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import os
import warnings
from ase.io import iread
from ase.geometry.dimensionality import analyze_dimensionality
class CLICommand:
"""Analyze the dimensionality of the bonded clusters in a structure, using
the scoring parameter described in:
"Definition of a scoring parameter to identify low-dimensional materials
components", P.M. Larsen, M. Pandey, M. Strange, and K. W. Jacobsen
Phys. Rev. Materials 3 034003, 2019,
https://doi.org/10.1103/PhysRevMaterials.3.034003
https://arxiv.org/abs/1808.02114
A score in the range [0-1] is assigned to each possible dimensionality
classification. The scores sum to 1. A bonded cluster can be a molecular
(0D), chain (1D), layer (2D), or bulk (3D) cluster. Mixed dimensionalities,
such as 0D+3D are possible. Input files may use any format supported by
ASE.
Example usage:
* ase dimensionality --display-all structure.cif
* ase dimensionality structure1.cif structure2.cif
For each structure the following data is printed:
* type - the dimensionalities present
* score - the score of the classification
* a - the start of the k-interval (see paper)
* b - the end of the k-interval (see paper)
* component counts - the number of clusters with each dimensionality type
If the `--display-all` option is used, all dimensionality classifications
are displayed.
"""
@staticmethod
def add_arguments(parser):
add = parser.add_argument
add('filenames', nargs='+', help='input file(s) to analyze')
add('--display-all', dest='full', action='store_true',
help='display all dimensionality classifications')
add('--no-merge', dest='no_merge', action='store_true',
help='do not merge k-intervals with same dimensionality')
@staticmethod
def run(args, parser):
files = [os.path.split(path)[1] for path in args.filenames]
lmax = max([len(f) for f in files]) + 2
print('file'.ljust(lmax) +
'type score a b component counts')
print('=' * lmax + '===============================================')
merge = not args.no_merge
# reading CIF files can produce a ton of distracting warnings
with warnings.catch_warnings():
warnings.filterwarnings('ignore')
for path, f in zip(args.filenames, files):
for atoms in iread(path):
result = analyze_dimensionality(atoms, merge=merge)
if not args.full:
result = result[:1]
for i, entry in enumerate(result):
dimtype = entry.dimtype.rjust(4)
score = '{:.3f}'.format(entry.score).ljust(5)
a = '{:.3f}'.format(entry.a).ljust(5)
b = '{:.3f}'.format(entry.b).ljust(5)
if i == 0:
name = f.ljust(lmax)
else:
name = ' ' * lmax
line = ('{}{}' + ' {}' * 4).format(name, dimtype,
score, a, b,
entry.h)
print(line)
if args.full:
print()
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