#include <field.hpp>

Public Member Functions
int	atomic_number (int atom_index) const
	Atomic number of one atom, from its element symbol.

std::vector< int >	atoms_per_species () const
	How many atoms each species has, in species order, for formats that group atoms so.

Vector3D	cartesian_position_bohr (int atom_index) const
	Cartesian position of one atom, in bohr.

Real	cell_volume_bohr3 () const

Real	integral () const

int	number_of_atoms () const

int	number_of_grid_points () const

Real	value (int index_1, int index_2, int index_3) const
	The sample at grid point (i1, i2, i3), third index fastest.

Public Attributes
std::vector< Vector3D >	atom_positions_crystal
	Fractional (crystal) coordinates, parallel to `atom_species_indices`.

std::vector< int >	atom_species_indices
	Species of each atom, an index into `species_symbols`.

std::string	description
	Free text for a format's comment line, e.g. "charge density".

std::array< int, 3 >	grid_dimensions = {0, 0, 0}
	Grid point counts along a1, a2, a3.

bool	is_a_density = false

Matrix3x3	lattice_vectors_bohr {}
	Rows are a1, a2, a3, Cartesian, in bohr.

std::vector< std::string >	species_symbols
	Element symbols, one per species.

std::vector< Real >	species_valence_charges
	Valence charge of each species, parallel to `species_symbols`.

std::string	unit
	The unit `values` is in, e.g. "e/bohr^3".

std::vector< Real >	values
	The samples themselves, `number_of_grid_points()` of them.

Detailed Description

Definition at line 40 of file field.hpp.

Member Function Documentation

◆ atomic_number()

int q3::VolumetricField::atomic_number ( int atom_index ) const

inline

Atomic number of one atom, from its element symbol.

Definition at line 123 of file field.hpp.

References atom_species_indices, q3::PeriodicTable::atomic_number_by_element_symbol(), and species_symbols.

Referenced by q3::CubeVolumetricFieldWriter::write(), and q3::XsfVolumetricFieldWriter::write().

◆ atoms_per_species()

std::vector< int > q3::VolumetricField::atoms_per_species ( ) const

inline

How many atoms each species has, in species order, for formats that group atoms so.

Definition at line 129 of file field.hpp.

References atom_species_indices, and species_symbols.

◆ cartesian_position_bohr()

Vector3D q3::VolumetricField::cartesian_position_bohr ( int atom_index ) const

inline

Cartesian position of one atom, in bohr.

Definition at line 111 of file field.hpp.

References atom_positions_crystal, lattice_vectors_bohr, q3::Vector3D::x, q3::Vector3D::y, and q3::Vector3D::z.

Referenced by q3::CubeVolumetricFieldWriter::write(), and q3::XsfVolumetricFieldWriter::write().

◆ cell_volume_bohr3()

Real q3::VolumetricField::cell_volume_bohr3 ( ) const

inline

Definition at line 82 of file field.hpp.

References q3::Matrix3x3::determinant(), and lattice_vectors_bohr.

Referenced by integral(), and q3::VolumetricCommand::run().

◆ integral()

Real q3::VolumetricField::integral ( ) const

inline

The field integrated over the cell by the midpoint rule the grid is a sample of: Omega / N * sum(values).

For a charge density this is the electron count, which is the one number that says whether a written file is right — a transposed grid or a missed unit changes it, and a viewer's isosurface does not.

Definition at line 103 of file field.hpp.

References cell_volume_bohr3(), number_of_grid_points(), and values.

Referenced by q3::VolumetricCommand::run().

◆ number_of_atoms()

int q3::VolumetricField::number_of_atoms ( ) const

inline

Definition at line 78 of file field.hpp.

References atom_species_indices.

Referenced by q3::CubeVolumetricFieldWriter::write(), and q3::XsfVolumetricFieldWriter::write().

◆ number_of_grid_points()

int q3::VolumetricField::number_of_grid_points ( ) const

inline

Definition at line 74 of file field.hpp.

References grid_dimensions.

Referenced by integral(), and q3::CubeVolumetricFieldReader::read().

◆ value()

Real q3::VolumetricField::value	(	int	index_1,
		int	index_2,
		int	index_3
	)		const

inline

The sample at grid point (i1, i2, i3), third index fastest.

Definition at line 87 of file field.hpp.

References grid_dimensions, and values.

Referenced by q3::CubeVolumetricFieldWriter::write(), and q3::XsfVolumetricFieldWriter::write().

Member Data Documentation

◆ atom_positions_crystal

std::vector<Vector3D> q3::VolumetricField::atom_positions_crystal

Fractional (crystal) coordinates, parallel to atom_species_indices.

Definition at line 53 of file field.hpp.

Referenced by cartesian_position_bohr(), and q3::CubeVolumetricFieldReader::read().

◆ atom_species_indices

std::vector<int> q3::VolumetricField::atom_species_indices

Species of each atom, an index into species_symbols.

Definition at line 51 of file field.hpp.

Referenced by atomic_number(), atoms_per_species(), number_of_atoms(), q3::CubeVolumetricFieldReader::read(), and q3::CubeVolumetricFieldWriter::write().

◆ description

std::string q3::VolumetricField::description

Free text for a format's comment line, e.g. "charge density".

Definition at line 58 of file field.hpp.

Referenced by q3::CubeVolumetricFieldReader::read(), q3::VolumetricCommand::run(), q3::CubeVolumetricFieldWriter::write(), and q3::XsfVolumetricFieldWriter::write().

◆ grid_dimensions

std::array<int, 3> q3::VolumetricField::grid_dimensions = {0, 0, 0}

Grid point counts along a1, a2, a3.

Definition at line 42 of file field.hpp.

Referenced by number_of_grid_points(), q3::CubeVolumetricFieldReader::read(), value(), q3::CubeVolumetricFieldWriter::write(), and q3::XsfVolumetricFieldWriter::write().

◆ is_a_density

bool q3::VolumetricField::is_a_density = false

Whether integral() is a particle count — true for the charge density and for a band's probability density, false for a potential.

Formats disagree about what they hold, and the disagreement is silent: one format stores the density multiplied by the cell volume, so that summing it and dividing by the point count gives electrons, while a potential in the same file shape is stored unscaled. A writer that cannot honour the distinction refuses the field rather than applying the wrong one.

Definition at line 72 of file field.hpp.

Referenced by q3::VolumetricCommand::run().

◆ lattice_vectors_bohr

Matrix3x3 q3::VolumetricField::lattice_vectors_bohr {}

Rows are a1, a2, a3, Cartesian, in bohr.

Definition at line 44 of file field.hpp.

Referenced by cartesian_position_bohr(), cell_volume_bohr3(), q3::CubeVolumetricFieldReader::read(), q3::CubeVolumetricFieldWriter::write(), and q3::XsfVolumetricFieldWriter::write().

◆ species_symbols

std::vector<std::string> q3::VolumetricField::species_symbols

Element symbols, one per species.

Definition at line 47 of file field.hpp.

Referenced by atomic_number(), and atoms_per_species().

◆ species_valence_charges

std::vector<Real> q3::VolumetricField::species_valence_charges

Valence charge of each species, parallel to species_symbols.

Definition at line 49 of file field.hpp.

Referenced by q3::CubeVolumetricFieldWriter::write().

◆ unit

std::string q3::VolumetricField::unit

The unit values is in, e.g. "e/bohr^3".

Definition at line 60 of file field.hpp.

Referenced by q3::VolumetricCommand::run(), q3::CubeVolumetricFieldWriter::write(), and q3::XsfVolumetricFieldWriter::write().

◆ values

std::vector<Real> q3::VolumetricField::values

The samples themselves, number_of_grid_points() of them.

Definition at line 56 of file field.hpp.

Referenced by integral(), q3::CubeVolumetricFieldReader::read(), and value().

The documentation for this struct was generated from the following file:

src/io/volumetric/field.hpp

Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

◆ atomic_number()

◆ atoms_per_species()

◆ cartesian_position_bohr()

◆ cell_volume_bohr3()

◆ integral()

◆ number_of_atoms()

◆ number_of_grid_points()

◆ value()

Member Data Documentation

◆ atom_positions_crystal

◆ atom_species_indices

◆ description

◆ grid_dimensions

◆ is_a_density

◆ lattice_vectors_bohr

◆ species_symbols

◆ species_valence_charges

◆ unit

◆ values