SimpleStructure.hh

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#ifndef SIMPLESTRUCTURE_HH
#define SIMPLESTRUCTURE_HH
 
#include <map>
#include <set>
#include <string>
#include <vector>
 
#include "casm/external/Eigen/Dense"
#include "casm/global/definitions.hh"
 
namespace CASM {
namespace xtal {
 
namespace SimpleStructureTools {
// TODO: Capitalize so it looks the same as COORD_MODE? Put it in some
// crystallography declarations file?
enum class SpeciesMode { ATOM, MOL };
}  // namespace SimpleStructureTools
 
class SimpleStructure {
 public:
  using SpeciesMode = SimpleStructureTools::SpeciesMode;
 
  struct Info {
    using Coord = Eigen::MatrixXd::ColXpr;
    using ConstCoord = Eigen::MatrixXd::ConstColXpr;
 
    std::vector<std::string> names;
 
    Eigen::MatrixXd coords;
 
    std::map<std::string, Eigen::MatrixXd> properties;
 
    std::vector<Index> sort_by_name();
 
    Coord cart_coord(Index i) { return coords.col(i); }
 
    ConstCoord cart_coord(Index i) const { return coords.col(i); }
 
    void resize(Index N) {
      names.resize(N, "Va");
      coords.setZero(3, N);
      for (auto &el : properties) el.second.setZero(Eigen::NoChange, N);
    }
 
    Index size() const { return names.size(); }
  };
 
  Index n_mol() const { return mol_info.size(); }
 
  Index n_atom() const { return atom_info.size(); }
 
  Info &info(SpeciesMode _mode) {
    return _mode == SpeciesMode::MOL ? mol_info : atom_info;
  }
 
  Info const &info(SpeciesMode _mode) const {
    return _mode == SpeciesMode::MOL ? mol_info : atom_info;
  }
 
  void within(double tol = TOL);
 
  void deform_coords(Eigen::Ref<const Eigen::Matrix3d> const &_F);
 
  void rotate_coords(Eigen::Ref<const Eigen::Matrix3d> const &_R);
 
  Eigen::Matrix3d lat_column_mat;
 
  // Use occupation vector in order to avoid messy molecule-name aliasing issues
  Info mol_info;
 
  Info atom_info;
 
  std::map<std::string, Eigen::MatrixXd> properties;
};
 
}  // namespace xtal
}  // namespace CASM
 
#endif