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41 #include "md_support.h"
48 #include "gromacs/domdec/domdec.h"
49 #include "gromacs/gmxlib/network.h"
50 #include "gromacs/gmxlib/nrnb.h"
51 #include "gromacs/math/units.h"
52 #include "gromacs/math/utilities.h"
53 #include "gromacs/math/vec.h"
54 #include "gromacs/mdlib/coupling.h"
55 #include "gromacs/mdlib/gmx_omp_nthreads.h"
56 #include "gromacs/mdlib/simulationsignal.h"
57 #include "gromacs/mdlib/stat.h"
58 #include "gromacs/mdlib/tgroup.h"
59 #include "gromacs/mdlib/update.h"
60 #include "gromacs/mdlib/vcm.h"
61 #include "gromacs/mdtypes/commrec.h"
62 #include "gromacs/mdtypes/df_history.h"
63 #include "gromacs/mdtypes/enerdata.h"
64 #include "gromacs/mdtypes/energyhistory.h"
65 #include "gromacs/mdtypes/forcerec.h"
66 #include "gromacs/mdtypes/group.h"
67 #include "gromacs/mdtypes/inputrec.h"
68 #include "gromacs/mdtypes/md_enums.h"
69 #include "gromacs/mdtypes/mdatom.h"
70 #include "gromacs/mdtypes/state.h"
71 #include "gromacs/pbcutil/pbc.h"
72 #include "gromacs/pulling/pull.h"
73 #include "gromacs/timing/wallcycle.h"
74 #include "gromacs/topology/mtop_util.h"
75 #include "gromacs/trajectory/trajectoryframe.h"
76 #include "gromacs/utility/arrayref.h"
77 #include "gromacs/utility/cstringutil.h"
78 #include "gromacs/utility/fatalerror.h"
79 #include "gromacs/utility/gmxassert.h"
80 #include "gromacs/utility/logger.h"
81 #include "gromacs/utility/smalloc.h"
82 #include "gromacs/utility/snprintf.h"
84 static void calc_ke_part_normal(gmx::ArrayRef<const gmx::RVec> v,
85 const t_grpopts* opts,
87 gmx_ekindata_t* ekind,
92 gmx::ArrayRef<t_grp_tcstat> tcstat = ekind->tcstat;
94 /* three main: VV with AveVel, vv with AveEkin, leap with AveEkin. Leap with AveVel is also
95 an option, but not supported now.
96 bEkinAveVel: If TRUE, we sum into ekin, if FALSE, into ekinh.
99 // Now accumulate the partial global and groups ekin.
100 for (g = 0; (g < opts->ngtc); g++)
102 copy_mat(tcstat[g].ekinh, tcstat[g].ekinh_old);
105 clear_mat(tcstat[g].ekinf);
106 tcstat[g].ekinscalef_nhc = 1.0; /* need to clear this -- logic is complicated! */
110 clear_mat(tcstat[g].ekinh);
113 ekind->dekindl_old = ekind->dekindl;
114 int nthread = gmx_omp_nthreads_get(emntUpdate);
116 #pragma omp parallel for num_threads(nthread) schedule(static)
117 for (int thread = 0; thread < nthread; thread++)
119 // This OpenMP only loops over arrays and does not call any functions
120 // or memory allocation. It should not be able to throw, so for now
121 // we do not need a try/catch wrapper.
122 int start_t, end_t, n;
129 start_t = ((thread + 0) * md->homenr) / nthread;
130 end_t = ((thread + 1) * md->homenr) / nthread;
132 ekin_sum = ekind->ekin_work[thread];
133 dekindl_sum = ekind->dekindl_work[thread];
135 for (gt = 0; gt < opts->ngtc; gt++)
137 clear_mat(ekin_sum[gt]);
142 for (n = start_t; n < end_t; n++)
148 hm = 0.5 * md->massT[n];
150 for (d = 0; (d < DIM); d++)
152 for (m = 0; (m < DIM); m++)
154 /* if we're computing a full step velocity, v[d] has v(t). Otherwise, v(t+dt/2) */
155 ekin_sum[gt][m][d] += hm * v[n][m] * v[n][d];
158 if (md->nMassPerturbed && md->bPerturbed[n])
160 *dekindl_sum += 0.5 * (md->massB[n] - md->massA[n]) * iprod(v[n], v[n]);
166 for (int thread = 0; thread < nthread; thread++)
168 for (g = 0; g < opts->ngtc; g++)
172 m_add(tcstat[g].ekinf, ekind->ekin_work[thread][g], tcstat[g].ekinf);
176 m_add(tcstat[g].ekinh, ekind->ekin_work[thread][g], tcstat[g].ekinh);
180 ekind->dekindl += *ekind->dekindl_work[thread];
183 inc_nrnb(nrnb, eNR_EKIN, md->homenr);
186 static void calc_ke_part_visc(const matrix box,
187 gmx::ArrayRef<const gmx::RVec> x,
188 gmx::ArrayRef<const gmx::RVec> v,
189 const t_grpopts* opts,
191 gmx_ekindata_t* ekind,
193 gmx_bool bEkinAveVel)
195 int start = 0, homenr = md->homenr;
196 int g, d, n, m, gt = 0;
199 gmx::ArrayRef<t_grp_tcstat> tcstat = ekind->tcstat;
200 t_cos_acc* cosacc = &(ekind->cosacc);
205 for (g = 0; g < opts->ngtc; g++)
207 copy_mat(ekind->tcstat[g].ekinh, ekind->tcstat[g].ekinh_old);
208 clear_mat(ekind->tcstat[g].ekinh);
210 ekind->dekindl_old = ekind->dekindl;
212 fac = 2 * M_PI / box[ZZ][ZZ];
215 for (n = start; n < start + homenr; n++)
221 hm = 0.5 * md->massT[n];
223 /* Note that the times of x and v differ by half a step */
224 /* MRS -- would have to be changed for VV */
225 cosz = std::cos(fac * x[n][ZZ]);
226 /* Calculate the amplitude of the new velocity profile */
227 mvcos += 2 * cosz * md->massT[n] * v[n][XX];
229 copy_rvec(v[n], v_corrt);
230 /* Subtract the profile for the kinetic energy */
231 v_corrt[XX] -= cosz * cosacc->vcos;
232 for (d = 0; (d < DIM); d++)
234 for (m = 0; (m < DIM); m++)
236 /* if we're computing a full step velocity, v_corrt[d] has v(t). Otherwise, v(t+dt/2) */
239 tcstat[gt].ekinf[m][d] += hm * v_corrt[m] * v_corrt[d];
243 tcstat[gt].ekinh[m][d] += hm * v_corrt[m] * v_corrt[d];
247 if (md->nPerturbed && md->bPerturbed[n])
249 /* The minus sign here might be confusing.
250 * The kinetic contribution from dH/dl doesn't come from
251 * d m(l)/2 v^2 / dl, but rather from d p^2/2m(l) / dl,
252 * where p are the momenta. The difference is only a minus sign.
254 dekindl -= 0.5 * (md->massB[n] - md->massA[n]) * iprod(v_corrt, v_corrt);
257 ekind->dekindl = dekindl;
258 cosacc->mvcos = mvcos;
260 inc_nrnb(nrnb, eNR_EKIN, homenr);
263 static void calc_ke_part(gmx::ArrayRef<const gmx::RVec> x,
264 gmx::ArrayRef<const gmx::RVec> v,
266 const t_grpopts* opts,
268 gmx_ekindata_t* ekind,
270 gmx_bool bEkinAveVel)
272 if (ekind->cosacc.cos_accel == 0)
274 calc_ke_part_normal(v, opts, md, ekind, nrnb, bEkinAveVel);
278 calc_ke_part_visc(box, x, v, opts, md, ekind, nrnb, bEkinAveVel);
282 /* TODO Specialize this routine into init-time and loop-time versions?
283 e.g. bReadEkin is only true when restoring from checkpoint */
284 void compute_globals(gmx_global_stat* gstat,
286 const t_inputrec* ir,
288 gmx_ekindata_t* ekind,
289 gmx::ArrayRef<const gmx::RVec> x,
290 gmx::ArrayRef<const gmx::RVec> v,
292 const t_mdatoms* mdatoms,
295 gmx_wallcycle_t wcycle,
296 gmx_enerdata_t* enerd,
301 gmx::ArrayRef<real> constraintsRmsdData,
302 gmx::SimulationSignaller* signalCoordinator,
303 const matrix lastbox,
304 gmx_bool* bSumEkinhOld,
307 gmx_bool bEner, bPres, bTemp;
308 gmx_bool bStopCM, bGStat, bReadEkin, bEkinAveVel, bScaleEkin, bConstrain;
309 gmx_bool bCheckNumberOfBondedInteractions;
312 /* translate CGLO flags to gmx_booleans */
313 bStopCM = ((flags & CGLO_STOPCM) != 0);
314 bGStat = ((flags & CGLO_GSTAT) != 0);
315 bReadEkin = ((flags & CGLO_READEKIN) != 0);
316 bScaleEkin = ((flags & CGLO_SCALEEKIN) != 0);
317 bEner = ((flags & CGLO_ENERGY) != 0);
318 bTemp = ((flags & CGLO_TEMPERATURE) != 0);
319 bPres = ((flags & CGLO_PRESSURE) != 0);
320 bConstrain = ((flags & CGLO_CONSTRAINT) != 0);
321 bCheckNumberOfBondedInteractions = ((flags & CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS) != 0);
323 /* we calculate a full state kinetic energy either with full-step velocity verlet
324 or half step where we need the pressure */
326 bEkinAveVel = (ir->eI == IntegrationAlgorithm::VV
327 || (ir->eI == IntegrationAlgorithm::VVAK && bPres) || bReadEkin);
329 /* in initalization, it sums the shake virial in vv, and to
330 sums ekinh_old in leapfrog (or if we are calculating ekinh_old) for other reasons */
332 /* ########## Kinetic energy ############## */
338 calc_ke_part(x, v, box, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
342 /* Calculate center of mass velocity if necessary, also parallellized */
345 calc_vcm_grp(*mdatoms, x, v, vcm);
348 if (bTemp || bStopCM || bPres || bEner || bConstrain || bCheckNumberOfBondedInteractions)
352 /* We will not sum ekinh_old,
353 * so signal that we still have to do it.
355 *bSumEkinhOld = TRUE;
359 gmx::ArrayRef<real> signalBuffer = signalCoordinator->getCommunicationBuffer();
362 wallcycle_start(wcycle, ewcMoveE);
371 bStopCM ? vcm : nullptr,
376 wallcycle_stop(wcycle, ewcMoveE);
378 signalCoordinator->finalizeSignals();
379 *bSumEkinhOld = FALSE;
385 /* Calculate the amplitude of the cosine velocity profile */
386 ekind->cosacc.vcos = ekind->cosacc.mvcos / mdatoms->tmass;
391 /* Sum the kinetic energies of the groups & calc temp */
392 /* compute full step kinetic energies if vv, or if vv-avek and we are computing the pressure with inputrecNptTrotter */
393 /* three maincase: VV with AveVel (md-vv), vv with AveEkin (md-vv-avek), leap with AveEkin (md).
394 Leap with AveVel is not supported; it's not clear that it will actually work.
395 bEkinAveVel: If TRUE, we simply multiply ekin by ekinscale to get a full step kinetic energy.
396 If FALSE, we average ekinh_old and ekinh*ekinscale_nhc to get an averaged half step kinetic energy.
398 enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &dvdl_ekin, bEkinAveVel, bScaleEkin);
399 enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Mass] = static_cast<double>(dvdl_ekin);
401 enerd->term[F_EKIN] = trace(ekind->ekin);
404 /* ########## Now pressure ############## */
405 // TODO: For the VV integrator bConstrain is needed in the conditional. This is confusing, so get rid of this.
406 if (bPres || bConstrain)
408 m_add(force_vir, shake_vir, total_vir);
410 /* Calculate pressure and apply LR correction if PPPM is used.
411 * Use the box from last timestep since we already called update().
414 enerd->term[F_PRES] = calc_pres(fr->pbcType, ir->nwall, lastbox, ekind->ekin, total_vir, pres);
418 static void min_zero(int* n, int i)
420 if (i > 0 && (*n == 0 || i < *n))
426 static int lcd4(int i1, int i2, int i3, int i4)
437 gmx_incons("All 4 inputs for determining nstglobalcomm are <= 0");
441 && ((i1 > 0 && i1 % nst != 0) || (i2 > 0 && i2 % nst != 0) || (i3 > 0 && i3 % nst != 0)
442 || (i4 > 0 && i4 % nst != 0)))
450 int computeGlobalCommunicationPeriod(const t_inputrec* ir)
452 int nstglobalcomm = 10;
454 // Set up the default behaviour
455 if (!(ir->nstcalcenergy > 0 || ir->nstlist > 0 || ir->etc != TemperatureCoupling::No
456 || ir->epc != PressureCoupling::No))
458 /* The user didn't choose the period for anything
459 important, so we just make sure we can send signals and
460 write output suitably. */
461 if (ir->nstenergy > 0 && ir->nstenergy < nstglobalcomm)
463 nstglobalcomm = ir->nstenergy;
468 /* The user has made a choice (perhaps implicitly), so we
469 * ensure that we do timely intra-simulation communication
470 * for (possibly) each of the four parts that care.
472 * TODO Does the Verlet scheme (+ DD) need any
473 * communication at nstlist steps? Is the use of nstlist
474 * here a leftover of the twin-range scheme? Can we remove
475 * nstlist when we remove the group scheme?
477 nstglobalcomm = lcd4(ir->nstcalcenergy,
479 ir->etc != TemperatureCoupling::No ? ir->nsttcouple : 0,
480 ir->epc != PressureCoupling::No ? ir->nstpcouple : 0);
483 return nstglobalcomm;
486 int computeGlobalCommunicationPeriod(const gmx::MDLogger& mdlog, const t_inputrec* ir, const t_commrec* cr)
488 const int nstglobalcomm = computeGlobalCommunicationPeriod(ir);
493 .appendTextFormatted("Intra-simulation communication will occur every %d steps.\n",
496 return nstglobalcomm;
499 void rerun_parallel_comm(t_commrec* cr, t_trxframe* fr, gmx_bool* bLastStep)
503 if (MASTER(cr) && *bLastStep)
509 gmx_bcast(sizeof(*fr), fr, cr->mpi_comm_mygroup);
513 *bLastStep = (fr->natoms < 0);
516 // TODO Most of this logic seems to belong in the respective modules
517 void set_state_entries(t_state* state, const t_inputrec* ir, bool useModularSimulator)
519 /* The entries in the state in the tpx file might not correspond
520 * with what is needed, so we correct this here.
523 if (ir->efep != FreeEnergyPerturbationType::No || ir->bExpanded)
525 state->flags |= enumValueToBitMask(StateEntry::Lambda);
526 state->flags |= enumValueToBitMask(StateEntry::FepState);
528 state->flags |= enumValueToBitMask(StateEntry::X);
529 GMX_RELEASE_ASSERT(state->x.size() == state->natoms,
530 "We should start a run with an initialized state->x");
531 if (EI_DYNAMICS(ir->eI))
533 state->flags |= enumValueToBitMask(StateEntry::V);
537 if (ir->pbcType != PbcType::No)
539 state->flags |= enumValueToBitMask(StateEntry::Box);
540 if (inputrecPreserveShape(ir))
542 state->flags |= enumValueToBitMask(StateEntry::BoxRel);
544 if ((ir->epc == PressureCoupling::ParrinelloRahman) || (ir->epc == PressureCoupling::Mttk))
546 state->flags |= enumValueToBitMask(StateEntry::BoxV);
547 if (!useModularSimulator)
549 state->flags |= enumValueToBitMask(StateEntry::PressurePrevious);
552 if (inputrecNptTrotter(ir) || (inputrecNphTrotter(ir)))
555 state->flags |= enumValueToBitMask(StateEntry::Nhpresxi);
556 state->flags |= enumValueToBitMask(StateEntry::Nhpresvxi);
557 state->flags |= enumValueToBitMask(StateEntry::SVirPrev);
558 state->flags |= enumValueToBitMask(StateEntry::FVirPrev);
559 state->flags |= enumValueToBitMask(StateEntry::Veta);
560 state->flags |= enumValueToBitMask(StateEntry::Vol0);
562 if (ir->epc == PressureCoupling::Berendsen || ir->epc == PressureCoupling::CRescale)
564 state->flags |= enumValueToBitMask(StateEntry::BarosInt);
568 if (ir->etc == TemperatureCoupling::NoseHoover)
570 state->flags |= enumValueToBitMask(StateEntry::Nhxi);
571 state->flags |= enumValueToBitMask(StateEntry::Nhvxi);
574 if (ir->etc == TemperatureCoupling::VRescale || ir->etc == TemperatureCoupling::Berendsen)
576 state->flags |= enumValueToBitMask(StateEntry::ThermInt);
579 init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
580 init_ekinstate(&state->ekinstate, ir);
584 snew(state->dfhist, 1);
585 init_df_history(state->dfhist, ir->fepvals->n_lambda);
588 if (ir->pull && ir->pull->bSetPbcRefToPrevStepCOM)
590 state->flags |= enumValueToBitMask(StateEntry::PullComPrevStep);