aiida_crystal17.parsers.geometry module

This module deals with reading/creating .gui files for use with the EXTERNAL keyword

File Format

dimesionality origin_setting crystal_type energy(optional)
    a_x a_y a_z
    b_x b_y b_z
    c_x c_y c_z
num_symm_ops (in cartesian coordinates)
    op1_rot_00 op1_rot_01 op1_rot_02
    op1_rot_10 op1_rot_11 op1_rot_12
    op1_rot_20 op1_rot_21 op1_rot_22
    op1_trans_0 op1_trans_1 op1_trans_2
    ...
num_atoms (if cryversion<17 irreducible atoms only)
    atomic_number x y z (in cartesian coordinates)
    ...
space_group_int_num num_symm_ops

aiida_crystal17.parsers.geometry.ase_to_structdict(atoms)

convert ase.Atoms to struct dict

Return structdict:  dict containing ‘lattice’, ‘atomic_numbers’, ‘pbc’, ‘ccoords’, ‘equivalent’

aiida_crystal17.parsers.geometry.cart2frac(lattice, ccoords)

a function that takes the cell parameters, in angstrom, and a list of Cartesian coordinates and returns the structure in fractional coordinates

aiida_crystal17.parsers.geometry.compute_symmetry_3d(structdata, standardize, primitive, idealize, symprec, angletol)

create 3d geometry input for CRYSTAL17

Parameters:

• structdata – “lattice”, “atomic_numbers”, “ccoords”, “pbc” and (optionally) “equivalent”
• standardize – whether to standardize the structure
• primitive – whether to create a primitive structure
• idealize – whether to idealize the structure
• symprec – symmetry precision to parse to spglib
• angletol – angletol to parse to spglib

Returns:

(structdata, symmdata)

aiida_crystal17.parsers.geometry.crystal17_gui_string(structdata, symmdata, fractional_ops=True)

create string of gui file content (for CRYSTAL17)

Parameters:

• structdata – dictionary of structure data with keys: ‘pbc’, ‘atomic_numbers’, ‘ccoords’, ‘lattice’
• symmdata – dictionary of symmetry data with keys: ‘crystal_type’, ‘centring_code’, ‘space_group’, ‘operations’
• fractional_ops – whether the symmetry operations are in fractional coordinates

Returns:

aiida_crystal17.parsers.geometry.dict_to_structure(structdict, logger=None)

create a dictionary of structure properties per atom

Param:dictionary containing; ‘lattice’, ‘atomic_numbers’ (or ‘symbols’), ‘ccoords’, ‘pbc’, ‘kinds’, ‘equivalent’ Parameters:logger – a logger with a warning method Return structure:  the input structure Rtype structure:  aiida.orm.data.structure.StructureData

aiida_crystal17.parsers.geometry.frac2cart(lattice, fcoords)

a function that takes the cell parameters, in angstrom, and a list of fractional coordinates and returns the structure in cartesian coordinates

aiida_crystal17.parsers.geometry.get_centering_code(sg_number, sg_symbol)

get crystal centering codes, to convert from primitive to conventional

Parameters:

• sg_number – the space group number
• sg_symbol – the space group symbol

Returns:

CRYSTAL centering code

aiida_crystal17.parsers.geometry.get_crystal_system(sg_number, as_number=False)

Get the crystal system for the structure, e.g., (triclinic, orthorhombic, cubic, etc.) from the space group number

Parameters:

• sg_number – the spacegroup number
• as_number – return the system as a number (recognized by CRYSTAL) or a str

Returns:

Crystal system for structure or None if system cannot be detected.

aiida_crystal17.parsers.geometry.get_lattice_type(sg_number)

Get the lattice for the structure, e.g., (triclinic, orthorhombic, cubic, etc.).This is the same than the crystal system with the exception of the hexagonal/rhombohedral lattice

Parameters:sg_number – space group number Returns:Lattice type for structure or None if type cannot be detected.

aiida_crystal17.parsers.geometry.ops_cart_to_frac(ops_flat, lattice)

convert a list of flattened cartesian symmetry operations to fractional

aiida_crystal17.parsers.geometry.ops_frac_to_cart(ops_flat, lattice)

convert a list of flattened fractional symmetry operations to cartesian

aiida_crystal17.parsers.geometry.read_gui_file(fpath, cryversion=17)

read CRYSTAL geometry (.gui) file

Parameters:

• fpath (str or pathlib.Path) – path to file
• cryversion (int) – version of CRYSTAL

Returns:

aiida_crystal17.parsers.geometry.structdict_to_ase(structdict)

convert struct dict to ase.Atoms

Parameters:structdict – dict containing ‘lattice’, ‘atomic_numbers’, ‘pbc’, ‘ccoords’, ‘equivalent’ Return type:ase.Atoms

aiida_crystal17.parsers.geometry.structure_to_dict(structure)

create a dictionary of structure properties per atom

Parameters:structure (aiida.orm.data.structure.StructureData) – the input structure Returns:dictionary containing; lattice, atomic_numbers, ccoords, pbc, kinds, equivalent Return type:dict