SimpleStructureTools.hh

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#ifndef SIMPLESTRUCTURETOOLS_HH
#define SIMPLESTRUCTURETOOLS_HH
 
#include <set>
#include <string>
#include <vector>
 
#include "casm/crystallography/DoFDecl.hh"
#include "casm/crystallography/SymType.hh"
#include "casm/external/Eigen/Dense"
#include "casm/global/definitions.hh"
 
namespace CASM {
 
namespace xtal {
 
// TODO: Move this into crystallography declarations or something of the sort
namespace SimpleStructureTools {
// Defined in SimpleStructure.hh
enum class SpeciesMode;
}  // namespace SimpleStructureTools
 
class SimpleStructure;
class Site;
class Molecule;
class BasicStructure;
 
SimpleStructure make_superstructure(Eigen::Ref<const Eigen::Matrix3i> const &_T,
                                    SimpleStructure const &_sstruc);
 
std::vector<Index> superstructure_basis_idx(
    Eigen::Ref<const Eigen::Matrix3i> const &_T,
    SimpleStructure const &_sstruc);
 
SimpleStructure make_simple_structure(BasicStructure const &_struc);
 
std::vector<std::set<Index>> atom_site_compatibility(
    SimpleStructure const &sstruc, BasicStructure const &_prim);
 
std::vector<std::set<Index>> mol_site_compatibility(
    SimpleStructure const &sstruc, BasicStructure const &_prim);
 
void _atomize(SimpleStructure &_sstruc,
              Eigen::Ref<const Eigen::VectorXi> const &_mol_occ,
              BasicStructure const &_reference);
 
BasicStructure make_basic_structure(
    SimpleStructure const &_sstruc, std::vector<DoFKey> const &_all_dofs,
    SimpleStructureTools::SpeciesMode mode,
    std::vector<std::vector<Molecule>> _allowed_occupants = {});
 
std::vector<Eigen::MatrixXd> generate_invariant_shuffle_modes(
    const std::vector<xtal::SymOp> &factor_group,
    const std::vector<Eigen::PermutationMatrix<Eigen::Dynamic, Eigen::Dynamic,
                                               Index>> &permute_group);
}  // namespace xtal
 
}  // namespace CASM
#endif