def _main():
# read a file, including orbitals and basis sets, and test
# if the output orbitals are orthogonal.
def rmsd(a):
return np.mean(a.flatten()**2)**.5
FileName = "benzene.xml"
#FileName = "/home/cgk/dev/xml-molpro/test1.xml"
XmlData = ReadMolproXml(FileName,SkipVirtual=True)
print("Atoms from file [a.u.]:\n{}".format(XmlData.Atoms.MakeXyz(NumFmt="%20.15f",Scale=1/wmme.ToAng)))
OrbBasis = XmlData.OrbBasis
#BasisLibs = ["def2-nzvpp-jkfit.libmol"]
BasisLibs = []
ic = wmme.FIntegralContext(XmlData.Atoms, XmlData.OrbBasis, FitBasis="univ-JKFIT", BasisLibs=BasisLibs)
from wmme import mdot
C = XmlData.Orbs
S = ic.MakeOverlap()
print("Orbital matrix shape: {} (loaded from '{}')".format(C.shape, FileName))
print("Overlap matrix shape: {} (made via WMME)".format(S.shape))
np.set_printoptions(precision=4,linewidth=10000,edgeitems=3,suppress=False)
SMo = mdot(C.T, S, C)
print("Read orbitals:")
for OrbInfo in XmlData.Orbitals:
print("{:30s}".format(OrbInfo.Desc))
print("MO deviation from orthogonality: {:.2e}".format(rmsd(SMo - np.eye(SMo.shape[0]))))
pass
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 _run_with_pyscf(FileNameXml):
from pyscf import gto
from pyscf import scf
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))
# this gives you data from MolproXmlfile ready for use in PySCF
Atoms, Basis, COrb = ConvertMolproXmlToPyscfInput(XmlData)
mol = gto.Mole()
mol.build(
verbose=0,
atom=Atoms,
basis=Basis,
)
# compute overlap matrix with PySCF
S = mol.intor_symmetric('int1e_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 _main():
# read a file, including orbitals and basis sets, and test
# if the output orbitals are orthogonal.
def rmsd(a):
return np.mean(a.flatten()**2)**.5
FileName = "benzene.xml"
#FileName = "/home/cgk/dev/xml-molpro/test1.xml"
XmlData = ReadMolproXml(FileName,SkipVirtual=True)
print "Atoms from file [a.u.]:\n%s" % XmlData.Atoms.MakeXyz(NumFmt="%20.15f",Scale=1/wmme.ToAng)
OrbBasis = XmlData.OrbBasis
#BasisLibs = ["def2-nzvpp-jkfit.libmol"]
BasisLibs = []
ic = wmme.FIntegralContext(XmlData.Atoms, XmlData.OrbBasis, FitBasis="univ-JKFIT", BasisLibs=BasisLibs)
from wmme import mdot
C = XmlData.Orbs
S = ic.MakeOverlap()
print "Orbital matrix shape: %s (loaded from '%s')" % (C.shape, FileName)
print "Overlap matrix shape: %s (made via WMME)" % (S.shape,)
np.set_printoptions(precision=4,linewidth=10000,edgeitems=3,suppress=False)
SMo = mdot(C.T, S, C)
print "Read orbitals:"
for OrbInfo in XmlData.Orbitals:
print "%30s" % OrbInfo.Desc
print "MO deviation from orthogonality: %.2e" % rmsd(SMo - np.eye(SMo.shape[0]))
pass
def _run_with_pyscf(FileNameXml):
from pyscf import gto
from pyscf import scf
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)
# this gives you data from MolproXmlfile ready for use in PySCF
Atoms, Basis, COrb = ConvertMolproXmlToPyscfInput(XmlData)
mol = gto.Mole()
mol.build(
verbose = 0,
atom = Atoms,
basis = Basis,
)
# 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 _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