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_zipwith3():
"""
zipWith f xs ys zs == map (f) (zip xs ys zs)
"""
@curry
def f(x, y, z):
return x * y + z
xs = range(3)
ys = range(3, 6)
zs = range(6, 9)
assert zipWith3(f)(xs)(ys)(zs) == [
f(x, y, z) for (x, y, z) in zip(xs, ys, zs)
]
def readCp2KBasis(path):
"""
Read the Contracted Gauss function primitives format from a text file.
:param path: Path to the file containing the basis.
:type path: String
"""
bss = topParseBasis.parseFile(path)
atoms = ["".join(xs.atom[:]).lower() for xs in bss]
names = [" ".join(xs.basisName[:]).upper() for xs in bss]
formats = [list(map(int, xs.format[:])) for xs in bss]
# for example 2 0 3 7 3 3 2 1 there are sum(3 3 2 1) =9 Lists
# of Coefficients + 1 lists of exponents
nCoeffs = [int(sum(xs[4:]) + 1) for xs in formats]
rss = zipWith(swapCoeff2)(nCoeffs)(list(map(float, cs.coeffs[:]))
for cs in bss)
tss = [headTail(xs) for xs in rss]
basisData = [AtomBasisData(xs[0], xs[1]) for xs in tss]
basiskey = zipWith3(AtomBasisKey)(atoms)(names)(formats)
return (basiskey, basisData)