unitcell Namespace Reference

Functions
void	bcast_atoms_tau (Atom *atoms, const int ntype)
	broadcast the tau array of the atoms
void	bcast_atoms_pseudo (Atom *atoms, const int ntype)
	broadcast the pseduo of the atoms
void	bcast_Lattice (Lattice &lat)
	broadcast the lattice
void	bcast_magnetism (Magnetism &magnet, const int ntype)
	broadcast the magnetism
void	bcast_unitcell (UnitCell &ucell)
	broadcast the unitcell
void	check_atomic_stru (UnitCell &ucell, const double &factor)
void	print_tau (Atom *atoms, const std::string &Coordinate, const int ntype, const double lat0, std::ofstream &ofs)
void	print_stru_file (const UnitCell &ucell, const Atom *atoms, const ModuleBase::Matrix3 &latvec, const std::string &fn, const int &nspin=1, const bool &direct=false, const bool &vel=false, const bool &magmom=false, const bool &orb=false, const bool &dpks_desc=false, const int &iproc=0)
	UnitCell class is too heavy, this function would be moved elsewhere. Print STRU file respect to given setting.
bool	read_atom_species (std::ifstream &ifa, std::ofstream &ofs_running, UnitCell &ucell)
bool	read_lattice_constant (std::ifstream &ifa, std::ofstream &ofs_running, Lattice &lat)
bool	validate_coordinate_system (const std::string &Coordinate, std::ofstream &ofs_warning)
	Validate coordinate system type.
void	allocate_atom_properties (Atom &atom, int na, double mass)
	Allocate and initialize atom property vectors.
void	set_atom_movement_flags (Atom &atom, int ia, const ModuleBase::Vector3< int > &mv)
	Set atom movement constraints based on fixed_atoms parameter.
void	autoset_magnetization (UnitCell &ucell, int nspin, std::ofstream &ofs_running)
	Set default magnetization if not explicitly specified.
bool	finalize_atom_positions (UnitCell &ucell, std::ofstream &ofs_running, std::ofstream &ofs_warning)
	Perform final validation and output.
ModuleBase::Vector3< double >	calculate_lattice_center (const ModuleBase::Matrix3 &latvec, const std::string &center_mode)
	Calculate lattice center for different centering modes.
void	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	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	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	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)
bool	check_tau (const Atom *atoms, const int &ntype, const double &lat0)
void	check_dtau (Atom *atoms, const int &ntype, const double &lat0, ModuleBase::Matrix3 &latvec)
bool	read_atom_positions (UnitCell &ucell, std::ifstream &ifpos, std::ofstream &ofs_running, std::ofstream &ofs_warning)
void	remake_cell (Lattice &lat)
void	setup_cell_after_vc (UnitCell &ucell, std::ofstream &log)
void	update_pos_tau (const Lattice &lat, const double *pos, const int ntype, const int nat, Atom *atoms)
	update the position and tau of the atoms
void	update_pos_taud (const Lattice &lat, const double *posd_in, const int ntype, const int nat, Atom *atoms)
	update the position and tau of the atoms
void	update_pos_taud (const Lattice &lat, const ModuleBase::Vector3< double > *posd_in, const int ntype, const int nat, Atom *atoms)
	update the velocity of the atoms
void	update_vel (const ModuleBase::Vector3< double > *vel_in, const int ntype, const int nat, Atom *atoms)
	update the velocity of the atoms
void	periodic_boundary_adjustment (Atom *atoms, const ModuleBase::Matrix3 &latvec, const int ntype)
	check the boundary of the cell, for each atom,the taud in three directions should be in the range of [-1,1)
void	reset_remake_cell_mock ()
bool	was_remake_cell_called ()

Detailed Description

• Tested Functions:
  • Ions_Move_Methods::allocate()
  • Ions_Move_Methods::cal_movement()
  • Ions_Move_Methods::get_converged()
  • Ions_Move_Methods::get_ediff()
  • Ions_Move_Methods::get_largest_grad()
  • Ions_Move_Methods::get_trust_radius()
  • Ions_Move_Methods::get_update_iter()

Function Documentation

allocate_atom_properties()

void unitcell::allocate_atom_properties	(	Atom &	atom,
		int	na,
		double	mass
	)

Allocate and initialize atom property vectors.

Parameters

atom	The atom object to allocate properties for
na	Number of atoms
mass	Atomic mass

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autoset_magnetization()

void unitcell::autoset_magnetization	(	UnitCell &	ucell,
		int	nspin,
		std::ofstream &	ofs_running
	)

Set default magnetization if not explicitly specified.

Parameters

ucell	Unit cell object
nspin	Number of spin components
ofs_running	Output stream for running information

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bcast_atoms_pseudo()

void unitcell::bcast_atoms_pseudo	(	Atom *	atoms,
		const int	ntype
	)

broadcast the pseduo of the atoms

Parameters

atoms	the atoms to be broadcasted [in/out]
ntype	the number of types of the atoms [in]

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bcast_atoms_tau()

void unitcell::bcast_atoms_tau	(	Atom *	atoms,
		const int	ntype
	)

broadcast the tau array of the atoms

Parameters

atoms	the atoms to be broadcasted [in/out]
ntype	the number of types of the atoms [in]

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bcast_Lattice()

void unitcell::bcast_Lattice

(

Lattice &

lat

)

broadcast the lattice

Parameters

lat	the lattice to be broadcasted [in/out]

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bcast_magnetism()

void unitcell::bcast_magnetism	(	Magnetism &	magnet,
		const int	ntype
	)

broadcast the magnetism

Parameters

magnet	the magnetism to be broadcasted [in/out]
nytpe	the number of types of the atoms [in]

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bcast_unitcell()

void unitcell::bcast_unitcell

(

UnitCell &

ucell

)

broadcast the unitcell

Parameters

ucell

the unitcell to be broadcasted [in/out]

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calculate_lattice_center()

ModuleBase::Vector3< double > unitcell::calculate_lattice_center	(	const ModuleBase::Matrix3 &	latvec,
		const std::string &	center_mode
	)

Calculate lattice center for different centering modes.

Parameters

latvec	Lattice vectors
center_mode	Centering mode: "xy", "xz", "yz", or "xyz"

Returns

Lattice center coordinates

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check_atomic_stru()

void unitcell::check_atomic_stru	(	UnitCell &	ucell,
		const double &	factor
	)

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check_dtau()

void unitcell::check_dtau	(	Atom *	atoms,
		const int &	ntype,
		const double &	lat0,
		ModuleBase::Matrix3 &	latvec
	)

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check_tau()

bool unitcell::check_tau	(	const Atom *	atoms,
		const int &	ntype,
		const double &	lat0
	)

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finalize_atom_positions()

bool unitcell::finalize_atom_positions	(	UnitCell &	ucell,
		std::ofstream &	ofs_running,
		std::ofstream &	ofs_warning
	)

Perform final validation and output.

Parameters

ucell	Unit cell object
ofs_running	Output stream for running information
ofs_warning	Output stream for warnings

Returns

true if validation passes, false otherwise

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parse_atom_properties()

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)

Parameters

ifpos	Input file stream
atom	The atom object
ia	Atom index
mv	Movement vector (output parameter)
input_vec_mag	Whether vector magnetization was input (output parameter)
input_angle_mag	Whether angle magnetization was input (output parameter)
set_element_mag_zero	Whether to reset element magnetization (output parameter)

Returns

true if parsing succeeds, false otherwise

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periodic_boundary_adjustment()

void unitcell::periodic_boundary_adjustment	(	Atom *	atoms,
		const ModuleBase::Matrix3 &	latvec,
		const int	ntype
	)

check the boundary of the cell, for each atom,the taud in three directions should be in the range of [-1,1)

Parameters

atoms	the atoms to be adjusted [in]
latvec	the lattice of the atoms [in]
ntype	the number of types of the atoms [in]

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print_stru_file()

void unitcell::print_stru_file	(	const UnitCell &	ucell,
		const Atom *	atoms,
		const ModuleBase::Matrix3 &	latvec,
		const std::string &	fn,
		const int &	nspin = 1,
		const bool &	direct = false,
		const bool &	vel = false,
		const bool &	magmom = false,
		const bool &	orb = false,
		const bool &	dpks_desc = false,
		const int &	iproc = 0
	)

UnitCell class is too heavy, this function would be moved elsewhere. Print STRU file respect to given setting.

Parameters

ucell	reference of unitcell
atoms	Atom list
latvec	lattice const parmater vector
fn	STRU file name
nspin	PARAM.inp.nspin feed in
direct	true for direct coords, false for cartesian coords
vol	true for printing velocities
magmom	true for printing Mulliken population analysis produced magmom
orb	true for printing NUMERICAL_ORBITAL section
dpks_desc	true for printing NUMERICAL_DESCRIPTOR section
iproc	GlobalV::MY_RANK feed in

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print_tau()

void unitcell::print_tau	(	Atom *	atoms,
		const std::string &	Coordinate,
		const int	ntype,
		const double	lat0,
		std::ofstream &	ofs
	)

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process_magnetization()

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.

Parameters

atom	The atom object
it	Atom type index
ia	Atom index
nspin	Number of spin components
input_vec_mag	Whether vector magnetization was input
input_angle_mag	Whether angle magnetization was input
ofs_running	Output stream for running information

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read_atom_positions()

bool unitcell::read_atom_positions	(	UnitCell &	ucell,
		std::ifstream &	ifpos,
		std::ofstream &	ofs_running,
		std::ofstream &	ofs_warning
	)

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read_atom_species()

bool unitcell::read_atom_species	(	std::ifstream &	ifa,
		std::ofstream &	ofs_running,
		UnitCell &	ucell
	)

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read_atom_type_header()

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)

Parameters

it	Atom type index
ucell	Unit cell object
ifpos	Input file stream
ofs_running	Output stream for running information
ofs_warning	Output stream for warnings
set_element_mag_zero	Whether to reset element magnetization (output parameter)

Returns

true if reading succeeds, false otherwise

liuyu update 2023-05-11 In order to employ the DP model as esolver, all atom types must be specified in the STRU in the order consistent with that of the DP model, even if the number of ucell.atoms is zero!

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read_lattice_constant()

bool unitcell::read_lattice_constant	(	std::ifstream &	ifa,
		std::ofstream &	ofs_running,
		Lattice &	lat
	)

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remake_cell()

void unitcell::remake_cell

(

Lattice &

lat

)

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reset_remake_cell_mock()

void unitcell::reset_remake_cell_mock

(

)

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set_atom_movement_flags()

void unitcell::set_atom_movement_flags	(	Atom &	atom,
		int	ia,
		const ModuleBase::Vector3< int > &	mv
	)

Set atom movement constraints based on fixed_atoms parameter.

Parameters

atom	The atom object
ia	Atom index
mv	Movement vector (1=movable, 0=fixed)

setup_cell_after_vc()

void unitcell::setup_cell_after_vc	(	UnitCell &	ucell,
		std::ofstream &	log
	)

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transform_atom_coordinates()

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.

Parameters

atom	The atom object
ia	Atom index
Coordinate	Coordinate system type
v	Input position vector
latvec	Lattice vectors
lat0	Lattice constant
latcenter	Lattice center (output parameter)

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update_pos_tau()

void unitcell::update_pos_tau	(	const Lattice &	lat,
		const double *	pos,
		const int	ntype,
		const int	nat,
		Atom *	atoms
	)

update the position and tau of the atoms

Parameters

lat	the lattice of the atoms [in]
pos	the position of the atoms [in]
ntype	the number of types of the atoms [in]
nat	the number of atoms [in]
atoms	the atoms to be updated [out]

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update_pos_taud() [1/2]

void unitcell::update_pos_taud	(	const Lattice &	lat,
		const double *	posd_in,
		const int	ntype,
		const int	nat,
		Atom *	atoms
	)

update the position and tau of the atoms

Parameters

lat	the lattice of the atoms [in]
pos_in	the position of the atoms in direct coordinate system [in]
ntype	the number of types of the atoms [in]
nat	the number of atoms [in]
atoms	the atoms to be updated [out]

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update_pos_taud() [2/2]

void unitcell::update_pos_taud	(	const Lattice &	lat,
		const ModuleBase::Vector3< double > *	posd_in,
		const int	ntype,
		const int	nat,
		Atom *	atoms
	)

update the velocity of the atoms

Parameters

lat	the lattice of the atoms [in]
pos_in	the position of the atoms in direct coordinate system in ModuleBase::Vector3 version [in]
ntype	the number of types of the atoms [in]
nat	the number of atoms [in]
atoms	the atoms to be updated [out]

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update_vel()

void unitcell::update_vel	(	const ModuleBase::Vector3< double > *	vel_in,
		const int	ntype,
		const int	nat,
		Atom *	atoms
	)

update the velocity of the atoms

Parameters

vel_in	the velocity of the atoms [in]
ntype	the number of types of the atoms [in]
nat	the number of atoms [in]
atoms	the atoms to be updated [out]

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validate_coordinate_system()

bool unitcell::validate_coordinate_system	(	const std::string &	Coordinate,
		std::ofstream &	ofs_warning
	)

Validate coordinate system type.

Parameters

Coordinate	The coordinate system string to validate
ofs_warning	Output stream for warnings

Returns

true if valid, false otherwise

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was_remake_cell_called()

bool unitcell::was_remake_cell_called

(

)

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