Structure

The structure module contains classes for constructing unit and supercells.

class SuperCell(filename, nu=1, nv=1, nw=1, tol=0.01)

Supercell.

Parameters:

filenamestr

Name of CIF file.

nu, nv, nwint

Extents \(N_1\), \(N_2\), \(N_3\) along the \(a\), \(b\), and \(c\)-axis of the supercell.

tolfloat, optional

Tolerance of unique atom coordinates.

Methods

save()	Save supercell data.
load()	Load supercell data.
get_super_cell_extents()	Number of cells along each dimension.
set_super_cell_extents()	Update number of cells along each dimension.
get_super_cell_size()	Total number of cells.
get_number_atoms_per_super_cell()	Total number of atoms.
get_cartesian_lattice_points()	Position of lattice points in Cartesian coordinates.
get_super_cell_cartesian_atomic_coordinates()	Average atom positions in Cartesian coordinates.
get_super_cell_cartesian_displaced_atomic_coordinates()	Displaced atom positions in Cartesian coordinates.
get_super_cell_occupancies()	Occupancies.
get_super_cell_cartesian_magnetic_moments()	Magnetic moments in Cartesian coordinates.

displacement_correlations_1d(fract, tol, average=False)

Spherically-averaged displacement correlations.

Parameters:

fractfloat

Fraction of longest distance for radial cutoff.

tolfloat

Tolerance of distances for unique pairs.

Returns:

corr1d array

Correlation.

coll1d array

Collinearity.

d1d array

Separation distance magnitude.

pairs1d array, str

Atom, ion, or isotope-pairs.

displacement_correlations_3d(fract, tol, average=False, laue=None)

Three-dimensional displacement correlations.

Parameters:

fractfloat

Fraction of longest distance for radial cutoff.

tolfloat

Tolerance of distances for unique pairs.

Returns:

corr1d array

Correlation.

coll1d array

Collinearity.

dx, dy, dz1d array

Separation distance vector.

pairs1d array, str

Atom, ion, or isotope-pairs.

displacive_single_crystal_intensity(extents, bins, W, laue=None, order=2, centering='P')

Calculate displacive single crystal intensity.

Parameters:

extentslist of lists, float

Reciprocal space extents.

binslist, int

Number of bins.

W2d array

Projection matrix.

lauestr, optional

Laue symmetry.

Returns:

I1d array

Displacive scattering intensity.

get_cartesian_lattice_points()

Position of lattice points in Cartesian coordinates,

Returns:

Rx, Ry, Rz1d array

Lattice vectors \(R_x\), \(R_y\), and \(R_z\).

get_number_atoms_per_super_cell()

Total number of atoms.

Returns:

nint

Number of atoms \(n\) in the supercell.

get_super_cell_cartesian_atomic_coordinates()

Average atom positions in Cartesian coordinates.

Returns:

rx, ry, rz1d array

Spatial vectors \(r_x\), \(r_y\), and \(r_z\).

atms1d array, str

Atoms, ions, or isotopes.

get_super_cell_cartesian_displaced_atomic_coordinates()

Displaced atom positions in Cartesian coordinates.

Returns:

px, py, pzlist, 1d array

Spatial vectors \(r_x\), \(r_y\), and \(r_z\).

get_super_cell_cartesian_magnetic_moments()

Magnetic moments in Cartesian coordinates

Returns:

mu_x, mu_y, mu_zlist, 1d array

Magnetic moments \(\mu_x\), \(\mu_y\), and \(\mu_z\).

get_super_cell_extents()

Number of cells along each dimension.

Returns:

nu, nv, nwint

Extents \(N_1\), \(N_2\), \(N_3\) along the \(a\), \(b\), and \(c\)-axis of the supercell.

get_super_cell_occupancies()

Occupancies.

Returns:

deltalist, 1d array

Spatial vectors \(r_x\), \(r_y\), and \(r_z\).

get_super_cell_size()

Total number of cells.

Returns:

n_uvwint

Supercell size \(N_1N_2N_3\).

load(filename)

Load supercell data.

Parameters:

filenamestr

Name of HDF5 file.

magnetic_powder_intensity(extents, bins)

Calculate magnetic powder intensity.

Parameters:

extentslist, float

Reciprocal space extents.

binsint

Number of bins.

Returns:

I1d array

Magnetic scattering intensity.

magnetic_single_crystal_intensity(extents, bins, W, laue=None)

Calculate magnetic single crystal intensity.

Parameters:

extentslist of lists, float

Reciprocal space extents.

binslist, int

Number of bins.

W2d array

Projection matrix.

lauestr, optional

Laue symmetry.

Returns:

I1d array

Magnetic scattering intensity.

occupancy_correlations_1d(fract, tol, average=False)

Spherically-averaged occupancy correlations.

Parameters:

fractfloat

Fraction of longest distance for radial cutoff.

tolfloat

Tolerance of distances for unique pairs.

Returns:

corr1d array

Correlation.

d1d array

Separation distance magnitude.

pairs1d array, str

Atom, ion, or isotope-pairs.

occupancy_correlations_3d(fract, tol, average=False, laue=None)

Three-dimensional occupancy correlations.

Parameters:

fractfloat

Fraction of longest distance for radial cutoff.

tolfloat

Tolerance of distances for unique pairs.

Returns:

corr1d array

Correlation.

dx, dy, dz1d array

Separation distance vector.

pairs1d array, str

Atom, ion, or isotope-pairs.

occupational_single_crystal_intensity(extents, bins, W, laue=None)

Calculate occupational single crystal intensity.

Parameters:

extentslist of lists, float

Reciprocal space extents.

binslist, int

Number of bins.

W2d array

Projection matrix.

lauestr, optional

Laue symmetry.

Returns:

I1d array

Occupational scattering intensity.

randomize_atomic_displacements()

Generate random atomic displacements.

randomize_magnetic_moments()

Generate random spin vectors.

randomize_site_occupancies()

Generate random site occupancies.

reset_disorder()

Reset data arrays.

save(filename)

Save supercell data.

Parameters:

filenamestr

Name of HDF5 file.

save_correlations_3d(filename, data, coordinates, pairs)

Save three-dimensional correlations.

Vector	Scalar
Correlation and collinearity	Correlation

Parameters:

filenamestr

Name of file to be saved.

data2-tuple or 4-tuple of 1d-array

List of correlation data.

coordinates3-tuple of 1d-array

Separation vector in Cartesian coordinates.

pairs1d-array, str

Pair identifier.

save_data(filename, signal, sigma_sq, extents, bins)

Save the dataset to a h5 binary file.

Parameters:

filenamestr

Name of file to be saved.

signal3d-array

THe data signal.

sigma_sq3d-array

The error weights.

bins3-tuple, int

Number of voxels along each dimension.

extents3-tuple of 2-list, float

The (min, max) limits along each dimension.

save_intensity_3d(filename, I, extents, W=array([[1., 0., 0.], [0., 1., 0.], [0., 0., 1.]]))

Save the intensity to VTK file.

Parameters:

filenamestr

Name of file to be saved.

I1d-array

Intensity data.

extents3-tuple of 2-list, float

The (min, max) limits along each dimension.

W2d-array, optional

Projection matrix of the intensity file. The default is np.eye(3).

set_super_cell_extents(nu, nv, nw)

Update number of cells along each dimension.

Parameters:

nu, nv, nwint

Extents \(N_1\), \(N_2\), \(N_3\) along the \(a\), \(b\), and \(c\)-axis of the supercell.

single_crystal_intensity_blur(I, sigma)

Perform an approximate Gaussian blur to the intensity dataset.

Parameters:

I1d-array

Intensity data.

sigma3-tuple, float or float

Blur width in voxels.

Returns:

I_blur3d-array

Gaussian blurred intensity.

spin_correlations_1d(fract, tol, average=False)

Spherically-averaged spin correlations.

Parameters:

fractfloat

Fraction of longest distance for radial cutoff.

tolfloat

Tolerance of distances for unique pairs.

Returns:

corr1d array

Correlation.

coll1d array

Collinearity.

d1d array

Separation distance magnitude.

pairs1d array, str

Atom, ion, or isotope-pairs.

spin_correlations_3d(fract, tol, average=False, laue=None)

Three-dimensional spin correlations.

Parameters:

fractfloat

Fraction of longest distance for radial cutoff.

tolfloat

Tolerance of distances for unique pairs.

Returns:

corr1d array

Correlation.

coll1d array

Collinearity.

dx, dy, dz1d array

Separation distance vector.

pairs1d array, str

Atom, ion, or isotope-pairs.

class UnitCell(filename, tol=0.01)

Unit cell.

Parameters:

filenamestr

Name of CIF file.

tolfloat, optional

Tolerance of unique atom coordinates.

Methods

save()	Save unit cell data.
load()	Load unit cell data.
get_filepath()	Path of CIF file.
get_filename()	Name of CIF file.
get_sites()	Atom sites in the unit cell.
get_atom_sites()	Atom sites in the unit cell.
get_active_sites()	Active atom sites in the unit cell.
set_active_sites()	Update active atom sites in the unit cell.
get_number_atoms_per_unit_cell()	Total number of atoms in the unit cell.
get_fractional_coordinates()	Fractional coordiantes.
set_fractional_coordinates()	Update fractional coordiantes of active atoms.
get_unit_cell_cartesian_atomic_coordinates()	Cartesian coordiantes.
get_unit_cell_atoms()	Atom symbols of active atoms.
set_unit_cell_atoms()	Update atom symbols.
get_unit_cell_charge_numbers()	Charge numbers of active ions.
set_unit_cell_charge_numbers()	Update charge numbers of active ions.
get_unit_cell_isotope_numbers()	Mass numbers of active isotopes.
set_unit_cell_isotope_numbers()	Update mass numbers of active isotopes.
get_occupancies()	Occupancies.
set_occupancies()	Update occupancies.
get_anisotropic_displacement_parameters()	Anisotropic displacement parameters in crystal coordinates.
set_anisotropic_displacement_parameters()	Update anisotropic displacement parameters in crystal coordinates.
get_isotropic_displacement_parameter()	Isotropic displacement parameters.
set_isotropic_displacement_parameter()	Update isotropic displacement parameters.
get_principal_displacement_parameters()	Principal displacement parameters in Cartesian coordinates.
get_cartesian_anisotropic_displacement_parameters()	Anisotropic displacement parameters in Cartesian coordinates.
get_crystal_axis_magnetic_moments()	Magnetic moments in crystal coordinates.
set_crystal_axis_magnetic_moments()	Update magnetic moments in crystal coordinates.
get_magnetic_moment_magnitude()	Magnitude of magnetic moments.
get_cartesian_magnetic_moments()	Magnetic moments in Cartesian coordinates.
get_g_factors()	g-factors.
set_g_factors()	Update g-factors.
get_lattice_constants()	Lattice parameters.
set_lattice_constants()	Update lattice parameters.
get_all_lattice_constants()	All lattice parameters.
get_reciprocal_lattice_constants()	Reciprocal lattice parameters.
get_symmetry_operators()	Symmetry operators.
get_magnetic_symmetry_operators()	Magnetic symmetry operators.
get_lattice_system()	Lattice system of unit cell.
get_lattice_volume()	Lattice volume of unit cell.
get_reciprocal_lattice_volume()	Reciprocal lattice volume of reciprocal cell.
get_metric_tensor()	Unit cell metric tensor.
get_reciprocal_metric_tensor()	Reciprocal cell metric tensor.
get_fractional_cartesian_transform()	Fractional to Cartesian coordinates transform matrix.
get_miller_cartesian_transform()	Miller to Cartesian coordinates transform matrix.
get_cartesian_rotation()	Transform matrix between Cartesian axes of real and reciprocal lattice.
get_moment_cartesian_transform()	Magnetic moment components crystal to Cartesian transfomrmation matrix.
get_atomic_displacement_cartesian_transform()	Atomic displacement parameters crystal to Cartesian transfomrmation matrix.
get_space_group_symbol()	Space group symbol.
get_space_group_number()	Space group number.
get_laue()	Laue class.
get_site_symmetries()	Site symmetry operators.
get_wyckoff_special_positions()	Wyckoff special positions.
get_site_multiplicities()	Site multiplicites.
get_twins()	Twin transformation matrices and mass fractions.
set_twins()	Update twin transformation matrices and mass fractions.
get_space_group_symmetry_operators()	All symmetry operators.
get_atom_colors()	Color of each atom.
get_atom_radii()	Radius of each atom.

get_active_sites()

Active atom sites in the unit cell.

Returns:

sites1d array, int

All active site numbers.

get_all_lattice_constants()

All lattice parameters.

Returns:

constantstuple

Lattice constants and angles. Angles in radians.

get_anisotropic_displacement_parameters()

Anisotropic displacement parameters in crystal coordinates of active atoms.

Returns:

U11, U22, U33, U23, U13, U121d array

Atomic displacement parameters \(U_{11}\), \(U_{22}\), \(U_{33}\), \(U_{23}\), \(U_{13}\), and \(U_{12}\).

get_atom_colors()

Color of each atom.

Parameters:

colors1d array

Colors of atoms in RGB.

get_atom_radii(radii='empirical')

Radius of each atom.

Parameters:

r1d array

Radii of atoms in angstroms. One of 'empirical', 'calculated', or 'van der waals'. Default 'empirical'.

get_atom_sites()

Atom site symbols in the unit cell.

Returns:

atms1d array, int

All atom sites.

get_atomic_displacement_cartesian_transform()

Transform matrix between crystal and Cartesian coordinates for atomic displacement parameters.

\[\begin{split}\begin{bmatrix} U_{xx} & U_{xy} & U_{xz} \\ U_{yx} & U_{yy} & U_{yz} \\ U_{zx} & U_{zy} & U_{zz} \end{bmatrix} = \begin{bmatrix} D_{11} & D_{12} & D_{13} \\ D_{21} & D_{22} & D_{23} \\ D_{31} & D_{32} & D_{33} \end{bmatrix} \begin{bmatrix} U_{11} & U_{12} & U_{13} \\ U_{21} & U_{22} & U_{23} \\ U_{31} & U_{32} & U_{33} \end{bmatrix} \begin{bmatrix} D_{11} & D_{21} & D_{31} \\ D_{12} & D_{22} & D_{32} \\ D_{13} & D_{23} & D_{33} \end{bmatrix}\end{split}\]

Returns:

D2d array

Components of the \(D\) matrix.

get_cartesian_anisotropic_displacement_parameters()

Anisotropic displacement parameters in Cartesian coordinates of active atoms.

Returns:

Uxx, Uyy, Uzz, Uyz, Uxz, Uxy1d array

Atomic displacement parameters \(U_{xx}\), \(U_{yy}\), \(U_{zz}\), \(U_{yz}\), \(U_{xz}\), and \(U_{xy}\).

get_cartesian_magnetic_moments()

Magnetic moments in Cartesian coordinates of active atoms.

Returns:

mu_x, mu_y, mu_z1d array

Magnetic moments \(\mu_x\), \(\mu_y\), and \(\mu_z\).

get_cartesian_rotation()

Transform matrix between Cartesian axes of real and reciprocal lattice.

\[\begin{split}\begin{bmatrix} Q_x \\ Q_y \\ Q_z \end{bmatrix} = 2\pi \begin{bmatrix} R_{11} & R_{12} & R_{13} \\ R_{21} & R_{22} & R_{23} \\ R_{31} & R_{32} & R_{33} \end{bmatrix} \begin{bmatrix} B_{11} & B_{12} & B_{13} \\ 0 & B_{22} & B_{23} \\ 0 & 0 & B_{33} \end{bmatrix} \begin{bmatrix} h \\ k \\ l \end{bmatrix}\end{split}\]

Returns:

R2d array

Components of the \(R\) matrix.

get_crystal_axis_magnetic_moments()

Magnetic moments in crystal coordinates of active atoms.

Returns:

mu1, mu2, mu31d array

Magnetic moments \(\mu_1\), \(\mu_2\), and \(\mu_3\).

get_filename()

Name of CIF file.

Returns:

filenamestr

Name of file excluding path.

get_filepath()

Path of CIF file.

Returns:

filepathstr

Name of path excluding filename.

get_fractional_cartesian_transform()

Trasform matrix from fractional to Cartesian coordinates.

\[\begin{split}\begin{bmatrix} r_x \\ r_y \\ r_z \end{bmatrix} = \begin{bmatrix} A_{11} & A_{12} & A_{13} \\ 0 & A_{22} & A_{23} \\ 0 & 0 & A_{33} \end{bmatrix} \begin{bmatrix} u \\ v \\ w \end{bmatrix}\end{split}\]

Returns:

A2d array

Components of the \(A\) matrix.

get_fractional_coordinates()

Fractional coordiantes of active atoms

Returns:

u, v, w1d array

Fractional coordiantes \(u\), \(v\), and \(w\).

get_g_factors()

g-factors of active ions.

Returns:

g1d array

Magnetic \(g\)-factors.

get_isotropic_displacement_parameter()

Isotropic displacement parameters of active atoms.

Returns:

Uiso1d array

Isotropic atomic displacement parameters \(U_\mathrm{iso}\).

get_lattice_constants()

Lattice parameters.

Cell	Parameters
Cubic	a
Hexagonal	a, c
Rhombohedral	a, alpha
Tetragonal	a, c
Orthorhombic	a, b, c
Monoclinic	a, b, c, alpha, beta or gamma
Triclinic	a, b, c, alpha, beta, gamma

Returns:

constantstuple

Non-constrained lattice constants and angles. Angles in radians.

get_lattice_system()

Lattice system of unit cell.

Returns:

systemstr

One of 'Cubic', 'Hexagonal', 'Rhombohedral', 'Tetragonal', 'Orthorhombic', 'Monoclinic', or 'Triclinic'.

get_lattice_volume()

Lattice volume of unit cell.

\[V = abc\sqrt{1-\cos^2{\alpha}-\cos^2{\beta}-\cos^2{\gamma} +2\cos{\alpha}\cos{\beta}\cos{\gamma}}\]

Returns:

Vfloat

Unit cell volume \(V\).

get_laue()

Laue class.

Returns:

lauestr

One of '-1', '2/m', 'mmm', '4/m', '4/mmm', '-3', '-3m', '6/m', '6/mmm', 'm-3', or 'm-3m'.

get_magnetic_moment_magnitude()

Magnitude of magnetic moments of active atoms.

Returns:

mu1d array

Moment of magnetic moments \(\mu\).

get_magnetic_symmetry_operators()

Magnetic symmetry operators of active atoms.

Returns:

mag_op1d array, str

Magnetic symmetry operator of each site.

get_metric_tensor()

Unit cell metric tensor.

\[\begin{split}G = \begin{bmatrix} a^2 & ab\cos{\gamma} & ac\cos{\beta} \\ ba\cos{\gamma} & b^2 & bc\cos{\alpha} \\ ca\cos{\beta} & cb\cos{\alpha} & c^2 \end{bmatrix}\end{split}\]

Returns:

G2d array

Components of the \(G\) metric tensor.

get_miller_cartesian_transform()

Trasform matrix from Miller to Cartesian coordinates.

\[\begin{split}\begin{bmatrix} Q_x \\ Q_y \\ Q_z \end{bmatrix} = 2\pi \begin{bmatrix} R_{11} & R_{12} & R_{13} \\ R_{21} & R_{22} & R_{23} \\ R_{31} & R_{32} & R_{33} \end{bmatrix} \begin{bmatrix} B_{11} & B_{12} & B_{13} \\ 0 & B_{22} & B_{23} \\ 0 & 0 & B_{33} \end{bmatrix} \begin{bmatrix} h \\ k \\ l \end{bmatrix}\end{split}\]

Returns:

B2d array

Components of the \(B\) matrix.

get_moment_cartesian_transform()

Transform matrix between crystal and Cartesian coordinates for magnetic moments.

\[\begin{split}\begin{bmatrix} \mu_x \\ \mu_y \\ \mu_z \end{bmatrix} = \begin{bmatrix} C_{11} & C_{12} & C_{13} \\ C_{21} & C_{22} & C_{23} \\ C_{31} & C_{32} & C_{33} \end{bmatrix} \begin{bmatrix} \mu_1 \\ \mu_2 \\ \mu_3 \end{bmatrix}\end{split}\]

Returns:

C2d array

Components of the \(C\) matrix.

get_number_atoms_per_unit_cell()

Total number of atoms in the unit cell.

Returns:

n_atmint

All active atoms.

get_occupancies()

Occupancies of active atoms.

Returns:

occ1d array

Site occupancies.

get_principal_displacement_parameters()

Principal displacement parameters in Cartesian coordinates of active atoms.

Returns:

U1, U2, U31d array

Atomic displacement parameters \(U_1\), \(U_2\), and \(U_3\).

get_reciprocal_lattice_constants()

Reciprocal lattice parameters.

Returns:

a_, b_, c_, alpha_, beta_, gamma_float

Reciprocal lattice constants and angles \(a^*\), \(b^*\), \(c^*\), \(\alpha^*\), \(\beta^*\) and \(\gamma^*\). Angles in radians.

get_reciprocal_lattice_volume()

Reciprocal lattice volume of reciprocal cell.

\[V^* = a^*b^*c^*\sqrt{1-\cos^2{\alpha^*}-\cos^2{\beta^*} -\cos^2{\gamma^*}+2\cos{\alpha^*} \cos{\beta^*}\cos{\gamma^*}}\]

Returns:

V_float

Reciprocal unit cell volume \(V^*\).

get_reciprocal_metric_tensor()

Reciprocal cell metric tensor.

\[\begin{split}G^* = \begin{bmatrix} (a^*)^2 & a^*b^*\cos{\gamma} & a^*c^*\cos{\beta} \\ b^*a^*\cos{\gamma} & (b^*)^2 & b^*c^*\cos{\alpha} \\ c^*a^*\cos{\beta} & c^*b^*\cos{\alpha} & (c^*)^2 \end{bmatrix}\end{split}\]

Returns:

G_2d array

Components of the \(G^*\) metric tensor.

get_site_multiplicities()

Site multiplicites of active atoms.

Returns:

mult1d array, int

Multiplicity of each site.

get_site_symmetries()

Site symmetry operators.

Returns:

pg1d array, str

Point group symmetry of each site.

get_sites()

Atom sites in the unit cell.

Returns:

sites1d array, int

All site numbers.

get_space_group_number()

Space group number.

Returns:

groupint

Number between 1 and 230.

get_space_group_symbol()

Space group symbol.

Returns:

hmstr

Symbol in Hermann–Mauguin notation.

get_space_group_symmetry_operators()

All symmetry operators.

Returns:

sym_ops1d array, str

Space group symmetry operators.

get_symmetry_operators()

Symmetry operators of active atoms.

Returns:

op1d array, str

Symmetry operator of each site.

get_twins()

Twin transformation matrices and mass fractions.

\[\begin{split}\begin{bmatrix} h^\prime \\ k^\prime \\ l^\prime \end{bmatrix} = \begin{bmatrix} T_{11} & T_{12} & T_{13} \\ T_{21} & T_{22} & T_{23} \\ T_{31} & T_{32} & T_{33} \end{bmatrix} \begin{bmatrix} h \\ k \\ l \end{bmatrix}\end{split}\]

Returns:

T3d array

Twin transformation matrices.

weights1d array

Twin mass fractions.

get_unit_cell_atoms()

Atom symbols of active atoms.

Returns:

atm1d array, str

Atom symbols.

get_unit_cell_cartesian_atomic_coordinates()

Cartesian coordiantes of active atoms.

Returns:

rx, ry, rz1d array

Cartesian coordiantes \(r_x\), \(r_y\), and \(r_z\).

get_unit_cell_charge_numbers()

Charge numbers of active ions.

Returns:

ion1d array, str

Valence charge number of active ions.

get_unit_cell_ions()

Ion symbols of active ions.

Returns:

ion1d array, str

Ion symbols.

get_unit_cell_isotopes()

Isotopes symbols of active isotopes.

Returns:

iso1d array, str

Isotopes symbols.

get_unit_cell_mass_numbers()

Mass numbers of active isotopes.

Returns:

iso1d array, str

Nuclide charge number of active ions.

get_wyckoff_special_positions()

Wyckoff special positions of active atoms.

Returns:

sp_pos1d array, str

Special position of each site

load(filename)

Load unit cell data.

Parameters:

filenamestr

Name of HDF5 file.

save(filename)

Save unit cell data.

Parameters:

filenamestr

Name of HDF5 file.

set_active_sites(act)

Update active atom sites in the unit cell.

Parameters:

act1d array, int

All active site numbers.

set_anisotropic_displacement_parameters(U11, U22, U33, U23, U13, U12)

Update anisotropic displacement parameters in crystal coordinates of active atoms.

Parameters:

U11, U22, U33, U23, U13, U121d array

Atomic displacement parameters \(U_{11}\), \(U_{22}\), \(U_{33}\), \(U_{23}\), \(U_{13}\), and \(U_{12}\).

set_crystal_axis_magnetic_moments(mu1, mu2, mu3)

Update magnetic moments in crystal coordinates of active atoms.

Parameters:

mu1, mu2, mu31d array

Magnetic moments \(\mu_1\), \(\mu_2\), and \(\mu_3\).

set_fractional_coordinates(u, v, w)

Update fractional coordiantes of active atoms.

Parameters:

u, v, w1d array

Fractional coordiantes \(u\), \(v\), and \(w\).

set_g_factors(g)

Update g-factors of active ions.

Parameters:

g1d array

Magnetic \(g\)-factors.

set_isotropic_displacement_parameter(Uiso)

Update isotropic displacement parameters of active atoms.

Parameters:

Uiso1d array

Isotropic atomic displacement parameters \(U_\mathrm{iso}\).

set_lattice_constants(constants)

Update lattice parameters.

Cell	Parameters
Cubic	a
Hexagonal	a, c
Rhombohedral	a, alpha
Tetragonal	a, c
Orthorhombic	a, b, c
Monoclinic	a, b, c, alpha, beta or gamma
Triclinic	a, b, c, alpha, beta, gamma

Parameters:

constantstuple

Non-constrained lattice constants and angles. Angles in radians.

set_occupancies(occ)

Update occupancies of active atoms.

Parameters:

occ1d array

Site occupancies.

set_twins(T, weights)

Update twin transformation matrices and mass fractions.

Parameters:

T3d array

Twin transformation matrices.

weights1d array

Twin mass fractions.

set_unit_cell_atoms(atm)

Update atom symbols of active atoms.

Parameters:

atm1d array, str

Atom symbols.

set_unit_cell_charge_numbers(ion)

Update charge numbers of active ions.

Parameters:

ion1d array, str

Valence charge number of active ions.

set_unit_cell_mass_numbers(iso)

Update mass numbers of active isotopes.

Parameters:

iso1d array, str

Nuclide mass number of active ions.