Source code for pyscf.gto.basis.parse_cp2k
#!/usr/bin/env python
# Copyright 2014-2023 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Author: Timothy Berkelbach <tim.berkelbach@gmail.com>
#
'''
parse CP2K format
'''
import re
from pyscf.lib.exceptions import BasisNotFoundError
from pyscf.gto.basis import parse_nwchem
from pyscf.gto.basis.parse_nwchem import _search_basis_block
from pyscf import __config__
DISABLE_EVAL = getattr(__config__, 'DISABLE_EVAL', False)
MAXL = 8
[docs]
def parse(string, symb=None, optimize=False):
'''Parse the basis text which is in CP2K format, return an internal
basis format which can be assigned to :attr:`Mole.basis`
Lines started with # are ignored.
Examples:
>>> cell = gto.Cell()
>>> cell.basis = {'C': pyscf.gto.basis.parse_cp2k.parse("""
... C DZVP-GTH
... 2
... 2 0 1 4 2 2
... 4.3362376436 0.1490797872 0.0000000000 -0.0878123619 0.0000000000
... 1.2881838513 -0.0292640031 0.0000000000 -0.2775560300 0.0000000000
... 0.4037767149 -0.6882040510 0.0000000000 -0.4712295093 0.0000000000
... 0.1187877657 -0.3964426906 1.0000000000 -0.4058039291 1.0000000000
... 3 2 2 1 1
... 0.5500000000 1.0000000000
... #
... """)}
'''
if symb is not None:
raw_data = list(filter(None, re.split(BASIS_SET_DELIMITER, string)))
string = _search_basis_block(raw_data, symb)
if not string:
raise BasisNotFoundError(f'Basis not found for {symb}')
bastxt = []
for dat in string.splitlines():
x = dat.split('#')[0].strip()
if (x and not x.startswith('END') and not x.startswith('BASIS')):
bastxt.append(x)
return _parse(bastxt, optimize)
[docs]
def load(basisfile, symb, optimize=False):
return _parse(search_seg(basisfile, symb), optimize)
def _parse(blines, optimize=False):
blines_iter = iter(blines)
try:
header_ln = next(blines_iter) # noqa: F841
nsets = int(next(blines_iter))
except Exception:
raise BasisNotFoundError('Not basis data')
basis = []
try:
for n in range(nsets):
comp = [int(p) for p in next(blines_iter).split()]
lmin, lmax, nexps, ncontractions = comp[1], comp[2], comp[3], comp[4:]
basis_n = [[l] for l in range(lmin,lmax+1)]
for nexp in range(nexps):
line = next(blines_iter)
dat = line.split()
try:
bfun = [float(x) for x in dat]
except ValueError:
if DISABLE_EVAL:
raise ValueError('Failed to parse %s' % line)
else:
bfun = eval(','.join(dat))
if len(bfun) != sum(ncontractions) + 1:
raise ValueError('Basis data incomplete')
bfun_iter = iter(bfun)
exp = next(bfun_iter)
for i,l in enumerate(range(lmin,lmax+1)):
cl = [exp]
for c in range(ncontractions[i]):
cl.append(next(bfun_iter))
basis_n[i].append(cl)
basis.extend(basis_n)
except StopIteration:
raise ValueError('Basis data incomplete')
basis_sorted = []
for l in range(MAXL):
basis_sorted.extend([b for b in basis if b[0] == l])
if not basis_sorted:
raise BasisNotFoundError('Basis data not found')
if optimize:
basis_sorted = parse_nwchem.optimize_contraction(basis_sorted)
basis_sorted = parse_nwchem.remove_zero(basis_sorted)
return basis_sorted
BASIS_SET_DELIMITER = re.compile('# *BASIS SET.*\n')
[docs]
def search_seg(basisfile, symb):
with open(basisfile, 'r') as fin:
fdata = re.split(BASIS_SET_DELIMITER, fin.read())
raw_basis = _search_basis_block(fdata[1:], symb)
if not raw_basis:
raise BasisNotFoundError(f'Basis for {symb} not found in {basisfile}')
return [x.strip() for x in raw_basis.splitlines()
if x.strip() and 'END' not in x]
