ConfigDoF.hh

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#ifndef ConfigDoF_HH
#define ConfigDoF_HH

#include "casm/container/Array.hh"
#include "casm/clex/Correlation.hh"
//#include "casm/symmetry/PermuteIterator.hh"

namespace CASM {


  class PermuteIterator;
  class PrimClex;
  class Supercell;
  class Clexulator;


  class ConfigDoF {

  public:

    // typedefs to provide flexibility if we eventually change to a Eigen::Matrix<3,Eigen::Dynamic>
    typedef Eigen::MatrixXd displacement_matrix_t;

    // Can treat as a Eigen::VectorXd
    typedef displacement_matrix_t::ColXpr displacement_t;
    typedef displacement_matrix_t::ConstColXpr const_displacement_t;

    EIGEN_MAKE_ALIGNED_OPERATOR_NEW

    ConfigDoF(Index N = 0, double _tol = TOL);

    ConfigDoF(const Array<int> &_occupation, double _tol = TOL);

    ConfigDoF(const Array<int> &_occupation, const Eigen::MatrixXd &_displacement, const Eigen::Matrix3d &_deformation, double _tol = TOL);

  public:

    Index size() const {
      return m_N;
    }

    double tol()const {
      return m_tol;
    }

    int &occ(Index i) {
      return m_occupation[i];
    };

    const int &occ(Index i) const {
      return m_occupation[i];
    };

    const Array<int> &occupation() const {
      return m_occupation;
    };

    displacement_t disp(Index i) {
      return m_displacement.col(i);
    };

    const_displacement_t disp(Index i) const {
      return m_displacement.col(i);
    };

    const displacement_matrix_t &displacement() const {
      return m_displacement;
    };

    const Eigen::Matrix3d &deformation() const {
      return m_deformation;
    }

    const double &F(Index i, Index j) const {
      return m_deformation(i, j);
    }

    double &F(Index i, Index j) {
      assert(has_deformation() && "Non-const method ConfigDoF::F() should only be called after ConfigDoF::set_deformation()!!!");
      return m_deformation(i, j);
    }

    bool has_deformation() const {
      return m_has_deformation;
    }

    bool has_displacement() const {
      return size() != 0 && displacement().cols() == size();
    }

    bool has_occupation() const {
      return size() != 0 && occupation().size() == size();
    }

    //**** MUTATORS ****
    void set_occupation(const Array<int> &_occupation);

    void set_displacement(const displacement_matrix_t &_displacement);

    void set_deformation(const Eigen::Matrix3d &_deformation);

    void clear();

    void clear_occupation();
    void clear_displacement();
    void clear_deformation();

    void swap(ConfigDoF &RHS);

    //**** I/O ****
    jsonParser &to_json(jsonParser &json) const;
    void from_json(const jsonParser &json);


  private:

    // ***DON'T FORGET: If you add something here, also update ConfigDoF::swap!!


    Index m_N;

    Array<int> m_occupation;

    displacement_matrix_t m_displacement;

    Eigen::Matrix3d m_deformation;

    bool m_has_deformation;

    mutable double m_tol;

    // *** PRIVATE NON-CONST ACCESS
    Array<int> &_occupation() {
      return m_occupation;
    };

    displacement_matrix_t &_displacement() {
      return m_displacement;
    };

    Eigen::Matrix3d &_deformation() {
      return m_deformation;
    }

  };

  jsonParser &to_json(const ConfigDoF &value, jsonParser &json);

  void from_json(ConfigDoF &value, const jsonParser &json);

  // Calculate transformed ConfigDoF from PermuteIterator via
  //   apply(permute_iterator, dof)
  ConfigDoF &apply(const PermuteIterator &it, ConfigDoF &dof);

  void swap(ConfigDoF &A, ConfigDoF &B);

  Correlation correlations(const ConfigDoF &configdof, const Supercell &scel, Clexulator &clexulator);

  Eigen::VectorXd correlations_vec(const ConfigDoF &configdof, const Supercell &scel, Clexulator &clexulator);

  ReturnArray<int> get_num_each_molecule(const ConfigDoF &configdof, const Supercell &scel);

  Eigen::VectorXi get_num_each_molecule_vec(const ConfigDoF &configdof, const Supercell &scel);

  Eigen::VectorXd comp_n(const ConfigDoF &configdof, const Supercell &scel);

  inline
  void reset_properties(ConfigDoF &_dof) {
    return;
  }

}

#endif