src/gromacs/mdlib/mdatoms.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
   7  * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   9  * and including many others, as listed in the AUTHORS file in the
  10  * top-level source directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
  18  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
  24  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
  28  * consider that scientific software is very special. Version
  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
  33  * official version at http://www.gromacs.org.
  34  *
  35  * To help us fund GROMACS development, we humbly ask that you cite
  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  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/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"
  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_->typeB);
  79     /* mdatoms->chargeA and mdatoms->chargeB point at chargeA_.data()
  80      * and chargeB_.data() respectively. They get freed automatically. */
  81     sfree(mdatoms_->sqrt_c6A);
  82     sfree(mdatoms_->sigmaA);
  83     sfree(mdatoms_->sigma3A);
  84     sfree(mdatoms_->sqrt_c6B);
  85     sfree(mdatoms_->sigmaB);
  86     sfree(mdatoms_->sigma3B);
  87     sfree(mdatoms_->ptype);
  88     sfree(mdatoms_->cTC);
  89     sfree(mdatoms_->cENER);
  90     sfree(mdatoms_->cACC);
  91     sfree(mdatoms_->cFREEZE);
  92     sfree(mdatoms_->cVCM);
  93     sfree(mdatoms_->cORF);
  94     sfree(mdatoms_->bPerturbed);
  95     sfree(mdatoms_->cU1);
  96     sfree(mdatoms_->cU2);
  97 }
  98
  99 void MDAtoms::resizeChargeA(const int newSize)
 100 {
 101     chargeA_.resizeWithPadding(newSize);
 102     mdatoms_->chargeA = chargeA_.data();
 103 }
 104
 105 void MDAtoms::resizeChargeB(const int newSize)
 106 {
 107     chargeB_.resizeWithPadding(newSize);
 108     mdatoms_->chargeB = chargeB_.data();
 109 }
 110
 111 void MDAtoms::reserveChargeA(const int newCapacity)
 112 {
 113     chargeA_.reserveWithPadding(newCapacity);
 114     mdatoms_->chargeA = chargeA_.data();
 115 }
 116
 117 void MDAtoms::reserveChargeB(const int newCapacity)
 118 {
 119     chargeB_.reserveWithPadding(newCapacity);
 120     mdatoms_->chargeB = chargeB_.data();
 121 }
 122
 123 std::unique_ptr<MDAtoms> makeMDAtoms(FILE* fp, const gmx_mtop_t& mtop, const t_inputrec& ir, const bool rankHasPmeGpuTask)
 124 {
 125     auto mdAtoms = std::make_unique<MDAtoms>();
 126     // GPU transfers may want to use a suitable pinning mode.
 127     if (rankHasPmeGpuTask)
 128     {
 129         changePinningPolicy(&mdAtoms->chargeA_, pme_get_pinning_policy());
 130         changePinningPolicy(&mdAtoms->chargeB_, pme_get_pinning_policy());
 131     }
 132     t_mdatoms* md;
 133     snew(md, 1);
 134     mdAtoms->mdatoms_.reset(md);
 135
 136     md->nenergrp = mtop.groups.groups[SimulationAtomGroupType::EnergyOutput].size();
 137     md->bVCMgrps = FALSE;
 138     for (int i = 0; i < mtop.natoms; i++)
 139     {
 140         if (getGroupType(mtop.groups, SimulationAtomGroupType::MassCenterVelocityRemoval, i) > 0)
 141         {
 142             md->bVCMgrps = TRUE;
 143         }
 144     }
 145
 146     /* Determine the total system mass and perturbed atom counts */
 147     double totalMassA = 0.0;
 148     double totalMassB = 0.0;
 149
 150     md->haveVsites                  = FALSE;
 151     gmx_mtop_atomloop_block_t aloop = gmx_mtop_atomloop_block_init(&mtop);
 152     const t_atom*             atom;
 153     int                       nmol;
 154     while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
 155     {
 156         totalMassA += nmol * atom->m;
 157         totalMassB += nmol * atom->mB;
 158
 159         if (atom->ptype == eptVSite)
 160         {
 161             md->haveVsites = TRUE;
 162         }
 163
 164         if (ir.efep != efepNO && PERTURBED(*atom))
 165         {
 166             md->nPerturbed++;
 167             if (atom->mB != atom->m)
 168             {
 169                 md->nMassPerturbed += nmol;
 170             }
 171             if (atom->qB != atom->q)
 172             {
 173                 md->nChargePerturbed += nmol;
 174             }
 175             if (atom->typeB != atom->type)
 176             {
 177                 md->nTypePerturbed += nmol;
 178             }
 179         }
 180     }
 181
 182     md->tmassA = totalMassA;
 183     md->tmassB = totalMassB;
 184
 185     if (ir.efep != efepNO && fp)
 186     {
 187         fprintf(fp, "There are %d atoms and %d charges for free energy perturbation\n",
 188                 md->nPerturbed, md->nChargePerturbed);
 189     }
 190
 191     md->havePartiallyFrozenAtoms = FALSE;
 192     for (int g = 0; g < ir.opts.ngfrz; g++)
 193     {
 194         for (int d = YY; d < DIM; d++)
 195         {
 196             if (ir.opts.nFreeze[g][d] != ir.opts.nFreeze[g][XX])
 197             {
 198                 md->havePartiallyFrozenAtoms = TRUE;
 199             }
 200         }
 201     }
 202
 203     md->bOrires = (gmx_mtop_ftype_count(&mtop, F_ORIRES) != 0);
 204
 205     return mdAtoms;
 206 }
 207
 208 } // namespace gmx
 209
 210 void atoms2md(const gmx_mtop_t*  mtop,
 211               const t_inputrec*  ir,
 212               int                nindex,
 213               gmx::ArrayRef<int> index,
 214               int                homenr,
 215               gmx::MDAtoms*      mdAtoms)
 216 {
 217     gmx_bool         bLJPME;
 218     const t_grpopts* opts;
 219     int nthreads gmx_unused;
 220
 221     bLJPME = EVDW_PME(ir->vdwtype);
 222
 223     opts = &ir->opts;
 224
 225     const SimulationGroups& groups = mtop->groups;
 226
 227     auto md = mdAtoms->mdatoms();
 228     /* nindex>=0 indicates DD where we use an index */
 229     if (nindex >= 0)
 230     {
 231         md->nr = nindex;
 232     }
 233     else
 234     {
 235         md->nr = mtop->natoms;
 236     }
 237
 238     if (md->nr > md->nalloc)
 239     {
 240         md->nalloc = over_alloc_dd(md->nr);
 241
 242         if (md->nMassPerturbed)
 243         {
 244             srenew(md->massA, md->nalloc);
 245             srenew(md->massB, md->nalloc);
 246         }
 247         srenew(md->massT, md->nalloc);
 248         /* The SIMD version of the integrator needs this aligned and padded.
 249          * The padding needs to be with zeros, which we set later below.
 250          */
 251         gmx::AlignedAllocationPolicy::free(md->invmass);
 252         md->invmass = new (gmx::AlignedAllocationPolicy::malloc(
 253                 (md->nalloc + GMX_REAL_MAX_SIMD_WIDTH) * sizeof(*md->invmass))) real;
 254         srenew(md->invMassPerDim, md->nalloc);
 255         // TODO eventually we will have vectors and just resize
 256         // everything, but for now the semantics of md->nalloc being
 257         // the capacity are preserved by keeping vectors within
 258         // mdAtoms having the same properties as the other arrays.
 259         mdAtoms->reserveChargeA(md->nalloc);
 260         mdAtoms->resizeChargeA(md->nr);
 261         if (md->nPerturbed > 0)
 262         {
 263             mdAtoms->reserveChargeB(md->nalloc);
 264             mdAtoms->resizeChargeB(md->nr);
 265         }
 266         srenew(md->typeA, md->nalloc);
 267         if (md->nPerturbed)
 268         {
 269             srenew(md->typeB, md->nalloc);
 270         }
 271         if (bLJPME)
 272         {
 273             srenew(md->sqrt_c6A, md->nalloc);
 274             srenew(md->sigmaA, md->nalloc);
 275             srenew(md->sigma3A, md->nalloc);
 276             if (md->nPerturbed)
 277             {
 278                 srenew(md->sqrt_c6B, md->nalloc);
 279                 srenew(md->sigmaB, md->nalloc);
 280                 srenew(md->sigma3B, md->nalloc);
 281             }
 282         }
 283         srenew(md->ptype, md->nalloc);
 284         if (opts->ngtc > 1)
 285         {
 286             srenew(md->cTC, md->nalloc);
 287             /* We always copy cTC with domain decomposition */
 288         }
 289         srenew(md->cENER, md->nalloc);
 290         if (opts->ngacc > 1)
 291         {
 292             srenew(md->cACC, md->nalloc);
 293         }
 294         if (opts->nFreeze
 295             && (opts->ngfrz > 1 || opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
 296         {
 297             srenew(md->cFREEZE, md->nalloc);
 298         }
 299         if (md->bVCMgrps)
 300         {
 301             srenew(md->cVCM, md->nalloc);
 302         }
 303         if (md->bOrires)
 304         {
 305             srenew(md->cORF, md->nalloc);
 306         }
 307         if (md->nPerturbed)
 308         {
 309             srenew(md->bPerturbed, md->nalloc);
 310         }
 311
 312         /* Note that these user t_mdatoms array pointers are NULL
 313          * when there is only one group present.
 314          * Therefore, when adding code, the user should use something like:
 315          * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
 316          */
 317         if (!mtop->groups.groupNumbers[SimulationAtomGroupType::User1].empty())
 318         {
 319             srenew(md->cU1, md->nalloc);
 320         }
 321         if (!mtop->groups.groupNumbers[SimulationAtomGroupType::User2].empty())
 322         {
 323             srenew(md->cU2, md->nalloc);
 324         }
 325     }
 326
 327     int molb = 0;
 328
 329     nthreads = gmx_omp_nthreads_get(emntDefault);
 330 #pragma omp parallel for num_threads(nthreads) schedule(static) firstprivate(molb)
 331     for (int i = 0; i < md->nr; i++)
 332     {
 333         try
 334         {
 335             int  g, ag;
 336             real mA, mB, fac;
 337             real c6, c12;
 338
 339             if (index.empty())
 340             {
 341                 ag = i;
 342             }
 343             else
 344             {
 345                 ag = index[i];
 346             }
 347             const t_atom& atom = mtopGetAtomParameters(mtop, ag, &molb);
 348
 349             if (md->cFREEZE)
 350             {
 351                 md->cFREEZE[i] = getGroupType(groups, SimulationAtomGroupType::Freeze, ag);
 352             }
 353             if (EI_ENERGY_MINIMIZATION(ir->eI))
 354             {
 355                 /* Displacement is proportional to F, masses used for constraints */
 356                 mA = 1.0;
 357                 mB = 1.0;
 358             }
 359             else if (ir->eI == eiBD)
 360             {
 361                 /* With BD the physical masses are irrelevant.
 362                  * To keep the code simple we use most of the normal MD code path
 363                  * for BD. Thus for constraining the masses should be proportional
 364                  * to the friction coefficient. We set the absolute value such that
 365                  * m/2<(dx/dt)^2> = m/2*2kT/fric*dt = kT/2 => m=fric*dt/2
 366                  * Then if we set the (meaningless) velocity to v=dx/dt, we get the
 367                  * correct kinetic energy and temperature using the usual code path.
 368                  * Thus with BD v*dt will give the displacement and the reported
 369                  * temperature can signal bad integration (too large time step).
 370                  */
 371                 if (ir->bd_fric > 0)
 372                 {
 373                     mA = 0.5 * ir->bd_fric * ir->delta_t;
 374                     mB = 0.5 * ir->bd_fric * ir->delta_t;
 375                 }
 376                 else
 377                 {
 378                     /* The friction coefficient is mass/tau_t */
 379                     fac = ir->delta_t
 380                           / opts->tau_t[md->cTC ? groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag] : 0];
 381                     mA = 0.5 * atom.m * fac;
 382                     mB = 0.5 * atom.mB * fac;
 383                 }
 384             }
 385             else
 386             {
 387                 mA = atom.m;
 388                 mB = atom.mB;
 389             }
 390             if (md->nMassPerturbed)
 391             {
 392                 md->massA[i] = mA;
 393                 md->massB[i] = mB;
 394             }
 395             md->massT[i] = mA;
 396
 397             if (mA == 0.0)
 398             {
 399                 md->invmass[i]           = 0;
 400                 md->invMassPerDim[i][XX] = 0;
 401                 md->invMassPerDim[i][YY] = 0;
 402                 md->invMassPerDim[i][ZZ] = 0;
 403             }
 404             else if (md->cFREEZE)
 405             {
 406                 g = md->cFREEZE[i];
 407                 GMX_ASSERT(opts->nFreeze != nullptr,
 408                            "Must have freeze groups to initialize masses");
 409                 if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
 410                 {
 411                     /* Set the mass of completely frozen particles to ALMOST_ZERO
 412                      * iso 0 to avoid div by zero in lincs or shake.
 413                      */
 414                     md->invmass[i] = ALMOST_ZERO;
 415                 }
 416                 else
 417                 {
 418                     /* Note: Partially frozen particles use the normal invmass.
 419                      * If such particles are constrained, the frozen dimensions
 420                      * should not be updated with the constrained coordinates.
 421                      */
 422                     md->invmass[i] = 1.0 / mA;
 423                 }
 424                 for (int d = 0; d < DIM; d++)
 425                 {
 426                     md->invMassPerDim[i][d] = (opts->nFreeze[g][d] ? 0 : 1.0 / mA);
 427                 }
 428             }
 429             else
 430             {
 431                 md->invmass[i] = 1.0 / mA;
 432                 for (int d = 0; d < DIM; d++)
 433                 {
 434                     md->invMassPerDim[i][d] = 1.0 / mA;
 435                 }
 436             }
 437
 438             md->chargeA[i] = atom.q;
 439             md->typeA[i]   = atom.type;
 440             if (bLJPME)
 441             {
 442                 c6  = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c6;
 443                 c12 = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c12;
 444                 md->sqrt_c6A[i] = sqrt(c6);
 445                 if (c6 == 0.0 || c12 == 0)
 446                 {
 447                     md->sigmaA[i] = 1.0;
 448                 }
 449                 else
 450                 {
 451                     md->sigmaA[i] = gmx::sixthroot(c12 / c6);
 452                 }
 453                 md->sigma3A[i] = 1 / (md->sigmaA[i] * md->sigmaA[i] * md->sigmaA[i]);
 454             }
 455             if (md->nPerturbed)
 456             {
 457                 md->bPerturbed[i] = PERTURBED(atom);
 458                 md->chargeB[i]    = atom.qB;
 459                 md->typeB[i]      = atom.typeB;
 460                 if (bLJPME)
 461                 {
 462                     c6  = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c6;
 463                     c12 = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c12;
 464                     md->sqrt_c6B[i] = sqrt(c6);
 465                     if (c6 == 0.0 || c12 == 0)
 466                     {
 467                         md->sigmaB[i] = 1.0;
 468                     }
 469                     else
 470                     {
 471                         md->sigmaB[i] = gmx::sixthroot(c12 / c6);
 472                     }
 473                     md->sigma3B[i] = 1 / (md->sigmaB[i] * md->sigmaB[i] * md->sigmaB[i]);
 474                 }
 475             }
 476             md->ptype[i] = atom.ptype;
 477             if (md->cTC)
 478             {
 479                 md->cTC[i] = groups.groupNumbers[SimulationAtomGroupType::TemperatureCoupling][ag];
 480             }
 481             md->cENER[i] = getGroupType(groups, SimulationAtomGroupType::EnergyOutput, ag);
 482             if (md->cACC)
 483             {
 484                 md->cACC[i] = groups.groupNumbers[SimulationAtomGroupType::Acceleration][ag];
 485             }
 486             if (md->cVCM)
 487             {
 488                 md->cVCM[i] = groups.groupNumbers[SimulationAtomGroupType::MassCenterVelocityRemoval][ag];
 489             }
 490             if (md->cORF)
 491             {
 492                 md->cORF[i] = getGroupType(groups, SimulationAtomGroupType::OrientationRestraintsFit, ag);
 493             }
 494
 495             if (md->cU1)
 496             {
 497                 md->cU1[i] = groups.groupNumbers[SimulationAtomGroupType::User1][ag];
 498             }
 499             if (md->cU2)
 500             {
 501                 md->cU2[i] = groups.groupNumbers[SimulationAtomGroupType::User2][ag];
 502             }
 503         }
 504         GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 505     }
 506
 507     if (md->nr > 0)
 508     {
 509         /* Pad invmass with 0 so a SIMD MD update does not change v and x */
 510         for (int i = md->nr; i < md->nr + GMX_REAL_MAX_SIMD_WIDTH; i++)
 511         {
 512             md->invmass[i] = 0;
 513         }
 514     }
 515
 516     md->homenr = homenr;
 517     /* We set mass, invmass, invMassPerDim and tmass for lambda=0.
 518      * For free-energy runs, these should be updated using update_mdatoms().
 519      */
 520     md->tmass  = md->tmassA;
 521     md->lambda = 0;
 522 }
 523
 524 void update_mdatoms(t_mdatoms* md, real lambda)
 525 {
 526     if (md->nMassPerturbed && lambda != md->lambda)
 527     {
 528         real L1 = 1 - lambda;
 529
 530         /* Update masses of perturbed atoms for the change in lambda */
 531         int gmx_unused nthreads = gmx_omp_nthreads_get(emntDefault);
 532 #pragma omp parallel for num_threads(nthreads) schedule(static)
 533         for (int i = 0; i < md->nr; i++)
 534         {
 535             if (md->bPerturbed[i])
 536             {
 537                 md->massT[i] = L1 * md->massA[i] + lambda * md->massB[i];
 538                 /* Atoms with invmass 0 or ALMOST_ZERO are massless or frozen
 539                  * and their invmass does not depend on lambda.
 540                  */
 541                 if (md->invmass[i] > 1.1 * ALMOST_ZERO)
 542                 {
 543                     md->invmass[i] = 1.0 / md->massT[i];
 544                     for (int d = 0; d < DIM; d++)
 545                     {
 546                         if (md->invMassPerDim[i][d] > 1.1 * ALMOST_ZERO)
 547                         {
 548                             md->invMassPerDim[i][d] = md->invmass[i];
 549                         }
 550                     }
 551                 }
 552             }
 553         }
 554
 555         /* Update the system mass for the change in lambda */
 556         md->tmass = L1 * md->tmassA + lambda * md->tmassB;
 557     }
 558
 559     md->lambda = lambda;
 560 }