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46 #include "gromacs/ewald/pme.h"
47 #include "gromacs/gpu_utils/hostallocator.h"
48 #include "gromacs/math/functions.h"
49 #include "gromacs/mdlib/gmx_omp_nthreads.h"
50 #include "gromacs/mdtypes/inputrec.h"
51 #include "gromacs/mdtypes/md_enums.h"
52 #include "gromacs/mdtypes/mdatom.h"
53 #include "gromacs/topology/mtop_lookup.h"
54 #include "gromacs/topology/mtop_util.h"
55 #include "gromacs/topology/topology.h"
56 #include "gromacs/utility/exceptions.h"
57 #include "gromacs/utility/smalloc.h"
59 #define ALMOST_ZERO 1e-30
64 MDAtoms::MDAtoms() : mdatoms_(nullptr) {}
68 if (mdatoms_ == nullptr)
72 sfree(mdatoms_->massA);
73 sfree(mdatoms_->massB);
74 sfree(mdatoms_->massT);
75 gmx::AlignedAllocationPolicy::free(mdatoms_->invmass);
76 sfree(mdatoms_->invMassPerDim);
77 sfree(mdatoms_->typeA);
78 sfree(mdatoms_->chargeB);
79 sfree(mdatoms_->typeB);
80 sfree(mdatoms_->sqrt_c6A);
81 sfree(mdatoms_->sigmaA);
82 sfree(mdatoms_->sigma3A);
83 sfree(mdatoms_->sqrt_c6B);
84 sfree(mdatoms_->sigmaB);
85 sfree(mdatoms_->sigma3B);
86 sfree(mdatoms_->ptype);
88 sfree(mdatoms_->cENER);
89 sfree(mdatoms_->cACC);
90 sfree(mdatoms_->cFREEZE);
91 sfree(mdatoms_->cVCM);
92 sfree(mdatoms_->cORF);
93 sfree(mdatoms_->bPerturbed);
98 void MDAtoms::resize(int newSize)
100 chargeA_.resizeWithPadding(newSize);
101 mdatoms_->chargeA = chargeA_.data();
104 void MDAtoms::reserve(int newCapacity)
106 chargeA_.reserveWithPadding(newCapacity);
107 mdatoms_->chargeA = chargeA_.data();
110 std::unique_ptr<MDAtoms> makeMDAtoms(FILE* fp, const gmx_mtop_t& mtop, const t_inputrec& ir, const bool rankHasPmeGpuTask)
112 auto mdAtoms = std::make_unique<MDAtoms>();
113 // GPU transfers may want to use a suitable pinning mode.
114 if (rankHasPmeGpuTask)
116 changePinningPolicy(&mdAtoms->chargeA_, pme_get_pinning_policy());
120 mdAtoms->mdatoms_.reset(md);
122 md->nenergrp = mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size();
123 md->bVCMgrps = FALSE;
124 for (int i = 0; i < mtop.natoms; i++)
126 if (getGroupType(mtop.groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i) > 0)
132 /* Determine the total system mass and perturbed atom counts */
133 double totalMassA = 0.0;
134 double totalMassB = 0.0;
136 md->haveVsites = FALSE;
137 gmx_mtop_atomloop_block_t aloop = gmx_mtop_atomloop_block_init(&mtop);
140 while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
142 totalMassA += nmol * atom->m;
143 totalMassB += nmol * atom->mB;
145 if (atom->ptype == eptVSite)
147 md->haveVsites = TRUE;
150 if (ir.efep != efepNO && PERTURBED(*atom))
153 if (atom->mB != atom->m)
155 md->nMassPerturbed += nmol;
157 if (atom->qB != atom->q)
159 md->nChargePerturbed += nmol;
161 if (atom->typeB != atom->type)
163 md->nTypePerturbed += nmol;
168 md->tmassA = totalMassA;
169 md->tmassB = totalMassB;
171 if (ir.efep != efepNO && fp)
173 fprintf(fp, "There are %d atoms and %d charges for free energy perturbation\n",
174 md->nPerturbed, md->nChargePerturbed);
177 md->havePartiallyFrozenAtoms = FALSE;
178 for (int g = 0; g < ir.opts.ngfrz; g++)
180 for (int d = YY; d < DIM; d++)
182 if (ir.opts.nFreeze[g][d] != ir.opts.nFreeze[g][XX])
184 md->havePartiallyFrozenAtoms = TRUE;
189 md->bOrires = (gmx_mtop_ftype_count(&mtop, F_ORIRES) != 0);
196 void atoms2md(const gmx_mtop_t* mtop, const t_inputrec* ir, int nindex, const int* index, int homenr, gmx::MDAtoms* mdAtoms)
199 const t_grpopts* opts;
200 int nthreads gmx_unused;
202 bLJPME = EVDW_PME(ir->vdwtype);
206 const SimulationGroups& groups = mtop->groups;
208 auto md = mdAtoms->mdatoms();
209 /* nindex>=0 indicates DD where we use an index */
216 md->nr = mtop->natoms;
219 if (md->nr > md->nalloc)
221 md->nalloc = over_alloc_dd(md->nr);
223 if (md->nMassPerturbed)
225 srenew(md->massA, md->nalloc);
226 srenew(md->massB, md->nalloc);
228 srenew(md->massT, md->nalloc);
229 /* The SIMD version of the integrator needs this aligned and padded.
230 * The padding needs to be with zeros, which we set later below.
232 gmx::AlignedAllocationPolicy::free(md->invmass);
233 md->invmass = new (gmx::AlignedAllocationPolicy::malloc(
234 (md->nalloc + GMX_REAL_MAX_SIMD_WIDTH) * sizeof(*md->invmass))) real;
235 srenew(md->invMassPerDim, md->nalloc);
236 // TODO eventually we will have vectors and just resize
237 // everything, but for now the semantics of md->nalloc being
238 // the capacity are preserved by keeping vectors within
239 // mdAtoms having the same properties as the other arrays.
240 mdAtoms->reserve(md->nalloc);
241 mdAtoms->resize(md->nr);
242 srenew(md->typeA, md->nalloc);
245 srenew(md->chargeB, md->nalloc);
246 srenew(md->typeB, md->nalloc);
250 srenew(md->sqrt_c6A, md->nalloc);
251 srenew(md->sigmaA, md->nalloc);
252 srenew(md->sigma3A, md->nalloc);
255 srenew(md->sqrt_c6B, md->nalloc);
256 srenew(md->sigmaB, md->nalloc);
257 srenew(md->sigma3B, md->nalloc);
260 srenew(md->ptype, md->nalloc);
263 srenew(md->cTC, md->nalloc);
264 /* We always copy cTC with domain decomposition */
266 srenew(md->cENER, md->nalloc);
269 srenew(md->cACC, md->nalloc);
272 && (opts->ngfrz > 1 || opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
274 srenew(md->cFREEZE, md->nalloc);
278 srenew(md->cVCM, md->nalloc);
282 srenew(md->cORF, md->nalloc);
286 srenew(md->bPerturbed, md->nalloc);
289 /* Note that these user t_mdatoms array pointers are NULL
290 * when there is only one group present.
291 * Therefore, when adding code, the user should use something like:
292 * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
294 if (!mtop->groups.groupNumbers[SimulationAtomGroupType::User1].empty())
296 srenew(md->cU1, md->nalloc);
298 if (!mtop->groups.groupNumbers[SimulationAtomGroupType::User2].empty())
300 srenew(md->cU2, md->nalloc);
306 nthreads = gmx_omp_nthreads_get(emntDefault);
307 #pragma omp parallel for num_threads(nthreads) schedule(static) firstprivate(molb)
308 for (int i = 0; i < md->nr; i++)
316 if (index == nullptr)
324 const t_atom& atom = mtopGetAtomParameters(mtop, ag, &molb);
328 md->cFREEZE[i] = getGroupType(groups, SimulationAtomGroupType::Freeze, ag);
330 if (EI_ENERGY_MINIMIZATION(ir->eI))
332 /* Displacement is proportional to F, masses used for constraints */
336 else if (ir->eI == eiBD)
338 /* With BD the physical masses are irrelevant.
339 * To keep the code simple we use most of the normal MD code path
340 * for BD. Thus for constraining the masses should be proportional
341 * to the friction coefficient. We set the absolute value such that
342 * m/2<(dx/dt)^2> = m/2*2kT/fric*dt = kT/2 => m=fric*dt/2
343 * Then if we set the (meaningless) velocity to v=dx/dt, we get the
344 * correct kinetic energy and temperature using the usual code path.
345 * Thus with BD v*dt will give the displacement and the reported
346 * temperature can signal bad integration (too large time step).
350 mA = 0.5 * ir->bd_fric * ir->delta_t;
351 mB = 0.5 * ir->bd_fric * ir->delta_t;
355 /* The friction coefficient is mass/tau_t */
357 / opts->tau_t[md->cTC ? groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag] : 0];
358 mA = 0.5 * atom.m * fac;
359 mB = 0.5 * atom.mB * fac;
367 if (md->nMassPerturbed)
377 md->invMassPerDim[i][XX] = 0;
378 md->invMassPerDim[i][YY] = 0;
379 md->invMassPerDim[i][ZZ] = 0;
381 else if (md->cFREEZE)
384 GMX_ASSERT(opts->nFreeze != nullptr,
385 "Must have freeze groups to initialize masses");
386 if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
388 /* Set the mass of completely frozen particles to ALMOST_ZERO
389 * iso 0 to avoid div by zero in lincs or shake.
391 md->invmass[i] = ALMOST_ZERO;
395 /* Note: Partially frozen particles use the normal invmass.
396 * If such particles are constrained, the frozen dimensions
397 * should not be updated with the constrained coordinates.
399 md->invmass[i] = 1.0 / mA;
401 for (int d = 0; d < DIM; d++)
403 md->invMassPerDim[i][d] = (opts->nFreeze[g][d] ? 0 : 1.0 / mA);
408 md->invmass[i] = 1.0 / mA;
409 for (int d = 0; d < DIM; d++)
411 md->invMassPerDim[i][d] = 1.0 / mA;
415 md->chargeA[i] = atom.q;
416 md->typeA[i] = atom.type;
419 c6 = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c6;
420 c12 = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c12;
421 md->sqrt_c6A[i] = sqrt(c6);
422 if (c6 == 0.0 || c12 == 0)
428 md->sigmaA[i] = gmx::sixthroot(c12 / c6);
430 md->sigma3A[i] = 1 / (md->sigmaA[i] * md->sigmaA[i] * md->sigmaA[i]);
434 md->bPerturbed[i] = PERTURBED(atom);
435 md->chargeB[i] = atom.qB;
436 md->typeB[i] = atom.typeB;
439 c6 = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c6;
440 c12 = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c12;
441 md->sqrt_c6B[i] = sqrt(c6);
442 if (c6 == 0.0 || c12 == 0)
448 md->sigmaB[i] = gmx::sixthroot(c12 / c6);
450 md->sigma3B[i] = 1 / (md->sigmaB[i] * md->sigmaB[i] * md->sigmaB[i]);
453 md->ptype[i] = atom.ptype;
456 md->cTC[i] = groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag];
458 md->cENER[i] = getGroupType(groups, SimulationAtomGroupType::EnergyOutput, ag);
461 md->cACC[i] = groups.groupNumbers[SimulationAtomGroupType::Acceleration][ag];
465 md->cVCM[i] = groups.groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][ag];
469 md->cORF[i] = getGroupType(groups, SimulationAtomGroupType::OrientationRestraintsFit, ag);
474 md->cU1[i] = groups.groupNumbers[SimulationAtomGroupType::User1][ag];
478 md->cU2[i] = groups.groupNumbers[SimulationAtomGroupType::User2][ag];
481 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
486 /* Pad invmass with 0 so a SIMD MD update does not change v and x */
487 for (int i = md->nr; i < md->nr + GMX_REAL_MAX_SIMD_WIDTH; i++)
494 /* We set mass, invmass, invMassPerDim and tmass for lambda=0.
495 * For free-energy runs, these should be updated using update_mdatoms().
497 md->tmass = md->tmassA;
501 void update_mdatoms(t_mdatoms* md, real lambda)
503 if (md->nMassPerturbed && lambda != md->lambda)
505 real L1 = 1 - lambda;
507 /* Update masses of perturbed atoms for the change in lambda */
508 int gmx_unused nthreads = gmx_omp_nthreads_get(emntDefault);
509 #pragma omp parallel for num_threads(nthreads) schedule(static)
510 for (int i = 0; i < md->nr; i++)
512 if (md->bPerturbed[i])
514 md->massT[i] = L1 * md->massA[i] + lambda * md->massB[i];
515 /* Atoms with invmass 0 or ALMOST_ZERO are massless or frozen
516 * and their invmass does not depend on lambda.
518 if (md->invmass[i] > 1.1 * ALMOST_ZERO)
520 md->invmass[i] = 1.0 / md->massT[i];
521 for (int d = 0; d < DIM; d++)
523 if (md->invMassPerDim[i][d] > 1.1 * ALMOST_ZERO)
525 md->invMassPerDim[i][d] = md->invmass[i];
532 /* Update the system mass for the change in lambda */
533 md->tmass = L1 * md->tmassA + lambda * md->tmassB;