def GetBasis(gaussResult, quiet=False):
"""Get PyQuante representation of a basis from a gaussian output file"""
# Create representation of molecule within PyQuante
PQMol = cclib.bridge.makepyquante(gaussResult.atomcoords[-1], gaussResult.atomnos)
# Get PyQuante representation of basis set
basis = Ints.getbasis(PQMol, gaussResult.basisname)
# Check that PyQuante and g09 have the same basis set ordering
nbasis = gaussResult.nbasis
assert len(basis.bfs) == nbasis, (
"Gaussian and PyQuante have " "different basis sets. Did you specify the same basis for each?"
)
overlap_py = np.array(Ints.getS(basis))
maxdefect = 0.0
if hasattr(gaussResult, "mocoeffs_sao"):
sao = gaussResult.mocoeffs_sao
else:
sao = gaussResult.aooverlaps
if not quiet:
for i, vals in enumerate(zip(overlap_py.flat, sao.flat)):
pq, g9 = vals
x, y = np.unravel_index(i, (nbasis, nbasis))
denom = max(pq, g9)
if denom < 10 ** -13:
continue
if min(pq, g9) == 0:
denom = 1.0
defect = abs((pq - g9) / denom)
if defect > maxdefect:
maxdefect = defect
if defect > 1e-3 and x <= y:
print pq, g9, (x, y), 100 * abs(pq - g9) / denom
print "Maximum error between G09 and PyQuante overlap matrices:", maxdefect
if maxdefect > 1e-3:
print "WARNING!!!! Calculated overlap matrix does not match basis set!"
print "Basis sets might not match!\n\n\n"
return nbasis, basis
from PyQuante.NumWrap import eigh, matrixmultiply
from PyQuante import hartree_fock as HF
#Global Variables############################
convergenceLimit = 1.0 * pow(10, -6)
maxCycle = 50
#Section 1############################
#specify a molecule
molecule = Molecule("H2", [(1, (0, 0, 0)), (1, (0, 0, 1)), (8, (-1, 0, 0))])
basisSet = Ints.getbasis(molecule, "sto-3g")
#Section 2############################
#Overlap Matrix
S = Ints.getS(basisSet)
#Follwing Two matrices compose the core Hamiltonian
#KE Matrix
KE = Ints.getT(basisSet)
#External Potential, Nuclear - Electron Attraction
Vext = Ints.getV(basisSet, molecule)
#Form Hcore
Hcore = KE + Vext
#calculate two electron integrals
elecRepulsion = Ints.get2ints(basisSet)
#Section 3############################
