OrbitBranch.hh

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#ifndef ORBITBRANCH_HH
#define ORBITBRANCH_HH

#include <iostream>
#include <fstream>

#include "casm/clusterography/Orbit.hh"
#include "casm/clusterography/SiteCluster.hh"

namespace CASM {
  class Lattice;

  class Supercell;

  template<typename ClustType>
  class GenericOrbitBranch;

  template<typename ClustType>
  class GenericOrbitree;

  typedef GenericOrbitBranch<SiteCluster> SiteOrbitBranch;
  typedef GenericOrbitree<SiteCluster> SiteOrbitree;

  //GenericOrbitBranch Class definition begins here:
  template<typename ClustType>
  class GenericOrbitBranch : public Array< GenericOrbit<ClustType> > {
    Index m_num_sites;
  public:

    using Array< GenericOrbit<ClustType> > :: size;
    using Array< GenericOrbit<ClustType> > :: at;
    using Array< GenericOrbit<ClustType> > :: back;

    ClustType pivot;

    Array<Index> index;

    GenericOrbitBranch(const Lattice &init_home) : m_num_sites(-1), pivot(init_home) { };
    GenericOrbitBranch(const Lattice &init_home, Index tnum_sites) : m_num_sites(tnum_sites), pivot(init_home) { };
    GenericOrbitBranch(const ClustType &init_pivot) : m_num_sites(-1), pivot(init_pivot) { };
    GenericOrbitBranch(const ClustType &init_pivot, Index tnum_sites) : m_num_sites(tnum_sites), pivot(init_pivot) { };

    void clear();

    GenericOrbit<ClustType> &orbit(Index no);
    const GenericOrbit<ClustType> &orbit(Index no) const;

    Index num_sites() const {
      return m_num_sites;
    };

    ClustType &prototype(Index no);
    const ClustType &prototype(Index no) const;

    const ClustType &equiv(Index no, Index ne) const;
    ClustType &equiv(Index no, Index ne);

    Index size(Index no) const;

    void set_lattice(const Lattice &new_lat, COORD_TYPE mode);

    void set_pivot(const ClustType &new_pivot);

    void push_back(const GenericOrbit<ClustType> &new_orbit);

    void print(std::ostream &stream, COORD_TYPE mode = FRAC);

    void sort(); //Done - Alex

    // Alex did these
    Index find(const ClustType &test_clust, double tol)const;

    bool contains(const ClustType &test_clust, double tol)const;

    GenericOrbitBranch &apply_sym(const SymOp &op);

    void generate_asymmetric_unit(const Array<typename ClustType::WhichCoordType > &basis, const SymGroup &factor_group, double tol);

    bool extract_orbits_including(const ClustType &pivot, GenericOrbitBranch &flowerbranch, double tol) const;

    //Translation operators need to be defined
    GenericOrbitBranch &operator+=(const Coordinate &shift) {
      return (*this);
    };
    GenericOrbitBranch &operator-=(const Coordinate &shift) {
      return (*this);
    };

    jsonParser &to_json(jsonParser &json) const;

    void from_json(const jsonParser &json);

  };

  // Some template weirdness is not allowing this to compile on flux.
  //   So I'm specializing for SiteCluster in ClusterFunctions.hh/.cc
  /*
  template<typename ClustType>
  jsonParser &to_json(const GenericOrbitBranch<ClustType> &branch, jsonParser &json) {
    return branch.to_json(json);
  }

  template<typename ClustType>
  void from_json(GenericOrbitBranch<ClustType> &branch, const jsonParser &json) {
    branch.from_json(json);
  }
  */
};

#include "casm/clusterography/OrbitBranch_impl.hh"

#endif