# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.
import numpy as np
import structuretoolkit as stk
from pyiron_base import state
from pyiron_snippets.deprecate import Deprecator
import pyiron_atomistics.atomistics.structure.atoms
deprecate = Deprecator()
__author__ = "Sarath Menon, Jan Janssen"
__copyright__ = (
"Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
"Computational Materials Design (CM) Department"
)
__version__ = "1.0"
__maintainer__ = "Sarath Menon"
__email__ = "sarath.menon@rub.de"
__status__ = "development"
__date__ = "Nov 6, 2019"
[docs]
@deprecate(arguments={"clustering": "use n_clusters=None instead of clustering=False."})
def get_steinhardt_parameter_structure(
structure,
neighbor_method="cutoff",
cutoff=0,
n_clusters=2,
q=None,
averaged=False,
clustering=None,
):
"""
Calculate Steinhardts parameters
Args:
structure (Atoms): The structure to analyse.
neighbor_method (str) : can be ['cutoff', 'voronoi']. (Default is 'cutoff'.)
cutoff (float) : Can be 0 for adaptive cutoff or any other value. (Default is 0, adaptive.)
n_clusters (int/None) : Number of clusters for K means clustering or None to not cluster. (Default is 2.)
q (list) : Values can be integers from 2-12, the required q values to be calculated. (Default is None, which
uses (4, 6).)
averaged (bool) : If True, calculates the averaged versions of the parameter. (Default is False.)
Returns:
numpy.ndarray: (number of q's, number of atoms) shaped array of q parameters
numpy.ndarray: If `clustering=True`, an additional per-atom array of cluster ids is also returned
"""
if clustering == False:
n_clusters = None
state.publications.add(publication())
return stk.analyse.get_steinhardt_parameters(
structure=structure,
neighbor_method=neighbor_method,
cutoff=cutoff,
n_clusters=n_clusters,
q=q,
averaged=averaged,
)
[docs]
def analyse_centro_symmetry(structure, num_neighbors=12):
"""
Analyse centrosymmetry parameter
Args:
structure: Atoms object
num_neighbors (int) : number of neighbors
Returns:
csm (list) : list of centrosymmetry parameter
"""
state.publications.add(publication())
return stk.analyse.get_centro_symmetry_descriptors(
structure=structure, num_neighbors=num_neighbors
)
[docs]
def analyse_diamond_structure(structure, mode="total", ovito_compatibility=False):
"""
Analyse diamond structure
Args:
structure: Atoms object
mode ("total"/"numeric"/"str"): Controls the style and level
of detail of the output.
- total : return number of atoms belonging to each structure
- numeric : return a per atom list of numbers- 0 for unknown,
1 fcc, 2 hcp, 3 bcc and 4 icosa
- str : return a per atom string of sructures
ovito_compatibility(bool): use ovito compatiblity mode
Returns:
(depends on `mode`)
"""
state.publications.add(publication())
return stk.analyse.get_diamond_structure_descriptors(
structure=structure, mode=mode, ovito_compatibility=ovito_compatibility
)
[docs]
def analyse_cna_adaptive(structure, mode="total", ovito_compatibility=False):
"""
Use common neighbor analysis
Args:
structure (pyiron_atomistics.structure.atoms.Atoms): The structure to analyze.
mode ("total"/"numeric"/"str"): Controls the style and level
of detail of the output.
- total : return number of atoms belonging to each structure
- numeric : return a per atom list of numbers- 0 for unknown,
1 fcc, 2 hcp, 3 bcc and 4 icosa
- str : return a per atom string of sructures
ovito_compatibility(bool): use ovito compatiblity mode
Returns:
(depends on `mode`)
"""
state.publications.add(publication())
return stk.analyse.get_adaptive_cna_descriptors(
structure=structure, mode=mode, ovito_compatibility=ovito_compatibility
)
[docs]
def analyse_voronoi_volume(structure):
"""
Calculate the Voronoi volume of atoms
Args:
structure : (pyiron_atomistics.structure.atoms.Atoms): The structure to analyze.
"""
state.publications.add(publication())
return stk.analyse.get_voronoi_volumes(structure=structure)
[docs]
def pyiron_to_pyscal_system(structure):
"""
Converts atoms to ase atoms and than to a pyscal system.
Also adds the pyscal publication.
Args:
structure (pyiron atoms): Structure to convert.
Returns:
Pyscal system: See the pyscal documentation.
"""
state.publications.add(publication())
return stk.common.ase_to_pyscal(
pyiron_atomistics.atomistics.structure.atoms.pyiron_to_ase(structure)
)
[docs]
def analyse_find_solids(
structure,
neighbor_method="cutoff",
cutoff=0,
bonds=0.5,
threshold=0.5,
avgthreshold=0.6,
cluster=False,
q=6,
right=True,
return_sys=False,
):
"""
Get the number of solids or the corresponding pyscal system.
Calls necessary pyscal methods as described in https://pyscal.org/en/latest/methods/03_solidliquid.html.
Args:
neighbor_method (str, optional): Method used to get neighborlist. See pyscal documentation. Defaults to "cutoff".
cutoff (int, optional): Adaptive if 0. Defaults to 0.
bonds (float, optional): Number or fraction of bonds to consider atom as solid. Defaults to 0.5.
threshold (float, optional): See pyscal documentation. Defaults to 0.5.
avgthreshold (float, optional): See pyscal documentation. Defaults to 0.6.
cluster (bool, optional): See pyscal documentation. Defaults to False.
q (int, optional): Steinhard parameter to calculate. Defaults to 6.
right (bool, optional): See pyscal documentation. Defaults to True.
return_sys (bool, optional): Whether to return number of solid atoms or pyscal system. Defaults to False.
Returns:
int: number of solids,
pyscal system: pyscal system when return_sys=True
"""
state.publications.add(publication())
return stk.analyse.find_solids(
structure=structure,
neighbor_method=neighbor_method,
cutoff=cutoff,
bonds=bonds,
threshold=threshold,
avgthreshold=avgthreshold,
cluster=cluster,
q=q,
right=right,
return_sys=return_sys,
)
[docs]
def publication():
return {
"pyscal": {
"Menon2019": {
"doi": "10.21105/joss.01824",
"url": "https://doi.org/10.21105/joss.01824",
"year": "2019",
"volume": "4",
"number": "43",
"pages": "1824",
"author": ["Sarath Menon", "Grisell Diaz Leines", "Jutta Rogal"],
"title": "pyscal: A python module for structural analysis of atomic environments",
"journal": "Journal of Open Source Software",
}
}
}
