aiida.tools.data.array.kpoints package¶
Various utilities to deal with KpointsData instances or create new ones (e.g. band paths, kpoints from a parsed input text file, …)
Submodules¶
Tool to automatically determine k-points for a given structure using legacy custom implementation.
- aiida.tools.data.array.kpoints.legacy.analyze_cell(cell=None, pbc=None)[source]¶
A function executed by the __init__ or by set_cell. If a cell is set, properties like a1, a2, a3, cosalpha, reciprocal_cell are set as well, although they are not stored in the DB. :note: units are Angstrom for the cell parameters, 1/Angstrom for the reciprocal cell parameters.
- aiida.tools.data.array.kpoints.legacy.change_reference(reciprocal_cell, kpoints, to_cartesian=True)[source]¶
Change reference system, from cartesian to crystal coordinates (units of b1,b2,b3) or viceversa.
- Parameters
reciprocal_cell – a 3x3 array representing the cell lattice vectors in reciprocal space
kpoints – a list of (3) point coordinates
- Return kpoints
a list of (3) point coordinates in the new reference
- aiida.tools.data.array.kpoints.legacy.find_bravais_info(cell, pbc, epsilon_length=1e-05, epsilon_angle=1e-05)[source]¶
Finds the Bravais lattice of the cell passed in input to the Kpoint class :note: We assume that the cell given by the cell property is the primitive unit cell.
Note
in 3D, this implementation expects that the structure is already standardized according to the Setyawan paper. If this is not the case, the kpoints and band structure returned will be incorrect. The only case that is dealt correctly by the library is the case when axes are swapped, where the library correctly takes this swapping/rotation into account to assign kpoint labels and coordinates.
- Parameters
cell – 3x3 array representing the structure cell lattice vectors
pbc – 3-dimensional array of booleans signifying the periodic boundary conditions along each lattice vector passed in value as cartesian coordinates. Default: False.
epsilon_length (float) – threshold on lengths comparison, used to get the bravais lattice info. It has to be used if the user wants to be sure the right symmetries are recognized.
epsilon_angle (float) – threshold on angles comparison, used to get the bravais lattice info. It has to be used if the user wants to be sure the right symmetries are recognized.
- Returns
a dictionary, with keys short_name, extended_name, index (index of the Bravais lattice), and sometimes variation (name of the variation of the Bravais lattice) and extra (a dictionary with extra parameters used by the get_kpoints_path method)
- aiida.tools.data.array.kpoints.legacy.get_explicit_kpoints_path(value=None, cell=None, pbc=None, kpoint_distance=None, cartesian=False, epsilon_length=1e-05, epsilon_angle=1e-05)[source]¶
Set a path of kpoints in the Brillouin zone.
- Parameters
value –
description of the path, in various possible formats.
None: automatically sets all irreducible high symmetry paths. Requires that a cell was set
or:
[('G','M'), (...), ...] [('G','M',30), (...), ...] [('G',(0,0,0),'M',(1,1,1)), (...), ...] [('G',(0,0,0),'M',(1,1,1),30), (...), ...]
cell – 3x3 array representing the structure cell lattice vectors
pbc – 3-dimensional array of booleans signifying the periodic boundary conditions along each lattice vector
kpoint_distance (float) – parameter controlling the distance between kpoints. Distance is given in crystal coordinates, i.e. the distance is computed in the space of b1,b2,b3. The distance set will be the closest possible to this value, compatible with the requirement of putting equispaced points between two special points (since extrema are included).
cartesian (bool) – if set to true, reads the coordinates eventually passed in value as cartesian coordinates. Default: False.
epsilon_length (float) – threshold on lengths comparison, used to get the bravais lattice info. It has to be used if the user wants to be sure the right symmetries are recognized.
epsilon_angle (float) – threshold on angles comparison, used to get the bravais lattice info. It has to be used if the user wants to be sure the right symmetries are recognized.
- Returns
point_coordinates, path, bravais_info, explicit_kpoints, labels
- aiida.tools.data.array.kpoints.legacy.get_kpoints_path(cell, pbc=None, cartesian=False, epsilon_length=1e-05, epsilon_angle=1e-05)[source]¶
Get the special point and path of a given structure.
Note
in 3D, this implementation expects that the structure is already standardized according to the Setyawan paper. If this is not the case, the kpoints and band structure returned will be incorrect. The only case that is dealt correctly by the library is the case when axes are swapped, where the library correctly takes this swapping/rotation into account to assign kpoint labels and coordinates.
In 2D, coordinates are based on the paper: R. Ramirez and M. C. Bohm, Int. J. Quant. Chem., XXX, pp. 391-411 (1986)
In 3D, coordinates are based on the paper: W. Setyawan, S. Curtarolo, Comp. Mat. Sci. 49, 299 (2010)
- Parameters
cell – 3x3 array representing the structure cell lattice vectors
pbc – 3-dimensional array of booleans signifying the periodic boundary conditions along each lattice vector
cartesian – If true, returns points in cartesian coordinates. Crystal coordinates otherwise. Default=False
epsilon_length – threshold on lengths comparison, used to get the bravais lattice info
epsilon_angle – threshold on angles comparison, used to get the bravais lattice info
- Return special_points,path
special_points: a dictionary of point_name:point_coords key,values.
path: the suggested path which goes through all high symmetry lines. A list of lists for all path segments. e.g.
[('G','X'),('X','M'),...]
It’s not necessarily a continuous line.- Note
We assume that the cell given by the cell property is the primitive unit cell
Various utilities to deal with KpointsData instances or create new ones (e.g. band paths, kpoints from a parsed input text file, …)
- aiida.tools.data.array.kpoints.main._legacy_get_explicit_kpoints_path(structure, **kwargs)[source]¶
Call the get_explicit_kpoints_path of the legacy implementation
- Parameters
structure – a StructureData node
kpoint_distance (float) – parameter controlling the distance between kpoints. Distance is given in crystal coordinates, i.e. the distance is computed in the space of b1, b2, b3. The distance set will be the closest possible to this value, compatible with the requirement of putting equispaced points between two special points (since extrema are included).
cartesian (bool) – if set to true, reads the coordinates eventually passed in value as cartesian coordinates
epsilon_length (float) – threshold on lengths comparison, used to get the bravais lattice info
epsilon_angle (float) – threshold on angles comparison, used to get the bravais lattice info
- aiida.tools.data.array.kpoints.main._legacy_get_kpoints_path(structure, **kwargs)[source]¶
Call the get_kpoints_path of the legacy implementation
- Parameters
structure – a StructureData node
cartesian (bool) – if set to true, reads the coordinates eventually passed in value as cartesian coordinates
epsilon_length – threshold on lengths comparison, used to get the bravais lattice info
epsilon_angle – threshold on angles comparison, used to get the bravais lattice info
- aiida.tools.data.array.kpoints.main._seekpath_get_explicit_kpoints_path(structure, **kwargs)[source]¶
Call the get_explicit_kpoints_path wrapper function for Seekpath
- Parameters
structure – a StructureData node
with_time_reversal – if False, and the group has no inversion symmetry, additional lines are returned
reference_distance – a reference target distance between neighboring k-points in the path, in units of 1/ang. The actual value will be as close as possible to this value, to have an integer number of points in each path
recipe –
choose the reference publication that defines the special points and paths. Currently, the following value is implemented:
hpkot
: HPKOT paper: Y. Hinuma, G. Pizzi, Y. Kumagai, F. Oba, I. Tanaka, Band structure diagram paths based on crystallography, Comp. Mat. Sci. 128, 140 (2017). DOI: 10.1016/j.commatsci.2016.10.015
threshold – the threshold to use to verify if we are in and edge case (e.g., a tetragonal cell, but
a==c
). For instance, in the tI lattice, ifabs(a-c) < threshold
, aEdgeCaseWarning
is issued. Note that depending on the bravais lattice, the meaning of the threshold is different (angle, length, …)symprec – the symmetry precision used internally by SPGLIB
angle_tolerance – the angle_tolerance used internally by SPGLIB
- aiida.tools.data.array.kpoints.main._seekpath_get_kpoints_path(structure, **kwargs)[source]¶
Call the get_kpoints_path wrapper function for Seekpath
- Parameters
structure – a StructureData node
with_time_reversal – if False, and the group has no inversion symmetry, additional lines are returned
recipe –
choose the reference publication that defines the special points and paths. Currently, the following value is implemented:
hpkot
: HPKOT paper: Y. Hinuma, G. Pizzi, Y. Kumagai, F. Oba, I. Tanaka, Band structure diagram paths based on crystallography, Comp. Mat. Sci. 128, 140 (2017). DOI: 10.1016/j.commatsci.2016.10.015
threshold – the threshold to use to verify if we are in and edge case (e.g., a tetragonal cell, but
a==c
). For instance, in the tI lattice, ifabs(a-c) < threshold
, aEdgeCaseWarning
is issued. Note that depending on the bravais lattice, the meaning of the threshold is different (angle, length, …)symprec – the symmetry precision used internally by SPGLIB
angle_tolerance – the angle_tolerance used internally by SPGLIB
- aiida.tools.data.array.kpoints.main.get_explicit_kpoints_path(structure, method='seekpath', **kwargs)[source]¶
Returns a dictionary whose contents depend on the method but includes at least the following keys
parameters: Dict node
explicit_kpoints: KpointsData node with explicit kpoints path
The contents of the parameters depends on the method but contains at least the keys
‘point_coords’: a dictionary with ‘kpoints-label’: [float coordinates]
- ‘path’: a list of length-2 tuples, with the labels of the starting
and ending point of each label section
The ‘seekpath’ method which is the default also returns the following additional nodes
primitive_structure: StructureData with the primitive cell
conv_structure: StructureData with the conventional cell
Note that the generated kpoints for the seekpath method only apply on the returned primitive_structure and not on the input structure that was provided
- Parameters
structure – a StructureData node
method – the method to use for kpoint generation, options are ‘seekpath’ and ‘legacy’. It is strongly advised to use the default ‘seekpath’ as the ‘legacy’ implementation is known to have bugs for certain structure cells
kwargs – optional keyword arguments that depend on the selected method
- Returns
dictionary as described above in the docstring
- aiida.tools.data.array.kpoints.main.get_kpoints_path(structure, method='seekpath', **kwargs)[source]¶
Returns a dictionary whose contents depend on the method but includes at least the following keys
parameters: Dict node
The contents of the parameters depends on the method but contains at least the keys
‘point_coords’: a dictionary with ‘kpoints-label’: [float coordinates]
- ‘path’: a list of length-2 tuples, with the labels of the starting
and ending point of each label section
The ‘seekpath’ method which is the default also returns the following additional nodes
primitive_structure: StructureData with the primitive cell
conv_structure: StructureData with the conventional cell
Note that the generated kpoints for the seekpath method only apply on the returned primitive_structure and not on the input structure that was provided
- Parameters
structure – a StructureData node
method – the method to use for kpoint generation, options are ‘seekpath’ and ‘legacy’. It is strongly advised to use the default ‘seekpath’ as the ‘legacy’ implementation is known to have bugs for certain structure cells
kwargs – optional keyword arguments that depend on the selected method
- Returns
dictionary as described above in the docstring
Tool to automatically determine k-points for a given structure using SeeK-path.
- aiida.tools.data.array.kpoints.seekpath.get_explicit_kpoints_path(structure, parameters)[source]¶
Return the kpoint path for band structure (in scaled and absolute coordinates), given a crystal structure, using the paths proposed in the various publications (see description of the ‘recipe’ input parameter). The parameters are the same as get get_explicit_k_path in __init__, but here all structures are input and returned as AiiDA structures rather than tuples, and similarly k-points-related information as a AiiDA KpointsData class.
- Parameters
structure – The AiiDA StructureData for which we want to obtain the suggested path.
parameters – A dictionary whose key-value pairs are passed as additional kwargs to the
seekpath.get_explicit_k_path
function.
- Returns
A dictionary with four nodes:
explicit_kpoints
: a KpointsData with the (explicit) kpoints (with labels set).parameters
: a Dict, whose content is the same dictionary as returned by theseekpath.get_explicit_k_path
function (see seekpath documentation), except that:conv_lattice
,conv_positions
,conv_types
are removed and replaced by theconv_structure
output nodeprimitive_lattice
,primitive_positions
,primitive_types
are removed and replaced by the primitive_structure output nodereciprocal_primitive_lattice
,explicit_kpoints_abs
,explicit_kpoints_rel
andexplicit_kpoints_labels
are removed and replaced by theexplicit_kpoints
output node
primitive_structure
: A StructureData with the primitive structureconv_structure
: A StructureData with the primitive structure
- aiida.tools.data.array.kpoints.seekpath.get_kpoints_path(structure, parameters)[source]¶
Return the kpoint path information for band structure given a crystal structure, using the paths from the chosen recipe/reference. The parameters are the same as get get_path in __init__, but here all structures are input and returned as AiiDA structures rather than tuples.
If you use this module, please cite the paper of the corresponding recipe (see documentation of seekpath).
- Parameters
structure – The crystal structure for which we want to obtain the suggested path. It should be an AiiDA StructureData object.
parameters – A dictionary whose key-value pairs are passed as additional kwargs to the
seekpath.get_path
function.
- Returns
A dictionary with three nodes:
parameters
: a Dict, whose content is the same dictionary as returned by theseekpath.get_path
function (see seekpath documentation), except that:conv_lattice
,conv_positions
,conv_types
are removed and replaced by theconv_structure
output nodeprimitive_lattice
,primitive_positions
,primitive_types
are removed and replaced by theprimitive_structure
output node
primitive_structure
: A StructureData with the primitive structureconv_structure
: A StructureData with the primitive structure