fr
.box
) < gmx::square(fr
->rlist
))
452 gmx_fatal(FARGS
, "Rerun trajectory frame step %" PRId64
" time %f "
453 "has too small box dimensions", rerun_fr
.step
, rerun_fr
.time
);
458 GMX_LOG(mdlog
.info
).asParagraph().
459 appendText("Rerun does not report kinetic energy, total energy, temperature, virial and pressure.");
463 rerun_parallel_comm(cr
, &rerun_fr
, &isLastStep
);
466 if (ir
->ePBC
!= epbcNONE
)
468 /* Set the shift vectors.
469 * Necessary here when have a static box different from the tpr box.
471 calc_shifts(rerun_fr
.box
, fr
->shift_vec
);
474 auto stopHandler
= stopHandlerBuilder
->getStopHandlerMD(
475 compat::not_null
<SimulationSignal
*>(&signals
[eglsSTOPCOND
]), false,
476 MASTER(cr
), ir
->nstlist
, mdrunOptions
.reproducible
, nstglobalcomm
,
477 mdrunOptions
.maximumHoursToRun
, ir
->nstlist
== 0, fplog
, step
, bNS
, walltime_accounting
);
479 // we don't do counter resetting in rerun - finish will always be valid
480 walltime_accounting_set_valid_finish(walltime_accounting
);
482 const DDBalanceRegionHandler
ddBalanceRegionHandler(cr
);
484 step
= ir
->init_step
;
487 /* and stop now if we should */
488 isLastStep
= (isLastStep
|| (ir
->nsteps
>= 0 && step_rel
> ir
->nsteps
));
491 wallcycle_start(wcycle
, ewcSTEP
);
495 step
= rerun_fr
.step
;
496 step_rel
= step
- ir
->init_step
;
507 if (ir
->efep
!= efepNO
&& MASTER(cr
))
509 setCurrentLambdasRerun(step
, ir
->fepvals
, &rerun_fr
, lam0
, state_global
);
514 const bool constructVsites
= ((vsite
!= nullptr) && mdrunOptions
.rerunConstructVsites
);
515 if (constructVsites
&& DOMAINDECOMP(cr
))
517 gmx_fatal(FARGS
, "Vsite recalculation with -rerun is not implemented with domain decomposition, "
518 "use a single rank");
520 prepareRerunState(rerun_fr
, state_global
, constructVsites
, vsite
, top
.idef
, ir
->delta_t
, *fr
, graph
);
523 isLastStep
= isLastStep
|| stopHandler
->stoppingAfterCurrentStep(bNS
);
525 if (DOMAINDECOMP(cr
))
527 /* Repartition the domain decomposition */
528 const bool bMasterState
= true;
529 dd_partition_system(fplog
, mdlog
, step
, cr
,
530 bMasterState
, nstglobalcomm
,
531 state_global
, *top_global
, ir
,
532 state
, &f
, mdAtoms
, &top
, fr
,
535 mdrunOptions
.verbose
);
536 shouldCheckNumberOfBondedInteractions
= true;
541 print_ebin_header(fplog
, step
, t
); /* can we improve the information printed here? */
544 if (ir
->efep
!= efepNO
)
546 update_mdatoms(mdatoms
, state
->lambda
[efptMASS
]);
549 force_flags
= (GMX_FORCE_STATECHANGED
|
550 GMX_FORCE_DYNAMICBOX
|
551 GMX_FORCE_ALLFORCES
|
552 (GMX_GPU
? GMX_FORCE_VIRIAL
: 0) | // TODO: Get rid of this once #2649 is solved
554 (doFreeEnergyPerturbation
? GMX_FORCE_DHDL
: 0));
558 /* Now is the time to relax the shells */
559 relax_shell_flexcon(fplog
, cr
, ms
, mdrunOptions
.verbose
,
560 enforcedRotation
, step
,
561 ir
, bNS
, force_flags
, &top
,
563 state
, f
.arrayRefWithPadding(), force_vir
, mdatoms
,
564 nrnb
, wcycle
, graph
, groups
,
565 shellfc
, fr
, ppForceWorkload
, t
, mu_tot
,
567 ddBalanceRegionHandler
);
571 /* The coordinates (x) are shifted (to get whole molecules)
573 * This is parallellized as well, and does communication too.
574 * Check comments in sim_util.c
577 gmx_edsam
*ed
= nullptr;
578 do_force(fplog
, cr
, ms
, ir
, awh
, enforcedRotation
,
579 step
, nrnb
, wcycle
, &top
, groups
,
580 state
->box
, state
->x
.arrayRefWithPadding(), &state
->hist
,
581 f
.arrayRefWithPadding(), force_vir
, mdatoms
, enerd
, fcd
,
582 state
->lambda
, graph
,
583 fr
, ppForceWorkload
, vsite
, mu_tot
, t
, ed
,
584 GMX_FORCE_NS
| force_flags
,
585 ddBalanceRegionHandler
);
588 /* Now we have the energies and forces corresponding to the
589 * coordinates at time t.
592 const bool isCheckpointingStep
= false;
593 const bool doRerun
= true;
594 const bool bSumEkinhOld
= false;
595 do_md_trajectory_writing(fplog
, cr
, nfile
, fnm
, step
, step_rel
, t
,
596 ir
, state
, state_global
, observablesHistory
,
598 outf
, energyOutput
, ekind
, f
,
599 isCheckpointingStep
, doRerun
, isLastStep
,
600 mdrunOptions
.writeConfout
,
604 stopHandler
->setSignal();
608 /* Need to unshift here */
609 unshift_self(graph
, state
->box
, as_rvec_array(state
->x
.data()));
612 if (vsite
!= nullptr)
614 wallcycle_start(wcycle
, ewcVSITECONSTR
);
615 if (graph
!= nullptr)
617 shift_self(graph
, state
->box
, as_rvec_array(state
->x
.data()));
619 construct_vsites(vsite
, as_rvec_array(state
->x
.data()), ir
->delta_t
, as_rvec_array(state
->v
.data()),
620 top
.idef
.iparams
, top
.idef
.il
,
621 fr
->ePBC
, fr
->bMolPBC
, cr
, state
->box
);
623 if (graph
!= nullptr)
625 unshift_self(graph
, state
->box
, as_rvec_array(state
->x
.data()));
627 wallcycle_stop(wcycle
, ewcVSITECONSTR
);
631 const bool doInterSimSignal
= false;
632 const bool doIntraSimSignal
= true;
633 bool bSumEkinhOld
= false;
634 t_vcm
*vcm
= nullptr;
635 SimulationSignaller
signaller(&signals
, cr
, ms
, doInterSimSignal
, doIntraSimSignal
);
637 compute_globals(fplog
, gstat
, cr
, ir
, fr
, ekind
, state
, mdatoms
, nrnb
, vcm
,
638 wcycle
, enerd
, force_vir
, shake_vir
, total_vir
, pres
, mu_tot
,
641 &totalNumberOfBondedInteractions
, &bSumEkinhOld
,
642 CGLO_GSTAT
| CGLO_ENERGY
643 | (shouldCheckNumberOfBondedInteractions
? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
: 0)
645 checkNumberOfBondedInteractions(mdlog
, cr
, totalNumberOfBondedInteractions
,
646 top_global
, &top
, state
,
647 &shouldCheckNumberOfBondedInteractions
);
650 /* Note: this is OK, but there are some numerical precision issues with using the convergence of
651 the virial that should probably be addressed eventually. state->veta has better properies,
652 but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
653 generate the new shake_vir, but test the veta value for convergence. This will take some thought. */
655 if (ir
->efep
!= efepNO
)
657 /* Sum up the foreign energy and dhdl terms for md and sd.
658 Currently done every step so that dhdl is correct in the .edr */
659 sum_dhdl(enerd
, state
->lambda
, ir
->fepvals
);
665 const bool bCalcEnerStep
= true;
666 energyOutput
.addDataAtEnergyStep(doFreeEnergyPerturbation
, bCalcEnerStep
,
667 t
, mdatoms
->tmass
, enerd
, state
,
668 ir
->fepvals
, ir
->expandedvals
, state
->box
,
669 shake_vir
, force_vir
, total_vir
, pres
,
670 ekind
, mu_tot
, constr
);
672 const bool do_ene
= true;
673 const bool do_log
= true;
675 const bool do_dr
= ir
->nstdisreout
!= 0;
676 const bool do_or
= ir
->nstorireout
!= 0;
678 energyOutput
.printStepToEnergyFile(mdoutf_get_fp_ene(outf
), do_ene
, do_dr
, do_or
,
679 do_log
? fplog
: nullptr,
681 eprNORMAL
, fcd
, groups
, &(ir
->opts
), awh
);
683 if (do_per_step(step
, ir
->nstlog
))
685 if (fflush(fplog
) != 0)
687 gmx_fatal(FARGS
, "Cannot flush logfile - maybe you are out of disk space?");
692 /* Print the remaining wall clock time for the run */
693 if (isMasterSimMasterRank(ms
, cr
) &&
694 (mdrunOptions
.verbose
|| gmx_got_usr_signal()))
698 fprintf(stderr
, "\n");
700 print_time(stderr
, walltime_accounting
, step
, ir
, cr
);
703 /* Ion/water position swapping.
704 * Not done in last step since trajectory writing happens before this call
705 * in the MD loop and exchanges would be lost anyway. */
706 if ((ir
->eSwapCoords
!= eswapNO
) && (step
> 0) && !isLastStep
&&
707 do_per_step(step
, ir
->swap
->nstswap
))
709 const bool doRerun
= true;
710 do_swapcoords(cr
, step
, t
, ir
, wcycle
,
713 MASTER(cr
) && mdrunOptions
.verbose
,
719 /* read next frame from input trajectory */
720 isLastStep
= !read_next_frame(oenv
, status
, &rerun_fr
);
725 rerun_parallel_comm(cr
, &rerun_fr
, &isLastStep
);
728 cycles
= wallcycle_stop(wcycle
, ewcSTEP
);
729 if (DOMAINDECOMP(cr
) && wcycle
)
731 dd_cycles_add(cr
->dd
, cycles
, ddCyclStep
);
736 /* increase the MD step number */
741 /* End of main MD loop */
743 /* Closing TNG files can include compressing data. Therefore it is good to do that
744 * before stopping the time measurements. */
745 mdoutf_tng_close(outf
);
747 /* Stop measuring walltime */
748 walltime_accounting_end_time(walltime_accounting
);
755 if (!thisRankHasDuty(cr
, DUTY_PME
))
757 /* Tell the PME only node to finish */
758 gmx_pme_send_finish(cr
);
763 done_shellfc(fplog
, shellfc
, step_rel
);
765 // Clean up swapcoords
766 if (ir
->eSwapCoords
!= eswapNO
)
768 finish_swapcoords(ir
->swap
);
771 walltime_accounting_set_nsteps_done(walltime_accounting
, step_rel
);
773 destroy_enerdata(enerd
);