pyxtal.io module¶
This module handles reading and write crystal files.
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pyxtal.io.
read_cif
(filename)[source]¶ read the cif, mainly for pyxtal cif output Be cautious in using it to read other cif files
Parameters: filename – path of the structure file Returns: pyxtal structure
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pyxtal.io.
search_molecules_in_crystal
(struc, tol=0.2, once=False, ignore_HH=True)[source]¶ Function to perform to find the molecule in a Pymatgen structure
Parameters: - struc – Pymatgen Structure
- tol – tolerance value to check the connectivity
- once – search only one molecule or all molecules
- ignore_HH – whether or not ignore the short H-H in checking molecule
Returns: list of pymatgen molecules positions: list of center positions
Return type: molecules
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class
pyxtal.io.
structure_from_ext
(struc, ref_mols, tol=0.2, ignore_HH=False, add_H=False, hn=None)[source]¶ Bases:
object
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pyxtal.io.
write_cif
(struc, filename=None, header='', permission='w', sym_num=None, style='mp')[source]¶ Export the structure in cif format The default setting for _atom_site follows the materials project cif
Parameters: - struc – pyxtal structure object
- filename – path of the structure file
- header – additional information
- permission – write(w) or append(a+) to the given file
- sym_num – the number of symmetry operations, None means writing all symops
- style – icsd or mp (used in pymatgen)