def readTurbomoleBasis(path):
"""Read Turbomole basis set"""
bss = topParseB.parseFile(path)
atoms = [xs.atomLabel.lower() for xs in bss]
names = concat([xs.basisName.upper().split() for xs in bss])
formats = [xs.format[:] for xs in bss]
formats_int = map(lambda fss: [[int(x) for x in xs] for xs in fss], formats)
rss = [rs.coeffs[:] for rs in bss]
rawData = [[x.contractions[:] for x in rss[i]] for i in range(len(rss))]
fst = lambda xs: xs[0]
snd = lambda xs: xs[1]
expos = list(
map(
mapFloat,
[concatMap(fst, swapCoeff(2, rawData[i])) for i in range(len(rawData))],
)
)
coeffs = list(
map(
mapFloat,
[concatMap(snd, swapCoeff(2, rawData[i])) for i in range(len(rawData))],
)
)
basisData = zipWith(AtomBasisData)(expos)(coeffs)
basiskey = zipWith3(AtomBasisKey)(atoms)(names)(formats_int)
return basiskey, basisData
def test_concatMap():
"""
concatMap f == concat (map f)
"""
f = lambda x: [x * 2]
xs = [1, 2]
assert concatMap(f, xs) == list(concat(map(f, xs)))
def get_property(self, prop):
"""
Look for the optional arguments to parse a property, which are stored
in the properties dictionary.
"""
# Read the JSON dictionary than contains the parsers names
ds = self.prop_dict[prop]
# extension of the output file containing the property value
file_ext = ds['file_ext']
# If there is not work_dir returns None
work_dir = self.archive.get('work_dir')
# Plams dir
plams_dir = self.archive['plams_dir'].path
# Search for the specified output file in the folders
file_pattern = ds.get('file_pattern')
if file_pattern is None:
file_pattern = '{}.{}'.format(self.job_name, file_ext)
output_files = concatMap(partial(find_file_pattern, file_pattern),
[plams_dir, work_dir])
if output_files:
file_out = output_files[0]
fun = getattr(import_parser(ds), ds['function'])
# Read the keywords arguments from the properties dictionary
kwargs = ds.get('kwargs') if ds.get('kwargs') is not None else {}
kwargs['plams_dir'] = plams_dir
return ignored_unused_kwargs(fun, [file_out], kwargs)
else:
msg = "Property {} not found. No output file \
called: {}.\n".format(prop, file_pattern)
raise FileNotFoundError(msg)
def save_coordinates_charges(molecules, charges):
"""
write the charges and coordinates in XYZ format
"""
xs = concatMap(lambda t: format_xyz(*t), zip(molecules, charges))
with open('coordinates_charges.xyz', 'w') as f:
f.write(''.join(xs))
def go(t1, t2):
"""
Cp2k Basis have exactly the same number of contracts
for all angular quantum number (i.e S, P, D, Z) and all
the same exponent. Using this fact the contracts representation
is built sharing the exponents between all the contracts
"""
index, acc = t1
n, l = t2
xss = css[index:n + index]
rss = concatMap(expandBasis_cp2k(l, es), xss)
return (index + n, acc + rss)