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# Note:
# Try to avoid module level import statements here to reduce
# import time during CLI execution
class CLICommand:
""" Execute code on files.
The given python code is evaluated on the Atoms object read from
the input file for each frame of the file. Either of -e or -E
option should provided for evaluating code given as a string or
from a file, respectively.
Variables which can be used inside the python code:
- `index`: Index of the current Atoms object.
- `atoms`: Current Atoms object.
- `images`: List of all images given as input.
"""
@staticmethod
def add_arguments(parser):
add = parser.add_argument
add('input', nargs='+', metavar='input-file')
add('-e', '--exec-code',
help='Python code to execute on each atoms. The Atoms'
' object is available as `atoms`. '
'Example: For printing cell parameters from all the '
'frames, `print(atoms.cell.cellpar())`')
add('-E', '--exec-file',
help='Python source code file to execute on each '
'frame, usage is as for -e/--exec-code.')
add('-i', '--input-format', metavar='FORMAT',
help='Specify input FORMAT')
add('-n', '--image-number',
default=':', metavar='NUMBER',
help='Pick images from trajectory. NUMBER can be a '
'single number (use a negative number to count from '
'the back) or a range: start:stop:step, where the '
'":step" part can be left out - default values are '
'0:nimages:1.')
add('--read-args', nargs='+', action='store',
default={}, metavar="KEY=VALUE",
help='Additional keyword arguments to pass to '
'`ase.io.read()`.')
@staticmethod
def run(args, parser):
import runpy
from ase.io import read
if not (args.exec_code or args.exec_file):
parser.error("At least one of '-e' or '-E' must be provided")
if args.read_args:
args.read_args = eval("dict({})"
.format(', '.join(args.read_args)))
configs = []
for filename in args.input:
atoms = read(filename, args.image_number,
format=args.input_format, **args.read_args)
if isinstance(atoms, list):
configs.extend(atoms)
else:
configs.append(atoms)
variables = {'images': configs}
for index, atoms in enumerate(configs):
variables['atoms'] = atoms
variables['index'] = index
if args.exec_code:
exec(compile(args.exec_code, '<string>', 'exec'), variables)
if args.exec_file:
runpy.run_path(args.exec_file, init_globals=variables)
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