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45 #include "gromacs/compat/make_unique.h"
46 #include "gromacs/gpu_utils/hostallocator.h"
47 #include "gromacs/math/functions.h"
48 #include "gromacs/mdlib/gmx_omp_nthreads.h"
49 #include "gromacs/mdlib/qmmm.h"
50 #include "gromacs/mdtypes/inputrec.h"
51 #include "gromacs/mdtypes/md_enums.h"
52 #include "gromacs/topology/mtop_lookup.h"
53 #include "gromacs/topology/mtop_util.h"
54 #include "gromacs/topology/topology.h"
55 #include "gromacs/utility/exceptions.h"
56 #include "gromacs/utility/smalloc.h"
58 #define ALMOST_ZERO 1e-30
64 : mdatoms_(nullptr), chargeA_()
68 void MDAtoms::resize(int newSize)
70 chargeA_.resize(newSize);
71 mdatoms_->chargeA = chargeA_.data();
74 void MDAtoms::reserve(int newCapacity)
76 chargeA_.reserve(newCapacity);
77 mdatoms_->chargeA = chargeA_.data();
80 std::unique_ptr<MDAtoms>
81 makeMDAtoms(FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir,
84 auto mdAtoms = compat::make_unique<MDAtoms>();
85 // GPU transfers want to use the pinning mode.
86 changePinningPolicy(&mdAtoms->chargeA_, useGpuForPme ? PinningPolicy::CanBePinned : PinningPolicy::CannotBePinned);
89 mdAtoms->mdatoms_.reset(md);
91 md->nenergrp = mtop.groups.grps[egcENER].nr;
93 for (int i = 0; i < mtop.natoms; i++)
95 if (ggrpnr(&mtop.groups, egcVCM, i) > 0)
101 /* Determine the total system mass and perturbed atom counts */
102 double totalMassA = 0.0;
103 double totalMassB = 0.0;
105 md->haveVsites = FALSE;
106 gmx_mtop_atomloop_block_t aloop = gmx_mtop_atomloop_block_init(&mtop);
109 while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
111 totalMassA += nmol*atom->m;
112 totalMassB += nmol*atom->mB;
114 if (atom->ptype == eptVSite)
116 md->haveVsites = TRUE;
119 if (ir.efep != efepNO && PERTURBED(*atom))
122 if (atom->mB != atom->m)
124 md->nMassPerturbed += nmol;
126 if (atom->qB != atom->q)
128 md->nChargePerturbed += nmol;
130 if (atom->typeB != atom->type)
132 md->nTypePerturbed += nmol;
137 md->tmassA = totalMassA;
138 md->tmassB = totalMassB;
140 if (ir.efep != efepNO && fp)
143 "There are %d atoms and %d charges for free energy perturbation\n",
144 md->nPerturbed, md->nChargePerturbed);
147 md->havePartiallyFrozenAtoms = FALSE;
148 for (int g = 0; g < ir.opts.ngfrz; g++)
150 for (int d = YY; d < DIM; d++)
152 if (ir.opts.nFreeze[g][d] != ir.opts.nFreeze[g][XX])
154 md->havePartiallyFrozenAtoms = TRUE;
159 md->bOrires = gmx_mtop_ftype_count(&mtop, F_ORIRES);
166 void atoms2md(const gmx_mtop_t *mtop, const t_inputrec *ir,
167 int nindex, const int *index,
169 gmx::MDAtoms *mdAtoms)
172 const t_grpopts *opts;
173 const gmx_groups_t *groups;
174 int nthreads gmx_unused;
176 bLJPME = EVDW_PME(ir->vdwtype);
180 groups = &mtop->groups;
182 auto md = mdAtoms->mdatoms();
183 /* nindex>=0 indicates DD where we use an index */
190 md->nr = mtop->natoms;
193 if (md->nr > md->nalloc)
195 md->nalloc = over_alloc_dd(md->nr);
197 if (md->nMassPerturbed)
199 srenew(md->massA, md->nalloc);
200 srenew(md->massB, md->nalloc);
202 srenew(md->massT, md->nalloc);
203 /* The SIMD version of the integrator needs this aligned and padded.
204 * The padding needs to be with zeros, which we set later below.
206 gmx::AlignedAllocationPolicy::free(md->invmass);
207 md->invmass = new(gmx::AlignedAllocationPolicy::malloc((md->nalloc + GMX_REAL_MAX_SIMD_WIDTH)*sizeof(*md->invmass)))real;
208 srenew(md->invMassPerDim, md->nalloc);
209 // TODO eventually we will have vectors and just resize
210 // everything, but for now the semantics of md->nalloc being
211 // the capacity are preserved by keeping vectors within
212 // mdAtoms having the same properties as the other arrays.
213 mdAtoms->reserve(md->nalloc);
214 mdAtoms->resize(md->nr);
215 srenew(md->typeA, md->nalloc);
218 srenew(md->chargeB, md->nalloc);
219 srenew(md->typeB, md->nalloc);
223 srenew(md->sqrt_c6A, md->nalloc);
224 srenew(md->sigmaA, md->nalloc);
225 srenew(md->sigma3A, md->nalloc);
228 srenew(md->sqrt_c6B, md->nalloc);
229 srenew(md->sigmaB, md->nalloc);
230 srenew(md->sigma3B, md->nalloc);
233 srenew(md->ptype, md->nalloc);
236 srenew(md->cTC, md->nalloc);
237 /* We always copy cTC with domain decomposition */
239 srenew(md->cENER, md->nalloc);
242 srenew(md->cACC, md->nalloc);
246 opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
248 srenew(md->cFREEZE, md->nalloc);
252 srenew(md->cVCM, md->nalloc);
256 srenew(md->cORF, md->nalloc);
260 srenew(md->bPerturbed, md->nalloc);
263 /* Note that these user t_mdatoms array pointers are NULL
264 * when there is only one group present.
265 * Therefore, when adding code, the user should use something like:
266 * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
268 if (mtop->groups.grpnr[egcUser1] != nullptr)
270 srenew(md->cU1, md->nalloc);
272 if (mtop->groups.grpnr[egcUser2] != nullptr)
274 srenew(md->cU2, md->nalloc);
279 srenew(md->bQM, md->nalloc);
285 // cppcheck-suppress unreadVariable
286 nthreads = gmx_omp_nthreads_get(emntDefault);
287 #pragma omp parallel for num_threads(nthreads) schedule(static) firstprivate(molb)
288 for (int i = 0; i < md->nr; i++)
296 if (index == nullptr)
304 const t_atom &atom = mtopGetAtomParameters(mtop, ag, &molb);
308 md->cFREEZE[i] = ggrpnr(groups, egcFREEZE, ag);
310 if (EI_ENERGY_MINIMIZATION(ir->eI))
312 /* Displacement is proportional to F, masses used for constraints */
316 else if (ir->eI == eiBD)
318 /* With BD the physical masses are irrelevant.
319 * To keep the code simple we use most of the normal MD code path
320 * for BD. Thus for constraining the masses should be proportional
321 * to the friction coefficient. We set the absolute value such that
322 * m/2<(dx/dt)^2> = m/2*2kT/fric*dt = kT/2 => m=fric*dt/2
323 * Then if we set the (meaningless) velocity to v=dx/dt, we get the
324 * correct kinetic energy and temperature using the usual code path.
325 * Thus with BD v*dt will give the displacement and the reported
326 * temperature can signal bad integration (too large time step).
330 mA = 0.5*ir->bd_fric*ir->delta_t;
331 mB = 0.5*ir->bd_fric*ir->delta_t;
335 /* The friction coefficient is mass/tau_t */
336 fac = ir->delta_t/opts->tau_t[md->cTC ? groups->grpnr[egcTC][ag] : 0];
338 mB = 0.5*atom.mB*fac;
346 if (md->nMassPerturbed)
356 md->invMassPerDim[i][XX] = 0;
357 md->invMassPerDim[i][YY] = 0;
358 md->invMassPerDim[i][ZZ] = 0;
360 else if (md->cFREEZE)
363 if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
365 /* Set the mass of completely frozen particles to ALMOST_ZERO
366 * iso 0 to avoid div by zero in lincs or shake.
368 md->invmass[i] = ALMOST_ZERO;
372 /* Note: Partially frozen particles use the normal invmass.
373 * If such particles are constrained, the frozen dimensions
374 * should not be updated with the constrained coordinates.
376 md->invmass[i] = 1.0/mA;
378 for (int d = 0; d < DIM; d++)
380 md->invMassPerDim[i][d] = (opts->nFreeze[g][d] ? 0 : 1.0/mA);
385 md->invmass[i] = 1.0/mA;
386 for (int d = 0; d < DIM; d++)
388 md->invMassPerDim[i][d] = 1.0/mA;
392 md->chargeA[i] = atom.q;
393 md->typeA[i] = atom.type;
396 c6 = mtop->ffparams.iparams[atom.type*(mtop->ffparams.atnr+1)].lj.c6;
397 c12 = mtop->ffparams.iparams[atom.type*(mtop->ffparams.atnr+1)].lj.c12;
398 md->sqrt_c6A[i] = sqrt(c6);
399 if (c6 == 0.0 || c12 == 0)
405 md->sigmaA[i] = gmx::sixthroot(c12/c6);
407 md->sigma3A[i] = 1/(md->sigmaA[i]*md->sigmaA[i]*md->sigmaA[i]);
411 md->bPerturbed[i] = PERTURBED(atom);
412 md->chargeB[i] = atom.qB;
413 md->typeB[i] = atom.typeB;
416 c6 = mtop->ffparams.iparams[atom.typeB*(mtop->ffparams.atnr+1)].lj.c6;
417 c12 = mtop->ffparams.iparams[atom.typeB*(mtop->ffparams.atnr+1)].lj.c12;
418 md->sqrt_c6B[i] = sqrt(c6);
419 if (c6 == 0.0 || c12 == 0)
425 md->sigmaB[i] = gmx::sixthroot(c12/c6);
427 md->sigma3B[i] = 1/(md->sigmaB[i]*md->sigmaB[i]*md->sigmaB[i]);
430 md->ptype[i] = atom.ptype;
433 md->cTC[i] = groups->grpnr[egcTC][ag];
435 md->cENER[i] = ggrpnr(groups, egcENER, ag);
438 md->cACC[i] = groups->grpnr[egcACC][ag];
442 md->cVCM[i] = groups->grpnr[egcVCM][ag];
446 md->cORF[i] = ggrpnr(groups, egcORFIT, ag);
451 md->cU1[i] = groups->grpnr[egcUser1][ag];
455 md->cU2[i] = groups->grpnr[egcUser2][ag];
460 if (groups->grpnr[egcQMMM] == nullptr ||
461 groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1)
471 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
476 /* Pad invmass with 0 so a SIMD MD update does not change v and x */
477 for (int i = md->nr; i < md->nr + GMX_REAL_MAX_SIMD_WIDTH; i++)
484 /* We set mass, invmass, invMassPerDim and tmass for lambda=0.
485 * For free-energy runs, these should be updated using update_mdatoms().
487 md->tmass = md->tmassA;
491 void update_mdatoms(t_mdatoms *md, real lambda)
493 if (md->nMassPerturbed && lambda != md->lambda)
495 real L1 = 1 - lambda;
497 /* Update masses of perturbed atoms for the change in lambda */
498 // cppcheck-suppress unreadVariable
499 int gmx_unused nthreads = gmx_omp_nthreads_get(emntDefault);
500 #pragma omp parallel for num_threads(nthreads) schedule(static)
501 for (int i = 0; i < md->nr; i++)
503 if (md->bPerturbed[i])
505 md->massT[i] = L1*md->massA[i] + lambda*md->massB[i];
506 /* Atoms with invmass 0 or ALMOST_ZERO are massless or frozen
507 * and their invmass does not depend on lambda.
509 if (md->invmass[i] > 1.1*ALMOST_ZERO)
511 md->invmass[i] = 1.0/md->massT[i];
512 for (int d = 0; d < DIM; d++)
514 if (md->invMassPerDim[i][d] > 1.1*ALMOST_ZERO)
516 md->invMassPerDim[i][d] = md->invmass[i];
523 /* Update the system mass for the change in lambda */
524 md->tmass = L1*md->tmassA + lambda*md->tmassB;