text: /*
   * This file is part of the GROMACS molecular simulation package.
   *
   * Copyright (c) 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.
   *
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  /*! \libinternal \file
   *
   * \brief Declares the WholeMolecules class for generating whole molecules
   *
   * \author Berk Hess <hess@kth.se>
   * \ingroup module_mdlib
   * \inlibraryapi
   */
  #ifndef GMX_MDLIB_WHOLEMOLECULETRANSFORM_H
  #define GMX_MDLIB_WHOLEMOLECULETRANSFORM_H
  
  #include <vector>
  
  #include "gromacs/math/vectypes.h"
  #include "gromacs/pbcutil/mshift.h"
  #include "gromacs/utility/arrayref.h"
  
  struct gmx_mtop_t;
  enum class PbcType : int;
  
  namespace gmx
  {
  
  /*! \libinternal
   * \brief This class manages a coordinate buffer with molecules not split
   * over periodic boundary conditions for use in force calculations
   * which require whole molecules.
   *
   * Note: This class should not be used for computation of forces which
   *       have virial contributions through shift forces.
   */
  class WholeMoleculeTransform
  {
  public:
      /*! \brief Constructor */
      WholeMoleculeTransform(const gmx_mtop_t& mtop, PbcType pbcType);
  
      /*! \brief Updates the graph when atoms have been shifted by periodic vectors */
      void updateForAtomPbcJumps(ArrayRef<const RVec> x, const matrix box);
  
      /*! \brief Create and return coordinates with whole molecules for input coordinates \p x
       *
       * \param[in] x  Input coordinates, should not have periodic displacement compared
       *               with the coordinates passed in the last call to \p updateForAtomPbcJumps().
       * \param[in] box  The current periodic image vectors
       *
       * Note: this operation is not free. If you need whole molecules coordinates
       * more than once during the force calculation, store the result and reuse it.
       */
      ArrayRef<const RVec> wholeMoleculeCoordinates(ArrayRef<const RVec> x, const matrix box);
  
  private:
      //! The type of PBC
      PbcType pbcType_;
      //! The graph
      t_graph graph_;
      //! Buffer for storing coordinates for whole molecules
      std::vector<RVec> wholeMoleculeCoordinates_;
  };
  
  } // namespace gmx
  
  #endif
  