SimpleStructure.cc

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#include "casm/crystallography/SimpleStructure.hh"
 
#include "casm/misc/CASM_Eigen_math.hh"
 
namespace CASM {
namespace xtal {
 
std::vector<Index> SimpleStructure::Info::sort_by_name() {
  std::vector<Index> permute;
  permute.clear();
  std::map<std::string, std::vector<Index> > smap;
  for (Index i = 0; i < names.size(); ++i) {
    smap[names[i]].push_back(i);
  }
  for (auto const &name : smap) {
    permute.insert(permute.end(), name.second.begin(), name.second.end());
  }
  return permute;
}
 
//***************************************************************************
 
void SimpleStructure::within(double tol) {
  if (mol_info.size())
    mol_info.coords -=
        lat_column_mat *
        Eigen::floor(
            ((lat_column_mat.inverse() * mol_info.coords).array() + tol)
                .array())
            .matrix()
            .eval();
  if (atom_info.size())
    atom_info.coords -=
        lat_column_mat *
        Eigen::floor(
            ((lat_column_mat.inverse() * atom_info.coords).array() + tol)
                .array())
            .matrix()
            .eval();
}
 
//***************************************************************************
 
void SimpleStructure::deform_coords(
    Eigen::Ref<const Eigen::Matrix3d> const &_F) {
  lat_column_mat = _F * lat_column_mat;
  if (mol_info.coords.rows() == 3) mol_info.coords = _F * mol_info.coords;
  if (atom_info.coords.rows() == 3) atom_info.coords = _F * atom_info.coords;
}
 
//***************************************************************************
 
void SimpleStructure::rotate_coords(
    Eigen::Ref<const Eigen::Matrix3d> const &_R) {
  lat_column_mat = _R * lat_column_mat;
  if (mol_info.coords.rows() == 3) mol_info.coords = _R * mol_info.coords;
  if (atom_info.coords.rows() == 3) atom_info.coords = _R * atom_info.coords;
}
 
}  // namespace xtal
}  // namespace CASM