\(\newcommand{\AA}{\text{Å}}\)

CRYSTALpytools.geometry module

Class and methods to deal with geometries, including Pymatgen Structrue and Molecule geometries and CRYSTAL gui geometries

class Crystal_gui(dimensionality=None, lattice=None, symmops=None, atom_number=None, atom_positions=None, space_group=None)

Bases: object

This class can read a CRYSTAL gui file into an object or substrate information of the object to generate a gui file.

Parameters:

  • dimensionality (int) – Number of dimensions

  • lattice (array) – 3*3 lattice matrix in Angstrom

  • symmops (array) – n_symmops*4*3 matrices of symmetry operators

  • atom_number (array) – natom*1 int array of atomic numbers

  • atom_positions (array) – natom*3 array of Cartesian coordinates

  • space_group (int) – CRYSTAL space group number

read_pmg(struc, pbc=None, vacuum=500.0, symmetry=True, zconv=None, **kwargs)

Read a pymatgen Structure object into a CRYSTAL_gui object. Vacuum layer is set to 500 Angstrom as the default of CRYSTAL for low symmstry systems.

Parameters:

  • struc (Structure|Molecule) – Pymatgen Structure / Molecule object.

  • pbc (list) – 1*3 boolian list. Implements periodicity along x, y and z directions. If none, the code will read it from input structure.

  • vacuum (float) – Vacuum distance. Unit: Angstrom. Low dimensional systems only.

  • symmetry (bool) – Do symmetry analysis.

  • zconv (list[list[int, int]]) – 1st element: The index of atom; 2nd element: The new conventional atomic number.

  • **kwargs – Passed to Pymatgen SpacegroupAnalyzer object. Valid only if symmetry=True.

read_gui(gui_file)

Read CRYSTAL gui file and genreate a Crystal_gui object.

Parameters:

gui_file (str) – The CRYSTAL structure (gui) file

write_gui(gui_file, symm=True, pseudo_atoms=[])

Write a CRYSTAL gui file (to file)

Parameters:

  • gui_file (str) – The name of the gui that is going to be written ( including .gui).

  • symm (bool) – Whether to include symmetry operations.

  • pseudo_atoms (list[int]) – A list of atoms whose core is described by a pseudopotential (conventional atomic number = atomic number + 200)

class CStructure(lattice, species, coords, symmetry_group=1, pbc=None, standarize=False, **kwargs)

Bases: Structure

Inherited from Pymatgen Structure object with added methods.

Arguments not listed are the same as Pymatgen Structure

Parameters:

  • species (list[int]) – Same as pymatgen or a 1*nAtom list of conventional atomic numbers.

  • symmetry_group (int) – Symmetry group number or symbol in CRYSTAL convention.

  • pbc (list|tuple) – Periodicity.

  • standarize (bool) – Whether to use the CRYSTAL convention of periodic boundaries for low dimensional materials. It calls the standarize_pbc() method.

  • **kwargs – Other arguments passed to pymatgen Structure.

Returns:

self (CStructure) – CStructure object.

classmethod from_pmg(struc)

Get a CStructure object from Pymatgen structure. symmetry_group currently not available.

property ndimen

Dimensionality (1~3) of the system.

property species_symbol

Atom symbols.

property species_Z

Conventional atomic numbers

property crys_coords

Composite fractional / Cartesian atomic coordinates. Consistent with CRYSTAL conventions.

  • 3D: Fractional

  • 2D: Frac, Frac, Cart

  • 1D: Frac, Cart, Cart

  • 0D: Cart, Cart, Cart

standarize_pbc()

Use the CRYSTAL standard periodic boundary for low dimensional materials.

refine_geometry(**kwargs)

Get refined geometry. Useful when reducing the cell to the irrducible one. 3D only.

Parameters:

**kwargs – Passed to Pymatgen SpacegroupAnalyzer object.

Returns:

  • self (CStructure) – New attributes listed below

  • sg (int) – Space group number

  • pstruc (Structure) – Irrducible structure that is consistent with International Crystallographic Table

  • platt (list) – minimal set of crystallographic cell parameters

  • natom_irr (int) – number of irrducible atoms

  • atom (list) – natom*4 array. 1st element: atomic number; 2-4: fractional coordinates

get_sg_symmops(**kwargs)

Get space group number and corresponding symmetry operations. To keep consistency with International Crystallographic Table, refined geometry is suggested.

Parameters:

**kwargs – Passed to Pymatgen SpacegroupAnalyzer object.

Returns:

  • self (CStructure) – New attributes are listed below

  • sg (int) – Space group number

  • n_symmops (int) – number of symmetry operations

  • symmops (array) – n_symmops*4*3 array of symmetry operations

get_pcel(smx)

Restore the supercell to primitive cell, with the origin shifted to the middle of lattice to utilize symmetry (as the default of CRYSTAL).

Parameters:

smx (array) – 3*3 array of supercell expansion matrix. Inverse will be taken automatically.

Returns:

pcel (CStructure) – Pymatgen structure of primitive cell with CRYSTALpytools methods.

get_scel(smx)

Get the supercell from primitive cell, with the origin shifted to the middle of lattice to utilize symmetry (as the default of CRYSTAL).

Parameters:

smx (array) – 3*3 array of supercell expansion matrix

Returns:

scel (CStructure) – Pymatgen structure of supercell

rot_cel(vec1, vec2)

Rotate the geometry according to 2 vectors. A rotation vector is defined.

Parameters:

  • vec1 (array) – A Cartesian vector before rotation

  • vec2 (array) – A Cartesian vector after rotation

Returns:

rcel (CStructure) – Pymatgen structure of rotated cell

miller_norm(miller)

Find the norm vector of a specified Miller plane

Parameters:

miller (array | list) – Miller indices. 3*1 1D array or nmiller*3 3D array

Returns:

vec (array) – Norm vector, normalized to 1. 3*1 1D array or nmiller*3 3D array

write_gui(gui_file=None, pbc=None, vacuum=500.0, symmetry=True, zconv=None, **kwargs)

Read a pymatgen Structure object into a CRYSTAL_gui object. Vacuum layer is set to 500 Angstrom as the default of CRYSTAL for low symmstry systems.

Developing

Parameters:

  • struc (Structure|Molecule) – Pymatgen Structure / Molecule object.

  • pbc (list) – 1*3 boolian list. Implements periodicity along x, y and z directions. If none, the code will read it from input structure.

  • vacuum (float) – Vacuum distance. Unit: Angstrom. Low dimensional systems only.

  • symmetry (bool) – Do symmetry analysis.

  • zconv (list[list[int, int]]) – 1st element: The index of atom; 2nd element: The new conventional atomic number.

  • **kwargs – Passed to Pymatgen SpacegroupAnalyzer object. Valid only if symmetry=True.

_abc_impl = <_abc._abc_data object>
class CMolecule(coords, symmetry_group=1, **kwargs)

Bases: Molecule

Inherited from Pymatgen Molecule object with added methods.

Parameters:

  • species (list[int]) – Same as pymatgen or a 1*nAtom list of conventional atomic numbers.

  • symmetry_group (int) – Symmetry group number or symbol in CRYSTAL convention.

  • **kwargs – Other arguments passed to pymatgen Molecule.

Returns:

self (CMolecule) – CMolecule object.

_abc_impl = <_abc._abc_data object>