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import numpy as np
def write_py(fileobj, images):
"""Write to ASE-compatible python script."""
fileobj.write('import numpy as np\n\n')
fileobj.write('from ase import Atoms\n\n')
if hasattr(images, 'get_positions'):
images = [images]
fileobj.write('images = [\n')
for image in images:
fileobj.write(" Atoms(symbols='%s',\n"
" pbc=np.array(%s),\n"
" cell=np.array(\n%s),\n"
" positions=np.array(\n%s)),\n" % (
image.get_chemical_formula(mode='reduce'),
array_to_string(image.pbc, 0),
array_to_string(image.cell),
array_to_string(image.positions)))
fileobj.write(']\n')
def array_to_string(array, indent=14):
"""Converts given numpy array to a string, which when printed will pass
flake8 tests."""
text = np.array2string(
array,
separator=', ',
suppress_small=False,
formatter={'float': '{:.8f}'.format, 'bool': '{}'.format},
threshold=np.inf,
)
text = ' ' * indent + text.replace('\n', '\n' + ' ' * indent)
return text
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