read_atoms_helper.cpp File Reference

#include "read_atoms_helper.h"
#include "source_io/module_parameter/parameter.h"
#include "source_base/global_function.h"
#include "source_base/constants.h"
#include "source_base/mathzone.h"
#include "read_stru.h"
#include "print_cell.h"
#include "source_estate/read_orb.h"
#include <cmath>
#include <iostream>
#include <sstream>

Include dependency graph for read_atoms_helper.cpp:

Namespaces
namespace	unitcell

Functions
bool	unitcell::validate_coordinate_system (const std::string &Coordinate, std::ofstream &ofs_warning)
	Validate coordinate system type.
void	unitcell::allocate_atom_properties (Atom &atom, int na, double mass)
	Allocate and initialize atom property vectors.
void	unitcell::set_atom_movement_flags (Atom &atom, int ia, const ModuleBase::Vector3< int > &mv)
	Set atom movement constraints based on fixed_atoms parameter.
void	unitcell::autoset_magnetization (UnitCell &ucell, int nspin, std::ofstream &ofs_running)
	Set default magnetization if not explicitly specified.
bool	unitcell::finalize_atom_positions (UnitCell &ucell, std::ofstream &ofs_running, std::ofstream &ofs_warning)
	Perform final validation and output.
ModuleBase::Vector3< double >	unitcell::calculate_lattice_center (const ModuleBase::Matrix3 &latvec, const std::string &center_mode)
	Calculate lattice center for different centering modes.
void	unitcell::transform_atom_coordinates (Atom &atom, int ia, const std::string &Coordinate, const ModuleBase::Vector3< double > &v, const ModuleBase::Matrix3 &latvec, double lat0, ModuleBase::Vector3< double > &latcenter)
	Convert between different coordinate systems.
void	unitcell::process_magnetization (Atom &atom, int it, int ia, int nspin, bool input_vec_mag, bool input_angle_mag, std::ofstream &ofs_running)
	Convert between magnetization representations and output.
bool	unitcell::parse_atom_properties (std::ifstream &ifpos, Atom &atom, int ia, ModuleBase::Vector3< int > &mv, bool &input_vec_mag, bool &input_angle_mag, bool &set_element_mag_zero)
	Parse optional atom properties (mag, angle1, angle2, lambda, sc, m, v)
bool	unitcell::read_atom_type_header (int it, UnitCell &ucell, std::ifstream &ifpos, std::ofstream &ofs_running, std::ofstream &ofs_warning, bool &set_element_mag_zero)
	Read atom type metadata (label, magnetization, orbital info, atom count)