pyxtal.molecular_crystal module¶
Module for generating molecular crystals
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class
pyxtal.molecular_crystal.molecular_crystal(dim, group, molecules, numMols, factor=1.1, thickness=None, area=None, lattice=None, torsions=None, tm=<pyxtal.tolerance.Tol_matrix object>, sites=None, conventional=True, seed=None, use_hall=False)[source]¶ Bases:
objectClass for storing and generating molecular crystals based on symmetry constraints. Based on the crystal.random_crystal class for atomic crystals. Given a spacegroup, list of molecule objects, molecular stoichiometry, and a volume factor, generates a molecular crystal consistent with the given constraints.
Parameters: - dim – dimenion (1, 2, 3)
- group – the group number (1-75, 1-80, 1-230)
- molecules – a list of pymatgen.core.structure.Molecule objects for each type of molecule. Alternatively, you may supply a file path, or the name of molecules from the built_in database
- numMols – A list of the number of each type of molecule within the primitive cell (NOT the conventioal cell)
- factor – A volume factor used to generate a larger or smaller unit cell. Increasing this gives extra space between molecules
- lattice (optional) – the Lattice object to define the unit cell
- conventional (optional) – count the atomic numbers in a conventional cell
- tm (optional) – the Tol_matrix object to define the distances
- sites (optional) – pre-assigned wyckoff sites (e.g., [[“4a”], [“2b”]])
- seed (optional) – seeds
- use_hall – False
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set_crystal()[source]¶ The main code to generate a random molecular crystal. If successful, self.valid is True
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set_molecules(molecules, torsions)[source]¶ Get molecular information
Parameters: - molecules – list of molecules
- torsions – list of torsions
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set_orientations()[source]¶ Calculates the valid orientations for each Molecule and Wyckoff position. Returns a list with 4 indices:
- index 1: the molecular prototype’s index within self.molecules
- index 2: the WP’s 1st index (based on multiplicity)
- index 3: the WP’s 2nd index (within the group of same multiplicity)
- index 4: the index of a valid orientation for the molecule/WP pair
For example, self.valid_orientations[i][j][k] would be a list of valid orientations for self.molecules[i], in the Wyckoff position self.group.wyckoffs_organized[j][k]