src/gromacs/mdlib/mdatoms.cpp

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  38 #include "gmxpre.h"
  39
  40 #include "mdatoms.h"
  41
  42 #include <cmath>
  43
  44 #include <memory>
  45
  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"
  58
  59 #define ALMOST_ZERO 1e-30
  60
  61 namespace gmx
  62 {
  63
  64 MDAtoms::MDAtoms() : mdatoms_(nullptr) {}
  65
  66 MDAtoms::~MDAtoms()
  67 {
  68     if (mdatoms_ == nullptr)
  69     {
  70         return;
  71     }
  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);
  87     sfree(mdatoms_->cTC);
  88     sfree(mdatoms_->cENER);
  89     sfree(mdatoms_->cACC);
  90     sfree(mdatoms_->cFREEZE);
  91     sfree(mdatoms_->cVCM);
  92     sfree(mdatoms_->cORF);
  93     sfree(mdatoms_->bPerturbed);
  94     sfree(mdatoms_->cU1);
  95     sfree(mdatoms_->cU2);
  96     sfree(mdatoms_->bQM);
  97 }
  98
  99 void MDAtoms::resize(int newSize)
 100 {
 101     chargeA_.resizeWithPadding(newSize);
 102     mdatoms_->chargeA = chargeA_.data();
 103 }
 104
 105 void MDAtoms::reserve(int newCapacity)
 106 {
 107     chargeA_.reserveWithPadding(newCapacity);
 108     mdatoms_->chargeA = chargeA_.data();
 109 }
 110
 111 std::unique_ptr<MDAtoms> makeMDAtoms(FILE* fp, const gmx_mtop_t& mtop, const t_inputrec& ir, const bool rankHasPmeGpuTask)
 112 {
 113     auto mdAtoms = std::make_unique<MDAtoms>();
 114     // GPU transfers may want to use a suitable pinning mode.
 115     if (rankHasPmeGpuTask)
 116     {
 117         changePinningPolicy(&mdAtoms->chargeA_, pme_get_pinning_policy());
 118     }
 119     t_mdatoms* md;
 120     snew(md, 1);
 121     mdAtoms->mdatoms_.reset(md);
 122
 123     md->nenergrp = mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size();
 124     md->bVCMgrps = FALSE;
 125     for (int i = 0; i < mtop.natoms; i++)
 126     {
 127         if (getGroupType(mtop.groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i) > 0)
 128         {
 129             md->bVCMgrps = TRUE;
 130         }
 131     }
 132
 133     /* Determine the total system mass and perturbed atom counts */
 134     double totalMassA = 0.0;
 135     double totalMassB = 0.0;
 136
 137     md->haveVsites                  = FALSE;
 138     gmx_mtop_atomloop_block_t aloop = gmx_mtop_atomloop_block_init(&mtop);
 139     const t_atom*             atom;
 140     int                       nmol;
 141     while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
 142     {
 143         totalMassA += nmol * atom->m;
 144         totalMassB += nmol * atom->mB;
 145
 146         if (atom->ptype == eptVSite)
 147         {
 148             md->haveVsites = TRUE;
 149         }
 150
 151         if (ir.efep != efepNO && PERTURBED(*atom))
 152         {
 153             md->nPerturbed++;
 154             if (atom->mB != atom->m)
 155             {
 156                 md->nMassPerturbed += nmol;
 157             }
 158             if (atom->qB != atom->q)
 159             {
 160                 md->nChargePerturbed += nmol;
 161             }
 162             if (atom->typeB != atom->type)
 163             {
 164                 md->nTypePerturbed += nmol;
 165             }
 166         }
 167     }
 168
 169     md->tmassA = totalMassA;
 170     md->tmassB = totalMassB;
 171
 172     if (ir.efep != efepNO && fp)
 173     {
 174         fprintf(fp, "There are %d atoms and %d charges for free energy perturbation\n",
 175                 md->nPerturbed, md->nChargePerturbed);
 176     }
 177
 178     md->havePartiallyFrozenAtoms = FALSE;
 179     for (int g = 0; g < ir.opts.ngfrz; g++)
 180     {
 181         for (int d = YY; d < DIM; d++)
 182         {
 183             if (ir.opts.nFreeze[g][d] != ir.opts.nFreeze[g][XX])
 184             {
 185                 md->havePartiallyFrozenAtoms = TRUE;
 186             }
 187         }
 188     }
 189
 190     md->bOrires = (gmx_mtop_ftype_count(&mtop, F_ORIRES) != 0);
 191
 192     return mdAtoms;
 193 }
 194
 195 } // namespace gmx
 196
 197 void atoms2md(const gmx_mtop_t* mtop, const t_inputrec* ir, int nindex, const int* index, int homenr, gmx::MDAtoms* mdAtoms)
 198 {
 199     gmx_bool         bLJPME;
 200     const t_grpopts* opts;
 201     int nthreads gmx_unused;
 202
 203     bLJPME = EVDW_PME(ir->vdwtype);
 204
 205     opts = &ir->opts;
 206
 207     const SimulationGroups& groups = mtop->groups;
 208
 209     auto md = mdAtoms->mdatoms();
 210     /* nindex>=0 indicates DD where we use an index */
 211     if (nindex >= 0)
 212     {
 213         md->nr = nindex;
 214     }
 215     else
 216     {
 217         md->nr = mtop->natoms;
 218     }
 219
 220     if (md->nr > md->nalloc)
 221     {
 222         md->nalloc = over_alloc_dd(md->nr);
 223
 224         if (md->nMassPerturbed)
 225         {
 226             srenew(md->massA, md->nalloc);
 227             srenew(md->massB, md->nalloc);
 228         }
 229         srenew(md->massT, md->nalloc);
 230         /* The SIMD version of the integrator needs this aligned and padded.
 231          * The padding needs to be with zeros, which we set later below.
 232          */
 233         gmx::AlignedAllocationPolicy::free(md->invmass);
 234         md->invmass = new (gmx::AlignedAllocationPolicy::malloc(
 235                 (md->nalloc + GMX_REAL_MAX_SIMD_WIDTH) * sizeof(*md->invmass))) real;
 236         srenew(md->invMassPerDim, md->nalloc);
 237         // TODO eventually we will have vectors and just resize
 238         // everything, but for now the semantics of md->nalloc being
 239         // the capacity are preserved by keeping vectors within
 240         // mdAtoms having the same properties as the other arrays.
 241         mdAtoms->reserve(md->nalloc);
 242         mdAtoms->resize(md->nr);
 243         srenew(md->typeA, md->nalloc);
 244         if (md->nPerturbed)
 245         {
 246             srenew(md->chargeB, md->nalloc);
 247             srenew(md->typeB, md->nalloc);
 248         }
 249         if (bLJPME)
 250         {
 251             srenew(md->sqrt_c6A, md->nalloc);
 252             srenew(md->sigmaA, md->nalloc);
 253             srenew(md->sigma3A, md->nalloc);
 254             if (md->nPerturbed)
 255             {
 256                 srenew(md->sqrt_c6B, md->nalloc);
 257                 srenew(md->sigmaB, md->nalloc);
 258                 srenew(md->sigma3B, md->nalloc);
 259             }
 260         }
 261         srenew(md->ptype, md->nalloc);
 262         if (opts->ngtc > 1)
 263         {
 264             srenew(md->cTC, md->nalloc);
 265             /* We always copy cTC with domain decomposition */
 266         }
 267         srenew(md->cENER, md->nalloc);
 268         if (opts->ngacc > 1)
 269         {
 270             srenew(md->cACC, md->nalloc);
 271         }
 272         if (opts->nFreeze
 273             && (opts->ngfrz > 1 || opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
 274         {
 275             srenew(md->cFREEZE, md->nalloc);
 276         }
 277         if (md->bVCMgrps)
 278         {
 279             srenew(md->cVCM, md->nalloc);
 280         }
 281         if (md->bOrires)
 282         {
 283             srenew(md->cORF, md->nalloc);
 284         }
 285         if (md->nPerturbed)
 286         {
 287             srenew(md->bPerturbed, md->nalloc);
 288         }
 289
 290         /* Note that these user t_mdatoms array pointers are NULL
 291          * when there is only one group present.
 292          * Therefore, when adding code, the user should use something like:
 293          * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
 294          */
 295         if (!mtop->groups.groupNumbers[SimulationAtomGroupType::User1].empty())
 296         {
 297             srenew(md->cU1, md->nalloc);
 298         }
 299         if (!mtop->groups.groupNumbers[SimulationAtomGroupType::User2].empty())
 300         {
 301             srenew(md->cU2, md->nalloc);
 302         }
 303
 304         if (ir->bQMMM)
 305         {
 306             srenew(md->bQM, md->nalloc);
 307         }
 308     }
 309
 310     int molb = 0;
 311
 312     nthreads = gmx_omp_nthreads_get(emntDefault);
 313 #pragma omp parallel for num_threads(nthreads) schedule(static) firstprivate(molb)
 314     for (int i = 0; i < md->nr; i++)
 315     {
 316         try
 317         {
 318             int  g, ag;
 319             real mA, mB, fac;
 320             real c6, c12;
 321
 322             if (index == nullptr)
 323             {
 324                 ag = i;
 325             }
 326             else
 327             {
 328                 ag = index[i];
 329             }
 330             const t_atom& atom = mtopGetAtomParameters(mtop, ag, &molb);
 331
 332             if (md->cFREEZE)
 333             {
 334                 md->cFREEZE[i] = getGroupType(groups, SimulationAtomGroupType::Freeze, ag);
 335             }
 336             if (EI_ENERGY_MINIMIZATION(ir->eI))
 337             {
 338                 /* Displacement is proportional to F, masses used for constraints */
 339                 mA = 1.0;
 340                 mB = 1.0;
 341             }
 342             else if (ir->eI == eiBD)
 343             {
 344                 /* With BD the physical masses are irrelevant.
 345                  * To keep the code simple we use most of the normal MD code path
 346                  * for BD. Thus for constraining the masses should be proportional
 347                  * to the friction coefficient. We set the absolute value such that
 348                  * m/2<(dx/dt)^2> = m/2*2kT/fric*dt = kT/2 => m=fric*dt/2
 349                  * Then if we set the (meaningless) velocity to v=dx/dt, we get the
 350                  * correct kinetic energy and temperature using the usual code path.
 351                  * Thus with BD v*dt will give the displacement and the reported
 352                  * temperature can signal bad integration (too large time step).
 353                  */
 354                 if (ir->bd_fric > 0)
 355                 {
 356                     mA = 0.5 * ir->bd_fric * ir->delta_t;
 357                     mB = 0.5 * ir->bd_fric * ir->delta_t;
 358                 }
 359                 else
 360                 {
 361                     /* The friction coefficient is mass/tau_t */
 362                     fac = ir->delta_t
 363                           / opts->tau_t[md->cTC ? groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag] : 0];
 364                     mA = 0.5 * atom.m * fac;
 365                     mB = 0.5 * atom.mB * fac;
 366                 }
 367             }
 368             else
 369             {
 370                 mA = atom.m;
 371                 mB = atom.mB;
 372             }
 373             if (md->nMassPerturbed)
 374             {
 375                 md->massA[i] = mA;
 376                 md->massB[i] = mB;
 377             }
 378             md->massT[i] = mA;
 379
 380             if (mA == 0.0)
 381             {
 382                 md->invmass[i]           = 0;
 383                 md->invMassPerDim[i][XX] = 0;
 384                 md->invMassPerDim[i][YY] = 0;
 385                 md->invMassPerDim[i][ZZ] = 0;
 386             }
 387             else if (md->cFREEZE)
 388             {
 389                 g = md->cFREEZE[i];
 390                 GMX_ASSERT(opts->nFreeze != nullptr,
 391                            "Must have freeze groups to initialize masses");
 392                 if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
 393                 {
 394                     /* Set the mass of completely frozen particles to ALMOST_ZERO
 395                      * iso 0 to avoid div by zero in lincs or shake.
 396                      */
 397                     md->invmass[i] = ALMOST_ZERO;
 398                 }
 399                 else
 400                 {
 401                     /* Note: Partially frozen particles use the normal invmass.
 402                      * If such particles are constrained, the frozen dimensions
 403                      * should not be updated with the constrained coordinates.
 404                      */
 405                     md->invmass[i] = 1.0 / mA;
 406                 }
 407                 for (int d = 0; d < DIM; d++)
 408                 {
 409                     md->invMassPerDim[i][d] = (opts->nFreeze[g][d] ? 0 : 1.0 / mA);
 410                 }
 411             }
 412             else
 413             {
 414                 md->invmass[i] = 1.0 / mA;
 415                 for (int d = 0; d < DIM; d++)
 416                 {
 417                     md->invMassPerDim[i][d] = 1.0 / mA;
 418                 }
 419             }
 420
 421             md->chargeA[i] = atom.q;
 422             md->typeA[i]   = atom.type;
 423             if (bLJPME)
 424             {
 425                 c6  = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c6;
 426                 c12 = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c12;
 427                 md->sqrt_c6A[i] = sqrt(c6);
 428                 if (c6 == 0.0 || c12 == 0)
 429                 {
 430                     md->sigmaA[i] = 1.0;
 431                 }
 432                 else
 433                 {
 434                     md->sigmaA[i] = gmx::sixthroot(c12 / c6);
 435                 }
 436                 md->sigma3A[i] = 1 / (md->sigmaA[i] * md->sigmaA[i] * md->sigmaA[i]);
 437             }
 438             if (md->nPerturbed)
 439             {
 440                 md->bPerturbed[i] = PERTURBED(atom);
 441                 md->chargeB[i]    = atom.qB;
 442                 md->typeB[i]      = atom.typeB;
 443                 if (bLJPME)
 444                 {
 445                     c6  = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c6;
 446                     c12 = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c12;
 447                     md->sqrt_c6B[i] = sqrt(c6);
 448                     if (c6 == 0.0 || c12 == 0)
 449                     {
 450                         md->sigmaB[i] = 1.0;
 451                     }
 452                     else
 453                     {
 454                         md->sigmaB[i] = gmx::sixthroot(c12 / c6);
 455                     }
 456                     md->sigma3B[i] = 1 / (md->sigmaB[i] * md->sigmaB[i] * md->sigmaB[i]);
 457                 }
 458             }
 459             md->ptype[i] = atom.ptype;
 460             if (md->cTC)
 461             {
 462                 md->cTC[i] = groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag];
 463             }
 464             md->cENER[i] = getGroupType(groups, SimulationAtomGroupType::EnergyOutput, ag);
 465             if (md->cACC)
 466             {
 467                 md->cACC[i] = groups.groupNumbers[SimulationAtomGroupType::Acceleration][ag];
 468             }
 469             if (md->cVCM)
 470             {
 471                 md->cVCM[i] = groups.groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][ag];
 472             }
 473             if (md->cORF)
 474             {
 475                 md->cORF[i] = getGroupType(groups, SimulationAtomGroupType::OrientationRestraintsFit, ag);
 476             }
 477
 478             if (md->cU1)
 479             {
 480                 md->cU1[i] = groups.groupNumbers[SimulationAtomGroupType::User1][ag];
 481             }
 482             if (md->cU2)
 483             {
 484                 md->cU2[i] = groups.groupNumbers[SimulationAtomGroupType::User2][ag];
 485             }
 486
 487             if (ir->bQMMM)
 488             {
 489                 if (groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics].empty()
 490                     || groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][ag]
 491                                < groups.groups[SimulationAtomGroupType::QuantumMechanics].size() - 1)
 492                 {
 493                     md->bQM[i] = TRUE;
 494                 }
 495                 else
 496                 {
 497                     md->bQM[i] = FALSE;
 498                 }
 499             }
 500         }
 501         GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 502     }
 503
 504     if (md->nr > 0)
 505     {
 506         /* Pad invmass with 0 so a SIMD MD update does not change v and x */
 507         for (int i = md->nr; i < md->nr + GMX_REAL_MAX_SIMD_WIDTH; i++)
 508         {
 509             md->invmass[i] = 0;
 510         }
 511     }
 512
 513     md->homenr = homenr;
 514     /* We set mass, invmass, invMassPerDim and tmass for lambda=0.
 515      * For free-energy runs, these should be updated using update_mdatoms().
 516      */
 517     md->tmass  = md->tmassA;
 518     md->lambda = 0;
 519 }
 520
 521 void update_mdatoms(t_mdatoms* md, real lambda)
 522 {
 523     if (md->nMassPerturbed && lambda != md->lambda)
 524     {
 525         real L1 = 1 - lambda;
 526
 527         /* Update masses of perturbed atoms for the change in lambda */
 528         int gmx_unused nthreads = gmx_omp_nthreads_get(emntDefault);
 529 #pragma omp parallel for num_threads(nthreads) schedule(static)
 530         for (int i = 0; i < md->nr; i++)
 531         {
 532             if (md->bPerturbed[i])
 533             {
 534                 md->massT[i] = L1 * md->massA[i] + lambda * md->massB[i];
 535                 /* Atoms with invmass 0 or ALMOST_ZERO are massless or frozen
 536                  * and their invmass does not depend on lambda.
 537                  */
 538                 if (md->invmass[i] > 1.1 * ALMOST_ZERO)
 539                 {
 540                     md->invmass[i] = 1.0 / md->massT[i];
 541                     for (int d = 0; d < DIM; d++)
 542                     {
 543                         if (md->invMassPerDim[i][d] > 1.1 * ALMOST_ZERO)
 544                         {
 545                             md->invMassPerDim[i][d] = md->invmass[i];
 546                         }
 547                     }
 548                 }
 549             }
 550         }
 551
 552         /* Update the system mass for the change in lambda */
 553         md->tmass = L1 * md->tmassA + lambda * md->tmassB;
 554     }
 555
 556     md->lambda = lambda;
 557 }