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45 #include "gromacs/compat/make_unique.h"
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/mdlib/qmmm.h"
51 #include "gromacs/mdtypes/inputrec.h"
52 #include "gromacs/mdtypes/md_enums.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
71 if (mdatoms_ == nullptr)
75 sfree(mdatoms_->massA);
76 sfree(mdatoms_->massB);
77 sfree(mdatoms_->massT);
78 gmx::AlignedAllocationPolicy::free(mdatoms_->invmass);
79 sfree(mdatoms_->invMassPerDim);
80 sfree(mdatoms_->typeA);
81 sfree(mdatoms_->chargeB);
82 sfree(mdatoms_->typeB);
83 sfree(mdatoms_->sqrt_c6A);
84 sfree(mdatoms_->sigmaA);
85 sfree(mdatoms_->sigma3A);
86 sfree(mdatoms_->sqrt_c6B);
87 sfree(mdatoms_->sigmaB);
88 sfree(mdatoms_->sigma3B);
89 sfree(mdatoms_->ptype);
91 sfree(mdatoms_->cENER);
92 sfree(mdatoms_->cACC);
93 sfree(mdatoms_->cFREEZE);
94 sfree(mdatoms_->cVCM);
95 sfree(mdatoms_->cORF);
96 sfree(mdatoms_->bPerturbed);
102 void MDAtoms::resize(int newSize)
104 chargeA_.resize(newSize);
105 mdatoms_->chargeA = chargeA_.data();
108 void MDAtoms::reserve(int newCapacity)
110 chargeA_.reserve(newCapacity);
111 mdatoms_->chargeA = chargeA_.data();
114 std::unique_ptr<MDAtoms>
115 makeMDAtoms(FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir,
116 const bool rankHasPmeGpuTask)
118 auto mdAtoms = compat::make_unique<MDAtoms>();
119 // GPU transfers may want to use a suitable pinning mode.
120 if (rankHasPmeGpuTask)
122 changePinningPolicy(&mdAtoms->chargeA_, pme_get_pinning_policy());
126 mdAtoms->mdatoms_.reset(md);
128 md->nenergrp = mtop.groups.grps[egcENER].nr;
129 md->bVCMgrps = FALSE;
130 for (int i = 0; i < mtop.natoms; i++)
132 if (ggrpnr(&mtop.groups, egcVCM, i) > 0)
138 /* Determine the total system mass and perturbed atom counts */
139 double totalMassA = 0.0;
140 double totalMassB = 0.0;
142 md->haveVsites = FALSE;
143 gmx_mtop_atomloop_block_t aloop = gmx_mtop_atomloop_block_init(&mtop);
146 while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
148 totalMassA += nmol*atom->m;
149 totalMassB += nmol*atom->mB;
151 if (atom->ptype == eptVSite)
153 md->haveVsites = TRUE;
156 if (ir.efep != efepNO && PERTURBED(*atom))
159 if (atom->mB != atom->m)
161 md->nMassPerturbed += nmol;
163 if (atom->qB != atom->q)
165 md->nChargePerturbed += nmol;
167 if (atom->typeB != atom->type)
169 md->nTypePerturbed += nmol;
174 md->tmassA = totalMassA;
175 md->tmassB = totalMassB;
177 if (ir.efep != efepNO && fp)
180 "There are %d atoms and %d charges for free energy perturbation\n",
181 md->nPerturbed, md->nChargePerturbed);
184 md->havePartiallyFrozenAtoms = FALSE;
185 for (int g = 0; g < ir.opts.ngfrz; g++)
187 for (int d = YY; d < DIM; d++)
189 if (ir.opts.nFreeze[g][d] != ir.opts.nFreeze[g][XX])
191 md->havePartiallyFrozenAtoms = TRUE;
196 md->bOrires = gmx_mtop_ftype_count(&mtop, F_ORIRES);
203 void atoms2md(const gmx_mtop_t *mtop, const t_inputrec *ir,
204 int nindex, const int *index,
206 gmx::MDAtoms *mdAtoms)
209 const t_grpopts *opts;
210 const gmx_groups_t *groups;
211 int nthreads gmx_unused;
213 bLJPME = EVDW_PME(ir->vdwtype);
217 groups = &mtop->groups;
219 auto md = mdAtoms->mdatoms();
220 /* nindex>=0 indicates DD where we use an index */
227 md->nr = mtop->natoms;
230 if (md->nr > md->nalloc)
232 md->nalloc = over_alloc_dd(md->nr);
234 if (md->nMassPerturbed)
236 srenew(md->massA, md->nalloc);
237 srenew(md->massB, md->nalloc);
239 srenew(md->massT, md->nalloc);
240 /* The SIMD version of the integrator needs this aligned and padded.
241 * The padding needs to be with zeros, which we set later below.
243 gmx::AlignedAllocationPolicy::free(md->invmass);
244 md->invmass = new(gmx::AlignedAllocationPolicy::malloc((md->nalloc + GMX_REAL_MAX_SIMD_WIDTH)*sizeof(*md->invmass)))real;
245 srenew(md->invMassPerDim, md->nalloc);
246 // TODO eventually we will have vectors and just resize
247 // everything, but for now the semantics of md->nalloc being
248 // the capacity are preserved by keeping vectors within
249 // mdAtoms having the same properties as the other arrays.
250 mdAtoms->reserve(md->nalloc);
251 mdAtoms->resize(md->nr);
252 srenew(md->typeA, md->nalloc);
255 srenew(md->chargeB, md->nalloc);
256 srenew(md->typeB, md->nalloc);
260 srenew(md->sqrt_c6A, md->nalloc);
261 srenew(md->sigmaA, md->nalloc);
262 srenew(md->sigma3A, md->nalloc);
265 srenew(md->sqrt_c6B, md->nalloc);
266 srenew(md->sigmaB, md->nalloc);
267 srenew(md->sigma3B, md->nalloc);
270 srenew(md->ptype, md->nalloc);
273 srenew(md->cTC, md->nalloc);
274 /* We always copy cTC with domain decomposition */
276 srenew(md->cENER, md->nalloc);
279 srenew(md->cACC, md->nalloc);
283 opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
285 srenew(md->cFREEZE, md->nalloc);
289 srenew(md->cVCM, md->nalloc);
293 srenew(md->cORF, md->nalloc);
297 srenew(md->bPerturbed, md->nalloc);
300 /* Note that these user t_mdatoms array pointers are NULL
301 * when there is only one group present.
302 * Therefore, when adding code, the user should use something like:
303 * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
305 if (mtop->groups.grpnr[egcUser1] != nullptr)
307 srenew(md->cU1, md->nalloc);
309 if (mtop->groups.grpnr[egcUser2] != nullptr)
311 srenew(md->cU2, md->nalloc);
316 srenew(md->bQM, md->nalloc);
322 nthreads = gmx_omp_nthreads_get(emntDefault);
323 #pragma omp parallel for num_threads(nthreads) schedule(static) firstprivate(molb)
324 for (int i = 0; i < md->nr; i++)
332 if (index == nullptr)
340 const t_atom &atom = mtopGetAtomParameters(mtop, ag, &molb);
344 md->cFREEZE[i] = ggrpnr(groups, egcFREEZE, ag);
346 if (EI_ENERGY_MINIMIZATION(ir->eI))
348 /* Displacement is proportional to F, masses used for constraints */
352 else if (ir->eI == eiBD)
354 /* With BD the physical masses are irrelevant.
355 * To keep the code simple we use most of the normal MD code path
356 * for BD. Thus for constraining the masses should be proportional
357 * to the friction coefficient. We set the absolute value such that
358 * m/2<(dx/dt)^2> = m/2*2kT/fric*dt = kT/2 => m=fric*dt/2
359 * Then if we set the (meaningless) velocity to v=dx/dt, we get the
360 * correct kinetic energy and temperature using the usual code path.
361 * Thus with BD v*dt will give the displacement and the reported
362 * temperature can signal bad integration (too large time step).
366 mA = 0.5*ir->bd_fric*ir->delta_t;
367 mB = 0.5*ir->bd_fric*ir->delta_t;
371 /* The friction coefficient is mass/tau_t */
372 fac = ir->delta_t/opts->tau_t[md->cTC ? groups->grpnr[egcTC][ag] : 0];
374 mB = 0.5*atom.mB*fac;
382 if (md->nMassPerturbed)
392 md->invMassPerDim[i][XX] = 0;
393 md->invMassPerDim[i][YY] = 0;
394 md->invMassPerDim[i][ZZ] = 0;
396 else if (md->cFREEZE)
399 if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
401 /* Set the mass of completely frozen particles to ALMOST_ZERO
402 * iso 0 to avoid div by zero in lincs or shake.
404 md->invmass[i] = ALMOST_ZERO;
408 /* Note: Partially frozen particles use the normal invmass.
409 * If such particles are constrained, the frozen dimensions
410 * should not be updated with the constrained coordinates.
412 md->invmass[i] = 1.0/mA;
414 for (int d = 0; d < DIM; d++)
416 md->invMassPerDim[i][d] = (opts->nFreeze[g][d] ? 0 : 1.0/mA);
421 md->invmass[i] = 1.0/mA;
422 for (int d = 0; d < DIM; d++)
424 md->invMassPerDim[i][d] = 1.0/mA;
428 md->chargeA[i] = atom.q;
429 md->typeA[i] = atom.type;
432 c6 = mtop->ffparams.iparams[atom.type*(mtop->ffparams.atnr+1)].lj.c6;
433 c12 = mtop->ffparams.iparams[atom.type*(mtop->ffparams.atnr+1)].lj.c12;
434 md->sqrt_c6A[i] = sqrt(c6);
435 if (c6 == 0.0 || c12 == 0)
441 md->sigmaA[i] = gmx::sixthroot(c12/c6);
443 md->sigma3A[i] = 1/(md->sigmaA[i]*md->sigmaA[i]*md->sigmaA[i]);
447 md->bPerturbed[i] = PERTURBED(atom);
448 md->chargeB[i] = atom.qB;
449 md->typeB[i] = atom.typeB;
452 c6 = mtop->ffparams.iparams[atom.typeB*(mtop->ffparams.atnr+1)].lj.c6;
453 c12 = mtop->ffparams.iparams[atom.typeB*(mtop->ffparams.atnr+1)].lj.c12;
454 md->sqrt_c6B[i] = sqrt(c6);
455 if (c6 == 0.0 || c12 == 0)
461 md->sigmaB[i] = gmx::sixthroot(c12/c6);
463 md->sigma3B[i] = 1/(md->sigmaB[i]*md->sigmaB[i]*md->sigmaB[i]);
466 md->ptype[i] = atom.ptype;
469 md->cTC[i] = groups->grpnr[egcTC][ag];
471 md->cENER[i] = ggrpnr(groups, egcENER, ag);
474 md->cACC[i] = groups->grpnr[egcACC][ag];
478 md->cVCM[i] = groups->grpnr[egcVCM][ag];
482 md->cORF[i] = ggrpnr(groups, egcORFIT, ag);
487 md->cU1[i] = groups->grpnr[egcUser1][ag];
491 md->cU2[i] = groups->grpnr[egcUser2][ag];
496 if (groups->grpnr[egcQMMM] == nullptr ||
497 groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1)
507 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
512 /* Pad invmass with 0 so a SIMD MD update does not change v and x */
513 for (int i = md->nr; i < md->nr + GMX_REAL_MAX_SIMD_WIDTH; i++)
520 /* We set mass, invmass, invMassPerDim and tmass for lambda=0.
521 * For free-energy runs, these should be updated using update_mdatoms().
523 md->tmass = md->tmassA;
527 void update_mdatoms(t_mdatoms *md, real lambda)
529 if (md->nMassPerturbed && lambda != md->lambda)
531 real L1 = 1 - lambda;
533 /* Update masses of perturbed atoms for the change in lambda */
534 int gmx_unused nthreads = gmx_omp_nthreads_get(emntDefault);
535 #pragma omp parallel for num_threads(nthreads) schedule(static)
536 for (int i = 0; i < md->nr; i++)
538 if (md->bPerturbed[i])
540 md->massT[i] = L1*md->massA[i] + lambda*md->massB[i];
541 /* Atoms with invmass 0 or ALMOST_ZERO are massless or frozen
542 * and their invmass does not depend on lambda.
544 if (md->invmass[i] > 1.1*ALMOST_ZERO)
546 md->invmass[i] = 1.0/md->massT[i];
547 for (int d = 0; d < DIM; d++)
549 if (md->invMassPerDim[i][d] > 1.1*ALMOST_ZERO)
551 md->invMassPerDim[i][d] = md->invmass[i];
558 /* Update the system mass for the change in lambda */
559 md->tmass = L1*md->tmassA + lambda*md->tmassB;