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  #ifndef GMX_TOPOLOGY_TOPOLOGY_H
  #define GMX_TOPOLOGY_TOPOLOGY_H
  
  #include <cstdio>
  
  #include <vector>
  
  #include "gromacs/math/vectypes.h"
  #include "gromacs/topology/atoms.h"
  #include "gromacs/topology/block.h"
  #include "gromacs/topology/forcefieldparameters.h"
  #include "gromacs/topology/idef.h"
  #include "gromacs/topology/symtab.h"
  #include "gromacs/utility/enumerationhelpers.h"
  #include "gromacs/utility/listoflists.h"
  #include "gromacs/utility/unique_cptr.h"
  
  enum class SimulationAtomGroupType : int
  {
      TemperatureCoupling,
      EnergyOutput,
      Acceleration,
      Freeze,
      User1,
      User2,
      MassCenterVelocityRemoval,
      CompressedPositionOutput,
      OrientationRestraintsFit,
      QuantumMechanics,
      Count
  };
  
  //! Short strings used for describing atom groups in log and energy files
  const char* shortName(SimulationAtomGroupType type);
  
  // const char *shortName(int type); // if necessary
  
  /*! \brief Molecules type data: atoms, interactions and exclusions */
  struct gmx_moltype_t
  {
      gmx_moltype_t();
  
      ~gmx_moltype_t();
  
      /*! \brief Deleted copy assignment operator to avoid (not) freeing pointers */
      gmx_moltype_t& operator=(const gmx_moltype_t&) = delete;
  
      /*! \brief Default copy constructor */
      gmx_moltype_t(const gmx_moltype_t&) = default;
  
      char**                name;  /**< Name of the molecule type            */
      t_atoms               atoms; /**< The atoms in this molecule           */
      InteractionLists      ilist; /**< Interaction list with local indices  */
      gmx::ListOfLists<int> excls; /**< The exclusions                       */
  };
  
  /*! \brief Block of molecules of the same type, used in gmx_mtop_t */
  struct gmx_molblock_t
  {
      int                    type = -1; /**< The molecule type index in mtop.moltype  */
      int                    nmol = 0;  /**< The number of molecules in this block    */
      std::vector<gmx::RVec> posres_xA; /**< Position restraint coordinates for top A */
      std::vector<gmx::RVec> posres_xB; /**< Position restraint coordinates for top B */
  };
  
  /*! \brief Indices for a gmx_molblock_t, derived from other gmx_mtop_t contents */
  struct MoleculeBlockIndices
  {
      int numAtomsPerMolecule; /**< Number of atoms in a molecule in the block */
      int globalAtomStart;     /**< Global atom index of the first atom in the block */
      int globalAtomEnd;       /**< Global atom index + 1 of the last atom in the block */
      int globalResidueStart;  /**< Global residue index of the first residue in the block */
      int residueNumberStart; /**< Residue numbers start from this value if the number of residues per molecule is <= maxres_renum */
      int moleculeIndexStart; /**< Global molecule indexing starts from this value */
  };
  
  /*! \brief Contains the simulation atom groups.
   *
   * Organized as containers for the different
   * SimulationAtomGroupTypes
   */
  struct SimulationGroups
  {
      // TODO: collect groups and groupNumbers in a struct for each group type
      //! Group numbers for each of the different SimulationAtomGroupType groups.
      gmx::EnumerationArray<SimulationAtomGroupType, AtomGroupIndices> groups;
      //! Names of groups, stored as pointer to the entries in the symbol table.
      std::vector<char**> groupNames;
      //! Indices into groups for each atom for each of the different SimulationAtomGroupType groups.
      gmx::EnumerationArray<SimulationAtomGroupType, std::vector<unsigned char>> groupNumbers;
  
      /*! \brief
       * Number of atoms for which group numbers are stored for a single SimulationGroup.
       *
       * \param[in] group  The group type.
       */
      int numberOfGroupNumbers(SimulationAtomGroupType group) const
      {
          return static_cast<int>(groupNumbers[group].size());
      }
  };
  
  /*! \brief
   * Returns group number of an input group for a given atom.
   *
   * Returns the group \p type for \p atom in \p group, or 0 if the
   * entries for all atoms in the group are 0 and the pointer is thus null.
   *
   * \param[in] group Group to check.
   * \param[in] type  Type of group to check.
   * \param[in] atom  Atom to check if it has an entry.
   */
  int getGroupType(const SimulationGroups& group, SimulationAtomGroupType type, int atom);
  
  /* The global, complete system topology struct, based on molecule types.
   * This structure should contain no data that is O(natoms) in memory.
   *
   * TODO: Find a solution for ensuring that the derived data is in sync
   *       with the primary data, possibly by converting to a class.
   */
  struct gmx_mtop_t //NOLINT(clang-analyzer-optin.performance.Padding)
  {
      gmx_mtop_t();
  
      ~gmx_mtop_t();
  
      //! Name of the topology.
      char** name = nullptr;
      //! Force field parameters used.
      gmx_ffparams_t ffparams;
      //! Vector of different molecule types.
      std::vector<gmx_moltype_t> moltype;
      //! Vector of different molecule blocks.
      std::vector<gmx_molblock_t> molblock;
      //! Are there intermolecular interactions?
      bool bIntermolecularInteractions = false;
      /* \brief
       * List of intermolecular interactions using system wide
       * atom indices, either NULL or size F_NRE
       */
      std::unique_ptr<InteractionLists> intermolecular_ilist = nullptr;
      //! Number of global atoms.
      int natoms = 0;
      //! Atomtype properties
      t_atomtypes atomtypes;
      //! Groups of atoms for different purposes
      SimulationGroups groups;
      //! The legacy symbol table
      t_symtab symtab;
      //! Tells whether we have valid molecule indices
      bool haveMoleculeIndices = false;
      /*! \brief List of global atom indices of atoms between which
       * non-bonded interactions must be excluded.
       */
      std::vector<int> intermolecularExclusionGroup;
  
      //! Maximum number of residues in molecule to trigger renumbering of residues
      int maxResiduesPerMoleculeToTriggerRenumber() const
      {
          return maxResiduesPerMoleculeToTriggerRenumber_;
      }
      //! Maximum residue number that is not renumbered.
      int maxResNumberNotRenumbered() const { return maxResNumberNotRenumbered_; }
      /*! \brief Finalize this data structure.
       *
       * Should be called after generating or reading mtop, to set some compute
       * intesive variables to avoid N^2 operations later on.
       *
       * \todo Move into a builder class, once available.
       */
      void finalize();
  
      /* Derived data below */
      //! Indices for each molblock entry for fast lookup of atom properties
      std::vector<MoleculeBlockIndices> moleculeBlockIndices;
  
  private:
      //! Build the molblock indices
      void buildMolblockIndices();
      //! Maximum number of residues in molecule to trigger renumbering of residues
      int maxResiduesPerMoleculeToTriggerRenumber_ = 0;
      //! The maximum residue number in moltype that is not renumbered
      int maxResNumberNotRenumbered_ = -1;
  };
  
  /*! \brief
   * The fully written out topology for a domain over its lifetime
   *
   * Also used in some analysis code.
   */
  struct gmx_localtop_t
  {
      //! Constructor used for normal operation, manages own resources.
      gmx_localtop_t(const gmx_ffparams_t& ffparams);
  
      //! The interaction function definition
      InteractionDefinitions idef;
      //! The exclusions
      gmx::ListOfLists<int> excls;
  };
  
  /* The old topology struct, completely written out, used in analysis tools */
  typedef struct t_topology
  {
      char**      name;                        /* Name of the topology                 */
      t_idef      idef;                        /* The interaction function definition  */
      t_atoms     atoms;                       /* The atoms                            */
      t_atomtypes atomtypes;                   /* Atomtype properties                  */
      t_block     mols;                        /* The molecules                        */
      gmx_bool    bIntermolecularInteractions; /* Inter.mol. int. ?   */
      /* Note that the exclusions are not stored in t_topology */
      t_symtab symtab; /* The symbol table                     */
  } t_topology;
  
  void init_top(t_topology* top);
  void done_top(t_topology* top);
  // Frees both t_topology and gmx_mtop_t when the former has been created from
  // the latter.
  void done_top_mtop(t_topology* top, gmx_mtop_t* mtop);
  
  bool gmx_mtop_has_masses(const gmx_mtop_t* mtop);
  bool gmx_mtop_has_charges(const gmx_mtop_t* mtop);
  bool gmx_mtop_has_perturbed_charges(const gmx_mtop_t& mtop);
  bool gmx_mtop_has_atomtypes(const gmx_mtop_t* mtop);
  bool gmx_mtop_has_pdbinfo(const gmx_mtop_t* mtop);
  
  void pr_mtop(FILE* fp, int indent, const char* title, const gmx_mtop_t* mtop, gmx_bool bShowNumbers, gmx_bool bShowParameters);
  void pr_top(FILE* fp, int indent, const char* title, const t_topology* top, gmx_bool bShowNumbers, gmx_bool bShowParameters);
  
  /*! \brief Compare two mtop topologies.
   *
   * \param[in] fp File pointer to write to.
   * \param[in] mtop1 First topology to compare.
   * \param[in] mtop2 Second topology to compare.
   * \param[in] relativeTolerance Relative tolerance for comparison.
   * \param[in] absoluteTolerance Absolute tolerance for comparison.
   */
  void compareMtop(FILE* fp, const gmx_mtop_t& mtop1, const gmx_mtop_t& mtop2, real relativeTolerance, real absoluteTolerance);
  
  /*! \brief Check perturbation parameters in topology.
   *
   * \param[in] fp File pointer to write to.
   * \param[in] mtop1 Topology to check perturbation parameters in.
   * \param[in] relativeTolerance Relative tolerance for comparison.
   * \param[in] absoluteTolerance Absolute tolerance for comparison.
   */
  void compareMtopAB(FILE* fp, const gmx_mtop_t& mtop1, real relativeTolerance, real absoluteTolerance);
  
  /*! \brief Compare groups.
   *
   * \param[in] fp File pointer to write to.
   * \param[in] g0 First group for comparison.
   * \param[in] g1 Second group for comparison.
   * \param[in] natoms0 Number of atoms for first group.
   * \param[in] natoms1 Number of atoms for second group.
   */
  void compareAtomGroups(FILE* fp, const SimulationGroups& g0, const SimulationGroups& g1, int natoms0, int natoms1);
  
  //! Typedef for gmx_localtop in analysis tools.
  using ExpandedTopologyPtr = std::unique_ptr<gmx_localtop_t>;
  
  void copy_moltype(const gmx_moltype_t* src, gmx_moltype_t* dst);
  
  #endif
  