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import sys
import io
from ase.io import read
from ase.cli.main import CLIError
template_help = """
Without argument, looks for ~/.ase/template.py. Otherwise,
expects the comma separated list of the fields to include
in their left-to-right order. Optionally, specify the
lexicographical sort hierarchy (0 is outermost sort) and if the
sort should be ascending or descending (1 or -1). By default,
sorting is descending, which makes sense for most things except
index (and rank, but one can just sort by the thing which is
ranked to get ascending ranks).
* example: ase diff start.cif stop.cif --template
* i:0:1,el,dx,dy,dz,d,rd
possible fields:
* i: index
* dx,dy,dz,d: displacement/displacement components
* dfx,dfy,dfz,df: difference force/force components
* afx,afy,afz,af: average force/force components
* p1x,p1y,p1z,p: first image positions/position components
* p2x,p2y,p2z,p: second image positions/position components
* f1x,f1y,f1z,f: first image forces/force components
* f2x,f2y,f2z,f: second image forces/force components
* an: atomic number
* el: atomic element
* t: atom tag
* r<col>: the rank of that atom with respect to the column
It is possible to change formatters in the template file."""
class CLICommand:
"""Print differences between atoms/calculations.
Supports taking differences between different calculation runs of
the same system as well as neighboring geometric images for one
calculation run of a system. As part of a difference table or as a
standalone display table, fields for non-difference quantities of image 1
and image 2 are also provided.
See the --template-help for the formatting exposed in the CLI. More
customization requires changing the input arguments to the Table
initialization and/or editing the templates file.
"""
@staticmethod
def add_arguments(parser):
add = parser.add_argument
add('file',
help="""Possible file entries are
* 2 non-trajectory files: difference between them
* 1 trajectory file: difference between consecutive images
* 2 trajectory files: difference between corresponding image numbers
* 1 trajectory file followed by hyphen-minus (ASCII 45): for display
Note deltas are defined as 2 - 1.
Use [FILE]@[SLICE] to select images.
""",
nargs='+')
add('-r',
'--rank-order',
metavar='FIELD',
nargs='?',
const='d',
type=str,
help="""Order atoms by rank, see --template-help for possible
fields.
The default value, when specified, is d. When not
specified, ordering is the same as that provided by the
generator. For hierarchical sorting, see template.""")
add('-c', '--calculator-outputs', action="store_true",
help="display calculator outputs of forces and energy")
add('--max-lines', metavar='N', type=int,
help="show only so many lines (atoms) in each table "
", useful if rank ordering")
add('-t', '--template', metavar='TEMPLATE', nargs='?', const='rc',
help="""See --template-help for the help on this option.""")
add('--template-help', help="""Prints the help for the template file.
Usage `ase diff - --template-help`""", action="store_true")
add('-s', '--summary-functions', metavar='SUMFUNCS', nargs='?',
help="""Specify the summary functions.
Possible values are `rmsd` and `dE`.
Comma separate more than one summary function.""")
add('--log-file', metavar='LOGFILE', help="print table to file")
add('--as-csv', action="store_true",
help="output table in csv format")
add('--precision', metavar='PREC',
default=2, type=int,
help="precision used in both display and sorting")
@staticmethod
def run(args, parser):
if args.template_help:
print(template_help)
return
encoding = 'utf-8'
if args.log_file is None:
out = io.TextIOWrapper(sys.stdout.buffer, encoding=encoding)
else:
out = open(args.log_file, 'w', encoding=encoding)
with out:
CLICommand.diff(args, out)
@staticmethod
def diff(args, out):
from ase.cli.template import (
Table,
TableFormat,
slice_split,
field_specs_on_conditions,
summary_functions_on_conditions,
rmsd,
energy_delta)
if args.template is None:
field_specs = field_specs_on_conditions(
args.calculator_outputs, args.rank_order)
else:
field_specs = args.template.split(',')
if not args.calculator_outputs:
for field_spec in field_specs:
if 'f' in field_spec:
raise CLIError(
"field requiring calculation outputs "
"without --calculator-outputs")
if args.summary_functions is None:
summary_functions = summary_functions_on_conditions(
args.calculator_outputs)
else:
summary_functions_dct = {
'rmsd': rmsd,
'dE': energy_delta}
summary_functions = args.summary_functions.split(',')
if not args.calculator_outputs:
for sf in summary_functions:
if sf == 'dE':
raise CLIError(
"summary function requiring calculation outputs "
"without --calculator-outputs")
summary_functions = [summary_functions_dct[i]
for i in summary_functions]
have_two_files = len(args.file) == 2
file1 = args.file[0]
actual_filename, index = slice_split(file1)
atoms1 = read(actual_filename, index)
natoms1 = len(atoms1)
if have_two_files:
if args.file[1] == '-':
atoms2 = atoms1
def header_fmt(c):
return 'image # {}'.format(c)
else:
file2 = args.file[1]
actual_filename, index = slice_split(file2)
atoms2 = read(actual_filename, index)
natoms2 = len(atoms2)
same_length = natoms1 == natoms2
one_l_one = natoms1 == 1 or natoms2 == 1
if not same_length and not one_l_one:
raise CLIError(
"Trajectory files are not the same length "
"and both > 1\n{}!={}".format(
natoms1, natoms2))
elif not same_length and one_l_one:
print(
"One file contains one image "
"and the other multiple images,\n"
"assuming you want to compare all images "
"with one reference image")
if natoms1 > natoms2:
atoms2 = natoms1 * atoms2
else:
atoms1 = natoms2 * atoms1
def header_fmt(c):
return 'sys-ref image # {}'.format(c)
else:
def header_fmt(c):
return 'sys2-sys1 image # {}'.format(c)
else:
atoms2 = atoms1.copy()
atoms1 = atoms1[:-1]
atoms2 = atoms2[1:]
natoms2 = natoms1 = natoms1 - 1
def header_fmt(c):
return 'images {}-{}'.format(c + 1, c)
natoms = natoms1 # = natoms2
output = ''
tableformat = TableFormat(precision=args.precision,
columnwidth=7 + args.precision)
table = Table(
field_specs,
max_lines=args.max_lines,
tableformat=tableformat,
summary_functions=summary_functions)
for counter in range(natoms):
table.title = header_fmt(counter)
output += table.make(atoms1[counter],
atoms2[counter], csv=args.as_csv) + '\n'
print(output, file=out)
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