mol = gto.M(
atom = '''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis = {'O': gto.parse('''
# Parse NWChem format basis string (see https://bse.pnl.gov/bse/portal).
# Comment lines are ignored
#BASIS SET: (6s,3p) -> [2s,1p]
O S
130.7093200 0.15432897
23.8088610 0.53532814
6.4436083 0.44463454
O SP
5.0331513 -0.09996723 0.15591627
1.1695961 0.39951283 0.60768372
0.3803890 0.70011547 0.39195739
'''),
'H1': gto.load(basis_file_from_user, 'H'),
'H2': gto.load('sto-3g', 'He') # or use basis of another atom
}
)
mol = gto.M(
atom = '''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis = {'O': 'unc-ccpvdz', # prefix "unc-" will uncontract the ccpvdz basis.
# It is equivalent to assigning
# 'O': gto.uncontract(gto.load('ccpvdz', 'O')),
'H': 'ccpvdz' # H1 H2 will use the same basis ccpvdz
}
)
mol = gto.M(
def test_format_basis(self):
mol = gto.M(atom='''O 0 0 0; 1 0 1 0; H 0 0 1''', basis={8: 'ccpvdz'})
self.assertEqual(mol.nao_nr(), 14)
mol = gto.M(atom='''O 0 0 0; H:1 0 1 0; H@2 0 0 1''',
basis={
'O': 'ccpvdz',
'H:1': 'sto3g',
'H': 'unc-iglo3'
})
self.assertEqual(mol.nao_nr(), 32)
mol = gto.M(atom='''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis={
'default': ('6-31g', [[0, [.05, 1.]], []]),
'H2': 'sto3g'
})
self.assertEqual(mol.nao_nr(), 14)
mol = gto.M(
atom='''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis={
'H1':
gto.parse('''
# Parse NWChem format basis string (see https://bse.pnl.gov/bse/portal).
# Comment lines are ignored
#BASIS SET: (6s,3p) -> [2s,1p]
H S
2.9412494 -0.09996723
0.6834831 0.39951283
0.2222899 0.70011547
H S
2.9412494 0.15591627
0.6834831 0.60768372
0.2222899 0.39195739
''',
optimize=True),
'O':
'unc-ccpvdz',
'H2':
gto.load('sto-3g', 'He') # or use basis of another atom
})
self.assertEqual(mol.nao_nr(), 29)
mol = gto.M(
atom='''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis={
'H': [
'sto3g', '''unc
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
'''
],
'O':
mol.expand_etbs([
(0, 4, 1.5, 2.2), # s-function
(1, 2, 0.5, 2.2)
]) # p-function
})
self.assertEqual(mol.nao_nr(), 42)
mol = gto.M(atom='''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis=('sto3g', 'ccpvdz', '3-21g',
gto.etbs([(0, 4, 1.5, 2.2), (1, 2, 0.5, 2.2)]),
[[0, numpy.array([1e3, 1.])]]))
self.assertEqual(mol.nao_nr(), 77)
mol.atom = 'Hg'
mol.basis = 'ccpvdz'
self.assertRaises(RuntimeError, mol.build)
This example illustrates how basis sets can be directly obtained from
a local copy of the Basis Set Exchange.
'''
mol = gto.M(
atom = '''
N 0.6683566134 0.2004327755 0.0000000000
H 0.9668193796 -0.3441960976 0.8071193402
H 0.9668193796 -0.3441960976 -0.8071193402
F -0.7347916126 -0.0467759204 0.0000000000
''',
basis = {
# The BSE returns the basis in NWChem format, which is then
# parsed in PySCF as usual. It is also easy to mix various
# basis sets, although this should only be done by experts.
'H' : gto.load(basis_set_exchange.api.get_basis('sto-2g', elements='H', fmt='nwchem'), 'H'),
'N' : gto.load(basis_set_exchange.api.get_basis('svp (dunning-hay)', elements='N', fmt='nwchem'), 'N'),
'F' : gto.load(basis_set_exchange.api.get_basis('2zapa-nr', elements='F', fmt='nwchem'), 'F'),
},
verbose = 4
)
mol = gto.M(
atom = '''
N 0.6683566134 0.2004327755 0.0000000000
H 0.9668193796 -0.3441960976 0.8071193402
H 0.9668193796 -0.3441960976 -0.8071193402
F -0.7347916126 -0.0467759204 0.0000000000
''',
basis = {
def test_format_basis(self):
mol = gto.M(atom = '''O 0 0 0; 1 0 1 0; H 0 0 1''',
basis = {8: 'ccpvdz'})
self.assertEqual(mol.nao_nr(), 14)
mol = gto.M(atom = '''O 0 0 0; H:1 0 1 0; H@2 0 0 1''',
basis = {'O': 'ccpvdz', 'H:1': 'sto3g', 'H': 'unc-iglo3'})
self.assertEqual(mol.nao_nr(), 32)
mol = gto.M(
atom = '''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis = {'default': ('6-31g', [[0, [.05, 1.]], []]), 'H2': 'sto3g'}
)
self.assertEqual(mol.nao_nr(), 14)
mol = gto.M(
atom = '''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis = {'H1': gto.parse('''
# Parse NWChem format basis string (see https://bse.pnl.gov/bse/portal).
# Comment lines are ignored
#BASIS SET: (6s,3p) -> [2s,1p]
H S
2.9412494 -0.09996723
0.6834831 0.39951283
0.2222899 0.70011547
H S
2.9412494 0.15591627
0.6834831 0.60768372
0.2222899 0.39195739
''', optimize=True),
'O': 'unc-ccpvdz',
'H2': gto.load('sto-3g', 'He') # or use basis of another atom
}
)
self.assertEqual(mol.nao_nr(), 29)
mol = gto.M(
atom = '''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis = {'H': ['sto3g', '''unc
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
'''],
'O': mol.expand_etbs([(0, 4, 1.5, 2.2), # s-function
(1, 2, 0.5, 2.2)]) # p-function
}
)
self.assertEqual(mol.nao_nr(), 42)
mol = gto.M(
atom = '''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis = ('sto3g', 'ccpvdz', '3-21g',
gto.etbs([(0, 4, 1.5, 2.2), (1, 2, 0.5, 2.2)]),
[[0, numpy.array([1e3, 1.])]])
)
self.assertEqual(mol.nao_nr(), 77)
mol.atom = 'Hg'
mol.basis = 'ccpvdz'
self.assertRaises(RuntimeError, mol.build)
def test_to_general_contraction(self):
b = gto.basis.to_general_contraction(gto.load('cc-pvtz', 'H'))
self.assertEqual(len(b), 3)
self.assertEqual(len(b[0]), 6)
self.assertEqual(len(b[1]), 3)
self.assertEqual(len(b[2]), 2)
atom = '''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis = {'O': gto.parse('''
# Parse NWChem format basis string (see https://bse.pnl.gov/bse/portal).
# Comment lines are ignored
#BASIS SET: (6s,3p) -> [2s,1p]
O S
130.7093200 0.15432897
23.8088610 0.53532814
6.4436083 0.44463454
O SP
5.0331513 -0.09996723 0.15591627
1.1695961 0.39951283 0.60768372
0.3803890 0.70011547 0.39195739
'''),
'H1': basis_file_from_user,
'H2': gto.load('sto-3g', 'He') # or use basis of another atom
}
)
#
# Uncontracted basis, decontracting basis.
#
mol = gto.M(
atom = '''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis = {'O': 'unc-ccpvdz', # prefix "unc-" will uncontract the ccpvdz basis.
# It is equivalent to assigning
# 'O': gto.uncontract(gto.load('ccpvdz', 'O')),
'H': 'ccpvdz' # H1 H2 will use the same basis ccpvdz
}
)