def test_template_classes(traj):
prec = 4
tableformat = TableFormat(precision=prec, representation='f', midrule='|')
table = Table(field_specs=('dx', 'dy', 'dz'), tableformat=tableformat)
traj = read(str(traj), ':')
table_out = table.make(traj[0], traj[1]).split('\n')
for counter, row in enumerate(table_out):
if '|' in row:
break
row = table_out[counter + 2]
assert 'E' not in table_out[counter + 2]
row = re.sub(r'\s+', ',', table_out[counter + 2]).split(',')[1:-1]
assert len(row[0]) >= prec
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)