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)
import pyscf.lib.parameters as param
mol0 = gto.Mole()
mol0.atom = [
[1, (0., 1., 1.)],
["O1", (0., 0., 0.)],
[1, (1., 1., 0.)],
]
mol0.nucmod = {"O": 'gaussian', 3: 'g'}
mol0.unit = 'ang'
mol0.basis = {
"O": [
(0, 0, (15, 1)),
] + gto.etbs((
(0, 4, 1, 1.8),
(1, 3, 2, 1.8),
(2, 2, 1, 1.8),
)),
"H": [
(0, 0, (1, 1, 0), (3, 3, 1), (5, 1, 0)),
(1, -2, (1, 1)),
]
}
mol0.symmetry = 1
mol0.charge = 1
mol0.spin = 1
mol0.verbose = 7
mol0.ecp = {'O1': 'lanl2dz'}
ftmp = tempfile.NamedTemporaryFile()
mol0.output = ftmp.name
mol0.build()
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)
import numpy
import scipy.linalg
from pyscf import gto
from pyscf import lib
import pyscf.lib.parameters as param
mol0 = gto.Mole()
mol0.atom = [
[1 , (0.,1.,1.)],
["O1", (0.,0.,0.)],
[1 , (1.,1.,0.)], ]
mol0.nucmod = { "O":'gaussian', 3:'g' }
mol0.unit = 'ang'
mol0.basis = {
"O": [(0, 0, (15, 1)), ] + gto.etbs(((0, 4, 1, 1.8),
(1, 3, 2, 1.8),
(2, 2, 1, 1.8),)),
"H": [(0, 0, (1, 1, 0), (3, 3, 1), (5, 1, 0)),
(1, -2, (1, 1)), ]}
mol0.symmetry = 1
mol0.charge = 1
mol0.spin = 1
mol0.verbose = 7
mol0.ecp = {'O1': 'lanl2dz'}
ftmp = tempfile.NamedTemporaryFile()
mol0.output = ftmp.name
mol0.build()
def tearDownModule():
global mol0, ftmp
mol0.stdout.close()
import scipy.linalg
from pyscf import gto
from pyscf import lib
import pyscf.lib.parameters as param
from pyscf.lib.exceptions import BasisNotFoundError
mol0 = gto.Mole()
mol0.atom = [
[1 , (0.,1.,1.)],
["O1", (0.,0.,0.)],
[1 , (1.,1.,0.)], ]
mol0.nucmod = { "O":'gaussian', 3:'g' }
mol0.unit = 'ang'
mol0.basis = {
"O": [(0, 0, (15, 1)), ] + gto.etbs(((0, 4, 1, 1.8),
(1, 3, 2, 1.8),
(2, 2, 1, 1.8),)),
"H": [(0, 0, (1, 1, 0), (3, 3, 1), (5, 1, 0)),
(1, -2, (1, 1)), ]}
mol0.symmetry = 1
mol0.charge = 1
mol0.spin = 1
mol0.verbose = 7
mol0.ecp = {'O1': 'lanl2dz'}
ftmp = tempfile.NamedTemporaryFile()
mol0.output = ftmp.name
mol0.build()
def tearDownModule():
global mol0, ftmp
mol0.stdout.close()
basis = {'O': 'ano@3s2p', # Truncate the ANO basis and keep only 9
# functions (3s, 2p) for O atom.
'H': 'ccpvdz@1s' # One s function from cc-pVDZ basis
}
)
#
# Even tempered gaussian basis
#
mol = gto.M(
atom = '''O 0 0 0; H1 0 1 0; H2 0 0 1''',
basis = {'H': 'sto3g',
# even-temper gaussians alpha*beta^i, where i = 0,..,n
# (l, n, alpha, beta)
'O': gto.etbs([(0, 4, 1.5, 2.2), # s-function
(1, 2, 0.5, 2.2)]) # p-function
}
)
#
# Internal format (not recommended). See also
# pyscf/gto/basis/dzp_dunning.py as an example of internal format
#
# basis = {atom_type1:[[angular_momentum
# (GTO-exp1, contract-coeff11, contract-coeff12),
# (GTO-exp2, contract-coeff21, contract-coeff22),
# (GTO-exp3, contract-coeff31, contract-coeff32),
# ...],
# [angular_momentum
# (GTO-exp1, contract-coeff11, contract-coeff12),
