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   * This file is part of the GROMACS molecular simulation package.
   *
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  /*! \libinternal \file
   * \brief Declares the VirtualSitesHandler class and vsite standalone functions
   *
   * \author Berk Hess <hess@kth.se>
   * \ingroup module_mdlib
   * \inlibraryapi
   */
  
  #ifndef GMX_MDLIB_VSITE_H
  #define GMX_MDLIB_VSITE_H
  
  #include <memory>
  
  #include "gromacs/math/vectypes.h"
  #include "gromacs/topology/idef.h"
  #include "gromacs/utility/real.h"
  
  struct gmx_domdec_t;
  struct gmx_mtop_t;
  struct t_commrec;
  struct InteractionList;
  struct t_nrnb;
  struct gmx_wallcycle;
  enum class PbcType : int;
  enum class ParticleType : int;
  
  namespace gmx
  {
  class RangePartitioning;
  template<typename T>
  class ArrayRef;
  
  /*! \brief The start value of the vsite indices in the ftype enum
   *
   * The validity of the start and end values is checked in makeVirtualSitesHandler().
   * This is used to avoid loops over all ftypes just to get the vsite entries.
   * (We should replace the fixed ilist array by only the used entries.)
   */
  static constexpr int c_ftypeVsiteStart = F_VSITE1;
  //! The start and end value of the vsite indices in the ftype enum
  static constexpr int c_ftypeVsiteEnd = F_VSITEN + 1;
  
  //! Type for storing PBC atom information for all vsite types in the system
  typedef std::array<std::vector<int>, c_ftypeVsiteEnd - c_ftypeVsiteStart> VsitePbc;
  
  //! Whether we calculate vsite positions, velocities, or both
  enum class VSiteOperation
  {
      Positions,              //!< Calculate only positions
      Velocities,             //!< Calculate only velocities
      PositionsAndVelocities, //!< Calculate both positions and velocities
      Count                   //!< The number of entries
  };
  
  /*! \libinternal
   * \brief Class that handles construction of vsites and spreading of vsite forces
   */
  class VirtualSitesHandler
  {
  public:
      //! Constructor, used only be the makeVirtualSitesHandler() factory function
      VirtualSitesHandler(const gmx_mtop_t&                 mtop,
                          gmx_domdec_t*                     domdec,
                          PbcType                           pbcType,
                          ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType);
  
      ~VirtualSitesHandler();
  
      //! Returns the number of virtual sites acting over multiple update groups
      int numInterUpdategroupVirtualSites() const;
  
      //! Set VSites and distribute VSite work over threads, should be called after each DD partitioning
      void setVirtualSites(ArrayRef<const InteractionList> ilist,
                           int                             numAtoms,
                           int                             homenr,
                           ArrayRef<const ParticleType>    ptype);
  
      /*! \brief Create positions of vsite atoms based for the local system
       *
       * \param[in,out] x          The coordinates
       * \param[in,out] v          The velocities, needed if operation requires it
       * \param[in]     box        The box
       * \param[in]     operation  Whether we calculate positions, velocities, or both
       */
      void construct(ArrayRef<RVec> x, ArrayRef<RVec> v, const matrix box, VSiteOperation operation) const;
  
      //! Tells how to handle virial contributions due to virtual sites
      enum class VirialHandling : int
      {
          None,     //!< Do not compute virial contributions
          Pbc,      //!< Add contributions working over PBC to shift forces
          NonLinear //!< Compute contributions due to non-linear virtual sites
      };
  
      /*! \brief Spread the force operating on the vsite atoms on the surrounding atoms.
       *
       * vsite should point to a valid object.
       * The virialHandling parameter determines how virial contributions are handled.
       * If this is set to Linear, shift forces are accumulated into fshift.
       * If this is set to NonLinear, non-linear contributions are added to virial.
       * This non-linear correction is required when the virial is not calculated
       * afterwards from the particle position and forces, but in a different way,
       * as for instance for the PME mesh contribution.
       */
      void spreadForces(ArrayRef<const RVec> x,
                        ArrayRef<RVec>       f,
                        VirialHandling       virialHandling,
                        ArrayRef<RVec>       fshift,
                        matrix               virial,
                        t_nrnb*              nrnb,
                        const matrix         box,
                        gmx_wallcycle*       wcycle);
  
  private:
      //! Implementation type.
      class Impl;
      //! Implementation object.
      std::unique_ptr<Impl> impl_;
  };
  
  /*! \brief Create positions of vsite atoms based for the local system
   *
   * \param[in,out] x        The coordinates
   * \param[in]     ip       Interaction parameters
   * \param[in]     ilist    The interaction list
   */
  void constructVirtualSites(ArrayRef<RVec>                  x,
                             ArrayRef<const t_iparams>       ip,
                             ArrayRef<const InteractionList> ilist);
  
  /*! \brief Create positions of vsite atoms for the whole system assuming all molecules are wholex
   *
   * \param[in]     mtop  The global topology
   * \param[in,out] x     The global coordinates
   */
  void constructVirtualSitesGlobal(const gmx_mtop_t& mtop, ArrayRef<RVec> x);
  
  //! Tells how to handle virial contributions due to virtual sites
  enum class VirtualSiteVirialHandling : int
  {
      None,     //!< Do not compute virial contributions
      Pbc,      //!< Add contributions working over PBC to shift forces
      NonLinear //!< Compute contributions due to non-linear virtual sites
  };
  
  //! Return the number of non-linear virtual site constructions in the system
  int countNonlinearVsites(const gmx_mtop_t& mtop);
  
  /*! \brief Return the number of virtual sites that cross update groups
   *
   * \param[in] mtop                           The global topology
   * \param[in] updateGroupingsPerMoleculeType  Update grouping per molecule type, pass empty when not using update groups
   */
  int countInterUpdategroupVsites(const gmx_mtop_t&                 mtop,
                                  ArrayRef<const RangePartitioning> updateGroupingsPerMoleculeType);
  
  /*! \brief Create the virtual site handler
   *
   * \param[in] mtop                           The global topology
   * \param[in] cr                             The communication record
   * \param[in] pbcType                        The type of PBC
   * \param[in] updateGroupingPerMoleculeType  Update grouping per molecule type, pass
   *                                           empty when not using update groups
   * \returns A valid vsite handler object or nullptr when there are no virtual sites
   */
  std::unique_ptr<VirtualSitesHandler>
  makeVirtualSitesHandler(const gmx_mtop_t&                 mtop,
                          const t_commrec*                  cr,
                          PbcType                           pbcType,
                          ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType);
  
  } // namespace gmx
  
  #endif
  