def getbfs(ccdata):
from cclib.bridge import cclib2pyquante
pymol = cclib2pyquante.makepyquante(ccdata)
bfs = []
for i, atom in enumerate(pymol): # `atom` is instance of pyquante2.geo.atom.atom class.
basis = ccdata.gbasis[i] # `basis` is basis coefficients stored in ccData.
for sym, primitives in basis:
for power in sym2powerlist[sym]: # `sym` is S, P, D, F and is used as key here.
exponentlist = []
coefficientlist = []
for exponents, coefficients in primitives:
exponentlist.append(exponents)
coefficientlist.append(coefficients)
basisfunction = cgbf(
atom.atuple()[1:4], powers=power, exps=exponentlist, coefs=coefficientlist,
)
basisfunction.normalize()
bfs.append(basisfunction)
del cclib2pyquante
return bfs
def getbfs(coords, gbasis):
"""Convenience function for both wavefunction and density based on PyQuante Ints.py."""
if not _HAS_PYQUANTE:
raise Exception("You need to have PyQuante installed")
mymol = cclib2pyquante.makepyquante(coords, [0 for _ in coords])
sym2powerlist = {
'S': [(0, 0, 0)],
'P': [(1, 0, 0), (0, 1, 0), (0, 0, 1)],
'D': [(2, 0, 0), (0, 2, 0), (0, 0, 2), (1, 1, 0), (0, 1, 1),
(1, 0, 1)],
'F': [(3, 0, 0), (2, 1, 0), (2, 0, 1), (1, 2, 0), (1, 1, 1), (1, 0, 2),
(0, 3, 0), (0, 2, 1), (0, 1, 2), (0, 0, 3)]
}
bfs = []
for i, atom in enumerate(mymol):
bs = gbasis[i]
for sym, prims in bs:
for power in sym2powerlist[sym]:
bf = CGBF(atom.pos(), power)
for expnt, coef in prims:
bf.add_primitive(expnt, coef)
bf.normalize()
bfs.append(bf)
return bfs
def getbfs(coords, gbasis):
"""Convenience function for both wavefunction and density based on PyQuante Ints.py."""
if not _HAS_PYQUANTE:
raise Exception("You need to have PyQuante installed")
mymol = cclib2pyquante.makepyquante(coords, [0 for _ in coords])
sym2powerlist = {
'S' : [(0, 0, 0)],
'P' : [(1, 0, 0), (0, 1, 0), (0, 0, 1)],
'D' : [(2, 0, 0), (0, 2, 0), (0, 0, 2), (1, 1, 0), (0, 1, 1), (1, 0, 1)],
'F' : [(3, 0, 0), (2, 1, 0), (2, 0, 1), (1, 2, 0), (1, 1, 1), (1, 0, 2),
(0, 3, 0), (0, 2, 1), (0, 1, 2), (0, 0, 3)]
}
bfs = []
for i, atom in enumerate(mymol):
bs = gbasis[i]
for sym, prims in bs:
for power in sym2powerlist[sym]:
bf = CGBF(atom.pos(), power)
for expnt, coef in prims:
bf.add_primitive(expnt, coef)
bf.normalize()
bfs.append(bf)
return bfs
def test_makepyquante(self):
from PyQuante.hartree_fock import hf
atomnos = numpy.array([1, 8, 1],"i")
a = numpy.array([[-1, 1, 0], [0, 0, 0], [1, 1, 0]], "f")
pyqmol = cclib2pyquante.makepyquante(a, atomnos)
en, orbe, orbs = hf(pyqmol)
ref = -75.824754
assert abs(en - ref) < 1.0e-6
def test_makepyquante(self):
from PyQuante.hartree_fock import hf
atomnos = numpy.array([1, 8, 1], "i")
a = numpy.array([[-1, 1, 0], [0, 0, 0], [1, 1, 0]], "f")
pyqmol = cclib2pyquante.makepyquante(a, atomnos)
en, orbe, orbs = hf(pyqmol)
ref = -75.824754
assert abs(en - ref) < 1.0e-6
def getbfs(ccdata):
from cclib.bridge import cclib2pyquante
pymol = cclib2pyquante.makepyquante(ccdata)
bfs = []
for i, atom in enumerate(pymol):
bs = ccdata.gbasis[i]
for sym, prims in bs:
for power in sym2powerlist[sym]:
bf = CGBF(atom.pos(), power)
for expnt, coef in prims:
bf.add_primitive(expnt, coef)
bf.normalize()
bfs.append(bf)
del cclib2pyquante
return bfs
def test_makepyquante(self):
# Test older PyQuante bridge
from PyQuante.hartree_fock import hf
from PyQuante.Molecule import Molecule
reference = Molecule(
"h2o",
[
(8, (0, 0, 0.119159)),
(1, (0, 0.790649, -0.476637)),
(1, (0, -0.790649, -0.476637)),
],
units="Angstroms",
)
refen, reforbe, reforbs = hf(reference)
pyqmol = cclib2pyquante.makepyquante(self.data)
en, orbe, orbs = hf(pyqmol)
self.assertAlmostEqual(en, refen, delta=1.0e-6)
def test_makepyquante(self):
# Test pyquante2 bridge
from pyquante2 import molecule, rhf, h2o, basisset
bfs = basisset(h2o)
# Copied from water_ccsd.log
refmol = molecule(
[(8, 0.0, 0.0, 0.119159), (1, 0, 0.790649, -0.476637),
(1, 0, -0.790649, -0.476637)],
units="Angstroms",
)
refsolver = rhf(refmol, bfs)
refsolver.converge()
pyqmol = cclib2pyquante.makepyquante(self.data)
pyqsolver = rhf(pyqmol, bfs)
pyqsolver.converge()
assert_array_almost_equal(refsolver.energies[-1],
pyqsolver.energies[-1],
decimal=6)