import logging
import numpy as np
import spglib
from collections import Counter
logger = logging.getLogger(__name__)
# DATADICT properties
# ------------------------------------------
bravais_lattice_dict = {
"b2": "https://www.wikidata.org/wiki/Q851536",
"bcc": "https://www.wikidata.org/wiki/Q851536",
"bct": "bct",
"cubic": "https://www.wikidata.org/wiki/Q473227",
"diamond": "https://www.wikidata.org/wiki/Q3006714",
"diatom": "https://www.wikidata.org/wiki/Q1751859",
"fcc": "https://www.wikidata.org/wiki/Q3006714",
"hcp": "https://www.wikidata.org/wiki/Q663314",
"monoclinic": "https://www.wikidata.org/wiki/Q624543",
"orthorhombic": "https://www.wikidata.org/wiki/Q648961",
"rhombohedral": "https://www.wikidata.org/wiki/Q13362463",
"sc": "https://www.wikidata.org/wiki/Q2242450",
"tetragonal": "https://www.wikidata.org/wiki/Q503601",
"l12": "https://www.wikidata.org/wiki/Q3006714",
"a15": "a15",
}
# SIMCELL properties
# --------------------------------------------
[docs]
def get_chemical_composition(structure):
"""
Get the chemical composition of the system.
Parameters
----------
system : object
The system object.
Returns
-------
composition : dict
A dictionary containing the chemical elements as keys and their corresponding counts as values.
"""
symbols = structure.get_chemical_symbols()
element_counts = Counter(symbols)
total_atoms = len(symbols)
composition = {
element: count / total_atoms for element, count in element_counts.items()
}
return composition
[docs]
def get_cell_volume(system):
"""
Get the volume of the simulation cell.
Parameters
----------
system : object
The system object.
Returns
-------
volume : float
The volume of the simulation cell.
"""
return system.get_volume()
[docs]
def get_number_of_atoms(system):
"""
Get the number of atoms in the system.
Parameters
----------
system : object
The system object.
Returns
-------
natoms : int
The number of atoms in the system.
"""
return len(system)
[docs]
def get_simulation_cell_length(system):
"""
Get the length of the simulation cell.
Parameters
----------
system : object
The system object.
Returns
-------
length : list
A list containing the length of each dimension of the simulation cell.
"""
return system.get_cell_lengths_and_angles()[:3]
[docs]
def get_simulation_cell_vector(system):
"""
Get the simulation cell vector of the given system.
Parameters
----------
system : object
The system object containing the simulation cell information.
Returns
-------
numpy.ndarray
The simulation cell vector of the system.
"""
return system.cell
[docs]
def get_simulation_cell_angle(system):
"""
Get the angles between the vectors of the simulation cell.
Parameters
----------
system : object
The system object containing the simulation cell information.
Returns
-------
angles : list
A list containing the angles between the vectors of the simulation cell.
"""
return system.get_cell_lengths_and_angles()[3:]
# LATTICE properties
# --------------------------------------------
[docs]
def get_lattice_angle(system):
"""
Calculate the lattice angles of a given system.
Parameters
----------
system : object
The system object containing the structure information.
Returns
-------
list
A list of three lattice angles in degrees. If the structure information is not available, [None, None, None] is returned.
"""
if system._structure_dict is None:
return [None, None, None]
if "box" in system._structure_dict.keys():
return [
_get_angle(
system._structure_dict["box"][0], system._structure_dict["box"][1]
),
_get_angle(
system._structure_dict["box"][1], system._structure_dict["box"][2]
),
_get_angle(
system._structure_dict["box"][2], system._structure_dict["box"][0]
),
]
else:
return [None, None, None]
[docs]
def get_lattice_parameter(system):
"""
Calculate the lattice parameters of a system.
Parameters
----------
system : object
The system object containing information about the atoms and structure.
Returns
-------
list
A list containing the lattice parameters of the system. If the lattice constant is not available,
[None, None, None] is returned. If the system structure is available, the lattice parameters are
calculated based on the box dimensions. Otherwise, the lattice constant is returned for all three
dimensions.
Examples
--------
>>> system = System()
>>> system.atoms._lattice_constant = 3.5
>>> system._structure_dict = {"box": [[1, 0, 0], [0, 1, 0], [0, 0, 1]]}
>>> get_lattice_parameter(system)
[3.5, 3.5, 3.5]
>>> system.atoms._lattice_constant = None
>>> get_lattice_parameter(system)
[None, None, None]
"""
if system.atoms._lattice_constant is None:
return [None, None, None]
else:
if system._structure_dict is not None:
if "box" in system._structure_dict.keys():
return [
np.linalg.norm(system._structure_dict["box"][0])
* system.atoms._lattice_constant,
np.linalg.norm(system._structure_dict["box"][1])
* system.atoms._lattice_constant,
np.linalg.norm(system._structure_dict["box"][2])
* system.atoms._lattice_constant,
]
return [
system.atoms._lattice_constant,
system.atoms._lattice_constant,
system.atoms._lattice_constant,
]
[docs]
def get_crystal_structure_name(system):
"""
Get the name of the crystal structure for a given system.
Parameters
----------
system : object
The system object containing the crystal structure information.
Returns
-------
str or None
The name of the crystal structure if available, otherwise None.
"""
if system._structure_dict is None:
return None
return system.atoms._lattice
def get_repetitions(system):
if system._structure_dict is None:
return [None, None, None]
if "repetitions" in system._structure_dict.keys():
return system._structure_dict["repetitions"]
return [None, None, None]
[docs]
def get_bravais_lattice(structure):
"""
Get the Bravais lattice of a given system.
Parameters
----------
system : object
The system object for which the Bravais lattice is to be determined.
Returns
-------
str or None
The Bravais lattice of the system, or None if the system's structure dictionary is not available or the lattice is not found in the dictionary.
"""
if structure in bravais_lattice_dict.keys():
return bravais_lattice_dict[structure]
return None
[docs]
def get_basis_positions(system):
"""
Get the basis positions from the given system.
Parameters
----------
system : object
The system object containing the structure dictionary.
Returns
-------
numpy.ndarray or None
The basis positions if available, otherwise None.
"""
if system._structure_dict is None:
return None
if "positions" in system._structure_dict.keys():
return system._structure_dict["positions"]
return None
[docs]
def get_lattice_vector(system):
"""
Get the lattice vector of a system.
Parameters
----------
system : object
The system object containing the structure information.
Returns
-------
list
A list representing the lattice vector of the system. If the structure
dictionary is not available or the lattice vector is not defined, it
returns [None, None, None].
"""
if system._structure_dict is None:
return [None, None, None]
if "box" in system._structure_dict.keys():
return system._structure_dict["box"]
return [None, None, None]
[docs]
def get_spacegroup_symbol(system):
"""
Get the symbol of the spacegroup for a given system.
Parameters:
system (object): The system object for which to retrieve the spacegroup symbol.
Returns:
str: The symbol of the spacegroup if available, otherwise None.
"""
try:
results = _get_symmetry_dict(system)
return results[0]
except Exception as e:
logger.debug("Spacegroup symbol lookup failed: %s", e)
return None
[docs]
def get_spacegroup_number(system):
"""
Get the spacegroup number of a given system.
Parameters
----------
system : object
The system object for which the spacegroup number is to be determined.
Returns
-------
int or None
The spacegroup number of the system if it is available, otherwise None.
"""
try:
results = _get_symmetry_dict(system)
return results[1]
except Exception as e:
logger.debug("Spacegroup number lookup failed: %s", e)
return None
# ATOM attributes
# --------------------------------------------
[docs]
def get_position(system):
"""
Get the positions of the atoms in the system.
Parameters
----------
system : object
The system object containing the atom positions.
Returns
-------
numpy.ndarray or None
The positions of the atoms if available, otherwise None.
"""
return system.atoms.positions
[docs]
def get_species(system):
"""
Get the species of atoms in the given system.
Parameters
----------
system : System
The system object containing atoms.
Returns
-------
list
A list of species of atoms in the system.
"""
return system.atoms.species
# SUPPORT functions
# --------------------------------------------
def _get_angle(vec1, vec2):
"""
Get angle between two vectors in degrees
Parameters
----------
vec1: list
first vector
vec2: list
second vector
Returns
-------
angle: float
angle in degrees
Notes
-----
Angle is rounded to two decimal points
"""
return np.round(
np.arccos(np.dot(vec1, vec2) / (np.linalg.norm(vec1) * np.linalg.norm(vec2)))
* 180
/ np.pi,
decimals=2,
)
def _get_symmetry_dict(system):
box = system.get_cell()
direct_coordinates = system.get_scaled_positions()
symbols = system.get_chemical_symbols()
atom_types = [list(dict.fromkeys(symbols).keys()).index(s) + 1 for s in symbols]
results = spglib.get_symmetry_dataset((box, direct_coordinates, atom_types))
return results.international, results.number
