#!/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: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Parsers for basis set in the NWChem format
'''
__all__ = ['parse', 'load', 'parse_ecp', 'load_ecp',
'convert_basis_to_nwchem', 'convert_ecp_to_nwchem',
'optimize_contraction', 'remove_zero', 'to_general_contraction']
import re
import numpy
import numpy as np
import scipy.linalg
from pyscf.data.elements import _std_symbol
from pyscf.lib.exceptions import BasisNotFoundError
from pyscf.gto.basis.parse_nwchem_ecp import DISABLE_EVAL, MAXL, SPDF, MAPSPDF
from pyscf.gto.basis.parse_nwchem_ecp import parse as parse_ecp
from pyscf.gto.basis.parse_nwchem_ecp import load as load_ecp
from pyscf.gto.basis.parse_nwchem_ecp import convert_ecp_to_nwchem
from pyscf import __config__
BASIS_SET_DELIMITER = re.compile('# *BASIS SET.*\n|END\n')
[docs]
def parse(string, symb=None, optimize=True):
'''Parse the basis text which is in NWChem format. Return an internal
basis format which can be assigned to attribute :attr:`Mole.basis`
Empty lines, or the lines started with #, or the lines of "BASIS SET" and
"END" will be ignored are ignored.
Args:
string : A string in NWChem basis format. Empty links and the lines of
"BASIS SET" and "END" will be ignored
Kwargs:
optimize : Optimize basis contraction. Convert the segment contracted
basis to the general contracted basis.
Examples:
>>> mol = gto.Mole()
>>> mol.basis = {'O': gto.basis.parse("""
... #BASIS SET: (6s,3p) -> [2s,1p]
... C S
... 71.6168370 0.15432897
... 13.0450960 0.53532814
... 3.5305122 0.44463454
... C SP
... 2.9412494 -0.09996723 0.15591627
... 0.6834831 0.39951283 0.60768372
... 0.2222899 0.70011547 0.39195739
... """)}
>>> gto.basis.parse("""
... He S
... 13.6267000 0.1752300
... 1.9993500 0.8934830
... 0.3829930 0.0000000
... He S
... 13.6267000 0.0000000
... 1.9993500 0.0000000
... 0.3829930 1.0000000
... """, optimize=True)
[[0, [13.6267, 0.17523, 0.0], [1.99935, 0.893483, 0.0], [0.382993, 0.0, 1.0]]]
'''
if symb is not None:
symb = _std_symbol(symb)
string = _search_basis_block(re.split(BASIS_SET_DELIMITER, string), symb)
if not string:
raise BasisNotFoundError('Basis not found for %s' % symb)
raw_basis = []
for dat in string.splitlines():
dat = dat.split('#')[0].strip() # Use # to start comments
dat_upper = dat.upper()
if (dat and not dat_upper.startswith('END') and not dat_upper.startswith('BASIS')):
raw_basis.append(dat)
return _parse(raw_basis, optimize)
[docs]
def load(basisfile, symb, optimize=True):
'''Load basis for atom of symb from file'''
raw_basis = search_seg(basisfile, symb)
return _parse(raw_basis, optimize)
def _parse(raw_basis, optimize=True):
basis_parsed = [[] for l in range(MAXL)]
key = None
for line in raw_basis:
dat = line.strip()
if not dat or dat.startswith('#'):
continue
elif dat[0].isalpha():
keys = dat.split()
if len(keys) == 1:
key = keys[0].upper()
else:
key = keys[1].upper()
if key == 'SP':
basis_parsed[0].append([0])
basis_parsed[1].append([1])
elif key in MAPSPDF:
l = MAPSPDF[key]
current_basis = [l]
basis_parsed[l].append(current_basis)
else:
raise BasisNotFoundError('Not basis data')
else:
dat = dat.replace('D','e').split()
try:
dat = [float(x) for x in dat]
except ValueError:
if DISABLE_EVAL:
raise ValueError('Failed to parse %s' % line)
else:
dat = list(eval(','.join(dat)))
except Exception as e:
raise BasisNotFoundError('\n' + str(e) +
'\nor the required basis file not existed.')
if key is None:
raise BasisNotFoundError('Not basis data')
elif key == 'SP':
basis_parsed[0][-1].append([dat[0], dat[1]])
basis_parsed[1][-1].append([dat[0], dat[2]])
else:
current_basis.append(dat)
basis_sorted = [b for bs in basis_parsed for b in bs]
if not basis_sorted:
raise BasisNotFoundError('Basis data not found')
if optimize:
basis_sorted = optimize_contraction(basis_sorted)
basis_sorted = remove_zero(basis_sorted)
return basis_sorted
def search_seg(basisfile, symb):
symb = _std_symbol(symb)
with open(basisfile, 'r') as fin:
fdata = re.split(BASIS_SET_DELIMITER, fin.read())
raw_basis = _search_basis_block(fdata, symb)
return [x for x in raw_basis.splitlines() if x and 'END' not in x]
def _search_basis_block(raw_data, symb):
raw_basis = ''
for dat in raw_data:
dat0 = dat.split(None, 1)
if dat0 and dat0[0] == symb:
raw_basis = dat
break
return raw_basis
[docs]
def convert_basis_to_nwchem(symb, basis):
'''Convert the internal basis format to NWChem format string'''
res = []
symb = _std_symbol(symb)
# pass 1: comment line
ls = [b[0] for b in basis]
nprims = [len(b[1:]) for b in basis]
nctrs = [len(b[1])-1 for b in basis]
prim_to_ctr = {}
for i, l in enumerate(ls):
if l in prim_to_ctr:
prim_to_ctr[l][0] += nprims[i]
prim_to_ctr[l][1] += nctrs[i]
else:
prim_to_ctr[l] = [nprims[i], nctrs[i]]
nprims = []
nctrs = []
for l in set(ls):
nprims.append(str(prim_to_ctr[l][0])+SPDF[l].lower())
nctrs.append(str(prim_to_ctr[l][1])+SPDF[l].lower())
res.append('#BASIS SET: (%s) -> [%s]' % (','.join(nprims), ','.join(nctrs)))
# pass 2: basis data
for bas in basis:
res.append('%-2s %s' % (symb, SPDF[bas[0]]))
for dat in bas[1:]:
res.append(' '.join('%15.9f'%x for x in dat))
return '\n'.join(res)
[docs]
def optimize_contraction(basis):
'''Search the basis segments which have the same exponents then merge them
to the general contracted sets.
Note the difference to the function :func:`to_general_contraction`. The
return value of this function may still have multiple segments for each
angular moment section.
'''
basdic = {}
for b in basis:
if isinstance(b[1], int): # kappa = b[1]
key = tuple(b[:2])
ec = numpy.array(b[2:]).T
else:
key = tuple(b[:1])
ec = numpy.array(b[1:]).T
es = ec[0]
cs = [c for c in ec[1:]]
if key not in basdic:
basdic[key] = []
if basdic[key]:
for e_cs in basdic[key]:
if numpy.array_equal(e_cs[0], es):
e_cs.extend(cs)
break
else:
basdic[key].append([es] + cs)
else:
basdic[key].append([es] + cs)
basis = []
for key in sorted(basdic.keys()):
l_kappa = list(key)
for e_cs in basdic[key]:
b = l_kappa + numpy.array(e_cs).T.tolist()
basis.append(b)
return basis
[docs]
def to_general_contraction(basis):
'''Segmented contracted basis -> general contracted basis.
Combine multiple basis segments to one segment for each angular moment
section.
Examples:
>>> gto.contract(gto.uncontract(gto.load('sto3g', 'He')))
[[0, [6.36242139, 1.0, 0.0, 0.0], [1.158923, 0.0, 1.0, 0.0], [0.31364979, 0.0, 0.0, 1.0]]]
'''
basdic = {}
for b in basis:
if isinstance(b[1], int): # kappa = b[1]
key = tuple(b[:2])
ec = numpy.array(b[2:])
else:
key = tuple(b[:1])
ec = numpy.array(b[1:])
if key in basdic:
basdic[key].append(ec)
else:
basdic[key] = [ec]
basis = []
for key in sorted(basdic.keys()):
l_kappa = list(key)
es = numpy.hstack([ec[:,0] for ec in basdic[key]])
cs = scipy.linalg.block_diag(*[ec[:,1:] for ec in basdic[key]])
es, e_idx, rev_idx = numpy.unique(es.round(9), True, True)
es = es[::-1] # sort the exponents from large to small
bcoeff = numpy.zeros((e_idx.size, cs.shape[1]))
for i, j in enumerate(rev_idx):
bcoeff[j] += cs[i]
bcoeff = bcoeff[::-1]
ec = numpy.hstack((es[:,None], bcoeff))
basis.append(l_kappa + ec.tolist())
return basis
[docs]
def remove_zero(basis):
'''
Remove exponents if their contraction coefficients are all zeros.
'''
new_basis = []
for b in basis:
if isinstance(b[1], int): # kappa = b[1]
key = list(b[:2])
ec = b[2:]
else:
key = list(b[:1])
ec = b[1:]
new_ec = [e_c for e_c in ec if any(c!=0 for c in e_c[1:])]
if new_ec:
new_basis.append(key + new_ec)
return new_basis
if __name__ == '__main__':
from pyscf import gto
mol = gto.M(atom='O', basis='6-31g')
print(load_ecp('lanl2dz.dat', 'Na'))
b = load('ano.dat', 'Na')
print(convert_basis_to_nwchem('Na', b))
b = load_ecp('lanl2dz.dat', 'Na')
print(convert_ecp_to_nwchem('Na', b))