src/gromacs/mdlib/mdatoms.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "mdatoms.h"
  40
  41 #include <cmath>
  42
  43 #include <memory>
  44
  45 #include "gromacs/ewald/pme.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"
  57
  58 #define ALMOST_ZERO 1e-30
  59
  60 namespace gmx
  61 {
  62
  63 MDAtoms::MDAtoms()
  64     : mdatoms_(nullptr)
  65 {
  66 }
  67
  68 MDAtoms::~MDAtoms()
  69 {
  70     if (mdatoms_ == nullptr)
  71     {
  72         return;
  73     }
  74     sfree(mdatoms_->massA);
  75     sfree(mdatoms_->massB);
  76     sfree(mdatoms_->massT);
  77     gmx::AlignedAllocationPolicy::free(mdatoms_->invmass);
  78     sfree(mdatoms_->invMassPerDim);
  79     sfree(mdatoms_->typeA);
  80     sfree(mdatoms_->chargeB);
  81     sfree(mdatoms_->typeB);
  82     sfree(mdatoms_->sqrt_c6A);
  83     sfree(mdatoms_->sigmaA);
  84     sfree(mdatoms_->sigma3A);
  85     sfree(mdatoms_->sqrt_c6B);
  86     sfree(mdatoms_->sigmaB);
  87     sfree(mdatoms_->sigma3B);
  88     sfree(mdatoms_->ptype);
  89     sfree(mdatoms_->cTC);
  90     sfree(mdatoms_->cENER);
  91     sfree(mdatoms_->cACC);
  92     sfree(mdatoms_->cFREEZE);
  93     sfree(mdatoms_->cVCM);
  94     sfree(mdatoms_->cORF);
  95     sfree(mdatoms_->bPerturbed);
  96     sfree(mdatoms_->cU1);
  97     sfree(mdatoms_->cU2);
  98     sfree(mdatoms_->bQM);
  99 }
 100
 101 void MDAtoms::resize(int newSize)
 102 {
 103     chargeA_.resizeWithPadding(newSize);
 104     mdatoms_->chargeA = chargeA_.data();
 105 }
 106
 107 void MDAtoms::reserve(int newCapacity)
 108 {
 109     chargeA_.reserveWithPadding(newCapacity);
 110     mdatoms_->chargeA = chargeA_.data();
 111 }
 112
 113 std::unique_ptr<MDAtoms>
 114 makeMDAtoms(FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir,
 115             const bool rankHasPmeGpuTask)
 116 {
 117     auto       mdAtoms = std::make_unique<MDAtoms>();
 118     // GPU transfers may want to use a suitable pinning mode.
 119     if (rankHasPmeGpuTask)
 120     {
 121         changePinningPolicy(&mdAtoms->chargeA_, pme_get_pinning_policy());
 122     }
 123     t_mdatoms *md;
 124     snew(md, 1);
 125     mdAtoms->mdatoms_.reset(md);
 126
 127     md->nenergrp = mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].nr;
 128     md->bVCMgrps = FALSE;
 129     for (int i = 0; i < mtop.natoms; i++)
 130     {
 131         if (getGroupType(mtop.groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i) > 0)
 132         {
 133             md->bVCMgrps = TRUE;
 134         }
 135     }
 136
 137     /* Determine the total system mass and perturbed atom counts */
 138     double                     totalMassA = 0.0;
 139     double                     totalMassB = 0.0;
 140
 141     md->haveVsites = FALSE;
 142     gmx_mtop_atomloop_block_t  aloop = gmx_mtop_atomloop_block_init(&mtop);
 143     const t_atom              *atom;
 144     int                        nmol;
 145     while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
 146     {
 147         totalMassA += nmol*atom->m;
 148         totalMassB += nmol*atom->mB;
 149
 150         if (atom->ptype == eptVSite)
 151         {
 152             md->haveVsites = TRUE;
 153         }
 154
 155         if (ir.efep != efepNO && PERTURBED(*atom))
 156         {
 157             md->nPerturbed++;
 158             if (atom->mB != atom->m)
 159             {
 160                 md->nMassPerturbed += nmol;
 161             }
 162             if (atom->qB != atom->q)
 163             {
 164                 md->nChargePerturbed += nmol;
 165             }
 166             if (atom->typeB != atom->type)
 167             {
 168                 md->nTypePerturbed += nmol;
 169             }
 170         }
 171     }
 172
 173     md->tmassA = totalMassA;
 174     md->tmassB = totalMassB;
 175
 176     if (ir.efep != efepNO && fp)
 177     {
 178         fprintf(fp,
 179                 "There are %d atoms and %d charges for free energy perturbation\n",
 180                 md->nPerturbed, md->nChargePerturbed);
 181     }
 182
 183     md->havePartiallyFrozenAtoms = FALSE;
 184     for (int g = 0; g < ir.opts.ngfrz; g++)
 185     {
 186         for (int d = YY; d < DIM; d++)
 187         {
 188             if (ir.opts.nFreeze[g][d] != ir.opts.nFreeze[g][XX])
 189             {
 190                 md->havePartiallyFrozenAtoms = TRUE;
 191             }
 192         }
 193     }
 194
 195     md->bOrires = (gmx_mtop_ftype_count(&mtop, F_ORIRES) != 0);
 196
 197     return mdAtoms;
 198 }
 199
 200 }  // namespace gmx
 201
 202 void atoms2md(const gmx_mtop_t *mtop, const t_inputrec *ir,
 203               int nindex, const int *index,
 204               int homenr,
 205               gmx::MDAtoms *mdAtoms)
 206 {
 207     gmx_bool              bLJPME;
 208     const t_grpopts      *opts;
 209     int                   nthreads gmx_unused;
 210
 211     bLJPME = EVDW_PME(ir->vdwtype);
 212
 213     opts = &ir->opts;
 214
 215     const SimulationGroups    &groups = mtop->groups;
 216
 217     auto                       md = mdAtoms->mdatoms();
 218     /* nindex>=0 indicates DD where we use an index */
 219     if (nindex >= 0)
 220     {
 221         md->nr = nindex;
 222     }
 223     else
 224     {
 225         md->nr = mtop->natoms;
 226     }
 227
 228     if (md->nr > md->nalloc)
 229     {
 230         md->nalloc = over_alloc_dd(md->nr);
 231
 232         if (md->nMassPerturbed)
 233         {
 234             srenew(md->massA, md->nalloc);
 235             srenew(md->massB, md->nalloc);
 236         }
 237         srenew(md->massT, md->nalloc);
 238         /* The SIMD version of the integrator needs this aligned and padded.
 239          * The padding needs to be with zeros, which we set later below.
 240          */
 241         gmx::AlignedAllocationPolicy::free(md->invmass);
 242         md->invmass = new(gmx::AlignedAllocationPolicy::malloc((md->nalloc + GMX_REAL_MAX_SIMD_WIDTH)*sizeof(*md->invmass)))real;
 243         srenew(md->invMassPerDim, md->nalloc);
 244         // TODO eventually we will have vectors and just resize
 245         // everything, but for now the semantics of md->nalloc being
 246         // the capacity are preserved by keeping vectors within
 247         // mdAtoms having the same properties as the other arrays.
 248         mdAtoms->reserve(md->nalloc);
 249         mdAtoms->resize(md->nr);
 250         srenew(md->typeA, md->nalloc);
 251         if (md->nPerturbed)
 252         {
 253             srenew(md->chargeB, md->nalloc);
 254             srenew(md->typeB, md->nalloc);
 255         }
 256         if (bLJPME)
 257         {
 258             srenew(md->sqrt_c6A, md->nalloc);
 259             srenew(md->sigmaA, md->nalloc);
 260             srenew(md->sigma3A, md->nalloc);
 261             if (md->nPerturbed)
 262             {
 263                 srenew(md->sqrt_c6B, md->nalloc);
 264                 srenew(md->sigmaB, md->nalloc);
 265                 srenew(md->sigma3B, md->nalloc);
 266             }
 267         }
 268         srenew(md->ptype, md->nalloc);
 269         if (opts->ngtc > 1)
 270         {
 271             srenew(md->cTC, md->nalloc);
 272             /* We always copy cTC with domain decomposition */
 273         }
 274         srenew(md->cENER, md->nalloc);
 275         if (opts->ngacc > 1)
 276         {
 277             srenew(md->cACC, md->nalloc);
 278         }
 279         if (opts->nFreeze &&
 280             (opts->ngfrz > 1 ||
 281              opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
 282         {
 283             srenew(md->cFREEZE, md->nalloc);
 284         }
 285         if (md->bVCMgrps)
 286         {
 287             srenew(md->cVCM, md->nalloc);
 288         }
 289         if (md->bOrires)
 290         {
 291             srenew(md->cORF, md->nalloc);
 292         }
 293         if (md->nPerturbed)
 294         {
 295             srenew(md->bPerturbed, md->nalloc);
 296         }
 297
 298         /* Note that these user t_mdatoms array pointers are NULL
 299          * when there is only one group present.
 300          * Therefore, when adding code, the user should use something like:
 301          * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
 302          */
 303         if (!mtop->groups.groupNumbers[SimulationAtomGroupType::User1].empty())
 304         {
 305             srenew(md->cU1, md->nalloc);
 306         }
 307         if (!mtop->groups.groupNumbers[SimulationAtomGroupType::User2].empty())
 308         {
 309             srenew(md->cU2, md->nalloc);
 310         }
 311
 312         if (ir->bQMMM)
 313         {
 314             srenew(md->bQM, md->nalloc);
 315         }
 316     }
 317
 318     int molb          = 0;
 319
 320     nthreads = gmx_omp_nthreads_get(emntDefault);
 321 #pragma omp parallel for num_threads(nthreads) schedule(static) firstprivate(molb)
 322     for (int i = 0; i < md->nr; i++)
 323     {
 324         try
 325         {
 326             int      g, ag;
 327             real     mA, mB, fac;
 328             real     c6, c12;
 329
 330             if (index == nullptr)
 331             {
 332                 ag = i;
 333             }
 334             else
 335             {
 336                 ag = index[i];
 337             }
 338             const t_atom &atom = mtopGetAtomParameters(mtop, ag, &molb);
 339
 340             if (md->cFREEZE)
 341             {
 342                 md->cFREEZE[i] = getGroupType(groups, SimulationAtomGroupType::Freeze, ag);
 343             }
 344             if (EI_ENERGY_MINIMIZATION(ir->eI))
 345             {
 346                 /* Displacement is proportional to F, masses used for constraints */
 347                 mA = 1.0;
 348                 mB = 1.0;
 349             }
 350             else if (ir->eI == eiBD)
 351             {
 352                 /* With BD the physical masses are irrelevant.
 353                  * To keep the code simple we use most of the normal MD code path
 354                  * for BD. Thus for constraining the masses should be proportional
 355                  * to the friction coefficient. We set the absolute value such that
 356                  * m/2<(dx/dt)^2> = m/2*2kT/fric*dt = kT/2 => m=fric*dt/2
 357                  * Then if we set the (meaningless) velocity to v=dx/dt, we get the
 358                  * correct kinetic energy and temperature using the usual code path.
 359                  * Thus with BD v*dt will give the displacement and the reported
 360                  * temperature can signal bad integration (too large time step).
 361                  */
 362                 if (ir->bd_fric > 0)
 363                 {
 364                     mA = 0.5*ir->bd_fric*ir->delta_t;
 365                     mB = 0.5*ir->bd_fric*ir->delta_t;
 366                 }
 367                 else
 368                 {
 369                     /* The friction coefficient is mass/tau_t */
 370                     fac = ir->delta_t/opts->tau_t[md->cTC ?
 371                                                   groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag] : 0];
 372                     mA  = 0.5*atom.m*fac;
 373                     mB  = 0.5*atom.mB*fac;
 374                 }
 375             }
 376             else
 377             {
 378                 mA = atom.m;
 379                 mB = atom.mB;
 380             }
 381             if (md->nMassPerturbed)
 382             {
 383                 md->massA[i]  = mA;
 384                 md->massB[i]  = mB;
 385             }
 386             md->massT[i]    = mA;
 387
 388             if (mA == 0.0)
 389             {
 390                 md->invmass[i]           = 0;
 391                 md->invMassPerDim[i][XX] = 0;
 392                 md->invMassPerDim[i][YY] = 0;
 393                 md->invMassPerDim[i][ZZ] = 0;
 394             }
 395             else if (md->cFREEZE)
 396             {
 397                 g = md->cFREEZE[i];
 398                 if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
 399                 {
 400                     /* Set the mass of completely frozen particles to ALMOST_ZERO
 401                      * iso 0 to avoid div by zero in lincs or shake.
 402                      */
 403                     md->invmass[i]  = ALMOST_ZERO;
 404                 }
 405                 else
 406                 {
 407                     /* Note: Partially frozen particles use the normal invmass.
 408                      * If such particles are constrained, the frozen dimensions
 409                      * should not be updated with the constrained coordinates.
 410                      */
 411                     md->invmass[i]  = 1.0/mA;
 412                 }
 413                 for (int d = 0; d < DIM; d++)
 414                 {
 415                     md->invMassPerDim[i][d] = (opts->nFreeze[g][d] ? 0 : 1.0/mA);
 416                 }
 417             }
 418             else
 419             {
 420                 md->invmass[i]  = 1.0/mA;
 421                 for (int d = 0; d < DIM; d++)
 422                 {
 423                     md->invMassPerDim[i][d] = 1.0/mA;
 424                 }
 425             }
 426
 427             md->chargeA[i]      = atom.q;
 428             md->typeA[i]        = atom.type;
 429             if (bLJPME)
 430             {
 431                 c6                = mtop->ffparams.iparams[atom.type*(mtop->ffparams.atnr+1)].lj.c6;
 432                 c12               = mtop->ffparams.iparams[atom.type*(mtop->ffparams.atnr+1)].lj.c12;
 433                 md->sqrt_c6A[i]   = sqrt(c6);
 434                 if (c6 == 0.0 || c12 == 0)
 435                 {
 436                     md->sigmaA[i] = 1.0;
 437                 }
 438                 else
 439                 {
 440                     md->sigmaA[i] = gmx::sixthroot(c12/c6);
 441                 }
 442                 md->sigma3A[i]    = 1/(md->sigmaA[i]*md->sigmaA[i]*md->sigmaA[i]);
 443             }
 444             if (md->nPerturbed)
 445             {
 446                 md->bPerturbed[i] = PERTURBED(atom);
 447                 md->chargeB[i]    = atom.qB;
 448                 md->typeB[i]      = atom.typeB;
 449                 if (bLJPME)
 450                 {
 451                     c6                = mtop->ffparams.iparams[atom.typeB*(mtop->ffparams.atnr+1)].lj.c6;
 452                     c12               = mtop->ffparams.iparams[atom.typeB*(mtop->ffparams.atnr+1)].lj.c12;
 453                     md->sqrt_c6B[i]   = sqrt(c6);
 454                     if (c6 == 0.0 || c12 == 0)
 455                     {
 456                         md->sigmaB[i] = 1.0;
 457                     }
 458                     else
 459                     {
 460                         md->sigmaB[i] = gmx::sixthroot(c12/c6);
 461                     }
 462                     md->sigma3B[i]    = 1/(md->sigmaB[i]*md->sigmaB[i]*md->sigmaB[i]);
 463                 }
 464             }
 465             md->ptype[i]    = atom.ptype;
 466             if (md->cTC)
 467             {
 468                 md->cTC[i]    = groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag];
 469             }
 470             md->cENER[i]    = getGroupType(groups, SimulationAtomGroupType::EnergyOutput, ag);
 471             if (md->cACC)
 472             {
 473                 md->cACC[i]   = groups.groupNumbers[SimulationAtomGroupType::Acceleration][ag];
 474             }
 475             if (md->cVCM)
 476             {
 477                 md->cVCM[i]       = groups.groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][ag];
 478             }
 479             if (md->cORF)
 480             {
 481                 md->cORF[i]       = getGroupType(groups, SimulationAtomGroupType::OrientationRestraintsFit, ag);
 482             }
 483
 484             if (md->cU1)
 485             {
 486                 md->cU1[i]        = groups.groupNumbers[SimulationAtomGroupType::User1][ag];
 487             }
 488             if (md->cU2)
 489             {
 490                 md->cU2[i]        = groups.groupNumbers[SimulationAtomGroupType::User2][ag];
 491             }
 492
 493             if (ir->bQMMM)
 494             {
 495                 if (groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics].empty() ||
 496                     groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][ag] < groups.groups[SimulationAtomGroupType::QuantumMechanics].nr-1)
 497                 {
 498                     md->bQM[i]      = TRUE;
 499                 }
 500                 else
 501                 {
 502                     md->bQM[i]      = FALSE;
 503                 }
 504             }
 505         }
 506         GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
 507     }
 508
 509     if (md->nr > 0)
 510     {
 511         /* Pad invmass with 0 so a SIMD MD update does not change v and x */
 512         for (int i = md->nr; i < md->nr + GMX_REAL_MAX_SIMD_WIDTH; i++)
 513         {
 514             md->invmass[i] = 0;
 515         }
 516     }
 517
 518     md->homenr = homenr;
 519     /* We set mass, invmass, invMassPerDim and tmass for lambda=0.
 520      * For free-energy runs, these should be updated using update_mdatoms().
 521      */
 522     md->tmass  = md->tmassA;
 523     md->lambda = 0;
 524 }
 525
 526 void update_mdatoms(t_mdatoms *md, real lambda)
 527 {
 528     if (md->nMassPerturbed && lambda != md->lambda)
 529     {
 530         real L1 = 1 - lambda;
 531
 532         /* Update masses of perturbed atoms for the change in lambda */
 533         int gmx_unused nthreads = gmx_omp_nthreads_get(emntDefault);
 534 #pragma omp parallel for num_threads(nthreads) schedule(static)
 535         for (int i = 0; i < md->nr; i++)
 536         {
 537             if (md->bPerturbed[i])
 538             {
 539                 md->massT[i] = L1*md->massA[i] + lambda*md->massB[i];
 540                 /* Atoms with invmass 0 or ALMOST_ZERO are massless or frozen
 541                  * and their invmass does not depend on lambda.
 542                  */
 543                 if (md->invmass[i] > 1.1*ALMOST_ZERO)
 544                 {
 545                     md->invmass[i] = 1.0/md->massT[i];
 546                     for (int d = 0; d < DIM; d++)
 547                     {
 548                         if (md->invMassPerDim[i][d] > 1.1*ALMOST_ZERO)
 549                         {
 550                             md->invMassPerDim[i][d] = md->invmass[i];
 551                         }
 552                     }
 553                 }
 554             }
 555         }
 556
 557         /* Update the system mass for the change in lambda */
 558         md->tmass  = L1*md->tmassA + lambda*md->tmassB;
 559     }
 560
 561     md->lambda = lambda;
 562 }