def load(filename_or_basisname, symb, optimize=OPTIMIZE_CONTRACTION):
'''Convert the basis of the given symbol to internal format
Args:
filename_or_basisname : str
Case insensitive basis set name. Special characters will be removed.
or a string of "path/to/file" which stores the basis functions
symb : str
Atomic symbol, Special characters will be removed.
Examples:
Load STO 3G basis of carbon to oxygen atom
>>> mol = gto.Mole()
>>> mol.basis = {'O': load('sto-3g', 'C')}
'''
symb = ''.join([i for i in symb if i.isalpha()])
if os.path.isfile(filename_or_basisname):
# read basis from given file
try:
return parse_nwchem.load(filename_or_basisname, symb, optimize)
except RuntimeError:
with open(filename_or_basisname, 'r') as fin:
return parse_nwchem.parse(fin.read(), symb)
name = _format_basis_name(filename_or_basisname)
if not (name in ALIAS or _is_pople_basis(name)):
try:
return parse_nwchem.parse(filename_or_basisname, symb)
except KeyError:
try:
return parse_nwchem.parse(filename_or_basisname)
except IndexError:
raise KeyError('Invalid basis name %s' % filename_or_basisname)
except IndexError:
raise KeyError('Basis %s not found' % filename_or_basisname)
if name in ALIAS:
basmod = ALIAS[name]
elif _is_pople_basis(name):
basmod = _parse_pople_basis(name, symb)
else:
raise RuntimeError('Basis %s not found' % filename_or_basisname)
if 'dat' in basmod:
b = parse_nwchem.load(os.path.join(_BASIS_DIR, basmod), symb, optimize)
elif isinstance(basmod, (tuple, list)) and isinstance(basmod[0], str):
b = []
for f in basmod:
b += parse_nwchem.load(os.path.join(_BASIS_DIR, f), symb, optimize)
else:
if sys.version_info < (2, 7):
fp, pathname, description = imp.find_module(basmod, __path__)
mod = imp.load_module(name, fp, pathname, description)
b = mod.__getattribute__(symb)
fp.close()
else:
mod = importlib.import_module('.' + basmod, __package__)
b = mod.__getattribute__(symb)
return b
def parse(string):
'''Parse the NWChem format basis or ECP text, return an internal basis (ECP)
format which can be assigned to :attr:`Mole.basis` or :attr:`Mole.ecp`
Args:
string : Blank linke and the lines of "BASIS SET" and "END" will be ignored
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
... """)}
'''
if 'ECP' in string:
return parse_nwchem.parse_ecp(string)
else:
return parse_nwchem.parse(string)
def parse(string):
'''Parse the NWChem format basis or ECP text, return an internal basis (ECP)
format which can be assigned to :attr:`Mole.basis` or :attr:`Mole.ecp`
Args:
string : Blank linke and the lines of "BASIS SET" and "END" will be ignored
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
... """)}
'''
if 'ECP' in string:
return parse_nwchem.parse_ecp(string)
else:
return parse_nwchem.parse(string)
def load(filename_or_basisname, symb):
'''Convert the basis of the given symbol to internal format
Args:
filename_or_basisname : str
Case insensitive basis set name. Special characters will be removed.
or a string of "path/to/file" which stores the basis functions
symb : str
Atomic symbol, Special characters will be removed.
Examples:
Load STO 3G basis of carbon to oxygen atom
>>> mol = gto.Mole()
>>> mol.basis = {'O': load('sto-3g', 'C')}
'''
if os.path.isfile(filename_or_basisname):
# read basis from given file
try:
return parse_nwchem.load(filename_or_basisname, symb)
except RuntimeError:
with open(filename_or_basisname, 'r') as fin:
return parse_nwchem.parse(fin.read())
name = filename_or_basisname.lower().replace(' ', '').replace('-',
'').replace(
'_', '')
if name not in ALIAS:
try:
return parse(filename_or_basisname)
except IndexError:
raise RuntimeError('basis %s not found' % filename_or_basisname)
basmod = ALIAS[name]
symb = ''.join([i for i in symb if i.isalpha()])
if 'dat' in basmod:
b = parse_nwchem.load(os.path.join(os.path.dirname(__file__), basmod),
symb)
else:
if sys.version_info < (2, 7):
fp, pathname, description = imp.find_module(basmod, __path__)
mod = imp.load_module(name, fp, pathname, description)
b = mod.__getattribute__(symb)
fp.close()
else:
mod = importlib.import_module('.' + basmod, __package__)
b = mod.__getattribute__(symb)
return b
def load(filename_or_basisname, symb):
'''Convert the basis of the given symbol to internal format
Args:
filename_or_basisname : str
Case insensitive basis set name. Special characters will be removed.
or a string of "path/to/file" which stores the basis functions
symb : str
Atomic symbol, Special characters will be removed.
Examples:
Load STO 3G basis of carbon to oxygen atom
>>> mol = gto.Mole()
>>> mol.basis = {'O': load('sto-3g', 'C')}
'''
if os.path.isfile(filename_or_basisname):
# read basis from given file
try:
return parse_nwchem.load(filename_or_basisname, symb)
except RuntimeError:
with open(filename_or_basisname, 'r') as fin:
return parse_nwchem.parse(fin.read())
name = filename_or_basisname.lower().replace(' ', '').replace('-', '').replace('_', '')
if name not in ALIAS:
return parse(filename_or_basisname)
basmod = ALIAS[name]
symb = ''.join([i for i in symb if i.isalpha()])
if 'dat' in basmod:
b = parse_nwchem.load(os.path.join(os.path.dirname(__file__), basmod), symb)
else:
if sys.version_info < (2,7):
fp, pathname, description = imp.find_module(basmod, __path__)
mod = imp.load_module(name, fp, pathname, description)
b = mod.__getattribute__(symb)
fp.close()
else:
mod = importlib.import_module('.'+basmod, __package__)
b = mod.__getattribute__(symb)
return b
def parse(string, symb=None, optimize=OPTIMIZE_CONTRACTION):
if 'ECP' in string:
return parse_nwchem.parse_ecp(string, symb)
else:
return parse_nwchem.parse(string, symb, optimize)
def load(filename_or_basisname, symb, optimize=OPTIMIZE_CONTRACTION):
'''Convert the basis of the given symbol to internal format
Args:
filename_or_basisname : str
Case insensitive basis set name. Special characters will be removed.
or a string of "path/to/file" which stores the basis functions
symb : str
Atomic symbol, Special characters will be removed.
Examples:
Load STO 3G basis of carbon to oxygen atom
>>> mol = gto.Mole()
>>> mol.basis = {'O': load('sto-3g', 'C')}
'''
symb = ''.join([i for i in symb if i.isalpha()])
if os.path.isfile(filename_or_basisname):
# read basis from given file
try:
return parse_nwchem.load(filename_or_basisname, symb, optimize)
except RuntimeError:
with open(filename_or_basisname, 'r') as fin:
return parse_nwchem.parse(fin.read(), symb)
name = _format_basis_name(filename_or_basisname)
if '@' in name:
split_name = name.split('@')
assert len(split_name) == 2
name = split_name[0]
contr_scheme = _convert_contraction(split_name[1])
else:
contr_scheme = 'Full'
if not (name in ALIAS or _is_pople_basis(name)):
try:
return parse_nwchem.parse(filename_or_basisname, symb)
except KeyError:
try:
return parse_nwchem.parse(filename_or_basisname)
except IndexError:
raise KeyError('Invalid basis name %s' % filename_or_basisname)
except IndexError:
raise KeyError('Basis %s not found' % filename_or_basisname)
if name in ALIAS:
basmod = ALIAS[name]
elif _is_pople_basis(name):
basmod = _parse_pople_basis(name, symb)
else:
raise RuntimeError('Basis %s not found' % filename_or_basisname)
if 'dat' in basmod:
b = parse_nwchem.load(os.path.join(_BASIS_DIR, basmod), symb, optimize)
elif isinstance(basmod, (tuple, list)) and isinstance(basmod[0], str):
b = []
for f in basmod:
b += parse_nwchem.load(os.path.join(_BASIS_DIR, f), symb, optimize)
else:
if sys.version_info < (2,7):
fp, pathname, description = imp.find_module(basmod, __path__)
mod = imp.load_module(name, fp, pathname, description)
b = mod.__getattribute__(symb)
fp.close()
else:
mod = importlib.import_module('.'+basmod, __package__)
b = mod.__getattribute__(symb)
if contr_scheme != 'Full':
b = _truncate(b, contr_scheme, symb, split_name)
return b
def parse(string, symb=None, optimize=OPTIMIZE_CONTRACTION):
if 'ECP' in string:
return parse_nwchem.parse_ecp(string, symb)
else:
return parse_nwchem.parse(string, symb, optimize)
def load(basis_name, symb):
'''Convert the basis of the given symbol to internal format
Args:
basis_name : str
Case insensitive basis set name. Special characters will be removed.
or a string of "path/to/file" which stores the basis functions
symb : str
Atomic symbol, Special characters will be removed.
Examples:
Load STO 3G basis of carbon to oxygen atom
>>> mol = gto.Mole()
>>> mol.basis = {'O': load('sto-3g', 'C')}
'''
alias = {
'ano' : 'ano.dat' ,
'anoroosdz' : 'roos-dz.dat' ,
'anoroostz' : 'roos-tz.dat' ,
'roosdz' : 'roos-dz.dat' ,
'roostz' : 'roos-tz.dat' ,
'ccpvdz' : 'cc-pvdz.dat' ,
'ccpvtz' : 'cc-pvtz.dat' ,
'ccpvqz' : 'cc-pvqz.dat' ,
'ccpv5z' : 'cc-pv5z.dat' ,
'augccpvdz' : 'aug-cc-pvdz.dat',
'augccpvtz' : 'aug-cc-pvtz.dat',
'augccpvqz' : 'aug-cc-pvqz.dat',
'ccpvdzdk' : 'cc-pvdz-dk.dat' ,
'ccpvtzdk' : 'cc-pvtz-dk.dat' ,
'ccpvqzdk' : 'cc-pvqz-dk.dat' ,
'ccpv5zdk' : 'cc-pv5z-dk.dat' ,
'augccpvdzdk': 'aug-cc-pvdz-dk.dat',
'augccpvtzdk': 'aug-cc-pvtz-dk.dat',
'augccpvqzdk': 'aug-cc-pvqz-dk.dat',
'ccpvdzdkh' : 'cc-pvdz-dk.dat' ,
'ccpvtzdkh' : 'cc-pvtz-dk.dat' ,
'ccpvqzdkh' : 'cc-pvqz-dk.dat' ,
'ccpv5zdkh' : 'cc-pv5z-dk.dat' ,
'augccpvdzdkh': 'aug-cc-pvdz-dk.dat',
'augccpvtzdkh': 'aug-cc-pvtz-dk.dat',
'augccpvqzdkh': 'aug-cc-pvqz-dk.dat',
'dyalldz' : 'dyall_dz' ,
'dyallqz' : 'dyall_qz' ,
'dyalltz' : 'dyall_tz' ,
'faegredz' : 'faegre_dz' ,
'iglo' : 'iglo3' ,
'iglo3' : 'iglo3' ,
'321g' : '3-21g.dat' ,
'431g' : '4-31g.dat' ,
'631g' : '6-31g.dat' ,
'631gs' : '6-31gs.dat' ,
'6311g' : '6-311g.dat' ,
'6311gs' : '6-311gs.dat' ,
'6311gsp' : '6-311gsp.dat' ,
'6311gps' : '6-311gsp.dat' ,
'631g*' : '6-31gs.dat' ,
'6311g*' : '6-311gs.dat' ,
'6311g*+' : '6-311gsp.dat' ,
'6311g+*' : '6-311gsp.dat' ,
'sto3g' : 'sto-3g.dat' ,
'sto6g' : 'sto-6g.dat' ,
'minao' : 'minao' ,
'dz' : 'dz.dat' ,
'dzpdunning' : 'dzp_dunning' ,
'dzp' : 'dzp.dat' ,
'tzp' : 'tzp.dat' ,
'qzp' : 'qzp.dat' ,
'dzpdk' : 'dzp-dkh.dat' ,
'tzpdk' : 'tzp-dkh.dat' ,
'qzpdk' : 'qzp-dkh.dat' ,
'dzpdkh' : 'dzp-dkh.dat' ,
'tzpdkh' : 'tzp-dkh.dat' ,
'qzpdkh' : 'qzp-dkh.dat' ,
'def2svp' : 'def2-svp.dat' ,
'def2svpd' : 'def2-svpd.dat' ,
'def2qzvpd' : 'def2-qzvpd.dat' ,
'def2qzvppd' : 'def2-qzvppd.dat',
'def2qzvpp' : 'def2-qzvpp.dat' ,
'def2qzvp' : 'def2-qzvp.dat' ,
'def2tzvpd' : 'def2-tzvpd.dat' ,
'def2tzvppd' : 'def2-tzvppd.dat',
'def2tzvpp' : 'def2-tzvpp.dat' ,
'def2tzvp' : 'def2-tzvp.dat' ,
'tzv' : 'tzv.dat' ,
'weigend' : 'weigend_cfit.dat',
'demon' : 'demon_cfit.dat' ,
'ahlrichs' : 'ahlrichs_cfit.dat',
'ccpvtzfit' : 'cc-pvtz_fit.dat',
'ccpvdzfit' : 'cc-pvdz_fit.dat',
'dgaussa1cfit': 'DgaussA1_dft_cfit.dat',
'dgaussa1xfit': 'DgaussA1_dft_xfit.dat',
'dgaussa2cfit': 'DgaussA2_dft_cfit.dat',
'dgaussa2xfit': 'DgaussA2_dft_xfit.dat',
}
if os.path.isfile(basis_name):
# read basis from given file
return parse_nwchem.parse(basis_name, symb)
name = basis_name.lower().replace(' ', '').replace('-', '').replace('_', '')
basmod = alias[name]
symb = ''.join(i for i in symb if i.isalpha())
if 'dat' in basmod:
b = parse_nwchem.parse(os.path.join(os.path.dirname(__file__), basmod), symb)
else:
fp, pathname, description = imp.find_module(basmod, __path__)
mod = imp.load_module(name, fp, pathname, description)
#mod = __import__(basmod, globals={'__path__': __path__, '__name__': __name__})
b = mod.__getattribute__(symb)
fp.close()
return b
