def _run_with_pyscf(FileNameXml):
# read Molpro XML file exported via {put,xml,filename}
print "\n* Reading: '%s'" % FileNameXml
XmlData = MolproXml.ReadMolproXml(FileNameXml, SkipVirtual=True)
# Note, that right now the default value is SkipVirtual =True, that means that Orbitals COrb include only those,
# which have non-zero occupation numbers in XML file. If you want virtual orbitals too, change SkipVirtual to False.
print "Atoms from file [a.u.]:\n%s" % XmlData.Atoms.MakeXyz(
NumFmt="%20.15f", Scale=1 / wmme.ToAng)
# convert data from XML file (atom positions, basis sets, MO coeffs) into format compatible
# with PySCF.
Atoms, Basis, COrb = MolproXmlToPyscf.ConvertMolproXmlToPyscfInput(XmlData)
# make pyscf Mole object
mol = gto.Mole()
mol.build(verbose=0, atom=Atoms, basis=Basis, spin=0)
# compute overlap matrix with PySCF
S = mol.intor_symmetric('cint1e_ovlp_sph')
# compute overlap matrix of MO basis overlap, using the MOs imported from the XML,
# and the overlap matrix computed with PySCF to check that MO were imported properly.
SMo = mdot(COrb.T, S, COrb)
PrintMatrix("MO-Basis overlap (should be unity!)", SMo)
print "RMSD(SMo-id): %8.2e" % rmsd(SMo - np.eye(SMo.shape[0]))
print
def get_1e_integrals_in_MOs_from_Molpro_for_SOC(FileNameXml):
# read Molpro XML file exported via {put,xml,filename}
print "\n* Reading: '%s'" % FileNameXml
XmlData = MolproXml.ReadMolproXml(FileNameXml, SkipVirtual=True)
print "Atoms from file [a.u.]:\n%s" % XmlData.Atoms.MakeXyz(
NumFmt="%20.15f", Scale=1 / wmme.ToAng)
# convert data from XML file (atom positions, basis sets, MO coeffs) into format compatible # with PySCF.
Atoms, Basis, COrb = MolproXmlToPyscf.ConvertMolproXmlToPyscfInput(XmlData)
# make pyscf Mole object
mol = gto.Mole()
mol.build(
verbose=0,
atom=Atoms,
basis=Basis,
# symmetry = 'D2h',
spin=0)
natoms = 1
norb = 11
nelec = 10
all_orbs = len(COrb)
# COrb is a list of orbs, you get the info about orbs in the output when reading orbs with a scheme above :
# # of an orb in COrb list, irrep in the point group used in Molpro calcs, # of orb in a given irrep in Molpro output
Orblist = [6, 7, 8, 9, 10, 18, 19, 24, 25, 27, 28]
ActOrb = np.zeros(shape=(all_orbs, norb))
ActOrb2 = np.zeros(shape=(all_orbs, norb))
for o1 in range(all_orbs):
for o2 in range(norb):
ActOrb[o1, o2] = COrb[o1, Orblist[o2]]
print "================================================="
print " Now print So1e integrals"
for id in range(natoms):
chg = mol.atom_charge(id)
mol.set_rinv_origin_(
mol.atom_coord(id)) # set the gauge origin to first atom
h1ao = abs(chg) * mol.intor('cint1e_prinvxp_sph',
comp=3) # comp=3 for x,y,z directions
h1 = []
for i in range(3):
h1.append(reduce(np.dot, (ActOrb.T, h1ao[i], ActOrb)))
for i in range(3):
for j in range(h1[i].shape[0]):
for k in range(h1[i].shape[1]):
print id, i + 1, j + 1, k + 1, h1[i][j, k]