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adapted shape_map script to new function in cosymlib
general cleaning
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,61 +1,126 @@ | ||
| #!/usr/bin/env python | ||
| import argparse | ||
| import sys | ||
| import yaml | ||
| from cosymlib import file_io | ||
| from cosymlib import Cosymlib | ||
|
|
||
| from cosymlib.file_io.tools import add_extra_keywords, print_header, print_footer, print_input_info | ||
| from cosymlib.file_io import read_generic_structure_file | ||
| from cosymlib.shape import tools | ||
| import argparse | ||
| import sys | ||
|
|
||
| parser = argparse.ArgumentParser(description='Shape_map ') | ||
| parser.add_argument(type=str, dest='input_file', help='input file name(+extension)') | ||
| parser.add_argument('-o', '--output_name', dest='output_name', default=None, help='save in file name') | ||
| parser.add_argument(type=str, dest="yaml_input", nargs='?', default=None, | ||
| help='Perform the calculations with the command file') | ||
| parser.add_argument('-c', '--central_atom', action='store', dest='central_atom', | ||
| type=int, default=0, help='position of the central atom if exist') | ||
| parser.add_argument('-custom_ref', action='store', dest='custom_ref', default=None, | ||
| help='take a given structure from the file and use it as reference') | ||
| parser.add_argument('-fix_perm', '--fix_permutation', dest='fix_permutation', action='store_true', default=False, | ||
| help='use the given permutation to perform a calculation') | ||
|
|
||
| # Shape input flags | ||
| group_shape = parser.add_argument_group('Shape') | ||
| group_shape.add_argument('-x', dest='x', action='store', default=False, | ||
| help='x axis label') | ||
| group_shape.add_argument('-y', dest='y', action='store', default=False, | ||
| help='y axis label') | ||
| group_shape.add_argument('-p', dest='p', action='store_true', default=False, | ||
| help='Print all the information') | ||
|
|
||
|
|
||
| args = parser.parse_args(sys.argv[1:]) | ||
|
|
||
| # positional arguments | ||
| parser.add_argument(type=str, | ||
| dest='input_file', | ||
| help='input file with structures') | ||
| parser.add_argument(type=str, | ||
| dest="yaml_input", | ||
| nargs='?', | ||
| default=None, | ||
| help='Input file with keywords') | ||
|
|
||
| # Main options | ||
| parser.add_argument('-m', '--map', | ||
| dest='map', | ||
| metavar='SH', | ||
| default=None, | ||
| nargs=2, | ||
| help='get map using shape 2 labels') | ||
| parser.add_argument('-cref', '--custom_ref', | ||
| dest='custom_ref', | ||
| metavar='filename', | ||
| default=None, | ||
| help='get map using custom 2 structures from a file') | ||
| parser.add_argument('-o', '--output_name', | ||
| dest='output_name', | ||
| metavar='filename', | ||
| default=None, | ||
| help='store the output into a file') | ||
| parser.add_argument('-c', '--central_atom', | ||
| dest='central_atom', | ||
| metavar='N', | ||
| type=int, | ||
| default=0, | ||
| help='define central atom as the atom in position N in the input structure') | ||
|
|
||
| # Extra options | ||
| parser.add_argument('-l', '--labels', action='store_true', | ||
| dest='labels', | ||
| default=False, | ||
| help='show the reference shape labels') | ||
| parser.add_argument('--info', | ||
| action='store_true', | ||
| default=False, | ||
| help='print information about the input structures') | ||
|
|
||
| # Modifiers | ||
| parser.add_argument('--fix_permutation', | ||
| dest='fix_permutation', | ||
| action='store_true', | ||
| help='do not permute atoms') | ||
| parser.add_argument('--min_dev', | ||
| dest='min_dev', | ||
| default=0.0, | ||
| help='minimum deviation') | ||
| parser.add_argument('--max_dev', | ||
| dest='max_dev', | ||
| default=100.0, | ||
| help='maximum deviation') | ||
| parser.add_argument('--min_gco', | ||
| dest='min_gco', | ||
| default=0.0, | ||
| help='minimum coordinates gradient') | ||
| parser.add_argument('--max_gco', | ||
| dest='max_gco', | ||
| action='store_true', | ||
| default=100.0, | ||
| help='maximum coordinates gradient') | ||
| parser.add_argument('--n_points', | ||
| dest='n_points', | ||
| default=20, | ||
| type=int, | ||
| help='number of path structures to calculate') | ||
|
|
||
| args = parser.parse_args() | ||
|
|
||
| if args.yaml_input: | ||
| with open(args.yaml_input, 'r') as stream: | ||
| input_parameters = yaml.load(stream) | ||
| add_extra_keywords(args, args.yaml_input) | ||
|
|
||
| for key, value in input_parameters.items(): | ||
| if key.lower() in args: | ||
| setattr(args, key.lower(), value) | ||
| else: | ||
| raise KeyError("Key %s is not valid" % key) | ||
| common_output = open(args.output_name, 'w') if args.output_name is not None else sys.stdout | ||
| print_header(common_output) | ||
|
|
||
| reference_polyhedron = [] | ||
| if args.input_file is not None: | ||
| structures = file_io.read_generic_structure_file(args.input_file, read_multiple=True) | ||
| symobj = Cosymlib(structures) | ||
| structures = read_generic_structure_file(args.input_file, read_multiple=True) | ||
| structure_set = Cosymlib(structures) | ||
| n_atoms = structure_set.get_n_atoms() | ||
|
|
||
| if args.custom_ref is not None: | ||
| if args.info: | ||
| print_input_info(structure_set.get_geometries(), output=common_output) | ||
| exit() | ||
|
|
||
| # Shape's commands | ||
| if args.labels: | ||
| common_output.write(tools.get_shape_label_info(n_atoms, with_central_atom=args.central_atom)) | ||
| exit() | ||
|
|
||
| reference_polyhedron = [] | ||
| if args.custom_ref: | ||
| reference_polyhedron = file_io.get_geometry_from_file_xyz(args.custom_ref, read_multiple=True) | ||
| [x.set_positions(args.central_atom - 1) for x in reference_polyhedron] | ||
|
|
||
| references = [geom for geom in reference_polyhedron] | ||
| args.map = 'custom' | ||
| else: | ||
| references = args.map | ||
|
|
||
| if not args.x: | ||
| args.x = reference_polyhedron[0] | ||
| elif not args.y: | ||
| args.y = reference_polyhedron[0] | ||
| if args.map: | ||
| structure_set.print_minimum_distortion_path_shape(references[0], | ||
| references[1], | ||
| central_atom=args.central_atom, | ||
| min_dev=args.min_dev, | ||
| max_dev=args.max_dev, | ||
| min_gco=args.min_gco, | ||
| max_gco=args.max_gco, | ||
| num_points=args.n_points, | ||
| output_name=args.output_name) | ||
|
|
||
| if args.x: | ||
| symobj.print_minimum_distortion_path_shape(args.x, | ||
| args.y, | ||
| central_atom=args.central_atom) | ||
| print_footer(common_output) |