BasicStructureTools.hh

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#ifndef BASICSTRUCTURETOOLS_HH
#define BASICSTRUCTURETOOLS_HH
 
#include <set>
#include <vector>
 
#include "casm/crystallography/Lattice.hh"
#include "casm/external/Eigen/Core"
#include "casm/global/definitions.hh"
#include "casm/global/eigen.hh"
 
namespace CASM {
namespace xtal {
class Site;
class Coordinate;
class BasicStructure;
struct SymOp;
 
Index find_index(const std::vector<Site> &basis, const Site &test_site,
                 double tol);
 
bool is_primitive(const BasicStructure &struc, double tol = TOL);
 
BasicStructure make_primitive(const BasicStructure &non_primitive_struc,
                              double tol = TOL);
 
std::pair<double, Eigen::Vector3d> calc_rotation_angle_and_axis(
    const SymOp &op, const Lattice &lat);
 
void sort_factor_group(std::vector<SymOp> &factor_group, const Lattice &lat);
 
std::vector<SymOp> make_factor_group(const BasicStructure &struc,
                                     double tol = TOL);
 
std::vector<Eigen::PermutationMatrix<Eigen::Dynamic, Eigen::Dynamic, Index>>
make_permutation_representation(const xtal::BasicStructure &struc,
                                const std::vector<SymOp> &factor_group);
 
std::set<std::set<Index>> make_asymmetric_unit(
    const xtal::BasicStructure &struc, const std::vector<SymOp> &factor_group);
 
std::set<std::set<Index>> make_asymmetric_unit(
    const xtal::BasicStructure &struc);
 
// TODO: Rename to symmetrize_basis and have it take vector<Site> and Lattice?
// seems like a symmetrize routine that takes a structure should also symmetrize
// the lattice.
BasicStructure symmetrize(const BasicStructure &structure,
                          const std::vector<SymOp> &enforced_group);
 
template <typename IntegralType, int Options = 0>
BasicStructure make_superstructure(
    const BasicStructure &tiling_unit,
    const Eigen::Matrix<IntegralType, 3, 3, Options> &transformation_matrix);
 
}  // namespace xtal
}  // namespace CASM
 
#endif