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40 #include "update_vv.h"
46 #include "gromacs/domdec/localtopologychecker.h"
47 #include "gromacs/gmxlib/nrnb.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/mdlib/constr.h"
50 #include "gromacs/mdlib/coupling.h"
51 #include "gromacs/mdlib/enerdata_utils.h"
52 #include "gromacs/mdlib/mdatoms.h"
53 #include "gromacs/mdlib/md_support.h"
54 #include "gromacs/mdlib/stat.h"
55 #include "gromacs/mdlib/tgroup.h"
56 #include "gromacs/mdlib/update.h"
57 #include "gromacs/mdrunutility/handlerestart.h"
58 #include "gromacs/mdtypes/commrec.h"
59 #include "gromacs/mdtypes/enerdata.h"
60 #include "gromacs/mdtypes/fcdata.h"
61 #include "gromacs/mdtypes/forcebuffers.h"
62 #include "gromacs/mdtypes/forcerec.h"
63 #include "gromacs/mdtypes/group.h"
64 #include "gromacs/mdtypes/inputrec.h"
65 #include "gromacs/mdtypes/mdatom.h"
66 #include "gromacs/mdtypes/state.h"
67 #include "gromacs/pulling/pull.h"
68 #include "gromacs/timing/wallcycle.h"
69 #include "gromacs/topology/topology.h"
71 void integrateVVFirstStep(int64_t step,
74 gmx::StartingBehavior startingBehavior,
84 gmx_enerdata_t* enerd,
85 gmx::ObservablesReducer* observablesReducer,
86 gmx_ekindata_t* ekind,
87 gmx_global_stat* gstat,
103 real* saved_conserved_quantity,
104 gmx::ForceBuffers* f,
106 gmx::Constraints* constr,
107 gmx::SimulationSignaller* nullSignaller,
108 gmx::EnumerationArray<TrotterSequence, std::vector<int>> trotter_seq,
111 gmx_wallcycle* wcycle)
113 if (!bFirstStep || startingBehavior == gmx::StartingBehavior::NewSimulation)
115 /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
116 rvec* vbuf = nullptr;
118 wallcycle_start(wcycle, WallCycleCounter::Update);
119 if (ir->eI == IntegrationAlgorithm::VV && bInitStep)
121 /* if using velocity verlet with full time step Ekin,
122 * take the first half step only to compute the
123 * virial for the first step. From there,
124 * revert back to the initial coordinates
125 * so that the input is actually the initial step.
127 snew(vbuf, state->natoms);
128 copy_rvecn(state->v.rvec_array(), vbuf, 0, state->natoms); /* should make this better for parallelizing? */
132 /* this is for NHC in the Ekin(t+dt/2) version of vv */
140 mdatoms->cTC ? gmx::arrayRefFromArray(mdatoms->cTC, mdatoms->nr)
141 : gmx::ArrayRef<const unsigned short>(),
142 gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
145 TrotterSequence::One);
148 upd->update_coords(*ir,
151 mdatoms->havePartiallyFrozenAtoms,
152 gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr),
153 gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
154 gmx::arrayRefFromArray(mdatoms->invMassPerDim, mdatoms->nr),
156 f->view().forceWithPadding(),
164 wallcycle_stop(wcycle, WallCycleCounter::Update);
165 constrain_velocities(constr, do_log, do_ene, step, state, nullptr, bCalcVir, shake_vir);
166 wallcycle_start(wcycle, WallCycleCounter::Update);
167 /* if VV, compute the pressure and constraints */
168 /* For VV2, we strictly only need this if using pressure
169 * control, but we really would like to have accurate pressures
171 * Think about ways around this in the future?
172 * For now, keep this choice in comments.
174 /*bPres = (ir->eI==IntegrationAlgorithm::VV || inputrecNptTrotter(ir)); */
175 /*bTemp = ((ir->eI==IntegrationAlgorithm::VV &&(!bInitStep)) || (ir->eI==IntegrationAlgorithm::VVAK && inputrecNptTrotter(ir)));*/
177 bool bTemp = ((ir->eI == IntegrationAlgorithm::VV && (!bInitStep))
178 || (ir->eI == IntegrationAlgorithm::VVAK));
179 if (bCalcEner && ir->eI == IntegrationAlgorithm::VVAK)
181 *bSumEkinhOld = TRUE;
183 /* for vv, the first half of the integration actually corresponds to the previous step.
184 So we need information from the last step in the first half of the integration */
185 if (bGStat || do_per_step(step - 1, nstglobalcomm))
187 wallcycle_stop(wcycle, WallCycleCounter::Update);
189 ((bGStat ? CGLO_GSTAT : 0) | (bCalcEner ? CGLO_ENERGY : 0)
190 | (bTemp ? CGLO_TEMPERATURE : 0) | (bPres ? CGLO_PRESSURE : 0)
191 | (bPres ? CGLO_CONSTRAINT : 0) | (bStopCM ? CGLO_STOPCM : 0) | CGLO_SCALEEKIN);
192 compute_globals(gstat,
197 makeConstArrayRef(state->x),
198 makeConstArrayRef(state->v),
215 /* explanation of above:
216 a) We compute Ekin at the full time step
217 if 1) we are using the AveVel Ekin, and it's not the
218 initial step, or 2) if we are using AveEkin, but need the full
219 time step kinetic energy for the pressure (always true now, since we want accurate statistics).
220 b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
221 EkinAveVel because it's needed for the pressure */
224 process_and_stopcm_grp(
225 fplog, vcm, *mdatoms, makeArrayRef(state->x), makeArrayRef(state->v));
226 inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
228 wallcycle_start(wcycle, WallCycleCounter::Update);
230 /* temperature scaling and pressure scaling to produce the extended variables at t+dt */
235 m_add(force_vir, shake_vir, total_vir); /* we need the un-dispersion corrected total vir here */
243 mdatoms->cTC ? gmx::arrayRefFromArray(mdatoms->cTC, mdatoms->nr)
244 : gmx::ArrayRef<const unsigned short>(),
245 gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
248 TrotterSequence::Two);
250 /* TODO This is only needed when we're about to write
251 * a checkpoint, because we use it after the restart
252 * (in a kludge?). But what should we be doing if
253 * the startingBehavior is NewSimulation or bInitStep are true? */
254 if (inputrecNptTrotter(ir) || inputrecNphTrotter(ir))
256 copy_mat(shake_vir, state->svir_prev);
257 copy_mat(force_vir, state->fvir_prev);
259 if ((inputrecNptTrotter(ir) || inputrecNvtTrotter(ir)) && ir->eI == IntegrationAlgorithm::VV)
261 /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
262 enerd->term[F_TEMP] = sum_ekin(
263 &(ir->opts), ekind, nullptr, (ir->eI == IntegrationAlgorithm::VV), FALSE);
264 enerd->term[F_EKIN] = trace(ekind->ekin);
269 wallcycle_stop(wcycle, WallCycleCounter::Update);
270 /* We need the kinetic energy at minus the half step for determining
271 * the full step kinetic energy and possibly for T-coupling.*/
272 /* This may not be quite working correctly yet . . . . */
273 compute_globals(gstat,
278 makeConstArrayRef(state->x),
279 makeConstArrayRef(state->v),
293 CGLO_GSTAT | CGLO_TEMPERATURE,
296 wallcycle_start(wcycle, WallCycleCounter::Update);
299 /* if it's the initial step, we performed this first step just to get the constraint virial */
300 if (ir->eI == IntegrationAlgorithm::VV && bInitStep)
302 copy_rvecn(vbuf, state->v.rvec_array(), 0, state->natoms);
305 wallcycle_stop(wcycle, WallCycleCounter::Update);
308 /* compute the conserved quantity */
309 *saved_conserved_quantity = NPT_energy(ir, state, MassQ);
310 if (ir->eI == IntegrationAlgorithm::VV)
312 *last_ekin = enerd->term[F_EKIN];
314 if ((ir->eDispCorr != DispersionCorrectionType::EnerPres)
315 && (ir->eDispCorr != DispersionCorrectionType::AllEnerPres))
317 *saved_conserved_quantity -= enerd->term[F_DISPCORR];
319 /* sum up the foreign kinetic energy and dK/dl terms for vv. currently done every step so that dhdl is correct in the .edr */
320 if (ir->efep != FreeEnergyPerturbationType::No)
322 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
326 void integrateVVSecondStep(int64_t step,
327 const t_inputrec* ir,
336 gmx_enerdata_t* enerd,
337 gmx::ObservablesReducer* observablesReducer,
338 gmx_ekindata_t* ekind,
339 gmx_global_stat* gstat,
352 gmx::ForceBuffers* f,
353 std::vector<gmx::RVec>* cbuf,
355 gmx::Constraints* constr,
356 gmx::SimulationSignaller* nullSignaller,
357 gmx::EnumerationArray<TrotterSequence, std::vector<int>> trotter_seq,
359 gmx_wallcycle* wcycle)
361 /* velocity half-step update */
362 upd->update_coords(*ir,
365 mdatoms->havePartiallyFrozenAtoms,
366 gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr),
367 gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
368 gmx::arrayRefFromArray(mdatoms->invMassPerDim, mdatoms->nr),
370 f->view().forceWithPadding(),
379 /* Above, initialize just copies ekinh into ekin,
380 * it doesn't copy position (for VV),
381 * and entire integrator for MD.
384 if (ir->eI == IntegrationAlgorithm::VVAK)
386 cbuf->resize(state->x.size());
387 std::copy(state->x.begin(), state->x.end(), cbuf->begin());
390 if (ir->bPull && ir->pull->bSetPbcRefToPrevStepCOM)
392 updatePrevStepPullCom(pull_work, state);
395 upd->update_coords(*ir,
398 mdatoms->havePartiallyFrozenAtoms,
399 gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr),
400 gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
401 gmx::arrayRefFromArray(mdatoms->invMassPerDim, mdatoms->nr),
403 f->view().forceWithPadding(),
411 wallcycle_stop(wcycle, WallCycleCounter::Update);
413 constrain_coordinates(
414 constr, do_log, do_ene, step, state, upd->xp()->arrayRefWithPadding(), dvdl_constr, bCalcVir, shake_vir);
416 upd->update_sd_second_half(*ir,
420 gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr),
421 gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
430 *ir, mdatoms->havePartiallyFrozenAtoms, mdatoms->homenr, state, wcycle, constr != nullptr);
432 if (ir->eI == IntegrationAlgorithm::VVAK)
434 /* erase F_EKIN and F_TEMP here? */
435 /* just compute the kinetic energy at the half step to perform a trotter step */
436 compute_globals(gstat,
441 makeConstArrayRef(state->x),
442 makeConstArrayRef(state->v),
456 (bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE,
459 wallcycle_start(wcycle, WallCycleCounter::Update);
467 mdatoms->cTC ? gmx::arrayRefFromArray(mdatoms->cTC, mdatoms->nr)
468 : gmx::ArrayRef<const unsigned short>(),
469 gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
472 TrotterSequence::Four);
473 /* now we know the scaling, we can compute the positions again */
474 std::copy(cbuf->begin(), cbuf->end(), state->x.begin());
476 upd->update_coords(*ir,
479 mdatoms->havePartiallyFrozenAtoms,
480 gmx::arrayRefFromArray(mdatoms->ptype, mdatoms->nr),
481 gmx::arrayRefFromArray(mdatoms->invmass, mdatoms->nr),
482 gmx::arrayRefFromArray(mdatoms->invMassPerDim, mdatoms->nr),
484 f->view().forceWithPadding(),
491 wallcycle_stop(wcycle, WallCycleCounter::Update);
493 /* do we need an extra constraint here? just need to copy out of as_rvec_array(state->v.data()) to upd->xp? */
494 /* are the small terms in the shake_vir here due
495 * to numerical errors, or are they important
496 * physically? I'm thinking they are just errors, but not completely sure.
497 * For now, will call without actually constraining, constr=NULL*/
498 upd->finish_update(*ir, mdatoms->havePartiallyFrozenAtoms, mdatoms->homenr, state, wcycle, false);
500 /* this factor or 2 correction is necessary
501 because half of the constraint force is removed
502 in the vv step, so we have to double it. See
503 the Issue #1255. It is not yet clear
504 if the factor of 2 is exact, or just a very
505 good approximation, and this will be
506 investigated. The next step is to see if this
507 can be done adding a dhdl contribution from the
508 rattle step, but this is somewhat more
509 complicated with the current code. Will be
510 investigated, hopefully for 4.6.3. However,
511 this current solution is much better than
512 having it completely wrong.
514 enerd->term[F_DVDL_CONSTR] += 2 * *dvdl_constr;