Structure.hh

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#ifndef STRUCTURE_HH
#define STRUCTURE_HH

#include <iostream>
#include <cstdlib>
#include <cmath>

#include "casm/crystallography/BasicStructure.hh"
#include "casm/crystallography/Site.hh"

namespace CASM {
  //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

  class MasterSymGroup;

  class SiteCluster;

  template<typename ClustType>
  class GenericOrbitree;

  typedef GenericOrbitree<SiteCluster> SiteOrbitree;

  class Structure : public BasicStructure<Site> {
  protected: //PROTECTED DATA MEMBERS

    mutable MasterSymGroup m_factor_group;
    mutable SymGroupRepID basis_perm_rep_ID;
    bool SD_flag;

  public: //PUBLIC DATA MEMBERS (Public for now)

    //std::string title;     // user-specified name of this structure
    //Lattice lattice;     // Lattice vectors that specifies periodicity of the crystal
    //Array<Site> basis;   // List of basis sites of the crystal.  Each site may host a molecule or a specie



  private: //PRIVATE METHODS

    void main_print(std::ostream &stream, COORD_TYPE mode, bool version5, int option) const;


  public: //PUBLIC METHODS

    //  ****Constructors****
    Structure() : BasicStructure<Site>() {}
    explicit Structure(const Lattice &init_lat) : BasicStructure<Site>(init_lat) {}
    explicit Structure(const BasicStructure<Site> &base) : BasicStructure<Site>(base) {}
    explicit Structure(const fs::path &filepath);

    Structure(const Structure &RHS);

    //  ****Inspectors/Accessors****
    //      - non-const versions try to populate data members before access
    const MasterSymGroup &factor_group() const;
    //const MasterSymGroup &factor_group();
    const SymGroup &point_group() const;
    //const SymGroup &point_group();
    SymGroupRep const *basis_permutation_symrep()const;
    SymGroupRepID basis_permutation_symrep_ID()const;

    std::vector<Specie> get_struc_specie() const;
    std::vector<Molecule> get_struc_molecule() const;
    std::vector<std::string> get_struc_molecule_name() const;
    Eigen::VectorXi get_num_each_specie() const;
    Eigen::VectorXi get_num_each_molecule() const;

    // ****Mutators****

    //   - Basic assignment/bookkeeping

    Structure &operator=(const Structure &RHS);

    void copy_attributes_from(const Structure &RHS);

    void reset();

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

    //   - Symmetry

    //Structure &apply_sym(const SymOp &op);  //Anna do this

    void generate_factor_group(double map_tol = TOL) const; // TOL is max distance for site equivalence, in Angstr.

    void generate_factor_group_slow(double map_tol = TOL) const; // TOL is max distance for site equivalence, in Angstr.

    void fg_converge(double large_tol);
    void fg_converge(double small_tol, double large_tol, double increment);

    SymGroupRepID generate_basis_permutation_representation(bool verbose = false) const;

    void symmetrize(const SymGroup &relaxed_factors);
    void symmetrize(const double &tolerace);


    //bool is_primitive(double prim_tol = TOL) const;          //Donghee do this

    //bool is_primitive(Structure &new_prim, double prim_tol = TOL) const;   //Donghee do this

    void fill_supercell(const Structure &prim, double map_tol = TOL); //Ivy

    Structure create_superstruc(const Lattice &scel_lat, double map_tol = TOL) const;

    void map_superstruc_to_prim(Structure &prim); //Added by Ivy 06/29/2013

    void set_occs(Array <int> occ_index);

    //    - Cluster related routines

    void generate_basis_bouquet(const SiteOrbitree &in_tree, SiteOrbitree &out_tree, Index num_sites, double tol);

    void generate_asym_bouquet(const SiteOrbitree &in_tree, SiteOrbitree &out_tree, Index num_sites, double tol);

    //John G 230913
    void generate_flowertrees_safe(const SiteOrbitree &in_tree, Array<SiteOrbitree> &out_trees, double tol = TOL);
    void generate_flowertrees(const SiteOrbitree &in_tree, Array<SiteOrbitree> &out_trees, double tol = TOL);
    //\John G 230913


    //John G 051112
    Structure stack_on(const Structure &understruc, bool override = 0) const;
    //\John G 051112

    //John G 121212
    Structure get_reflection() const;
    void clump_atoms(double maxdist, double tol); //Only for same atom types
    void sort_basis();
    //\John G 121212

    //John G 050513
    Structure stamp_with(SiteCluster stamp, bool lat_override = 0, bool im_override = 0) const;
    Array<Structure> bedazzle(Array<SiteCluster> stamps, bool lat_override = 0, bool im_override = 0) const;
    Array<Array<Array<double> > > get_NN_table(const double &maxr, SiteOrbitree &bouquet, double tol);
    Array<Array<Array<double> > > get_NN_table(const double &maxr, double tol);
    //\John G 050513

    void add_vacuum_shift(Structure &new_surface_struc, double vacuum_thickness, Eigen::Vector3d shift, COORD_TYPE mode) const;
    void add_vacuum_shift(Structure &new_surface_struc, double vacuum_thickness, Coordinate shift) const;  //Because Anton thought a coordinate would be better
    void add_vacuum(Structure &new_surface_struc, double vacuum_thickness) const;
    Structure &operator+=(const Coordinate &shift);
    Structure &operator-=(const Coordinate &shift);

    void intpol(Structure end_struc, int Nofimag, PERIODICITY_TYPE mode, Array<Structure> &images);

    // ****Input/Output****

    void print_site_symmetry(std::ostream &stream, COORD_TYPE mode, int shorttag, double tol);
    //void print_factor_group(std::ostream &stream) const;

    bool read_species(); //Ivy 11/27/12
    void assign_species(Array<std::string> &names, Array<double> &masses, Array<double> &magmoms, Array<double> &Us, Array<double> &Js); //Added by Ivy

    jsonParser &to_json(jsonParser &json) const;
    void from_json(const jsonParser &json);
  };

  //Structure operator*(const SymOp &LHS, const Structure &RHS);

  jsonParser &to_json(const Structure &structure, jsonParser &json);
  void from_json(Structure &structure, const jsonParser &json);

  Structure operator*(const Lattice &LHS, const Structure &RHS);

  //Translation operators -- not yet defined
  Structure operator+(const Coordinate &LHS, const Structure &RHS);
  Structure operator+(const Structure &LHS, const Coordinate &RHS);

  //Not yet sure how these will work
  Structure operator+(const Structure &LHS, const Structure &RHS);
  Structure operator+(const Structure &LHS, const Lattice &RHS);
  Structure operator+(const Lattice &LHS, const Structure &RHS);



  std::vector< std::vector<Index> > get_index_converter(const Structure &struc, std::vector<Molecule> mol_list);

  std::vector< std::vector<Index> > get_index_converter(const Structure &struc, std::vector<std::string> mol_name_list);

  std::vector< std::vector<Index> > get_index_converter_inverse(const Structure &struc, std::vector<std::string> mol_name_list);

};

//#include "casm/clusterography/Orbitree_impl.hh"

#endif