text: /*
   * This file is part of the GROMACS molecular simulation package.
   *
   * Copyright (c) 2019, 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
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  /*! \internal \file
   * \brief
   * Implements the PairSearch class
   *
   * \author Berk Hess <hess@kth.se>
   * \ingroup module_nbnxm
   */
  
  #include "gmxpre.h"
  
  #include "pairsearch.h"
  
  #include "gromacs/nbnxm/pairlist.h"
  #include "gromacs/utility/smalloc.h"
  
  
  void SearchCycleCounting::printCycles(FILE                               *fp,
                                        gmx::ArrayRef<const PairsearchWork> work) const
  {
      fprintf(fp, "\n");
      fprintf(fp, "ns %4d grid %4.1f search %4.1f",
              cc_[enbsCCgrid].count(),
              cc_[enbsCCgrid].averageMCycles(),
              cc_[enbsCCsearch].averageMCycles());
  
      if (work.size() > 1)
      {
          if (cc_[enbsCCcombine].count() > 0)
          {
              fprintf(fp, " comb %5.2f",
                      cc_[enbsCCcombine].averageMCycles());
          }
          fprintf(fp, " s. th");
          for (const PairsearchWork &workEntry : work)
          {
              fprintf(fp, " %4.1f",
                      workEntry.cycleCounter.averageMCycles());
          }
      }
      fprintf(fp, "\n");
  }
  
  /*! \brief Frees the contents of a legacy t_nblist struct */
  static void free_nblist(t_nblist *nl)
  {
      sfree(nl->iinr);
      sfree(nl->gid);
      sfree(nl->shift);
      sfree(nl->jindex);
      sfree(nl->jjnr);
      sfree(nl->excl_fep);
  }
  
  #ifndef DOXYGEN
  
  PairsearchWork::PairsearchWork() :
      cp0({{0}}
          ),
      buffer_flags({0, nullptr, 0}),
      ndistc(0),
      nbl_fep(new t_nblist),
      cp1({{0}})
  {
      nbnxn_init_pairlist_fep(nbl_fep.get());
  }
  
  #endif // !DOXYGEN
  
  PairsearchWork::~PairsearchWork()
  {
      sfree(buffer_flags.flag);
  
      free_nblist(nbl_fep.get());
  }
  
  PairSearch::PairSearch(const int                 ePBC,
                         const ivec               *numDDCells,
                         const gmx_domdec_zones_t *ddZones,
                         const PairlistType        pairlistType,
                         const bool                haveFep,
                         const int                 maxNumThreads) :
      gridSet_(ePBC, numDDCells, ddZones, pairlistType, haveFep, maxNumThreads),
      work_(maxNumThreads)
  {
      cycleCounting_.recordCycles_ = (getenv("GMX_NBNXN_CYCLE") != nullptr);
  }
  