src/gromacs/mdlib/constr.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) 2013,2014,2015,2016,2017 by the GROMACS development team.
   7  * Copyright (c) 2018,2019,2020,2021, 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  *
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  38 /*! \internal \file
  39  * \brief Defines the high-level constraint code.
  40  *
  41  * \author Berk Hess <hess@kth.se>
  42  * \author Mark Abraham <mark.j.abraham@gmail.com>
  43  * \ingroup module_mdlib
  44  */
  45 #include "gmxpre.h"
  46
  47 #include "constr.h"
  48
  49 #include <cassert>
  50 #include <cmath>
  51 #include <cstdlib>
  52
  53 #include <algorithm>
  54
  55 #include "gromacs/domdec/domdec.h"
  56 #include "gromacs/domdec/domdec_struct.h"
  57 #include "gromacs/essentialdynamics/edsam.h"
  58 #include "gromacs/fileio/confio.h"
  59 #include "gromacs/fileio/gmxfio.h"
  60 #include "gromacs/fileio/pdbio.h"
  61 #include "gromacs/gmxlib/nrnb.h"
  62 #include "gromacs/math/arrayrefwithpadding.h"
  63 #include "gromacs/math/utilities.h"
  64 #include "gromacs/math/vec.h"
  65 #include "gromacs/mdlib/gmx_omp_nthreads.h"
  66 #include "gromacs/mdlib/lincs.h"
  67 #include "gromacs/mdlib/settle.h"
  68 #include "gromacs/mdlib/shake.h"
  69 #include "gromacs/mdtypes/commrec.h"
  70 #include "gromacs/mdtypes/inputrec.h"
  71 #include "gromacs/mdtypes/md_enums.h"
  72 #include "gromacs/mdtypes/state.h"
  73 #include "gromacs/pbcutil/pbc.h"
  74 #include "gromacs/pulling/pull.h"
  75 #include "gromacs/timing/wallcycle.h"
  76 #include "gromacs/topology/ifunc.h"
  77 #include "gromacs/topology/mtop_lookup.h"
  78 #include "gromacs/topology/mtop_util.h"
  79 #include "gromacs/utility/arrayref.h"
  80 #include "gromacs/utility/exceptions.h"
  81 #include "gromacs/utility/fatalerror.h"
  82 #include "gromacs/utility/gmxassert.h"
  83 #include "gromacs/utility/listoflists.h"
  84 #include "gromacs/utility/pleasecite.h"
  85 #include "gromacs/utility/txtdump.h"
  86
  87 namespace gmx
  88 {
  89
  90 /* \brief Impl class for Constraints
  91  *
  92  * \todo Members like md, idef are valid only for the lifetime of a
  93  * domain, which would be good to make clearer in the structure of the
  94  * code. It should not be possible to call apply() if setConstraints()
  95  * has not been called. For example, this could be achieved if
  96  * setConstraints returned a valid object with such a method.  That
  97  * still requires that we manage the lifetime of that object
  98  * correctly, however. */
  99 class Constraints::Impl
 100 {
 101 public:
 102     Impl(const gmx_mtop_t&     mtop_p,
 103          const t_inputrec&     ir_p,
 104          pull_t*               pull_work,
 105          FILE*                 log_p,
 106          const t_commrec*      cr_p,
 107          const gmx_multisim_t* ms,
 108          t_nrnb*               nrnb,
 109          gmx_wallcycle*        wcycle_p,
 110          bool                  pbcHandlingRequired,
 111          int                   numConstraints,
 112          int                   numSettles);
 113     ~Impl();
 114     void setConstraints(gmx_localtop_t*                     top,
 115                         int                                 numAtoms,
 116                         int                                 numHomeAtoms,
 117                         gmx::ArrayRef<const real>           masses,
 118                         gmx::ArrayRef<const real>           inverseMasses,
 119                         bool                                hasMassPerturbedAtoms,
 120                         real                                lambda,
 121                         gmx::ArrayRef<const unsigned short> cFREEZE);
 122     bool apply(bool                      bLog,
 123                bool                      bEner,
 124                int64_t                   step,
 125                int                       delta_step,
 126                real                      step_scaling,
 127                ArrayRefWithPadding<RVec> x,
 128                ArrayRefWithPadding<RVec> xprime,
 129                ArrayRef<RVec>            min_proj,
 130                const matrix              box,
 131                real                      lambda,
 132                real*                     dvdlambda,
 133                ArrayRefWithPadding<RVec> v,
 134                bool                      computeVirial,
 135                tensor                    constraintsVirial,
 136                ConstraintVariable        econq);
 137     //! The total number of constraints.
 138     int ncon_tot = 0;
 139     //! The number of flexible constraints.
 140     int nflexcon = 0;
 141     //! A list of atoms to constraints for each moleculetype.
 142     std::vector<ListOfLists<int>> at2con_mt;
 143     //! A list of atoms to settles for each moleculetype
 144     std::vector<std::vector<int>> at2settle_mt;
 145     //! LINCS data.
 146     Lincs* lincsd = nullptr; // TODO this should become a unique_ptr
 147     //! SHAKE data.
 148     std::unique_ptr<shakedata> shaked;
 149     //! SETTLE data.
 150     std::unique_ptr<SettleData> settled;
 151     //! The maximum number of warnings.
 152     int maxwarn = 0;
 153     //! The number of warnings for LINCS.
 154     int warncount_lincs = 0;
 155     //! The number of warnings for SETTLE.
 156     int warncount_settle = 0;
 157     //! The essential dynamics data.
 158     gmx_edsam* ed = nullptr;
 159
 160     //! Thread-local virial contribution.
 161     tensor* threadConstraintsVirial = { nullptr };
 162     //! Did a settle error occur?
 163     bool* bSettleErrorHasOccurred = nullptr;
 164
 165     //! Pointer to the global topology - only used for printing warnings.
 166     const gmx_mtop_t& mtop;
 167     //! Parameters for the interactions in this domain.
 168     const InteractionDefinitions* idef = nullptr;
 169     //! Total number of atoms.
 170     int numAtoms_ = 0;
 171     //! Number of local atoms.
 172     int numHomeAtoms_ = 0;
 173     //! Atoms masses.
 174     gmx::ArrayRef<const real> masses_;
 175     //! Inverse masses.
 176     gmx::ArrayRef<const real> inverseMasses_;
 177     //! If there are atoms with perturbed mass (for FEP).
 178     bool hasMassPerturbedAtoms_;
 179     //! FEP lambda value.
 180     real lambda_;
 181     //! Freeze groups data
 182     gmx::ArrayRef<const unsigned short> cFREEZE_;
 183     //! Whether we need to do pbc for handling bonds.
 184     bool pbcHandlingRequired_ = false;
 185
 186     //! Logging support.
 187     FILE* log = nullptr;
 188     //! Communication support.
 189     const t_commrec* cr = nullptr;
 190     //! Multi-sim support.
 191     const gmx_multisim_t* ms = nullptr;
 192     //! Pulling code object, if any.
 193     pull_t* pull_work = nullptr;
 194     /*!\brief Input options.
 195      *
 196      * \todo Replace with IMdpOptions */
 197     const t_inputrec& ir;
 198     //! Flop counting support.
 199     t_nrnb* nrnb = nullptr;
 200     //! Tracks wallcycle usage.
 201     gmx_wallcycle* wcycle;
 202 };
 203
 204 Constraints::~Constraints() = default;
 205
 206 int Constraints::numFlexibleConstraints() const
 207 {
 208     return impl_->nflexcon;
 209 }
 210
 211 bool Constraints::havePerturbedConstraints() const
 212 {
 213     const gmx_ffparams_t& ffparams = impl_->mtop.ffparams;
 214
 215     for (size_t i = 0; i < ffparams.functype.size(); i++)
 216     {
 217         if ((ffparams.functype[i] == F_CONSTR || ffparams.functype[i] == F_CONSTRNC)
 218             && ffparams.iparams[i].constr.dA != ffparams.iparams[i].constr.dB)
 219         {
 220             return true;
 221         }
 222     }
 223
 224     return false;
 225 }
 226
 227 //! Clears constraint quantities for atoms in nonlocal region.
 228 static void clear_constraint_quantity_nonlocal(const gmx_domdec_t& dd, ArrayRef<RVec> q)
 229 {
 230     int nonlocal_at_start, nonlocal_at_end;
 231
 232     dd_get_constraint_range(dd, &nonlocal_at_start, &nonlocal_at_end);
 233
 234     for (int at = nonlocal_at_start; at < nonlocal_at_end; at++)
 235     {
 236         clear_rvec(q[at]);
 237     }
 238 }
 239
 240 void too_many_constraint_warnings(ConstraintAlgorithm eConstrAlg, int warncount)
 241 {
 242     gmx_fatal(FARGS,
 243               "Too many %s warnings (%d)\n"
 244               "If you know what you are doing you can %s"
 245               "set the environment variable GMX_MAXCONSTRWARN to -1,\n"
 246               "but normally it is better to fix the problem",
 247               (eConstrAlg == ConstraintAlgorithm::Lincs) ? "LINCS" : "SETTLE",
 248               warncount,
 249               (eConstrAlg == ConstraintAlgorithm::Lincs)
 250                       ? "adjust the lincs warning threshold in your mdp file\nor "
 251                       : "\n");
 252 }
 253
 254 //! Writes out coordinates.
 255 static void write_constr_pdb(const char*          fn,
 256                              const char*          title,
 257                              const gmx_mtop_t&    mtop,
 258                              int                  start,
 259                              int                  homenr,
 260                              const t_commrec*     cr,
 261                              ArrayRef<const RVec> x,
 262                              const matrix         box)
 263 {
 264     char          fname[STRLEN];
 265     FILE*         out;
 266     int           dd_ac0 = 0, dd_ac1 = 0, i, ii, resnr;
 267     gmx_domdec_t* dd;
 268     const char *  anm, *resnm;
 269
 270     dd = nullptr;
 271     if (DOMAINDECOMP(cr))
 272     {
 273         dd = cr->dd;
 274         dd_get_constraint_range(*dd, &dd_ac0, &dd_ac1);
 275         start  = 0;
 276         homenr = dd_ac1;
 277     }
 278
 279     if (PAR(cr))
 280     {
 281         sprintf(fname, "%s_n%d.pdb", fn, cr->sim_nodeid);
 282     }
 283     else
 284     {
 285         sprintf(fname, "%s.pdb", fn);
 286     }
 287
 288     out = gmx_fio_fopen(fname, "w");
 289
 290     fprintf(out, "TITLE     %s\n", title);
 291     gmx_write_pdb_box(out, PbcType::Unset, box);
 292     int molb = 0;
 293     for (i = start; i < start + homenr; i++)
 294     {
 295         if (dd != nullptr)
 296         {
 297             if (i >= dd_numHomeAtoms(*dd) && i < dd_ac0)
 298             {
 299                 continue;
 300             }
 301             ii = dd->globalAtomIndices[i];
 302         }
 303         else
 304         {
 305             ii = i;
 306         }
 307         mtopGetAtomAndResidueName(mtop, ii, &molb, &anm, &resnr, &resnm, nullptr);
 308         gmx_fprintf_pdb_atomline(out,
 309                                  PdbRecordType::Atom,
 310                                  ii + 1,
 311                                  anm,
 312                                  ' ',
 313                                  resnm,
 314                                  ' ',
 315                                  resnr,
 316                                  ' ',
 317                                  10 * x[i][XX],
 318                                  10 * x[i][YY],
 319                                  10 * x[i][ZZ],
 320                                  1.0,
 321                                  0.0,
 322                                  "");
 323     }
 324     fprintf(out, "TER\n");
 325
 326     gmx_fio_fclose(out);
 327 }
 328
 329 //! Writes out domain contents to help diagnose crashes.
 330 static void dump_confs(FILE*                log,
 331                        int64_t              step,
 332                        const gmx_mtop_t&    mtop,
 333                        int                  start,
 334                        int                  homenr,
 335                        const t_commrec*     cr,
 336                        ArrayRef<const RVec> x,
 337                        ArrayRef<const RVec> xprime,
 338                        const matrix         box)
 339 {
 340     char buf[STRLEN], buf2[22];
 341
 342     char* env = getenv("GMX_SUPPRESS_DUMP");
 343     if (env)
 344     {
 345         return;
 346     }
 347
 348     sprintf(buf, "step%sb", gmx_step_str(step, buf2));
 349     write_constr_pdb(buf, "initial coordinates", mtop, start, homenr, cr, x, box);
 350     sprintf(buf, "step%sc", gmx_step_str(step, buf2));
 351     write_constr_pdb(buf, "coordinates after constraining", mtop, start, homenr, cr, xprime, box);
 352     if (log)
 353     {
 354         fprintf(log, "Wrote pdb files with previous and current coordinates\n");
 355     }
 356     fprintf(stderr, "Wrote pdb files with previous and current coordinates\n");
 357 }
 358
 359 bool Constraints::apply(bool                      bLog,
 360                         bool                      bEner,
 361                         int64_t                   step,
 362                         int                       delta_step,
 363                         real                      step_scaling,
 364                         ArrayRefWithPadding<RVec> x,
 365                         ArrayRefWithPadding<RVec> xprime,
 366                         ArrayRef<RVec>            min_proj,
 367                         const matrix              box,
 368                         real                      lambda,
 369                         real*                     dvdlambda,
 370                         ArrayRefWithPadding<RVec> v,
 371                         bool                      computeVirial,
 372                         tensor                    constraintsVirial,
 373                         ConstraintVariable        econq)
 374 {
 375     return impl_->apply(bLog,
 376                         bEner,
 377                         step,
 378                         delta_step,
 379                         step_scaling,
 380                         std::move(x),
 381                         std::move(xprime),
 382                         min_proj,
 383                         box,
 384                         lambda,
 385                         dvdlambda,
 386                         std::move(v),
 387                         computeVirial,
 388                         constraintsVirial,
 389                         econq);
 390 }
 391
 392 bool Constraints::Impl::apply(bool                      bLog,
 393                               bool                      bEner,
 394                               int64_t                   step,
 395                               int                       delta_step,
 396                               real                      step_scaling,
 397                               ArrayRefWithPadding<RVec> x,
 398                               ArrayRefWithPadding<RVec> xprime,
 399                               ArrayRef<RVec>            min_proj,
 400                               const matrix              box,
 401                               real                      lambda,
 402                               real*                     dvdlambda,
 403                               ArrayRefWithPadding<RVec> v,
 404                               bool                      computeVirial,
 405                               tensor                    constraintsVirial,
 406                               ConstraintVariable        econq)
 407 {
 408     bool  bOK, bDump;
 409     int   start;
 410     real  scaled_delta_t;
 411     real  invdt, vir_fac = 0, t;
 412     int   nsettle;
 413     t_pbc pbc, *pbc_null;
 414     char  buf[22];
 415     int   nth;
 416
 417     wallcycle_start(wcycle, WallCycleCounter::Constr);
 418
 419     if (econq == ConstraintVariable::ForceDispl && !EI_ENERGY_MINIMIZATION(ir.eI))
 420     {
 421         gmx_incons(
 422                 "constrain called for forces displacements while not doing energy minimization, "
 423                 "can not do this while the LINCS and SETTLE constraint connection matrices are "
 424                 "mass weighted");
 425     }
 426
 427     bOK   = TRUE;
 428     bDump = FALSE;
 429
 430     start = 0;
 431
 432     scaled_delta_t = step_scaling * ir.delta_t;
 433
 434     /* Prepare time step for use in constraint implementations, and
 435        avoid generating inf when ir.delta_t = 0. */
 436     if (ir.delta_t == 0)
 437     {
 438         invdt = 0.0;
 439     }
 440     else
 441     {
 442         invdt = 1.0 / scaled_delta_t;
 443     }
 444
 445     if (ir.efep != FreeEnergyPerturbationType::No && EI_DYNAMICS(ir.eI))
 446     {
 447         /* Set the constraint lengths for the step at which this configuration
 448          * is meant to be. The invmasses should not be changed.
 449          */
 450         lambda += delta_step * ir.fepvals->delta_lambda;
 451     }
 452
 453     if (computeVirial)
 454     {
 455         clear_mat(constraintsVirial);
 456     }
 457     const InteractionList& settle = idef->il[F_SETTLE];
 458     nsettle                       = settle.size() / (1 + NRAL(F_SETTLE));
 459
 460     if (nsettle > 0)
 461     {
 462         nth = gmx_omp_nthreads_get(ModuleMultiThread::Settle);
 463     }
 464     else
 465     {
 466         nth = 1;
 467     }
 468
 469     /* We do not need full pbc when constraints do not cross update groups
 470      * i.e. when dd->constraint_comm==NULL.
 471      * Note that PBC for constraints is different from PBC for bondeds.
 472      * For constraints there is both forward and backward communication.
 473      */
 474     if (ir.pbcType != PbcType::No && (cr->dd || pbcHandlingRequired_)
 475         && !(cr->dd && cr->dd->constraint_comm == nullptr))
 476     {
 477         /* With pbc=screw the screw has been changed to a shift
 478          * by the constraint coordinate communication routine,
 479          * so that here we can use normal pbc.
 480          */
 481         pbc_null = set_pbc_dd(&pbc, ir.pbcType, DOMAINDECOMP(cr) ? cr->dd->numCells : nullptr, FALSE, box);
 482     }
 483     else
 484     {
 485         pbc_null = nullptr;
 486     }
 487
 488     /* Communicate the coordinates required for the non-local constraints
 489      * for LINCS and/or SETTLE.
 490      */
 491     if (cr->dd)
 492     {
 493         dd_move_x_constraints(cr->dd,
 494                               box,
 495                               x.unpaddedArrayRef(),
 496                               xprime.unpaddedArrayRef(),
 497                               econq == ConstraintVariable::Positions);
 498
 499         if (!v.empty())
 500         {
 501             /* We need to initialize the non-local components of v.
 502              * We never actually use these values, but we do increment them,
 503              * so we should avoid uninitialized variables and overflows.
 504              */
 505             clear_constraint_quantity_nonlocal(*cr->dd, v.unpaddedArrayRef());
 506         }
 507     }
 508
 509     if (lincsd != nullptr)
 510     {
 511         bOK = constrain_lincs(bLog || bEner,
 512                               ir,
 513                               step,
 514                               lincsd,
 515                               inverseMasses_,
 516                               cr,
 517                               ms,
 518                               x,
 519                               xprime,
 520                               min_proj,
 521                               box,
 522                               pbc_null,
 523                               hasMassPerturbedAtoms_,
 524                               lambda,
 525                               dvdlambda,
 526                               invdt,
 527                               v.unpaddedArrayRef(),
 528                               computeVirial,
 529                               constraintsVirial,
 530                               econq,
 531                               nrnb,
 532                               maxwarn,
 533                               &warncount_lincs);
 534         if (!bOK && maxwarn < INT_MAX)
 535         {
 536             if (log != nullptr)
 537             {
 538                 fprintf(log,
 539                         "Constraint error in algorithm %s at step %s\n",
 540                         enumValueToString(ConstraintAlgorithm::Lincs),
 541                         gmx_step_str(step, buf));
 542             }
 543             bDump = TRUE;
 544         }
 545     }
 546
 547     if (shaked != nullptr)
 548     {
 549         bOK = constrain_shake(log,
 550                               shaked.get(),
 551                               inverseMasses_,
 552                               *idef,
 553                               ir,
 554                               x.unpaddedArrayRef(),
 555                               xprime.unpaddedArrayRef(),
 556                               min_proj,
 557                               pbc_null,
 558                               nrnb,
 559                               lambda,
 560                               dvdlambda,
 561                               invdt,
 562                               v.unpaddedArrayRef(),
 563                               computeVirial,
 564                               constraintsVirial,
 565                               maxwarn < INT_MAX,
 566                               econq);
 567
 568         if (!bOK && maxwarn < INT_MAX)
 569         {
 570             if (log != nullptr)
 571             {
 572                 fprintf(log,
 573                         "Constraint error in algorithm %s at step %s\n",
 574                         enumValueToString(ConstraintAlgorithm::Shake),
 575                         gmx_step_str(step, buf));
 576             }
 577             bDump = TRUE;
 578         }
 579     }
 580
 581     if (nsettle > 0)
 582     {
 583         bool bSettleErrorHasOccurred0 = false;
 584
 585         switch (econq)
 586         {
 587             case ConstraintVariable::Positions:
 588 #pragma omp parallel for num_threads(nth) schedule(static)
 589                 for (int th = 0; th < nth; th++)
 590                 {
 591                     try
 592                     {
 593                         if (th > 0)
 594                         {
 595                             clear_mat(threadConstraintsVirial[th]);
 596                         }
 597
 598                         csettle(*settled,
 599                                 nth,
 600                                 th,
 601                                 pbc_null,
 602                                 x,
 603                                 xprime,
 604                                 invdt,
 605                                 v,
 606                                 computeVirial,
 607                                 th == 0 ? constraintsVirial : threadConstraintsVirial[th],
 608                                 th == 0 ? &bSettleErrorHasOccurred0 : &bSettleErrorHasOccurred[th]);
 609                     }
 610                     GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 611                 }
 612                 inc_nrnb(nrnb, eNR_SETTLE, nsettle);
 613                 if (!v.empty())
 614                 {
 615                     inc_nrnb(nrnb, eNR_CONSTR_V, nsettle * 3);
 616                 }
 617                 if (computeVirial)
 618                 {
 619                     inc_nrnb(nrnb, eNR_CONSTR_VIR, nsettle * 3);
 620                 }
 621                 break;
 622             case ConstraintVariable::Velocities:
 623             case ConstraintVariable::Derivative:
 624             case ConstraintVariable::Force:
 625             case ConstraintVariable::ForceDispl:
 626 #pragma omp parallel for num_threads(nth) schedule(static)
 627                 for (int th = 0; th < nth; th++)
 628                 {
 629                     try
 630                     {
 631                         int calcvir_atom_end;
 632
 633                         if (!computeVirial)
 634                         {
 635                             calcvir_atom_end = 0;
 636                         }
 637                         else
 638                         {
 639                             calcvir_atom_end = numHomeAtoms_;
 640                         }
 641
 642                         if (th > 0)
 643                         {
 644                             clear_mat(threadConstraintsVirial[th]);
 645                         }
 646
 647                         int start_th = (nsettle * th) / nth;
 648                         int end_th   = (nsettle * (th + 1)) / nth;
 649
 650                         if (start_th >= 0 && end_th - start_th > 0)
 651                         {
 652                             settle_proj(*settled,
 653                                         econq,
 654                                         end_th - start_th,
 655                                         settle.iatoms.data() + start_th * (1 + NRAL(F_SETTLE)),
 656                                         pbc_null,
 657                                         x.unpaddedArrayRef(),
 658                                         xprime.unpaddedArrayRef(),
 659                                         min_proj,
 660                                         calcvir_atom_end,
 661                                         th == 0 ? constraintsVirial : threadConstraintsVirial[th]);
 662                         }
 663                     }
 664                     GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 665                 }
 666                 /* This is an overestimate */
 667                 inc_nrnb(nrnb, eNR_SETTLE, nsettle);
 668                 break;
 669             case ConstraintVariable::Deriv_FlexCon:
 670                 /* Nothing to do, since the are no flexible constraints in settles */
 671                 break;
 672             default: gmx_incons("Unknown constraint quantity for settle");
 673         }
 674
 675         if (computeVirial)
 676         {
 677             /* Reduce the virial contributions over the threads */
 678             for (int th = 1; th < nth; th++)
 679             {
 680                 m_add(constraintsVirial, threadConstraintsVirial[th], constraintsVirial);
 681             }
 682         }
 683
 684         if (econq == ConstraintVariable::Positions)
 685         {
 686             for (int th = 1; th < nth; th++)
 687             {
 688                 bSettleErrorHasOccurred0 = bSettleErrorHasOccurred0 || bSettleErrorHasOccurred[th];
 689             }
 690
 691             if (bSettleErrorHasOccurred0)
 692             {
 693                 char buf[STRLEN];
 694                 sprintf(buf,
 695                         "\nstep "
 696                         "%" PRId64
 697                         ": One or more water molecules can not be settled.\n"
 698                         "Check for bad contacts and/or reduce the timestep if appropriate.\n",
 699                         step);
 700                 if (log)
 701                 {
 702                     fprintf(log, "%s", buf);
 703                 }
 704                 fprintf(stderr, "%s", buf);
 705                 warncount_settle++;
 706                 if (warncount_settle > maxwarn)
 707                 {
 708                     too_many_constraint_warnings(ConstraintAlgorithm::Count, warncount_settle);
 709                 }
 710                 bDump = TRUE;
 711
 712                 bOK = FALSE;
 713             }
 714         }
 715     }
 716
 717     if (computeVirial)
 718     {
 719         /* The normal uses of constrain() pass step_scaling = 1.0.
 720          * The call to constrain() for SD1 that passes step_scaling =
 721          * 0.5 also passes vir = NULL, so cannot reach this
 722          * assertion. This assertion should remain until someone knows
 723          * that this path works for their intended purpose, and then
 724          * they can use scaled_delta_t instead of ir.delta_t
 725          * below. */
 726         assert(gmx_within_tol(step_scaling, 1.0, GMX_REAL_EPS));
 727         switch (econq)
 728         {
 729             case ConstraintVariable::Positions: vir_fac = 0.5 / (ir.delta_t * ir.delta_t); break;
 730             case ConstraintVariable::Velocities: vir_fac = 0.5 / ir.delta_t; break;
 731             case ConstraintVariable::Force:
 732             case ConstraintVariable::ForceDispl: vir_fac = 0.5; break;
 733             default: gmx_incons("Unsupported constraint quantity for virial");
 734         }
 735
 736         if (EI_VV(ir.eI))
 737         {
 738             vir_fac *= 2; /* only constraining over half the distance here */
 739         }
 740         for (int i = 0; i < DIM; i++)
 741         {
 742             for (int j = 0; j < DIM; j++)
 743             {
 744                 constraintsVirial[i][j] *= vir_fac;
 745             }
 746         }
 747     }
 748
 749     if (bDump)
 750     {
 751         dump_confs(log, step, mtop, start, numHomeAtoms_, cr, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(), box);
 752     }
 753
 754     if (econq == ConstraintVariable::Positions)
 755     {
 756         if (ir.bPull && pull_have_constraint(*pull_work))
 757         {
 758             if (EI_DYNAMICS(ir.eI))
 759             {
 760                 t = ir.init_t + (step + delta_step) * ir.delta_t;
 761             }
 762             else
 763             {
 764                 t = ir.init_t;
 765             }
 766             set_pbc(&pbc, ir.pbcType, box);
 767             pull_constraint(pull_work,
 768                             masses_,
 769                             &pbc,
 770                             cr,
 771                             ir.delta_t,
 772                             t,
 773                             x.unpaddedArrayRef(),
 774                             xprime.unpaddedArrayRef(),
 775                             v.unpaddedArrayRef(),
 776                             constraintsVirial);
 777         }
 778         if (ed && delta_step > 0)
 779         {
 780             /* apply the essential dynamics constraints here */
 781             do_edsam(&ir, step, cr, xprime.unpaddedArrayRef(), v.unpaddedArrayRef(), box, ed);
 782         }
 783     }
 784     wallcycle_stop(wcycle, WallCycleCounter::Constr);
 785
 786     const bool haveVelocities = (!v.empty() || econq == ConstraintVariable::Velocities);
 787     if (haveVelocities && !cFREEZE_.empty())
 788     {
 789         /* Set the velocities of frozen dimensions to zero */
 790         ArrayRef<RVec> vRef;
 791         if (econq == ConstraintVariable::Velocities)
 792         {
 793             vRef = xprime.unpaddedArrayRef();
 794         }
 795         else
 796         {
 797             vRef = v.unpaddedArrayRef();
 798         }
 799
 800         int gmx_unused numThreads = gmx_omp_nthreads_get(ModuleMultiThread::Update);
 801
 802 #pragma omp parallel for num_threads(numThreads) schedule(static)
 803         for (int i = 0; i < numHomeAtoms_; i++)
 804         {
 805             int freezeGroup = cFREEZE_[i];
 806
 807             for (int d = 0; d < DIM; d++)
 808             {
 809                 if (ir.opts.nFreeze[freezeGroup][d])
 810                 {
 811                     vRef[i][d] = 0;
 812                 }
 813             }
 814         }
 815     }
 816
 817     return bOK;
 818 } // namespace gmx
 819
 820 ArrayRef<real> Constraints::rmsdData() const
 821 {
 822     if (impl_->lincsd)
 823     {
 824         return lincs_rmsdData(impl_->lincsd);
 825     }
 826     else
 827     {
 828         return {};
 829     }
 830 }
 831
 832 real Constraints::rmsd() const
 833 {
 834     if (impl_->lincsd)
 835     {
 836         return lincs_rmsd(impl_->lincsd);
 837     }
 838     else
 839     {
 840         return 0;
 841     }
 842 }
 843
 844 int Constraints::numConstraintsTotal()
 845 {
 846     return impl_->ncon_tot;
 847 }
 848
 849 FlexibleConstraintTreatment flexibleConstraintTreatment(bool haveDynamicsIntegrator)
 850 {
 851     if (haveDynamicsIntegrator)
 852     {
 853         return FlexibleConstraintTreatment::Include;
 854     }
 855     else
 856     {
 857         return FlexibleConstraintTreatment::Exclude;
 858     }
 859 }
 860
 861 /*! \brief Returns a block struct to go from atoms to constraints
 862  *
 863  * The block struct will contain constraint indices with lower indices
 864  * directly matching the order in F_CONSTR and higher indices matching
 865  * the order in F_CONSTRNC offset by the number of constraints in F_CONSTR.
 866  *
 867  * \param[in]  numAtoms  The number of atoms to construct the list for
 868  * \param[in]  ilists    The interaction lists, size F_NRE
 869  * \param[in]  iparams   Interaction parameters, can be null when
 870  *                       \p flexibleConstraintTreatment==Include
 871  * \param[in]  flexibleConstraintTreatment  The flexible constraint treatment,
 872  *                                          see enum above
 873  *
 874  * \returns a block struct with all constraints for each atom
 875  */
 876 static ListOfLists<int> makeAtomsToConstraintsList(int                             numAtoms,
 877                                                    ArrayRef<const InteractionList> ilists,
 878                                                    ArrayRef<const t_iparams>       iparams,
 879                                                    FlexibleConstraintTreatment flexibleConstraintTreatment)
 880 {
 881     GMX_ASSERT(flexibleConstraintTreatment == FlexibleConstraintTreatment::Include || !iparams.empty(),
 882                "With flexible constraint detection we need valid iparams");
 883
 884     std::vector<int> count(numAtoms);
 885
 886     for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
 887     {
 888         const InteractionList& ilist  = ilists[ftype];
 889         const int              stride = 1 + NRAL(ftype);
 890         for (int i = 0; i < ilist.size(); i += stride)
 891         {
 892             if (flexibleConstraintTreatment == FlexibleConstraintTreatment::Include
 893                 || !isConstraintFlexible(iparams, ilist.iatoms[i]))
 894             {
 895                 for (int j = 1; j < 3; j++)
 896                 {
 897                     int a = ilist.iatoms[i + j];
 898                     count[a]++;
 899                 }
 900             }
 901         }
 902     }
 903
 904     std::vector<int> listRanges(numAtoms + 1);
 905     for (int a = 0; a < numAtoms; a++)
 906     {
 907         listRanges[a + 1] = listRanges[a] + count[a];
 908         count[a]          = 0;
 909     }
 910     std::vector<int> elements(listRanges[numAtoms]);
 911
 912     /* The F_CONSTRNC constraints have constraint numbers
 913      * that continue after the last F_CONSTR constraint.
 914      */
 915     int numConstraints = 0;
 916     for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
 917     {
 918         const InteractionList& ilist  = ilists[ftype];
 919         const int              stride = 1 + NRAL(ftype);
 920         for (int i = 0; i < ilist.size(); i += stride)
 921         {
 922             if (flexibleConstraintTreatment == FlexibleConstraintTreatment::Include
 923                 || !isConstraintFlexible(iparams, ilist.iatoms[i]))
 924             {
 925                 for (int j = 1; j < 3; j++)
 926                 {
 927                     const int a                          = ilist.iatoms[i + j];
 928                     elements[listRanges[a] + count[a]++] = numConstraints;
 929                 }
 930             }
 931             numConstraints++;
 932         }
 933     }
 934
 935     return ListOfLists<int>(std::move(listRanges), std::move(elements));
 936 }
 937
 938 ListOfLists<int> make_at2con(int                             numAtoms,
 939                              ArrayRef<const InteractionList> ilist,
 940                              ArrayRef<const t_iparams>       iparams,
 941                              FlexibleConstraintTreatment     flexibleConstraintTreatment)
 942 {
 943     return makeAtomsToConstraintsList(numAtoms, ilist, iparams, flexibleConstraintTreatment);
 944 }
 945
 946 ListOfLists<int> make_at2con(const gmx_moltype_t&           moltype,
 947                              gmx::ArrayRef<const t_iparams> iparams,
 948                              FlexibleConstraintTreatment    flexibleConstraintTreatment)
 949 {
 950     return makeAtomsToConstraintsList(
 951             moltype.atoms.nr, makeConstArrayRef(moltype.ilist), iparams, flexibleConstraintTreatment);
 952 }
 953
 954 //! Return the number of flexible constraints in the \c ilist and \c iparams.
 955 int countFlexibleConstraints(ArrayRef<const InteractionList> ilist, ArrayRef<const t_iparams> iparams)
 956 {
 957     int nflexcon = 0;
 958     for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
 959     {
 960         const int numIatomsPerConstraint = 3;
 961         for (int i = 0; i < ilist[ftype].size(); i += numIatomsPerConstraint)
 962         {
 963             const int type = ilist[ftype].iatoms[i];
 964             if (iparams[type].constr.dA == 0 && iparams[type].constr.dB == 0)
 965             {
 966                 nflexcon++;
 967             }
 968         }
 969     }
 970
 971     return nflexcon;
 972 }
 973
 974 //! Returns the index of the settle to which each atom belongs.
 975 static std::vector<int> make_at2settle(int natoms, const InteractionList& ilist)
 976 {
 977     /* Set all to no settle */
 978     std::vector<int> at2s(natoms, -1);
 979
 980     const int stride = 1 + NRAL(F_SETTLE);
 981
 982     for (int s = 0; s < ilist.size(); s += stride)
 983     {
 984         at2s[ilist.iatoms[s + 1]] = s / stride;
 985         at2s[ilist.iatoms[s + 2]] = s / stride;
 986         at2s[ilist.iatoms[s + 3]] = s / stride;
 987     }
 988
 989     return at2s;
 990 }
 991
 992 void Constraints::Impl::setConstraints(gmx_localtop_t*                     top,
 993                                        int                                 numAtoms,
 994                                        int                                 numHomeAtoms,
 995                                        gmx::ArrayRef<const real>           masses,
 996                                        gmx::ArrayRef<const real>           inverseMasses,
 997                                        const bool                          hasMassPerturbedAtoms,
 998                                        const real                          lambda,
 999                                        gmx::ArrayRef<const unsigned short> cFREEZE)
1000 {
1001     numAtoms_              = numAtoms;
1002     numHomeAtoms_          = numHomeAtoms;
1003     masses_                = masses;
1004     inverseMasses_         = inverseMasses;
1005     hasMassPerturbedAtoms_ = hasMassPerturbedAtoms;
1006     lambda_                = lambda;
1007     cFREEZE_               = cFREEZE;
1008
1009     idef = &top->idef;
1010
1011     if (ncon_tot > 0)
1012     {
1013         /* With DD we might also need to call LINCS on a domain no constraints for
1014          * communicating coordinates to other nodes that do have constraints.
1015          */
1016         if (ir.eConstrAlg == ConstraintAlgorithm::Lincs)
1017         {
1018             set_lincs(*idef, numAtoms_, inverseMasses_, lambda_, EI_DYNAMICS(ir.eI), cr, lincsd);
1019         }
1020         if (ir.eConstrAlg == ConstraintAlgorithm::Shake)
1021         {
1022             if (cr->dd)
1023             {
1024                 // We are using the local topology, so there are only
1025                 // F_CONSTR constraints.
1026                 GMX_RELEASE_ASSERT(idef->il[F_CONSTRNC].empty(),
1027                                    "Here we should not have no-connect constraints");
1028                 make_shake_sblock_dd(shaked.get(), idef->il[F_CONSTR]);
1029             }
1030             else
1031             {
1032                 make_shake_sblock_serial(shaked.get(), &top->idef, numAtoms_);
1033             }
1034         }
1035     }
1036
1037     if (settled)
1038     {
1039         settled->setConstraints(idef->il[F_SETTLE], numHomeAtoms_, masses_, inverseMasses_);
1040     }
1041
1042     /* Make a selection of the local atoms for essential dynamics */
1043     if (ed && cr->dd)
1044     {
1045         dd_make_local_ed_indices(cr->dd, ed);
1046     }
1047 }
1048
1049 void Constraints::setConstraints(gmx_localtop_t*                     top,
1050                                  const int                           numAtoms,
1051                                  const int                           numHomeAtoms,
1052                                  gmx::ArrayRef<const real>           masses,
1053                                  gmx::ArrayRef<const real>           inverseMasses,
1054                                  const bool                          hasMassPerturbedAtoms,
1055                                  const real                          lambda,
1056                                  gmx::ArrayRef<const unsigned short> cFREEZE)
1057 {
1058     impl_->setConstraints(
1059             top, numAtoms, numHomeAtoms, masses, inverseMasses, hasMassPerturbedAtoms, lambda, cFREEZE);
1060 }
1061
1062 /*! \brief Makes a per-moleculetype container of mappings from atom
1063  * indices to constraint indices.
1064  *
1065  * Note that flexible constraints are only enabled with a dynamical integrator. */
1066 static std::vector<ListOfLists<int>> makeAtomToConstraintMappings(const gmx_mtop_t& mtop,
1067                                                                   FlexibleConstraintTreatment flexibleConstraintTreatment)
1068 {
1069     std::vector<ListOfLists<int>> mapping;
1070     mapping.reserve(mtop.moltype.size());
1071     for (const gmx_moltype_t& moltype : mtop.moltype)
1072     {
1073         mapping.push_back(make_at2con(moltype, mtop.ffparams.iparams, flexibleConstraintTreatment));
1074     }
1075     return mapping;
1076 }
1077
1078 Constraints::Constraints(const gmx_mtop_t&     mtop,
1079                          const t_inputrec&     ir,
1080                          pull_t*               pull_work,
1081                          FILE*                 log,
1082                          const t_commrec*      cr,
1083                          const gmx_multisim_t* ms,
1084                          t_nrnb*               nrnb,
1085                          gmx_wallcycle*        wcycle,
1086                          bool                  pbcHandlingRequired,
1087                          int                   numConstraints,
1088                          int                   numSettles) :
1089     impl_(new Impl(mtop, ir, pull_work, log, cr, ms, nrnb, wcycle, pbcHandlingRequired, numConstraints, numSettles))
1090 {
1091 }
1092
1093 Constraints::Impl::Impl(const gmx_mtop_t&     mtop_p,
1094                         const t_inputrec&     ir_p,
1095                         pull_t*               pull_work,
1096                         FILE*                 log_p,
1097                         const t_commrec*      cr_p,
1098                         const gmx_multisim_t* ms_p,
1099                         t_nrnb*               nrnb_p,
1100                         gmx_wallcycle*        wcycle_p,
1101                         bool                  pbcHandlingRequired,
1102                         int                   numConstraints,
1103                         int                   numSettles) :
1104     ncon_tot(numConstraints),
1105     mtop(mtop_p),
1106     pbcHandlingRequired_(pbcHandlingRequired),
1107     log(log_p),
1108     cr(cr_p),
1109     ms(ms_p),
1110     pull_work(pull_work),
1111     ir(ir_p),
1112     nrnb(nrnb_p),
1113     wcycle(wcycle_p)
1114 {
1115     if (numConstraints + numSettles > 0 && ir.epc == PressureCoupling::Mttk)
1116     {
1117         gmx_fatal(FARGS, "Constraints are not implemented with MTTK pressure control.");
1118     }
1119
1120     nflexcon = 0;
1121     if (numConstraints > 0)
1122     {
1123         at2con_mt = makeAtomToConstraintMappings(mtop, flexibleConstraintTreatment(EI_DYNAMICS(ir.eI)));
1124
1125         for (const gmx_molblock_t& molblock : mtop.molblock)
1126         {
1127             int count = countFlexibleConstraints(mtop.moltype[molblock.type].ilist, mtop.ffparams.iparams);
1128             nflexcon += molblock.nmol * count;
1129         }
1130
1131         if (nflexcon > 0)
1132         {
1133             if (log)
1134             {
1135                 fprintf(log, "There are %d flexible constraints\n", nflexcon);
1136                 if (ir.fc_stepsize == 0)
1137                 {
1138                     fprintf(log,
1139                             "\n"
1140                             "WARNING: step size for flexible constraining = 0\n"
1141                             "         All flexible constraints will be rigid.\n"
1142                             "         Will try to keep all flexible constraints at their original "
1143                             "length,\n"
1144                             "         but the lengths may exhibit some drift.\n\n");
1145                     nflexcon = 0;
1146                 }
1147             }
1148             if (nflexcon > 0)
1149             {
1150                 please_cite(log, "Hess2002");
1151             }
1152         }
1153
1154         if (ir.eConstrAlg == ConstraintAlgorithm::Lincs)
1155         {
1156             lincsd = init_lincs(log,
1157                                 mtop,
1158                                 nflexcon,
1159                                 at2con_mt,
1160                                 DOMAINDECOMP(cr) && ddHaveSplitConstraints(*cr->dd),
1161                                 ir.nLincsIter,
1162                                 ir.nProjOrder);
1163         }
1164
1165         if (ir.eConstrAlg == ConstraintAlgorithm::Shake)
1166         {
1167             if (DOMAINDECOMP(cr) && ddHaveSplitConstraints(*cr->dd))
1168             {
1169                 gmx_fatal(FARGS,
1170                           "SHAKE is not supported with domain decomposition and constraint that "
1171                           "cross domain boundaries, use LINCS");
1172             }
1173             if (nflexcon)
1174             {
1175                 gmx_fatal(FARGS,
1176                           "For this system also velocities and/or forces need to be constrained, "
1177                           "this can not be done with SHAKE, you should select LINCS");
1178             }
1179             please_cite(log, "Ryckaert77a");
1180             if (ir.bShakeSOR)
1181             {
1182                 please_cite(log, "Barth95a");
1183             }
1184
1185             shaked = std::make_unique<shakedata>();
1186         }
1187     }
1188
1189     if (numSettles > 0)
1190     {
1191         please_cite(log, "Miyamoto92a");
1192
1193         settled = std::make_unique<SettleData>(mtop);
1194
1195         /* Make an atom to settle index for use in domain decomposition */
1196         for (size_t mt = 0; mt < mtop.moltype.size(); mt++)
1197         {
1198             at2settle_mt.emplace_back(
1199                     make_at2settle(mtop.moltype[mt].atoms.nr, mtop.moltype[mt].ilist[F_SETTLE]));
1200         }
1201
1202         /* Allocate thread-local work arrays */
1203         int nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Settle);
1204         if (nthreads > 1 && threadConstraintsVirial == nullptr)
1205         {
1206             snew(threadConstraintsVirial, nthreads);
1207             snew(bSettleErrorHasOccurred, nthreads);
1208         }
1209     }
1210
1211     maxwarn   = 999;
1212     char* env = getenv("GMX_MAXCONSTRWARN");
1213     if (env)
1214     {
1215         maxwarn = 0;
1216         sscanf(env, "%8d", &maxwarn);
1217         if (maxwarn < 0)
1218         {
1219             maxwarn = INT_MAX;
1220         }
1221         if (log)
1222         {
1223             fprintf(log, "Setting the maximum number of constraint warnings to %d\n", maxwarn);
1224         }
1225         if (MASTER(cr))
1226         {
1227             fprintf(stderr, "Setting the maximum number of constraint warnings to %d\n", maxwarn);
1228         }
1229     }
1230     warncount_lincs  = 0;
1231     warncount_settle = 0;
1232 }
1233
1234 Constraints::Impl::~Impl()
1235 {
1236     if (bSettleErrorHasOccurred != nullptr)
1237     {
1238         sfree(bSettleErrorHasOccurred);
1239     }
1240     if (threadConstraintsVirial != nullptr)
1241     {
1242         sfree(threadConstraintsVirial);
1243     }
1244     done_lincs(lincsd);
1245 }
1246
1247 void Constraints::saveEdsamPointer(gmx_edsam* ed)
1248 {
1249     impl_->ed = ed;
1250 }
1251
1252 ArrayRef<const ListOfLists<int>> Constraints::atom2constraints_moltype() const
1253 {
1254     return impl_->at2con_mt;
1255 }
1256
1257 ArrayRef<const std::vector<int>> Constraints::atom2settle_moltype() const
1258 {
1259     return impl_->at2settle_mt;
1260 }
1261
1262 void do_constrain_first(FILE*                     fplog,
1263                         gmx::Constraints*         constr,
1264                         const t_inputrec*         ir,
1265                         int                       numAtoms,
1266                         int                       numHomeAtoms,
1267                         ArrayRefWithPadding<RVec> x,
1268                         ArrayRefWithPadding<RVec> v,
1269                         const matrix              box,
1270                         real                      lambda)
1271 {
1272     int     i, m, start, end;
1273     int64_t step;
1274     real    dt = ir->delta_t;
1275     real    dvdl_dum;
1276
1277     PaddedVector<RVec> savex(numAtoms);
1278
1279     start = 0;
1280     end   = numHomeAtoms;
1281
1282     if (debug)
1283     {
1284         fprintf(debug, "vcm: start=%d, homenr=%d, end=%d\n", start, numHomeAtoms, end);
1285     }
1286     /* Do a first constrain to reset particles... */
1287     step = ir->init_step;
1288     if (fplog)
1289     {
1290         char buf[STEPSTRSIZE];
1291         fprintf(fplog, "\nConstraining the starting coordinates (step %s)\n", gmx_step_str(step, buf));
1292     }
1293     dvdl_dum = 0;
1294
1295     bool needsLogging  = true;
1296     bool computeEnergy = false;
1297     bool computeVirial = false;
1298     /* constrain the current position */
1299     constr->apply(needsLogging,
1300                   computeEnergy,
1301                   step,
1302                   0,
1303                   1.0,
1304                   x,
1305                   x,
1306                   {},
1307                   box,
1308                   lambda,
1309                   &dvdl_dum,
1310                   {},
1311                   computeVirial,
1312                   nullptr,
1313                   gmx::ConstraintVariable::Positions);
1314     if (EI_VV(ir->eI))
1315     {
1316         /* constrain the inital velocity, and save it */
1317         /* also may be useful if we need the ekin from the halfstep for velocity verlet */
1318         constr->apply(needsLogging,
1319                       computeEnergy,
1320                       step,
1321                       0,
1322                       1.0,
1323                       x,
1324                       v,
1325                       v.unpaddedArrayRef(),
1326                       box,
1327                       lambda,
1328                       &dvdl_dum,
1329                       {},
1330                       computeVirial,
1331                       nullptr,
1332                       gmx::ConstraintVariable::Velocities);
1333     }
1334     /* constrain the inital velocities at t-dt/2 */
1335     if (EI_STATE_VELOCITY(ir->eI) && ir->eI != IntegrationAlgorithm::VV)
1336     {
1337         auto subX = x.paddedArrayRef().subArray(start, end);
1338         auto subV = v.paddedArrayRef().subArray(start, end);
1339         for (i = start; (i < end); i++)
1340         {
1341             for (m = 0; (m < DIM); m++)
1342             {
1343                 /* Reverse the velocity */
1344                 subV[i][m] = -subV[i][m];
1345                 /* Store the position at t-dt in buf */
1346                 savex[i][m] = subX[i][m] + dt * subV[i][m];
1347             }
1348         }
1349         /* Shake the positions at t=-dt with the positions at t=0
1350          * as reference coordinates.
1351          */
1352         if (fplog)
1353         {
1354             char buf[STEPSTRSIZE];
1355             fprintf(fplog, "\nConstraining the coordinates at t0-dt (step %s)\n", gmx_step_str(step, buf));
1356         }
1357         dvdl_dum = 0;
1358         constr->apply(needsLogging,
1359                       computeEnergy,
1360                       step,
1361                       -1,
1362                       1.0,
1363                       x,
1364                       savex.arrayRefWithPadding(),
1365                       {},
1366                       box,
1367                       lambda,
1368                       &dvdl_dum,
1369                       v,
1370                       computeVirial,
1371                       nullptr,
1372                       gmx::ConstraintVariable::Positions);
1373
1374         for (i = start; i < end; i++)
1375         {
1376             for (m = 0; m < DIM; m++)
1377             {
1378                 /* Re-reverse the velocities */
1379                 subV[i][m] = -subV[i][m];
1380             }
1381         }
1382     }
1383 }
1384
1385 void constrain_velocities(gmx::Constraints* constr,
1386                           bool              do_log,
1387                           bool              do_ene,
1388                           int64_t           step,
1389                           t_state*          state,
1390                           real*             dvdlambda,
1391                           gmx_bool          computeVirial,
1392                           tensor            constraintsVirial)
1393 {
1394     if (constr != nullptr)
1395     {
1396         constr->apply(do_log,
1397                       do_ene,
1398                       step,
1399                       1,
1400                       1.0,
1401                       state->x.arrayRefWithPadding(),
1402                       state->v.arrayRefWithPadding(),
1403                       state->v.arrayRefWithPadding().unpaddedArrayRef(),
1404                       state->box,
1405                       state->lambda[FreeEnergyPerturbationCouplingType::Bonded],
1406                       dvdlambda,
1407                       ArrayRefWithPadding<RVec>(),
1408                       computeVirial,
1409                       constraintsVirial,
1410                       ConstraintVariable::Velocities);
1411     }
1412 }
1413
1414 void constrain_coordinates(gmx::Constraints*         constr,
1415                            bool                      do_log,
1416                            bool                      do_ene,
1417                            int64_t                   step,
1418                            t_state*                  state,
1419                            ArrayRefWithPadding<RVec> xp,
1420                            real*                     dvdlambda,
1421                            gmx_bool                  computeVirial,
1422                            tensor                    constraintsVirial)
1423 {
1424     if (constr != nullptr)
1425     {
1426         constr->apply(do_log,
1427                       do_ene,
1428                       step,
1429                       1,
1430                       1.0,
1431                       state->x.arrayRefWithPadding(),
1432                       std::move(xp),
1433                       ArrayRef<RVec>(),
1434                       state->box,
1435                       state->lambda[FreeEnergyPerturbationCouplingType::Bonded],
1436                       dvdlambda,
1437                       state->v.arrayRefWithPadding(),
1438                       computeVirial,
1439                       constraintsVirial,
1440                       ConstraintVariable::Positions);
1441     }
1442 }
1443
1444 } // namespace gmx