text: /*
   * This file is part of the GROMACS molecular simulation package.
   *
   * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
   * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   * and including many others, as listed in the AUTHORS file in the
   * top-level source directory and at http://www.gromacs.org.
   *
   * GROMACS is free software; you can redistribute it and/or
   * modify it under the terms of the GNU Lesser General Public License
   * as published by the Free Software Foundation; either version 2.1
   * of the License, or (at your option) any later version.
   *
   * GROMACS is distributed in the hope that it will be useful,
   * but WITHOUT ANY WARRANTY; without even the implied warranty of
   * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
   * Lesser General Public License for more details.
   *
   * You should have received a copy of the GNU Lesser General Public
   * License along with GROMACS; if not, see
   * http://www.gnu.org/licenses, or write to the Free Software Foundation,
   * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
   *
   * If you want to redistribute modifications to GROMACS, please
   * consider that scientific software is very special. Version
   * control is crucial - bugs must be traceable. We will be happy to
   * consider code for inclusion in the official distribution, but
   * derived work must not be called official GROMACS. Details are found
   * in the README & COPYING files - if they are missing, get the
   * official version at http://www.gromacs.org.
   *
   * To help us fund GROMACS development, we humbly ask that you cite
   * the research papers on the package. Check out http://www.gromacs.org.
   */
  
  /*! \internal \file
   *
   * \brief Declares the loop for MiMiC QM/MM
   *
   * \author Viacheslav Bolnykh <v.bolnykh@hpc-leap.eu>
   * \ingroup module_mdrun
   */
  #include "gmxpre.h"
  
  #include <cinttypes>
  #include <cmath>
  #include <cstdio>
  #include <cstdlib>
  
  #include <algorithm>
  #include <memory>
  
  #include "gromacs/applied_forces/awh/awh.h"
  #include "gromacs/commandline/filenm.h"
  #include "gromacs/domdec/collect.h"
  #include "gromacs/domdec/dlbtiming.h"
  #include "gromacs/domdec/domdec.h"
  #include "gromacs/domdec/domdec_network.h"
  #include "gromacs/domdec/domdec_struct.h"
  #include "gromacs/domdec/mdsetup.h"
  #include "gromacs/domdec/partition.h"
  #include "gromacs/essentialdynamics/edsam.h"
  #include "gromacs/ewald/pme_load_balancing.h"
  #include "gromacs/ewald/pme_pp.h"
  #include "gromacs/fileio/trxio.h"
  #include "gromacs/gmxlib/network.h"
  #include "gromacs/gmxlib/nrnb.h"
  #include "gromacs/gpu_utils/gpu_utils.h"
  #include "gromacs/listed_forces/listed_forces.h"
  #include "gromacs/math/functions.h"
  #include "gromacs/math/utilities.h"
  #include "gromacs/math/vec.h"
  #include "gromacs/math/vectypes.h"
  #include "gromacs/mdlib/checkpointhandler.h"
  #include "gromacs/mdlib/compute_io.h"
  #include "gromacs/mdlib/constr.h"
  #include "gromacs/mdlib/ebin.h"
  #include "gromacs/mdlib/enerdata_utils.h"
  #include "gromacs/mdlib/energyoutput.h"
  #include "gromacs/mdlib/expanded.h"
  #include "gromacs/mdlib/force.h"
  #include "gromacs/mdlib/force_flags.h"
  #include "gromacs/mdlib/forcerec.h"
  #include "gromacs/mdlib/freeenergyparameters.h"
  #include "gromacs/mdlib/md_support.h"
  #include "gromacs/mdlib/mdatoms.h"
  #include "gromacs/mdlib/mdoutf.h"
  #include "gromacs/mdlib/membed.h"
  #include "gromacs/mdlib/resethandler.h"
  #include "gromacs/mdlib/sighandler.h"
  #include "gromacs/mdlib/simulationsignal.h"
  #include "gromacs/mdlib/stat.h"
  #include "gromacs/mdlib/stophandler.h"
  #include "gromacs/mdlib/tgroup.h"
  #include "gromacs/mdlib/trajectory_writing.h"
  #include "gromacs/mdlib/update.h"
  #include "gromacs/mdlib/vcm.h"
  #include "gromacs/mdlib/vsite.h"
  #include "gromacs/mdrunutility/handlerestart.h"
  #include "gromacs/mdrunutility/multisim.h"
  #include "gromacs/mdrunutility/printtime.h"
  #include "gromacs/mdtypes/awh_history.h"
  #include "gromacs/mdtypes/awh_params.h"
  #include "gromacs/mdtypes/commrec.h"
  #include "gromacs/mdtypes/df_history.h"
  #include "gromacs/mdtypes/enerdata.h"
  #include "gromacs/mdtypes/energyhistory.h"
  #include "gromacs/mdtypes/forcebuffers.h"
  #include "gromacs/mdtypes/forcerec.h"
  #include "gromacs/mdtypes/group.h"
  #include "gromacs/mdtypes/inputrec.h"
  #include "gromacs/mdtypes/interaction_const.h"
  #include "gromacs/mdtypes/md_enums.h"
  #include "gromacs/mdtypes/mdatom.h"
  #include "gromacs/mdtypes/mdrunoptions.h"
  #include "gromacs/mdtypes/observableshistory.h"
  #include "gromacs/mdtypes/state.h"
  #include "gromacs/mimic/communicator.h"
  #include "gromacs/mimic/utilities.h"
  #include "gromacs/pbcutil/pbc.h"
  #include "gromacs/pulling/pull.h"
  #include "gromacs/timing/wallcycle.h"
  #include "gromacs/timing/walltime_accounting.h"
  #include "gromacs/topology/atoms.h"
  #include "gromacs/topology/idef.h"
  #include "gromacs/topology/mtop_util.h"
  #include "gromacs/topology/topology.h"
  #include "gromacs/trajectory/trajectoryframe.h"
  #include "gromacs/utility/basedefinitions.h"
  #include "gromacs/utility/cstringutil.h"
  #include "gromacs/utility/fatalerror.h"
  #include "gromacs/utility/logger.h"
  #include "gromacs/utility/real.h"
  #include "gromacs/utility/smalloc.h"
  
  #include "legacysimulator.h"
  #include "replicaexchange.h"
  #include "shellfc.h"
  
  using gmx::SimulationSignaller;
  
  void gmx::LegacySimulator::do_mimic()
  {
      t_inputrec*       ir = inputrec;
      int64_t           step, step_rel;
      double            t;
      bool              isLastStep               = false;
      bool              doFreeEnergyPerturbation = false;
      unsigned int      force_flags;
      tensor            force_vir, shake_vir, total_vir, pres;
      rvec              mu_tot;
      ForceBuffers      f;
      gmx_global_stat_t gstat;
      gmx_shellfc_t*    shellfc;
  
      double cycles;
  
      /* Domain decomposition could incorrectly miss a bonded
         interaction, but checking for that requires a global
         communication stage, which does not otherwise happen in DD
         code. So we do that alongside the first global energy reduction
         after a new DD is made. These variables handle whether the
         check happens, and the result it returns. */
      bool shouldCheckNumberOfBondedInteractions = false;
      int  totalNumberOfBondedInteractions       = -1;
  
      SimulationSignals signals;
      // Most global communnication stages don't propagate mdrun
      // signals, and will use this object to achieve that.
      SimulationSignaller nullSignaller(nullptr, nullptr, nullptr, false, false);
  
      if (ir->bExpanded)
      {
          gmx_fatal(FARGS, "Expanded ensemble not supported by MiMiC.");
      }
      if (ir->bSimTemp)
      {
          gmx_fatal(FARGS, "Simulated tempering not supported by MiMiC.");
      }
      if (ir->bDoAwh)
      {
          gmx_fatal(FARGS, "AWH not supported by MiMiC.");
      }
      if (replExParams.exchangeInterval > 0)
      {
          gmx_fatal(FARGS, "Replica exchange not supported by MiMiC.");
      }
      if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
      {
          gmx_fatal(FARGS, "Essential dynamics not supported by MiMiC.");
      }
      if (ir->bIMD)
      {
          gmx_fatal(FARGS, "Interactive MD not supported by MiMiC.");
      }
      if (isMultiSim(ms))
      {
          gmx_fatal(FARGS, "Multiple simulations not supported by MiMiC.");
      }
      if (std::any_of(ir->opts.annealing, ir->opts.annealing + ir->opts.ngtc,
                      [](int i) { return i != eannNO; }))
      {
          gmx_fatal(FARGS, "Simulated annealing not supported by MiMiC.");
      }
  
      /* Settings for rerun */
      ir->nstlist              = 1;
      ir->nstcalcenergy        = 1;
      int        nstglobalcomm = 1;
      const bool bNS           = true;
  
      if (MASTER(cr))
      {
          MimicCommunicator::init();
          auto nonConstGlobalTopology = const_cast<gmx_mtop_t*>(top_global);
          MimicCommunicator::sendInitData(nonConstGlobalTopology, state_global->x);
          ir->nsteps = MimicCommunicator::getStepNumber();
      }
  
      ir->nstxout_compressed         = 0;
      const SimulationGroups* groups = &top_global->groups;
      {
          auto nonConstGlobalTopology                          = const_cast<gmx_mtop_t*>(top_global);
          nonConstGlobalTopology->intermolecularExclusionGroup = genQmmmIndices(*top_global);
      }
  
      initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda);
  
      const bool        simulationsShareState = false;
      gmx_mdoutf*       outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider,
                                     mdModulesNotifier, ir, top_global, oenv, wcycle,
                                     StartingBehavior::NewSimulation, simulationsShareState, ms);
      gmx::EnergyOutput energyOutput(mdoutf_get_fp_ene(outf), top_global, ir, pull_work,
                                     mdoutf_get_fp_dhdl(outf), true, StartingBehavior::NewSimulation,
                                     mdModulesNotifier);
  
      gstat = global_stat_init(ir);
  
      /* Check for polarizable models and flexible constraints */
      shellfc = init_shell_flexcon(fplog, top_global, constr ? constr->numFlexibleConstraints() : 0,
                                   ir->nstcalcenergy, DOMAINDECOMP(cr));
  
      {
          double io = compute_io(ir, top_global->natoms, *groups, energyOutput.numEnergyTerms(), 1);
          if ((io > 2000) && MASTER(cr))
          {
              fprintf(stderr, "\nWARNING: This run will generate roughly %.0f Mb of data\n\n", io);
          }
      }
  
      // Local state only becomes valid now.
      std::unique_ptr<t_state> stateInstance;
      t_state*                 state;
  
      gmx_localtop_t top(top_global->ffparams);
  
      if (DOMAINDECOMP(cr))
      {
          stateInstance = std::make_unique<t_state>();
          state         = stateInstance.get();
          dd_init_local_state(cr->dd, state_global, state);
  
          /* Distribute the charge groups over the nodes from the master node */
          dd_partition_system(fplog, mdlog, ir->init_step, cr, TRUE, 1, state_global, *top_global, ir,
                              imdSession, pull_work, state, &f, mdAtoms, &top, fr, vsite, constr,
                              nrnb, nullptr, FALSE);
          shouldCheckNumberOfBondedInteractions = true;
          gmx_bcast(sizeof(ir->nsteps), &ir->nsteps, cr->mpi_comm_mygroup);
      }
      else
      {
          state_change_natoms(state_global, state_global->natoms);
          /* Copy the pointer to the global state */
          state = state_global;
  
          mdAlgorithmsSetupAtomData(cr, ir, *top_global, &top, fr, &f, mdAtoms, constr, vsite, shellfc);
      }
  
      auto mdatoms = mdAtoms->mdatoms();
  
      // NOTE: The global state is no longer used at this point.
      // But state_global is still used as temporary storage space for writing
      // the global state to file and potentially for replica exchange.
      // (Global topology should persist.)
  
      update_mdatoms(mdatoms, state->lambda[efptMASS]);
  
      if (ir->efep != efepNO && ir->fepvals->nstdhdl != 0)
      {
          doFreeEnergyPerturbation = true;
      }
  
      {
          int cglo_flags =
                  (CGLO_GSTAT
                   | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
          bool   bSumEkinhOld = false;
          t_vcm* vcm          = nullptr;
          compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
                          makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd,
                          force_vir, shake_vir, total_vir, pres, constr, &nullSignaller, state->box,
                          &totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags);
      }
      checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global, &top,
                                      makeConstArrayRef(state->x), state->box,
                                      &shouldCheckNumberOfBondedInteractions);
  
      if (MASTER(cr))
      {
          fprintf(stderr, "starting MiMiC MD run '%s'\n\n", *(top_global->name));
          if (mdrunOptions.verbose)
          {
              fprintf(stderr,
                      "Calculated time to finish depends on nsteps from "
                      "run input file,\nwhich may not correspond to the time "
                      "needed to process input trajectory.\n\n");
          }
          fprintf(fplog, "\n");
      }
  
      walltime_accounting_start_time(walltime_accounting);
      wallcycle_start(wcycle, ewcRUN);
      print_start(fplog, cr, walltime_accounting, "mdrun");
  
      /***********************************************************
       *
       *             Loop over MD steps
       *
       ************************************************************/
  
      if (constr)
      {
          GMX_LOG(mdlog.info)
                  .asParagraph()
                  .appendText(
                          "Simulations has constraints. Constraints will "
                          "be handled by CPMD.");
      }
  
      GMX_LOG(mdlog.info)
              .asParagraph()
              .appendText(
                      "MiMiC does not report kinetic energy, total energy, temperature, virial and "
                      "pressure.");
  
      step     = ir->init_step;
      step_rel = 0;
  
      auto stopHandler = stopHandlerBuilder->getStopHandlerMD(
              compat::not_null<SimulationSignal*>(&signals[eglsSTOPCOND]), false, MASTER(cr),
              ir->nstlist, mdrunOptions.reproducible, nstglobalcomm, mdrunOptions.maximumHoursToRun,
              ir->nstlist == 0, fplog, step, bNS, walltime_accounting);
  
      // we don't do counter resetting in rerun - finish will always be valid
      walltime_accounting_set_valid_finish(walltime_accounting);
  
      const DDBalanceRegionHandler ddBalanceRegionHandler(cr);
  
      /* and stop now if we should */
      isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel > ir->nsteps));
      while (!isLastStep)
      {
          isLastStep = (isLastStep || (ir->nsteps >= 0 && step_rel == ir->nsteps));
          wallcycle_start(wcycle, ewcSTEP);
  
          t = step;
  
          if (MASTER(cr))
          {
              MimicCommunicator::getCoords(&state_global->x, state_global->natoms);
          }
  
          if (ir->efep != efepNO)
          {
              state->lambda = currentLambdas(step, *(ir->fepvals), state_global->fep_state);
          }
  
          if (MASTER(cr))
          {
              const bool constructVsites = ((vsite != nullptr) && mdrunOptions.rerunConstructVsites);
              if (constructVsites && DOMAINDECOMP(cr))
              {
                  gmx_fatal(FARGS,
                            "Vsite recalculation with -rerun is not implemented with domain "
                            "decomposition, "
                            "use a single rank");
              }
          }
  
          if (DOMAINDECOMP(cr))
          {
              /* Repartition the domain decomposition */
              const bool bMasterState = true;
              dd_partition_system(fplog, mdlog, step, cr, bMasterState, nstglobalcomm, state_global,
                                  *top_global, ir, imdSession, pull_work, state, &f, mdAtoms, &top,
                                  fr, vsite, constr, nrnb, wcycle, mdrunOptions.verbose);
              shouldCheckNumberOfBondedInteractions = true;
          }
  
          if (MASTER(cr))
          {
              EnergyOutput::printHeader(fplog, step, t); /* can we improve the information printed here? */
          }
  
          if (ir->efep != efepNO)
          {
              update_mdatoms(mdatoms, state->lambda[efptMASS]);
          }
  
          force_flags = (GMX_FORCE_STATECHANGED | GMX_FORCE_DYNAMICBOX | GMX_FORCE_ALLFORCES
                         | GMX_FORCE_VIRIAL | // TODO: Get rid of this once #2649 is solved
                         GMX_FORCE_ENERGY | (doFreeEnergyPerturbation ? GMX_FORCE_DHDL : 0));
  
          if (shellfc)
          {
              /* Now is the time to relax the shells */
              relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
                                  imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
                                  state->natoms, state->x.arrayRefWithPadding(),
                                  state->v.arrayRefWithPadding(), state->box, state->lambda,
                                  &state->hist, &f.view(), force_vir, mdatoms, nrnb, wcycle, shellfc,
                                  fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
          }
          else
          {
              /* The coordinates (x) are shifted (to get whole molecules)
               * in do_force.
               * This is parallellized as well, and does communication too.
               * Check comments in sim_util.c
               */
              Awh*       awh = nullptr;
              gmx_edsam* ed  = nullptr;
              do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
                       wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
                       &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork,
                       vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags, ddBalanceRegionHandler);
          }
  
          /* Now we have the energies and forces corresponding to the
           * coordinates at time t.
           */
          {
              const bool isCheckpointingStep = false;
              const bool doRerun             = false;
              const bool bSumEkinhOld        = false;
              do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
                                       state_global, observablesHistory, top_global, fr, outf,
                                       energyOutput, ekind, f.view().force(), isCheckpointingStep,
                                       doRerun, isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
          }
  
          stopHandler->setSignal();
  
          if (vsite != nullptr)
          {
              wallcycle_start(wcycle, ewcVSITECONSTR);
              vsite->construct(state->x, ir->delta_t, state->v, state->box);
              wallcycle_stop(wcycle, ewcVSITECONSTR);
          }
  
          {
              const bool          doInterSimSignal = false;
              const bool          doIntraSimSignal = true;
              bool                bSumEkinhOld     = false;
              t_vcm*              vcm              = nullptr;
              SimulationSignaller signaller(&signals, cr, ms, doInterSimSignal, doIntraSimSignal);
  
              compute_globals(gstat, cr, ir, fr, ekind, makeConstArrayRef(state->x),
                              makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, wcycle,
                              enerd, nullptr, nullptr, nullptr, nullptr, constr, &signaller,
                              state->box, &totalNumberOfBondedInteractions, &bSumEkinhOld,
                              CGLO_GSTAT | CGLO_ENERGY
                                      | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS
                                                                               : 0));
              checkNumberOfBondedInteractions(mdlog, cr, totalNumberOfBondedInteractions, top_global,
                                              &top, makeConstArrayRef(state->x), state->box,
                                              &shouldCheckNumberOfBondedInteractions);
          }
  
          {
              gmx::HostVector<gmx::RVec>     fglobal(top_global->natoms);
              gmx::ArrayRef<gmx::RVec>       ftemp;
              gmx::ArrayRef<const gmx::RVec> flocal = f.view().force();
              if (DOMAINDECOMP(cr))
              {
                  ftemp = gmx::makeArrayRef(fglobal);
                  dd_collect_vec(cr->dd, state->ddp_count, state->ddp_count_cg_gl, state->cg_gl,
                                 flocal, ftemp);
              }
              else
              {
                  ftemp = f.view().force();
              }
  
              if (MASTER(cr))
              {
                  MimicCommunicator::sendEnergies(enerd->term[F_EPOT]);
                  MimicCommunicator::sendForces(ftemp, state_global->natoms);
              }
          }
  
  
          /* Note: this is OK, but there are some numerical precision issues with using the convergence of
             the virial that should probably be addressed eventually. state->veta has better properies,
             but what we actually need entering the new cycle is the new shake_vir value. Ideally, we could
             generate the new shake_vir, but test the veta value for convergence.  This will take some thought. */
  
          if (ir->efep != efepNO)
          {
              /* Sum up the foreign energy and dhdl terms for md and sd.
                 Currently done every step so that dhdl is correct in the .edr */
              accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals);
          }
  
          /* Output stuff */
          if (MASTER(cr))
          {
              const bool bCalcEnerStep = true;
              energyOutput.addDataAtEnergyStep(
                      doFreeEnergyPerturbation, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals,
                      ir->expandedvals, state->box,
                      PTCouplingArrays({ state->boxv, state->nosehoover_xi, state->nosehoover_vxi,
                                         state->nhpres_xi, state->nhpres_vxi }),
                      state->fep_state, shake_vir, force_vir, total_vir, pres, ekind, mu_tot, constr);
  
              const bool do_ene = true;
              const bool do_log = true;
              Awh*       awh    = nullptr;
              const bool do_dr  = ir->nstdisreout != 0;
              const bool do_or  = ir->nstorireout != 0;
  
              EnergyOutput::printAnnealingTemperatures(do_log ? fplog : nullptr, groups, &(ir->opts));
              energyOutput.printStepToEnergyFile(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or,
                                                 do_log ? fplog : nullptr, step, t, fr->fcdata.get(), awh);
  
              if (do_per_step(step, ir->nstlog))
              {
                  if (fflush(fplog) != 0)
                  {
                      gmx_fatal(FARGS, "Cannot flush logfile - maybe you are out of disk space?");
                  }
              }
          }
  
          /* Print the remaining wall clock time for the run */
          if (isMasterSimMasterRank(ms, MASTER(cr)) && (mdrunOptions.verbose || gmx_got_usr_signal()))
          {
              if (shellfc)
              {
                  fprintf(stderr, "\n");
              }
              print_time(stderr, walltime_accounting, step, ir, cr);
          }
  
          cycles = wallcycle_stop(wcycle, ewcSTEP);
          if (DOMAINDECOMP(cr) && wcycle)
          {
              dd_cycles_add(cr->dd, cycles, ddCyclStep);
          }
  
          /* increase the MD step number */
          step++;
          step_rel++;
      }
      /* End of main MD loop */
  
      /* Closing TNG files can include compressing data. Therefore it is good to do that
       * before stopping the time measurements. */
      mdoutf_tng_close(outf);
  
      /* Stop measuring walltime */
      walltime_accounting_end_time(walltime_accounting);
  
      if (MASTER(cr))
      {
          MimicCommunicator::finalize();
      }
  
      if (!thisRankHasDuty(cr, DUTY_PME))
      {
          /* Tell the PME only node to finish */
          gmx_pme_send_finish(cr);
      }
  
      done_mdoutf(outf);
  
      done_shellfc(fplog, shellfc, step_rel);
  
      walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
  }
  