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          bool                  useUpdateGroups,
 108          const gmx_multisim_t* ms,
 109          t_nrnb*               nrnb,
 110          gmx_wallcycle*        wcycle_p,
 111          bool                  pbcHandlingRequired,
 112          int                   numConstraints,
 113          int                   numSettles);
 114     ~Impl();
 115     void setConstraints(gmx_localtop_t*                     top,
 116                         int                                 numAtoms,
 117                         int                                 numHomeAtoms,
 118                         gmx::ArrayRef<const real>           masses,
 119                         gmx::ArrayRef<const real>           inverseMasses,
 120                         bool                                hasMassPerturbedAtoms,
 121                         real                                lambda,
 122                         gmx::ArrayRef<const unsigned short> cFREEZE);
 123     bool apply(bool                      bLog,
 124                bool                      bEner,
 125                int64_t                   step,
 126                int                       delta_step,
 127                real                      step_scaling,
 128                ArrayRefWithPadding<RVec> x,
 129                ArrayRefWithPadding<RVec> xprime,
 130                ArrayRef<RVec>            min_proj,
 131                const matrix              box,
 132                real                      lambda,
 133                real*                     dvdlambda,
 134                ArrayRefWithPadding<RVec> v,
 135                bool                      computeVirial,
 136                tensor                    constraintsVirial,
 137                ConstraintVariable        econq);
 138     //! The total number of constraints.
 139     int ncon_tot = 0;
 140     //! The number of flexible constraints.
 141     int nflexcon = 0;
 142     //! A list of atoms to constraints for each moleculetype.
 143     std::vector<ListOfLists<int>> at2con_mt;
 144     //! A list of atoms to settles for each moleculetype
 145     std::vector<std::vector<int>> at2settle_mt;
 146     //! LINCS data.
 147     Lincs* lincsd = nullptr; // TODO this should become a unique_ptr
 148     //! SHAKE data.
 149     std::unique_ptr<shakedata> shaked;
 150     //! SETTLE data.
 151     std::unique_ptr<SettleData> settled;
 152     //! The maximum number of warnings.
 153     int maxwarn = 0;
 154     //! The number of warnings for LINCS.
 155     int warncount_lincs = 0;
 156     //! The number of warnings for SETTLE.
 157     int warncount_settle = 0;
 158     //! The essential dynamics data.
 159     gmx_edsam* ed = nullptr;
 160
 161     //! Thread-local virial contribution.
 162     tensor* threadConstraintsVirial = { nullptr };
 163     //! Did a settle error occur?
 164     bool* bSettleErrorHasOccurred = nullptr;
 165
 166     //! Pointer to the global topology - only used for printing warnings.
 167     const gmx_mtop_t& mtop;
 168     //! Parameters for the interactions in this domain.
 169     const InteractionDefinitions* idef = nullptr;
 170     //! Total number of atoms.
 171     int numAtoms_ = 0;
 172     //! Number of local atoms.
 173     int numHomeAtoms_ = 0;
 174     //! Atoms masses.
 175     gmx::ArrayRef<const real> masses_;
 176     //! Inverse masses.
 177     gmx::ArrayRef<const real> inverseMasses_;
 178     //! If there are atoms with perturbed mass (for FEP).
 179     bool hasMassPerturbedAtoms_;
 180     //! FEP lambda value.
 181     real lambda_;
 182     //! Freeze groups data
 183     gmx::ArrayRef<const unsigned short> cFREEZE_;
 184     //! Whether we need to do pbc for handling bonds.
 185     bool pbcHandlingRequired_ = false;
 186
 187     //! Logging support.
 188     FILE* log = nullptr;
 189     //! Communication support.
 190     const t_commrec* cr = nullptr;
 191     //! Multi-sim support.
 192     const gmx_multisim_t* ms = nullptr;
 193     //! Pulling code object, if any.
 194     pull_t* pull_work = nullptr;
 195     /*!\brief Input options.
 196      *
 197      * \todo Replace with IMdpOptions */
 198     const t_inputrec& ir;
 199     //! Flop counting support.
 200     t_nrnb* nrnb = nullptr;
 201     //! Tracks wallcycle usage.
 202     gmx_wallcycle* wcycle;
 203 };
 204
 205 Constraints::~Constraints() = default;
 206
 207 int Constraints::numFlexibleConstraints() const
 208 {
 209     return impl_->nflexcon;
 210 }
 211
 212 bool Constraints::havePerturbedConstraints() const
 213 {
 214     const gmx_ffparams_t& ffparams = impl_->mtop.ffparams;
 215
 216     for (size_t i = 0; i < ffparams.functype.size(); i++)
 217     {
 218         if ((ffparams.functype[i] == F_CONSTR || ffparams.functype[i] == F_CONSTRNC)
 219             && ffparams.iparams[i].constr.dA != ffparams.iparams[i].constr.dB)
 220         {
 221             return true;
 222         }
 223     }
 224
 225     return false;
 226 }
 227
 228 //! Clears constraint quantities for atoms in nonlocal region.
 229 static void clear_constraint_quantity_nonlocal(const gmx_domdec_t& dd, ArrayRef<RVec> q)
 230 {
 231     int nonlocal_at_start, nonlocal_at_end;
 232
 233     dd_get_constraint_range(dd, &nonlocal_at_start, &nonlocal_at_end);
 234
 235     for (int at = nonlocal_at_start; at < nonlocal_at_end; at++)
 236     {
 237         clear_rvec(q[at]);
 238     }
 239 }
 240
 241 void too_many_constraint_warnings(ConstraintAlgorithm eConstrAlg, int warncount)
 242 {
 243     gmx_fatal(FARGS,
 244               "Too many %s warnings (%d)\n"
 245               "If you know what you are doing you can %s"
 246               "set the environment variable GMX_MAXCONSTRWARN to -1,\n"
 247               "but normally it is better to fix the problem",
 248               (eConstrAlg == ConstraintAlgorithm::Lincs) ? "LINCS" : "SETTLE",
 249               warncount,
 250               (eConstrAlg == ConstraintAlgorithm::Lincs)
 251                       ? "adjust the lincs warning threshold in your mdp file\nor "
 252                       : "\n");
 253 }
 254
 255 //! Writes out coordinates.
 256 static void write_constr_pdb(const char*          fn,
 257                              const char*          title,
 258                              const gmx_mtop_t&    mtop,
 259                              int                  start,
 260                              int                  homenr,
 261                              const t_commrec*     cr,
 262                              ArrayRef<const RVec> x,
 263                              const matrix         box)
 264 {
 265     char          fname[STRLEN];
 266     FILE*         out;
 267     int           dd_ac0 = 0, dd_ac1 = 0, i, ii, resnr;
 268     gmx_domdec_t* dd;
 269     const char *  anm, *resnm;
 270
 271     dd = nullptr;
 272     if (DOMAINDECOMP(cr))
 273     {
 274         dd = cr->dd;
 275         dd_get_constraint_range(*dd, &dd_ac0, &dd_ac1);
 276         start  = 0;
 277         homenr = dd_ac1;
 278     }
 279
 280     if (PAR(cr))
 281     {
 282         sprintf(fname, "%s_n%d.pdb", fn, cr->sim_nodeid);
 283     }
 284     else
 285     {
 286         sprintf(fname, "%s.pdb", fn);
 287     }
 288
 289     out = gmx_fio_fopen(fname, "w");
 290
 291     fprintf(out, "TITLE     %s\n", title);
 292     gmx_write_pdb_box(out, PbcType::Unset, box);
 293     int molb = 0;
 294     for (i = start; i < start + homenr; i++)
 295     {
 296         if (dd != nullptr)
 297         {
 298             if (i >= dd_numHomeAtoms(*dd) && i < dd_ac0)
 299             {
 300                 continue;
 301             }
 302             ii = dd->globalAtomIndices[i];
 303         }
 304         else
 305         {
 306             ii = i;
 307         }
 308         mtopGetAtomAndResidueName(mtop, ii, &molb, &anm, &resnr, &resnm, nullptr);
 309         gmx_fprintf_pdb_atomline(out,
 310                                  PdbRecordType::Atom,
 311                                  ii + 1,
 312                                  anm,
 313                                  ' ',
 314                                  resnm,
 315                                  ' ',
 316                                  resnr,
 317                                  ' ',
 318                                  10 * x[i][XX],
 319                                  10 * x[i][YY],
 320                                  10 * x[i][ZZ],
 321                                  1.0,
 322                                  0.0,
 323                                  "");
 324     }
 325     fprintf(out, "TER\n");
 326
 327     gmx_fio_fclose(out);
 328 }
 329
 330 //! Writes out domain contents to help diagnose crashes.
 331 static void dump_confs(FILE*                log,
 332                        int64_t              step,
 333                        const gmx_mtop_t&    mtop,
 334                        int                  start,
 335                        int                  homenr,
 336                        const t_commrec*     cr,
 337                        ArrayRef<const RVec> x,
 338                        ArrayRef<const RVec> xprime,
 339                        const matrix         box)
 340 {
 341     char buf[STRLEN], buf2[22];
 342
 343     char* env = getenv("GMX_SUPPRESS_DUMP");
 344     if (env)
 345     {
 346         return;
 347     }
 348
 349     sprintf(buf, "step%sb", gmx_step_str(step, buf2));
 350     write_constr_pdb(buf, "initial coordinates", mtop, start, homenr, cr, x, box);
 351     sprintf(buf, "step%sc", gmx_step_str(step, buf2));
 352     write_constr_pdb(buf, "coordinates after constraining", mtop, start, homenr, cr, xprime, box);
 353     if (log)
 354     {
 355         fprintf(log, "Wrote pdb files with previous and current coordinates\n");
 356     }
 357     fprintf(stderr, "Wrote pdb files with previous and current coordinates\n");
 358 }
 359
 360 bool Constraints::apply(bool                      bLog,
 361                         bool                      bEner,
 362                         int64_t                   step,
 363                         int                       delta_step,
 364                         real                      step_scaling,
 365                         ArrayRefWithPadding<RVec> x,
 366                         ArrayRefWithPadding<RVec> xprime,
 367                         ArrayRef<RVec>            min_proj,
 368                         const matrix              box,
 369                         real                      lambda,
 370                         real*                     dvdlambda,
 371                         ArrayRefWithPadding<RVec> v,
 372                         bool                      computeVirial,
 373                         tensor                    constraintsVirial,
 374                         ConstraintVariable        econq)
 375 {
 376     return impl_->apply(bLog,
 377                         bEner,
 378                         step,
 379                         delta_step,
 380                         step_scaling,
 381                         std::move(x),
 382                         std::move(xprime),
 383                         min_proj,
 384                         box,
 385                         lambda,
 386                         dvdlambda,
 387                         std::move(v),
 388                         computeVirial,
 389                         constraintsVirial,
 390                         econq);
 391 }
 392
 393 bool Constraints::Impl::apply(bool                      bLog,
 394                               bool                      bEner,
 395                               int64_t                   step,
 396                               int                       delta_step,
 397                               real                      step_scaling,
 398                               ArrayRefWithPadding<RVec> x,
 399                               ArrayRefWithPadding<RVec> xprime,
 400                               ArrayRef<RVec>            min_proj,
 401                               const matrix              box,
 402                               real                      lambda,
 403                               real*                     dvdlambda,
 404                               ArrayRefWithPadding<RVec> v,
 405                               bool                      computeVirial,
 406                               tensor                    constraintsVirial,
 407                               ConstraintVariable        econq)
 408 {
 409     bool  bOK, bDump;
 410     int   start;
 411     real  scaled_delta_t;
 412     real  invdt, vir_fac = 0, t;
 413     int   nsettle;
 414     t_pbc pbc, *pbc_null;
 415     char  buf[22];
 416     int   nth;
 417
 418     wallcycle_start(wcycle, WallCycleCounter::Constr);
 419
 420     if (econq == ConstraintVariable::ForceDispl && !EI_ENERGY_MINIMIZATION(ir.eI))
 421     {
 422         gmx_incons(
 423                 "constrain called for forces displacements while not doing energy minimization, "
 424                 "can not do this while the LINCS and SETTLE constraint connection matrices are "
 425                 "mass weighted");
 426     }
 427
 428     bOK   = TRUE;
 429     bDump = FALSE;
 430
 431     start = 0;
 432
 433     scaled_delta_t = step_scaling * ir.delta_t;
 434
 435     /* Prepare time step for use in constraint implementations, and
 436        avoid generating inf when ir.delta_t = 0. */
 437     if (ir.delta_t == 0)
 438     {
 439         invdt = 0.0;
 440     }
 441     else
 442     {
 443         invdt = 1.0 / scaled_delta_t;
 444     }
 445
 446     if (ir.efep != FreeEnergyPerturbationType::No && EI_DYNAMICS(ir.eI))
 447     {
 448         /* Set the constraint lengths for the step at which this configuration
 449          * is meant to be. The invmasses should not be changed.
 450          */
 451         lambda += delta_step * ir.fepvals->delta_lambda;
 452     }
 453
 454     if (computeVirial)
 455     {
 456         clear_mat(constraintsVirial);
 457     }
 458     const InteractionList& settle = idef->il[F_SETTLE];
 459     nsettle                       = settle.size() / (1 + NRAL(F_SETTLE));
 460
 461     if (nsettle > 0)
 462     {
 463         nth = gmx_omp_nthreads_get(ModuleMultiThread::Settle);
 464     }
 465     else
 466     {
 467         nth = 1;
 468     }
 469
 470     /* We do not need full pbc when constraints do not cross update groups
 471      * i.e. when dd->constraint_comm==NULL.
 472      * Note that PBC for constraints is different from PBC for bondeds.
 473      * For constraints there is both forward and backward communication.
 474      */
 475     if (ir.pbcType != PbcType::No && (cr->dd || pbcHandlingRequired_)
 476         && !(cr->dd && cr->dd->constraint_comm == nullptr))
 477     {
 478         /* With pbc=screw the screw has been changed to a shift
 479          * by the constraint coordinate communication routine,
 480          * so that here we can use normal pbc.
 481          */
 482         pbc_null = set_pbc_dd(&pbc, ir.pbcType, DOMAINDECOMP(cr) ? cr->dd->numCells : nullptr, FALSE, box);
 483     }
 484     else
 485     {
 486         pbc_null = nullptr;
 487     }
 488
 489     /* Communicate the coordinates required for the non-local constraints
 490      * for LINCS and/or SETTLE.
 491      */
 492     if (cr->dd)
 493     {
 494         dd_move_x_constraints(cr->dd,
 495                               box,
 496                               x.unpaddedArrayRef(),
 497                               xprime.unpaddedArrayRef(),
 498                               econq == ConstraintVariable::Positions);
 499
 500         if (!v.empty())
 501         {
 502             /* We need to initialize the non-local components of v.
 503              * We never actually use these values, but we do increment them,
 504              * so we should avoid uninitialized variables and overflows.
 505              */
 506             clear_constraint_quantity_nonlocal(*cr->dd, v.unpaddedArrayRef());
 507         }
 508     }
 509
 510     if (lincsd != nullptr)
 511     {
 512         bOK = constrain_lincs(bLog || bEner,
 513                               ir,
 514                               step,
 515                               lincsd,
 516                               inverseMasses_,
 517                               cr,
 518                               ms,
 519                               x,
 520                               xprime,
 521                               min_proj,
 522                               box,
 523                               pbc_null,
 524                               hasMassPerturbedAtoms_,
 525                               lambda,
 526                               dvdlambda,
 527                               invdt,
 528                               v.unpaddedArrayRef(),
 529                               computeVirial,
 530                               constraintsVirial,
 531                               econq,
 532                               nrnb,
 533                               maxwarn,
 534                               &warncount_lincs);
 535         if (!bOK && maxwarn < INT_MAX)
 536         {
 537             if (log != nullptr)
 538             {
 539                 fprintf(log,
 540                         "Constraint error in algorithm %s at step %s\n",
 541                         enumValueToString(ConstraintAlgorithm::Lincs),
 542                         gmx_step_str(step, buf));
 543             }
 544             bDump = TRUE;
 545         }
 546     }
 547
 548     if (shaked != nullptr)
 549     {
 550         bOK = constrain_shake(log,
 551                               shaked.get(),
 552                               inverseMasses_,
 553                               *idef,
 554                               ir,
 555                               x.unpaddedArrayRef(),
 556                               xprime.unpaddedArrayRef(),
 557                               min_proj,
 558                               pbc_null,
 559                               nrnb,
 560                               lambda,
 561                               dvdlambda,
 562                               invdt,
 563                               v.unpaddedArrayRef(),
 564                               computeVirial,
 565                               constraintsVirial,
 566                               maxwarn < INT_MAX,
 567                               econq);
 568
 569         if (!bOK && maxwarn < INT_MAX)
 570         {
 571             if (log != nullptr)
 572             {
 573                 fprintf(log,
 574                         "Constraint error in algorithm %s at step %s\n",
 575                         enumValueToString(ConstraintAlgorithm::Shake),
 576                         gmx_step_str(step, buf));
 577             }
 578             bDump = TRUE;
 579         }
 580     }
 581
 582     if (nsettle > 0)
 583     {
 584         bool bSettleErrorHasOccurred0 = false;
 585
 586         switch (econq)
 587         {
 588             case ConstraintVariable::Positions:
 589 #pragma omp parallel for num_threads(nth) schedule(static)
 590                 for (int th = 0; th < nth; th++)
 591                 {
 592                     try
 593                     {
 594                         if (th > 0)
 595                         {
 596                             clear_mat(threadConstraintsVirial[th]);
 597                         }
 598
 599                         csettle(*settled,
 600                                 nth,
 601                                 th,
 602                                 pbc_null,
 603                                 x,
 604                                 xprime,
 605                                 invdt,
 606                                 v,
 607                                 computeVirial,
 608                                 th == 0 ? constraintsVirial : threadConstraintsVirial[th],
 609                                 th == 0 ? &bSettleErrorHasOccurred0 : &bSettleErrorHasOccurred[th]);
 610                     }
 611                     GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 612                 }
 613                 inc_nrnb(nrnb, eNR_SETTLE, nsettle);
 614                 if (!v.empty())
 615                 {
 616                     inc_nrnb(nrnb, eNR_CONSTR_V, nsettle * 3);
 617                 }
 618                 if (computeVirial)
 619                 {
 620                     inc_nrnb(nrnb, eNR_CONSTR_VIR, nsettle * 3);
 621                 }
 622                 break;
 623             case ConstraintVariable::Velocities:
 624             case ConstraintVariable::Derivative:
 625             case ConstraintVariable::Force:
 626             case ConstraintVariable::ForceDispl:
 627 #pragma omp parallel for num_threads(nth) schedule(static)
 628                 for (int th = 0; th < nth; th++)
 629                 {
 630                     try
 631                     {
 632                         int calcvir_atom_end;
 633
 634                         if (!computeVirial)
 635                         {
 636                             calcvir_atom_end = 0;
 637                         }
 638                         else
 639                         {
 640                             calcvir_atom_end = numHomeAtoms_;
 641                         }
 642
 643                         if (th > 0)
 644                         {
 645                             clear_mat(threadConstraintsVirial[th]);
 646                         }
 647
 648                         int start_th = (nsettle * th) / nth;
 649                         int end_th   = (nsettle * (th + 1)) / nth;
 650
 651                         if (start_th >= 0 && end_th - start_th > 0)
 652                         {
 653                             settle_proj(*settled,
 654                                         econq,
 655                                         end_th - start_th,
 656                                         settle.iatoms.data() + start_th * (1 + NRAL(F_SETTLE)),
 657                                         pbc_null,
 658                                         x.unpaddedArrayRef(),
 659                                         xprime.unpaddedArrayRef(),
 660                                         min_proj,
 661                                         calcvir_atom_end,
 662                                         th == 0 ? constraintsVirial : threadConstraintsVirial[th]);
 663                         }
 664                     }
 665                     GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 666                 }
 667                 /* This is an overestimate */
 668                 inc_nrnb(nrnb, eNR_SETTLE, nsettle);
 669                 break;
 670             case ConstraintVariable::Deriv_FlexCon:
 671                 /* Nothing to do, since the are no flexible constraints in settles */
 672                 break;
 673             default: gmx_incons("Unknown constraint quantity for settle");
 674         }
 675
 676         if (computeVirial)
 677         {
 678             /* Reduce the virial contributions over the threads */
 679             for (int th = 1; th < nth; th++)
 680             {
 681                 m_add(constraintsVirial, threadConstraintsVirial[th], constraintsVirial);
 682             }
 683         }
 684
 685         if (econq == ConstraintVariable::Positions)
 686         {
 687             for (int th = 1; th < nth; th++)
 688             {
 689                 bSettleErrorHasOccurred0 = bSettleErrorHasOccurred0 || bSettleErrorHasOccurred[th];
 690             }
 691
 692             if (bSettleErrorHasOccurred0)
 693             {
 694                 char buf[STRLEN];
 695                 sprintf(buf,
 696                         "\nstep "
 697                         "%" PRId64
 698                         ": One or more water molecules can not be settled.\n"
 699                         "Check for bad contacts and/or reduce the timestep if appropriate.\n",
 700                         step);
 701                 if (log)
 702                 {
 703                     fprintf(log, "%s", buf);
 704                 }
 705                 fprintf(stderr, "%s", buf);
 706                 warncount_settle++;
 707                 if (warncount_settle > maxwarn)
 708                 {
 709                     too_many_constraint_warnings(ConstraintAlgorithm::Count, warncount_settle);
 710                 }
 711                 bDump = TRUE;
 712
 713                 bOK = FALSE;
 714             }
 715         }
 716     }
 717
 718     if (computeVirial)
 719     {
 720         /* The normal uses of constrain() pass step_scaling = 1.0.
 721          * The call to constrain() for SD1 that passes step_scaling =
 722          * 0.5 also passes vir = NULL, so cannot reach this
 723          * assertion. This assertion should remain until someone knows
 724          * that this path works for their intended purpose, and then
 725          * they can use scaled_delta_t instead of ir.delta_t
 726          * below. */
 727         assert(gmx_within_tol(step_scaling, 1.0, GMX_REAL_EPS));
 728         switch (econq)
 729         {
 730             case ConstraintVariable::Positions: vir_fac = 0.5 / (ir.delta_t * ir.delta_t); break;
 731             case ConstraintVariable::Velocities: vir_fac = 0.5 / ir.delta_t; break;
 732             case ConstraintVariable::Force:
 733             case ConstraintVariable::ForceDispl: vir_fac = 0.5; break;
 734             default: gmx_incons("Unsupported constraint quantity for virial");
 735         }
 736
 737         if (EI_VV(ir.eI))
 738         {
 739             vir_fac *= 2; /* only constraining over half the distance here */
 740         }
 741         for (int i = 0; i < DIM; i++)
 742         {
 743             for (int j = 0; j < DIM; j++)
 744             {
 745                 constraintsVirial[i][j] *= vir_fac;
 746             }
 747         }
 748     }
 749
 750     if (bDump)
 751     {
 752         dump_confs(log, step, mtop, start, numHomeAtoms_, cr, x.unpaddedArrayRef(), xprime.unpaddedArrayRef(), box);
 753     }
 754
 755     if (econq == ConstraintVariable::Positions)
 756     {
 757         if (ir.bPull && pull_have_constraint(*pull_work))
 758         {
 759             if (EI_DYNAMICS(ir.eI))
 760             {
 761                 t = ir.init_t + (step + delta_step) * ir.delta_t;
 762             }
 763             else
 764             {
 765                 t = ir.init_t;
 766             }
 767             set_pbc(&pbc, ir.pbcType, box);
 768             pull_constraint(pull_work,
 769                             masses_,
 770                             pbc,
 771                             cr,
 772                             ir.delta_t,
 773                             t,
 774                             x.unpaddedArrayRef(),
 775                             xprime.unpaddedArrayRef(),
 776                             v.unpaddedArrayRef(),
 777                             constraintsVirial);
 778         }
 779         if (ed && delta_step > 0)
 780         {
 781             /* apply the essential dynamics constraints here */
 782             do_edsam(&ir, step, cr, xprime.unpaddedArrayRef(), v.unpaddedArrayRef(), box, ed);
 783         }
 784     }
 785     wallcycle_stop(wcycle, WallCycleCounter::Constr);
 786
 787     const bool haveVelocities = (!v.empty() || econq == ConstraintVariable::Velocities);
 788     if (haveVelocities && !cFREEZE_.empty())
 789     {
 790         /* Set the velocities of frozen dimensions to zero */
 791         ArrayRef<RVec> vRef;
 792         if (econq == ConstraintVariable::Velocities)
 793         {
 794             vRef = xprime.unpaddedArrayRef();
 795         }
 796         else
 797         {
 798             vRef = v.unpaddedArrayRef();
 799         }
 800
 801         int gmx_unused numThreads = gmx_omp_nthreads_get(ModuleMultiThread::Update);
 802
 803 #pragma omp parallel for num_threads(numThreads) schedule(static)
 804         for (int i = 0; i < numHomeAtoms_; i++)
 805         {
 806             int freezeGroup = cFREEZE_[i];
 807
 808             for (int d = 0; d < DIM; d++)
 809             {
 810                 if (ir.opts.nFreeze[freezeGroup][d])
 811                 {
 812                     vRef[i][d] = 0;
 813                 }
 814             }
 815         }
 816     }
 817
 818     return bOK;
 819 } // namespace gmx
 820
 821 ArrayRef<real> Constraints::rmsdData() const
 822 {
 823     if (impl_->lincsd)
 824     {
 825         return lincs_rmsdData(impl_->lincsd);
 826     }
 827     else
 828     {
 829         return {};
 830     }
 831 }
 832
 833 real Constraints::rmsd() const
 834 {
 835     if (impl_->lincsd)
 836     {
 837         return lincs_rmsd(impl_->lincsd);
 838     }
 839     else
 840     {
 841         return 0;
 842     }
 843 }
 844
 845 int Constraints::numConstraintsTotal()
 846 {
 847     return impl_->ncon_tot;
 848 }
 849
 850 FlexibleConstraintTreatment flexibleConstraintTreatment(bool haveDynamicsIntegrator)
 851 {
 852     if (haveDynamicsIntegrator)
 853     {
 854         return FlexibleConstraintTreatment::Include;
 855     }
 856     else
 857     {
 858         return FlexibleConstraintTreatment::Exclude;
 859     }
 860 }
 861
 862 /*! \brief Returns a block struct to go from atoms to constraints
 863  *
 864  * The block struct will contain constraint indices with lower indices
 865  * directly matching the order in F_CONSTR and higher indices matching
 866  * the order in F_CONSTRNC offset by the number of constraints in F_CONSTR.
 867  *
 868  * \param[in]  numAtoms  The number of atoms to construct the list for
 869  * \param[in]  ilists    The interaction lists, size F_NRE
 870  * \param[in]  iparams   Interaction parameters, can be null when
 871  *                       \p flexibleConstraintTreatment==Include
 872  * \param[in]  flexibleConstraintTreatment  The flexible constraint treatment,
 873  *                                          see enum above
 874  *
 875  * \returns a block struct with all constraints for each atom
 876  */
 877 static ListOfLists<int> makeAtomsToConstraintsList(int                             numAtoms,
 878                                                    ArrayRef<const InteractionList> ilists,
 879                                                    ArrayRef<const t_iparams>       iparams,
 880                                                    FlexibleConstraintTreatment flexibleConstraintTreatment)
 881 {
 882     GMX_ASSERT(flexibleConstraintTreatment == FlexibleConstraintTreatment::Include || !iparams.empty(),
 883                "With flexible constraint detection we need valid iparams");
 884
 885     std::vector<int> count(numAtoms);
 886
 887     for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
 888     {
 889         const InteractionList& ilist  = ilists[ftype];
 890         const int              stride = 1 + NRAL(ftype);
 891         for (int i = 0; i < ilist.size(); i += stride)
 892         {
 893             if (flexibleConstraintTreatment == FlexibleConstraintTreatment::Include
 894                 || !isConstraintFlexible(iparams, ilist.iatoms[i]))
 895             {
 896                 for (int j = 1; j < 3; j++)
 897                 {
 898                     int a = ilist.iatoms[i + j];
 899                     count[a]++;
 900                 }
 901             }
 902         }
 903     }
 904
 905     std::vector<int> listRanges(numAtoms + 1);
 906     for (int a = 0; a < numAtoms; a++)
 907     {
 908         listRanges[a + 1] = listRanges[a] + count[a];
 909         count[a]          = 0;
 910     }
 911     std::vector<int> elements(listRanges[numAtoms]);
 912
 913     /* The F_CONSTRNC constraints have constraint numbers
 914      * that continue after the last F_CONSTR constraint.
 915      */
 916     int numConstraints = 0;
 917     for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
 918     {
 919         const InteractionList& ilist  = ilists[ftype];
 920         const int              stride = 1 + NRAL(ftype);
 921         for (int i = 0; i < ilist.size(); i += stride)
 922         {
 923             if (flexibleConstraintTreatment == FlexibleConstraintTreatment::Include
 924                 || !isConstraintFlexible(iparams, ilist.iatoms[i]))
 925             {
 926                 for (int j = 1; j < 3; j++)
 927                 {
 928                     const int a                          = ilist.iatoms[i + j];
 929                     elements[listRanges[a] + count[a]++] = numConstraints;
 930                 }
 931             }
 932             numConstraints++;
 933         }
 934     }
 935
 936     return ListOfLists<int>(std::move(listRanges), std::move(elements));
 937 }
 938
 939 ListOfLists<int> make_at2con(int                             numAtoms,
 940                              ArrayRef<const InteractionList> ilist,
 941                              ArrayRef<const t_iparams>       iparams,
 942                              FlexibleConstraintTreatment     flexibleConstraintTreatment)
 943 {
 944     return makeAtomsToConstraintsList(numAtoms, ilist, iparams, flexibleConstraintTreatment);
 945 }
 946
 947 ListOfLists<int> make_at2con(const gmx_moltype_t&           moltype,
 948                              gmx::ArrayRef<const t_iparams> iparams,
 949                              FlexibleConstraintTreatment    flexibleConstraintTreatment)
 950 {
 951     return makeAtomsToConstraintsList(
 952             moltype.atoms.nr, makeConstArrayRef(moltype.ilist), iparams, flexibleConstraintTreatment);
 953 }
 954
 955 //! Return the number of flexible constraints in the \c ilist and \c iparams.
 956 int countFlexibleConstraints(ArrayRef<const InteractionList> ilist, ArrayRef<const t_iparams> iparams)
 957 {
 958     int nflexcon = 0;
 959     for (int ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
 960     {
 961         const int numIatomsPerConstraint = 3;
 962         for (int i = 0; i < ilist[ftype].size(); i += numIatomsPerConstraint)
 963         {
 964             const int type = ilist[ftype].iatoms[i];
 965             if (iparams[type].constr.dA == 0 && iparams[type].constr.dB == 0)
 966             {
 967                 nflexcon++;
 968             }
 969         }
 970     }
 971
 972     return nflexcon;
 973 }
 974
 975 //! Returns the index of the settle to which each atom belongs.
 976 static std::vector<int> make_at2settle(int natoms, const InteractionList& ilist)
 977 {
 978     /* Set all to no settle */
 979     std::vector<int> at2s(natoms, -1);
 980
 981     const int stride = 1 + NRAL(F_SETTLE);
 982
 983     for (int s = 0; s < ilist.size(); s += stride)
 984     {
 985         at2s[ilist.iatoms[s + 1]] = s / stride;
 986         at2s[ilist.iatoms[s + 2]] = s / stride;
 987         at2s[ilist.iatoms[s + 3]] = s / stride;
 988     }
 989
 990     return at2s;
 991 }
 992
 993 void Constraints::Impl::setConstraints(gmx_localtop_t*                     top,
 994                                        int                                 numAtoms,
 995                                        int                                 numHomeAtoms,
 996                                        gmx::ArrayRef<const real>           masses,
 997                                        gmx::ArrayRef<const real>           inverseMasses,
 998                                        const bool                          hasMassPerturbedAtoms,
 999                                        const real                          lambda,
1000                                        gmx::ArrayRef<const unsigned short> cFREEZE)
1001 {
1002     numAtoms_              = numAtoms;
1003     numHomeAtoms_          = numHomeAtoms;
1004     masses_                = masses;
1005     inverseMasses_         = inverseMasses;
1006     hasMassPerturbedAtoms_ = hasMassPerturbedAtoms;
1007     lambda_                = lambda;
1008     cFREEZE_               = cFREEZE;
1009
1010     idef = &top->idef;
1011
1012     if (ncon_tot > 0)
1013     {
1014         /* With DD we might also need to call LINCS on a domain no constraints for
1015          * communicating coordinates to other nodes that do have constraints.
1016          */
1017         if (ir.eConstrAlg == ConstraintAlgorithm::Lincs)
1018         {
1019             set_lincs(*idef, numAtoms_, inverseMasses_, lambda_, EI_DYNAMICS(ir.eI), cr, lincsd);
1020         }
1021         if (ir.eConstrAlg == ConstraintAlgorithm::Shake)
1022         {
1023             if (cr->dd)
1024             {
1025                 // We are using the local topology, so there are only
1026                 // F_CONSTR constraints.
1027                 GMX_RELEASE_ASSERT(idef->il[F_CONSTRNC].empty(),
1028                                    "Here we should not have no-connect constraints");
1029                 make_shake_sblock_dd(shaked.get(), idef->il[F_CONSTR]);
1030             }
1031             else
1032             {
1033                 make_shake_sblock_serial(shaked.get(), &top->idef, numAtoms_);
1034             }
1035         }
1036     }
1037
1038     if (settled)
1039     {
1040         settled->setConstraints(idef->il[F_SETTLE], numHomeAtoms_, masses_, inverseMasses_);
1041     }
1042
1043     /* Make a selection of the local atoms for essential dynamics */
1044     if (ed && cr->dd)
1045     {
1046         dd_make_local_ed_indices(cr->dd, ed);
1047     }
1048 }
1049
1050 void Constraints::setConstraints(gmx_localtop_t*                     top,
1051                                  const int                           numAtoms,
1052                                  const int                           numHomeAtoms,
1053                                  gmx::ArrayRef<const real>           masses,
1054                                  gmx::ArrayRef<const real>           inverseMasses,
1055                                  const bool                          hasMassPerturbedAtoms,
1056                                  const real                          lambda,
1057                                  gmx::ArrayRef<const unsigned short> cFREEZE)
1058 {
1059     impl_->setConstraints(
1060             top, numAtoms, numHomeAtoms, masses, inverseMasses, hasMassPerturbedAtoms, lambda, cFREEZE);
1061 }
1062
1063 /*! \brief Makes a per-moleculetype container of mappings from atom
1064  * indices to constraint indices.
1065  *
1066  * Note that flexible constraints are only enabled with a dynamical integrator. */
1067 static std::vector<ListOfLists<int>> makeAtomToConstraintMappings(const gmx_mtop_t& mtop,
1068                                                                   FlexibleConstraintTreatment flexibleConstraintTreatment)
1069 {
1070     std::vector<ListOfLists<int>> mapping;
1071     mapping.reserve(mtop.moltype.size());
1072     for (const gmx_moltype_t& moltype : mtop.moltype)
1073     {
1074         mapping.push_back(make_at2con(moltype, mtop.ffparams.iparams, flexibleConstraintTreatment));
1075     }
1076     return mapping;
1077 }
1078
1079 Constraints::Constraints(const gmx_mtop_t&     mtop,
1080                          const t_inputrec&     ir,
1081                          pull_t*               pull_work,
1082                          FILE*                 log,
1083                          const t_commrec*      cr,
1084                          const bool            useUpdateGroups,
1085                          const gmx_multisim_t* ms,
1086                          t_nrnb*               nrnb,
1087                          gmx_wallcycle*        wcycle,
1088                          bool                  pbcHandlingRequired,
1089                          int                   numConstraints,
1090                          int                   numSettles) :
1091     impl_(new Impl(mtop, ir, pull_work, log, cr, useUpdateGroups, ms, nrnb, wcycle, pbcHandlingRequired, numConstraints, numSettles))
1092 {
1093 }
1094
1095 Constraints::Impl::Impl(const gmx_mtop_t&     mtop_p,
1096                         const t_inputrec&     ir_p,
1097                         pull_t*               pull_work,
1098                         FILE*                 log_p,
1099                         const t_commrec*      cr_p,
1100                         const bool            useUpdateGroups,
1101                         const gmx_multisim_t* ms_p,
1102                         t_nrnb*               nrnb_p,
1103                         gmx_wallcycle*        wcycle_p,
1104                         bool                  pbcHandlingRequired,
1105                         int                   numConstraints,
1106                         int                   numSettles) :
1107     ncon_tot(numConstraints),
1108     mtop(mtop_p),
1109     pbcHandlingRequired_(pbcHandlingRequired),
1110     log(log_p),
1111     cr(cr_p),
1112     ms(ms_p),
1113     pull_work(pull_work),
1114     ir(ir_p),
1115     nrnb(nrnb_p),
1116     wcycle(wcycle_p)
1117 {
1118     if (numConstraints + numSettles > 0 && ir.epc == PressureCoupling::Mttk)
1119     {
1120         gmx_fatal(FARGS, "Constraints are not implemented with MTTK pressure control.");
1121     }
1122
1123     nflexcon = 0;
1124     if (numConstraints > 0)
1125     {
1126         at2con_mt = makeAtomToConstraintMappings(mtop, flexibleConstraintTreatment(EI_DYNAMICS(ir.eI)));
1127
1128         for (const gmx_molblock_t& molblock : mtop.molblock)
1129         {
1130             int count = countFlexibleConstraints(mtop.moltype[molblock.type].ilist, mtop.ffparams.iparams);
1131             nflexcon += molblock.nmol * count;
1132         }
1133
1134         if (nflexcon > 0)
1135         {
1136             if (log)
1137             {
1138                 fprintf(log, "There are %d flexible constraints\n", nflexcon);
1139                 if (ir.fc_stepsize == 0)
1140                 {
1141                     fprintf(log,
1142                             "\n"
1143                             "WARNING: step size for flexible constraining = 0\n"
1144                             "         All flexible constraints will be rigid.\n"
1145                             "         Will try to keep all flexible constraints at their original "
1146                             "length,\n"
1147                             "         but the lengths may exhibit some drift.\n\n");
1148                     nflexcon = 0;
1149                 }
1150             }
1151             if (nflexcon > 0)
1152             {
1153                 please_cite(log, "Hess2002");
1154             }
1155         }
1156
1157         // When there are multiple PP domains and update groups are
1158         // not in use, the constraints might be split across the
1159         // domains, needing particular handling.
1160         const bool mayHaveSplitConstraints = DOMAINDECOMP(cr) && !useUpdateGroups;
1161
1162         if (ir.eConstrAlg == ConstraintAlgorithm::Lincs)
1163         {
1164             lincsd = init_lincs(
1165                     log, mtop, nflexcon, at2con_mt, mayHaveSplitConstraints, ir.nLincsIter, ir.nProjOrder);
1166         }
1167
1168         if (ir.eConstrAlg == ConstraintAlgorithm::Shake)
1169         {
1170             if (mayHaveSplitConstraints)
1171             {
1172                 gmx_fatal(FARGS,
1173                           "SHAKE is not supported with domain decomposition and constraints that "
1174                           "cross domain boundaries, use LINCS");
1175             }
1176             if (nflexcon)
1177             {
1178                 gmx_fatal(FARGS,
1179                           "For this system also velocities and/or forces need to be constrained, "
1180                           "this can not be done with SHAKE, you should select LINCS");
1181             }
1182             please_cite(log, "Ryckaert77a");
1183             if (ir.bShakeSOR)
1184             {
1185                 please_cite(log, "Barth95a");
1186             }
1187
1188             shaked = std::make_unique<shakedata>();
1189         }
1190     }
1191
1192     if (numSettles > 0)
1193     {
1194         please_cite(log, "Miyamoto92a");
1195
1196         settled = std::make_unique<SettleData>(mtop);
1197
1198         // SETTLE with perturbed masses is not implemented. grompp now checks
1199         // for this, but old .tpr files that did this might still exist.
1200         if (haveFepPerturbedMassesInSettles(mtop))
1201         {
1202             gmx_fatal(FARGS,
1203                       "SETTLE is not implemented for atoms whose mass is perturbed. "
1204                       "You might\ninstead use normal constraints.");
1205         }
1206
1207         /* Make an atom to settle index for use in domain decomposition */
1208         for (size_t mt = 0; mt < mtop.moltype.size(); mt++)
1209         {
1210             at2settle_mt.emplace_back(
1211                     make_at2settle(mtop.moltype[mt].atoms.nr, mtop.moltype[mt].ilist[F_SETTLE]));
1212         }
1213
1214         /* Allocate thread-local work arrays */
1215         int nthreads = gmx_omp_nthreads_get(ModuleMultiThread::Settle);
1216         if (nthreads > 1 && threadConstraintsVirial == nullptr)
1217         {
1218             snew(threadConstraintsVirial, nthreads);
1219             snew(bSettleErrorHasOccurred, nthreads);
1220         }
1221     }
1222
1223     maxwarn   = 999;
1224     char* env = getenv("GMX_MAXCONSTRWARN");
1225     if (env)
1226     {
1227         maxwarn = 0;
1228         sscanf(env, "%8d", &maxwarn);
1229         if (maxwarn < 0)
1230         {
1231             maxwarn = INT_MAX;
1232         }
1233         if (log)
1234         {
1235             fprintf(log, "Setting the maximum number of constraint warnings to %d\n", maxwarn);
1236         }
1237         if (MASTER(cr))
1238         {
1239             fprintf(stderr, "Setting the maximum number of constraint warnings to %d\n", maxwarn);
1240         }
1241     }
1242     warncount_lincs  = 0;
1243     warncount_settle = 0;
1244 }
1245
1246 Constraints::Impl::~Impl()
1247 {
1248     if (bSettleErrorHasOccurred != nullptr)
1249     {
1250         sfree(bSettleErrorHasOccurred);
1251     }
1252     if (threadConstraintsVirial != nullptr)
1253     {
1254         sfree(threadConstraintsVirial);
1255     }
1256     done_lincs(lincsd);
1257 }
1258
1259 void Constraints::saveEdsamPointer(gmx_edsam* ed)
1260 {
1261     impl_->ed = ed;
1262 }
1263
1264 ArrayRef<const ListOfLists<int>> Constraints::atom2constraints_moltype() const
1265 {
1266     return impl_->at2con_mt;
1267 }
1268
1269 ArrayRef<const std::vector<int>> Constraints::atom2settle_moltype() const
1270 {
1271     return impl_->at2settle_mt;
1272 }
1273
1274 void do_constrain_first(FILE*                     fplog,
1275                         gmx::Constraints*         constr,
1276                         const t_inputrec*         ir,
1277                         int                       numAtoms,
1278                         int                       numHomeAtoms,
1279                         ArrayRefWithPadding<RVec> x,
1280                         ArrayRefWithPadding<RVec> v,
1281                         const matrix              box,
1282                         real                      lambda)
1283 {
1284     int     i, m, start, end;
1285     int64_t step;
1286     real    dt = ir->delta_t;
1287     real    dvdl_dum;
1288
1289     PaddedVector<RVec> savex(numAtoms);
1290
1291     start = 0;
1292     end   = numHomeAtoms;
1293
1294     if (debug)
1295     {
1296         fprintf(debug, "vcm: start=%d, homenr=%d, end=%d\n", start, numHomeAtoms, end);
1297     }
1298     /* Do a first constrain to reset particles... */
1299     step = ir->init_step;
1300     if (fplog)
1301     {
1302         char buf[STEPSTRSIZE];
1303         fprintf(fplog, "\nConstraining the starting coordinates (step %s)\n", gmx_step_str(step, buf));
1304     }
1305     dvdl_dum = 0;
1306
1307     bool needsLogging  = true;
1308     bool computeEnergy = false;
1309     bool computeVirial = false;
1310     /* constrain the current position */
1311     constr->apply(needsLogging,
1312                   computeEnergy,
1313                   step,
1314                   0,
1315                   1.0,
1316                   x,
1317                   x,
1318                   {},
1319                   box,
1320                   lambda,
1321                   &dvdl_dum,
1322                   {},
1323                   computeVirial,
1324                   nullptr,
1325                   gmx::ConstraintVariable::Positions);
1326     if (EI_VV(ir->eI))
1327     {
1328         /* constrain the inital velocity, and save it */
1329         /* also may be useful if we need the ekin from the halfstep for velocity verlet */
1330         constr->apply(needsLogging,
1331                       computeEnergy,
1332                       step,
1333                       0,
1334                       1.0,
1335                       x,
1336                       v,
1337                       v.unpaddedArrayRef(),
1338                       box,
1339                       lambda,
1340                       &dvdl_dum,
1341                       {},
1342                       computeVirial,
1343                       nullptr,
1344                       gmx::ConstraintVariable::Velocities);
1345     }
1346     /* constrain the inital velocities at t-dt/2 */
1347     if (EI_STATE_VELOCITY(ir->eI) && ir->eI != IntegrationAlgorithm::VV)
1348     {
1349         auto subX = x.paddedArrayRef().subArray(start, end);
1350         auto subV = v.paddedArrayRef().subArray(start, end);
1351         for (i = start; (i < end); i++)
1352         {
1353             for (m = 0; (m < DIM); m++)
1354             {
1355                 /* Reverse the velocity */
1356                 subV[i][m] = -subV[i][m];
1357                 /* Store the position at t-dt in buf */
1358                 savex[i][m] = subX[i][m] + dt * subV[i][m];
1359             }
1360         }
1361         /* Shake the positions at t=-dt with the positions at t=0
1362          * as reference coordinates.
1363          */
1364         if (fplog)
1365         {
1366             char buf[STEPSTRSIZE];
1367             fprintf(fplog, "\nConstraining the coordinates at t0-dt (step %s)\n", gmx_step_str(step, buf));
1368         }
1369         dvdl_dum = 0;
1370         constr->apply(needsLogging,
1371                       computeEnergy,
1372                       step,
1373                       -1,
1374                       1.0,
1375                       x,
1376                       savex.arrayRefWithPadding(),
1377                       {},
1378                       box,
1379                       lambda,
1380                       &dvdl_dum,
1381                       v,
1382                       computeVirial,
1383                       nullptr,
1384                       gmx::ConstraintVariable::Positions);
1385
1386         for (i = start; i < end; i++)
1387         {
1388             for (m = 0; m < DIM; m++)
1389             {
1390                 /* Re-reverse the velocities */
1391                 subV[i][m] = -subV[i][m];
1392             }
1393         }
1394     }
1395 }
1396
1397 void constrain_velocities(gmx::Constraints* constr,
1398                           bool              do_log,
1399                           bool              do_ene,
1400                           int64_t           step,
1401                           t_state*          state,
1402                           real*             dvdlambda,
1403                           gmx_bool          computeVirial,
1404                           tensor            constraintsVirial)
1405 {
1406     if (constr != nullptr)
1407     {
1408         constr->apply(do_log,
1409                       do_ene,
1410                       step,
1411                       1,
1412                       1.0,
1413                       state->x.arrayRefWithPadding(),
1414                       state->v.arrayRefWithPadding(),
1415                       state->v.arrayRefWithPadding().unpaddedArrayRef(),
1416                       state->box,
1417                       state->lambda[FreeEnergyPerturbationCouplingType::Bonded],
1418                       dvdlambda,
1419                       ArrayRefWithPadding<RVec>(),
1420                       computeVirial,
1421                       constraintsVirial,
1422                       ConstraintVariable::Velocities);
1423     }
1424 }
1425
1426 void constrain_coordinates(gmx::Constraints*         constr,
1427                            bool                      do_log,
1428                            bool                      do_ene,
1429                            int64_t                   step,
1430                            t_state*                  state,
1431                            ArrayRefWithPadding<RVec> xp,
1432                            real*                     dvdlambda,
1433                            gmx_bool                  computeVirial,
1434                            tensor                    constraintsVirial)
1435 {
1436     if (constr != nullptr)
1437     {
1438         constr->apply(do_log,
1439                       do_ene,
1440                       step,
1441                       1,
1442                       1.0,
1443                       state->x.arrayRefWithPadding(),
1444                       std::move(xp),
1445                       ArrayRef<RVec>(),
1446                       state->box,
1447                       state->lambda[FreeEnergyPerturbationCouplingType::Bonded],
1448                       dvdlambda,
1449                       state->v.arrayRefWithPadding(),
1450                       computeVirial,
1451                       constraintsVirial,
1452                       ConstraintVariable::Positions);
1453     }
1454 }
1455
1456 } // namespace gmx