Structure.hh

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#ifndef STRUCTURE_HH
#define STRUCTURE_HH
 
#include <cmath>
#include <cstdlib>
#include <iostream>
#include <memory>
#include <unordered_map>
#include <vector>
 
#include "casm/crystallography/BasicStructure.hh"
#include "casm/crystallography/Molecule.hh"
#include "casm/crystallography/Site.hh"
#include "casm/symmetry/SymGroup.hh"
 
namespace CASM {
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
//  template<typename ClustType>
//  class GenericOrbitree;
 
//  typedef GenericOrbitree<SiteCluster> SiteOrbitree;
 
class Structure {
 private:
  // TODO: Collect all the symmetry information and package it into a
  // StructureSymInfo class or the like. Then store alongside the BasicStructure
  // as a shared pointer. This will save you regenerating the factor group each
  // time you make a copy of *this. It'll also make the custom copy constructor
  // and assignment operators unnecessary.
 
  MasterSymGroup m_factor_group;
 
  SymGroupRepID m_basis_perm_rep_ID;
 
  std::vector<SymGroupRepID> m_occupant_symrep_IDs;
 
  std::vector<std::map<DoFKey, SymGroupRepID>> m_site_dof_symrep_IDs;
 
  std::unordered_map<std::string, SymGroupRepID> m_global_dof_symrep_IDs;
 
  // Flushes out every SymGroupRepID for each site (occupant DoF) and gives it a
  // default value of identity
  void _reset_occupant_symrep_IDs();
 
  // Flushes out every SymGroupRepID for each site (continuous DoF) and gives it
  // a default values
  void _reset_site_dof_symrep_IDs();
 
  void _generate_basis_symreps();
 
  void _generate_global_symreps();
 
  void _fg_converge(SymGroup &factor_group, double small_tol, double large_tol,
                    double increment);
 
  void generate_factor_group();  // TOL is max distance for site equivalence, in
                                 // Angstr.
 
  void copy_attributes_from(const Structure &RHS);
 
  // Don't ever even think about making this non-const, assignable or modifiable
  // in any way.
  std::shared_ptr<const xtal::BasicStructure> m_structure_ptr;
 
 public:
  // TODO: Do we even want automatic conversion?
  operator const xtal::BasicStructure &() const;
 
  const xtal::BasicStructure &structure() const {
    return *this->m_structure_ptr;
  }
 
  const std::shared_ptr<const xtal::BasicStructure> &shared_structure() const {
    return this->m_structure_ptr;
  }
 
  const Lattice &lattice() const { return this->structure().lattice(); }
 
  const std::vector<xtal::Site> &basis() const {
    return this->structure().basis();
  }
 
  // TODO: I tried getting rid of this but it seems to get used in almost every
  // casm command right now
  Structure();
  explicit Structure(const xtal::BasicStructure &base);
  explicit Structure(const fs::path &filepath);
 
  Structure(const Structure &RHS);
 
  ~Structure(){};
 
  const MasterSymGroup &factor_group() const;
  const SymGroup &point_group() const;
  SymGroupRep const *basis_permutation_symrep() const;
  SymGroupRepID basis_permutation_symrep_ID() const;
  std::vector<SymGroupRepID> occupant_symrep_IDs() const;
  std::vector<std::map<DoFKey, SymGroupRepID>> site_dof_symrep_IDs() const;
  SymGroupRepID global_dof_symrep_ID(const std::string dof_name) const;
 
  Structure &operator=(const Structure &RHS);
};
 
std::vector<std::vector<Index>> make_index_converter(
    const Structure &struc, std::vector<xtal::Molecule> mol_list);
 
std::vector<std::vector<Index>> make_index_converter(
    const Structure &struc, std::vector<std::string> mol_name_list);
 
std::vector<std::vector<Index>> make_index_converter_inverse(
    const Structure &struc, std::vector<std::string> mol_name_list);
 
//************************************************************************************
 
struct DoFSetInfo;
 
std::map<DoFKey, CASM::DoFSetInfo> global_dof_info(Structure const &_struc);
 
std::map<DoFKey, std::vector<CASM::DoFSetInfo>> local_dof_info(
    Structure const &_struc);
 
class SupercellSymInfo;
SupercellSymInfo make_supercell_sym_info(Structure const &prim,
                                         Lattice const &super_lattice);
 
}  // namespace CASM
 
#endif