def backtransform(chgeMol, permMol, chgeGrad=None, chgeDip=None):
"""Here, *chgeMol* and *chgeGrd* need to be turned into the native Cfour
orientation embodied by *permMol*. Currently for vpt2.
"""
# Set up array reorientation object
p4c4 = OrientMols(permMol, chgeMol) # opposite than usual
oriCoord = p4c4.transform_coordinates2(chgeMol)
p4Elem = []
for at in range(chgeMol.natom()):
p4Elem.append(chgeMol.Z(at))
oriElem = p4c4.transform_elementlist(p4Elem)
oriElemMap = p4c4.Catommap
oriGrad = None if chgeGrad is None else p4c4.transform_gradient(chgeGrad)
oriDip = None if chgeDip is None else p4c4.transform_vector(chgeDip)
if chgeGrad and chgeDip:
return oriElemMap, oriElem, oriCoord, oriGrad, oriDip
else:
return oriElemMap, oriElem, oriCoord
def harvest(p4Mol, c4out, **largs):
"""Parses all the pieces of output from Cfour: the stdout in
*c4out* and the contents of various scratch files like GRD stored
in their namesake keys in *largs*. Since all Cfour output uses
its own orientation and atom ordering for the given molecule,
a qcdb.Molecule *p4Mol*, if supplied, is used to transform the
Cfour output back into consistency with *p4Mol*.
"""
# Collect results from output file and subsidiary files
outPsivar, outMol, outGrad = harvest_output(c4out)
if 'GRD' in largs:
grdMol, grdGrad = harvest_GRD(largs['GRD'])
else:
grdMol, grdGrad = None, None
if 'FCMFINAL' in largs:
fcmHess = harvest_FCM(largs['FCMFINAL'])
else:
fcmHess = None
if 'DIPOL' in largs:
dipolDip = harvest_DIPOL(largs['DIPOL'])
else:
dipolDip = None
# Reconcile the coordinate information: several cases
# Case p4Mol GRD Check consistency Apply orientation? ReturnMol (1-19-2014)
# sp with mol thru cfour {} None None outMol N.C. outMol
# opt with mol thru cfour {} None grdMol outMol && grdMol N.C. grdMol
# sp with mol thru molecule {} p4Mol None p4Mol && outMol p4Mol <-- outMol p4Mol (same as input arg)
# opt with mol thru molecule {} p4Mol grdMol p4Mol && outMol && grdMol p4Mol <-- grdMol p4Mol (same as input arg)
if outMol:
if grdMol:
if abs(outMol.nuclear_repulsion_energy() - grdMol.nuclear_repulsion_energy()) > 1.0e-3:
raise ValidationError("""Cfour outfile (NRE: %f) inconsistent with Cfour GRD (NRE: %f).""" % \
(outMol.nuclear_repulsion_energy(), grdMol.nuclear_repulsion_energy()))
if p4Mol:
if abs(outMol.nuclear_repulsion_energy() - p4Mol.nuclear_repulsion_energy()) > 1.0e-3:
raise ValidationError("""Cfour outfile (NRE: %f) inconsistent with Psi4 input (NRE: %f).""" % \
(outMol.nuclear_repulsion_energy(), p4Mol.nuclear_repulsion_energy()))
else:
raise ValidationError("""No coordinate information extracted from Cfour output.""")
# print ' <<< [1] P4-MOL >>>'
# if p4Mol:
# p4Mol.print_out_in_bohr()
# print ' <<< [2] C4-OUT-MOL >>>'
# if outMol:
# outMol.print_out_in_bohr()
# print ' <<< [3] C4-GRD-MOL >>>'
# if grdMol:
# grdMol.print_out_in_bohr()
# Set up array reorientation object
if p4Mol and grdMol:
p4c4 = OrientMols(p4Mol, grdMol)
oriCoord = p4c4.transform_coordinates2(grdMol)
oriGrad = p4c4.transform_gradient(grdGrad)
oriDip = None if dipolDip is None else p4c4.transform_vector(dipolDip)
elif p4Mol and outMol:
p4c4 = OrientMols(p4Mol, outMol)
oriCoord = p4c4.transform_coordinates2(outMol)
oriGrad = None
oriDip = None if dipolDip is None else p4c4.transform_vector(dipolDip)
elif outMol:
oriCoord = None
oriGrad = None
oriDip = None if dipolDip is None else dipolDip
# print p4c4
# print ' <<< [4] C4-ORI-MOL >>>'
# if oriCoord is not None:
# for item in oriCoord:
# print(' %16.8f %16.8f %16.8f' % (item[0], item[1], item[2]))
#
# print ' <<< [1] C4-GRD-GRAD >>>'
# if grdGrad is not None:
# for item in grdGrad:
# print(' %16.8f %16.8f %16.8f' % (item[0], item[1], item[2]))
# print ' <<< [2] C4-ORI-GRAD >>>'
# if oriGrad is not None:
# for item in oriGrad:
# print(' %16.8f %16.8f %16.8f' % (item[0], item[1], item[2]))
retMol = None if p4Mol else grdMol
if oriDip:
outPsivar['CURRENT DIPOLE X'] = str(oriDip[0] * psi_dipmom_au2debye)
outPsivar['CURRENT DIPOLE Y'] = str(oriDip[1] * psi_dipmom_au2debye)
outPsivar['CURRENT DIPOLE Z'] = str(oriDip[2] * psi_dipmom_au2debye)
if oriGrad:
retGrad = oriGrad
elif grdGrad:
retGrad = grdGrad
else:
retGrad = None
return outPsivar, retGrad, retMol