jarvis.analysis.structure.spacegroup
¶
Modules for handling crystallographic Spacegroup related operations.
Module Contents¶
Classes¶
Provide spacegroup related data for Atoms object. |
Functions¶
Remove duplicate rows. |
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Get unique miller indices for max_index. |
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Parse Wyckoff.csv from spglib. |
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Read wyckoff_csv file. |
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Get all Wyckoff operations for Hall number. |
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Convert xyz info to translation and rotation vectors. |
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Operate affine method. |
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Obtain new coord from xyz string. |
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Check if a coordinate exists. |
Attributes¶
- jarvis.analysis.structure.spacegroup.symmetrically_distinct_miller_indices(max_index=3, cvn_atoms=None)[source]¶
Get unique miller indices for max_index.
- jarvis.analysis.structure.spacegroup.wyckoff_file¶
- jarvis.analysis.structure.spacegroup.parse_wyckoff_csv(wyckoff_file)[source]¶
Parse Wyckoff.csv from spglib.
There are 530 data sets. For one example: 9:C 1 2 1::::::: ::4:c:1:(x,y,z):(-x,y,-z):: ::2:b:2:(0,y,1/2)::: ::2:a:2:(0,y,0)::
- jarvis.analysis.structure.spacegroup.get_wyckoff_position_operators(hall_number)[source]¶
Get all Wyckoff operations for Hall number.
- class jarvis.analysis.structure.spacegroup.Spacegroup3D(atoms=[], dataset={}, symprec=0.01, angle_tolerance=5)[source]¶
Bases:
object
Provide spacegroup related data for Atoms object.
Currently uses spglib to derive spacegroup related information for 3D materials mainly
- property space_group_symbol¶
Get spacegroup symbol.
- property space_group_number¶
Get spacegroup number.
- property primitive_atoms¶
Get primitive atoms.
- property refined_atoms¶
Refine atoms based on spacegroup data.
- property crystal_system¶
Get crystal system.
- property lattice_system¶
Get lattice system.
- property point_group_symbol¶
Get pointgroup.
- property conventional_standard_structure¶
Give a conventional cell according to certain conventions.
The conventionss are defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput electronic band structure calculations: Challenges and tools. Computational Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010 They basically enforce as much as possible norm(a1)<norm(a2)<norm(a3) Returns:
The structure in a conventional standardized cell
- jarvis.analysis.structure.spacegroup.parse_xyz_string(xyz_string)[source]¶
Convert xyz info to translation and rotation vectors.
Adapted from pymatgen. Args:
- xyz_string: string of the form ‘x, y, z’, ‘-x, -y, z’,
‘-2y+1/2, 3x+1/2, z-y+1/2’, etc.
- Returns:
translation and rotation vectors.
- jarvis.analysis.structure.spacegroup.operate_affine(cart_coord=[], affine_matrix=[])[source]¶
Operate affine method.