def harvest_zmat(zmat):
"""Parses the contents of the Cfour ZMAT file into array and
coordinate information. The coordinate info is converted into a
rather dinky Molecule (no fragment, but does read charge, mult,
unit). Return qcdb.Molecule. Written for findif zmat* where
geometry always Cartesian and Bohr.
"""
zmat = zmat.splitlines()[1:] # skip comment line
Nat = 0
readCoord = True
isBohr = ''
charge = 0
mult = 1
molxyz = ''
cgeom = []
for line in zmat:
if line.strip() == '':
readCoord = False
elif readCoord:
lline = line.split()
molxyz += line + '\n'
Nat += 1
else:
if line.find('CHARGE') > -1:
idx = line.find('CHARGE')
charge = line[idx + 7:]
idxc = charge.find(',')
if idxc > -1:
charge = charge[:idxc]
charge = int(charge)
if line.find('MULTIPLICITY') > -1:
idx = line.find('MULTIPLICITY')
mult = line[idx + 13:]
idxc = mult.find(',')
if idxc > -1:
mult = mult[:idxc]
mult = int(mult)
if line.find('UNITS=BOHR') > -1:
isBohr = ' bohr'
molxyz = '%d%s\n%d %d\n' % (Nat, isBohr, charge, mult) + molxyz
mol = Molecule.init_with_xyz(molxyz, no_com=True, no_reorient=True, contentsNotFilename=True)
return mol
def jajo2mol(jajodic):
"""Returns a Molecule from entries in dictionary *jajodic* extracted
from JAINDX and JOBARC.
"""
map = jajodic['MAP2ZMAT']
elem = jajodic['ATOMCHRG']
coord = jajodic['COORD ']
Nat = len(elem)
molxyz = '%d bohr\n\n' % (Nat)
# TODO chgmult, though not really necessary for reorientation
for at in range(Nat):
posn = map[at] - 1
el = 'GH' if elem[posn] == 0 else z2el[elem[posn]]
posn *= 3
molxyz += '%s %21.15f %21.15f %21.15f\n' % (el, coord[posn], coord[posn + 1], coord[posn + 2])
mol = Molecule.init_with_xyz(molxyz, no_com=True, no_reorient=True, contentsNotFilename=True)
return mol
def harvest_GRD(grd):
"""Parses the contents *grd* of the Cfour GRD file into the gradient
array and coordinate information. The coordinate info is converted
into a rather dinky Molecule (no charge, multiplicity, or fragment),
but this is these coordinates that govern the reading of molecule
orientation by Cfour. Return qcdb.Molecule and gradient array.
"""
grd = grd.splitlines()
Nat = int(grd[0].split()[0])
molxyz = '%d bohr\n\n' % (Nat)
grad = []
for at in range(Nat):
mline = grd[at + 1].split()
el = 'GH' if int(float(mline[0])) == 0 else z2el[int(float(mline[0]))]
molxyz += '%s %16s %16s %16s\n' % (el, mline[-3], mline[-2], mline[-1])
lline = grd[at + 1 + Nat].split()
grad.append([float(lline[-3]), float(lline[-2]), float(lline[-1])])
mol = Molecule.init_with_xyz(molxyz, no_com=True, no_reorient=True, contentsNotFilename=True)
return mol, grad
def harvest_outfile_pass(outtext):
"""Function to read CFOUR output file *outtext* and parse important
quantum chemical information from it in
"""
psivar = PreservingDict()
psivar_coord = None
psivar_grad = None
# TODO: BCC
# CI
# QCISD(T)
# other ROHF tests
# vcc/ecc
NUMBER = "((?:[-+]?\\d*\\.\\d+(?:[DdEe][-+]?\\d+)?)|(?:[-+]?\\d+\\.\\d*(?:[DdEe][-+]?\\d+)?))"
# Process NRE
mobj = re.search(r'^\s+' + r'(?:Nuclear repulsion energy :)' + r'\s+' + NUMBER + r'\s+a\.u\.\s*$',
outtext, re.MULTILINE)
if mobj:
print('matched nre')
psivar['NUCLEAR REPULSION ENERGY'] = mobj.group(1)
# Process SCF
mobj = re.search(
r'^\s+' + r'(?:E\(SCF\))' + r'\s+=\s+' + NUMBER + r'\s+a\.u\.\s*$',
outtext, re.MULTILINE)
if mobj:
print('matched scf1')
psivar['SCF TOTAL ENERGY'] = mobj.group(1)
mobj = re.search(
r'^\s+' + r'(?:E\(SCF\)=)' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE)
if mobj:
print('matched scf2')
psivar['SCF TOTAL ENERGY'] = mobj.group(1)
mobj = re.search(
r'^\s+' + r'(?:SCF has converged.)' + r'\s*$' +
r'(?:.*?)' +
r'^\s+' + r'(?:\d+)' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
print('matched scf3')
psivar['SCF TOTAL ENERGY'] = mobj.group(1)
# Process MP2
mobj = re.search(
r'^\s+' + r'(?:E2\(AA\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:E2\(AB\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:E2\(TOT\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:Total MP2 energy)' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*$',
outtext, re.MULTILINE)
if mobj:
print('matched mp2r')
psivar['MP2 SAME-SPIN CORRELATION ENERGY'] = 2 * Decimal(mobj.group(1))
psivar['MP2 OPPOSITE-SPIN CORRELATION ENERGY'] = mobj.group(2)
psivar['MP2 CORRELATION ENERGY'] = 2 * Decimal(mobj.group(1)) + Decimal(mobj.group(2))
psivar['MP2 TOTAL ENERGY'] = mobj.group(4)
mobj = re.search(
r'^\s+' + r'(?:E2\(AA\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:E2\(BB\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:E2\(AB\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:E2\(TOT\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:Total MP2 energy)' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*$',
outtext, re.MULTILINE)
if mobj:
print('matched mp2u')
psivar['MP2 SAME-SPIN CORRELATION ENERGY'] = Decimal(mobj.group(1)) + Decimal(mobj.group(2))
psivar['MP2 OPPOSITE-SPIN CORRELATION ENERGY'] = mobj.group(3)
psivar['MP2 CORRELATION ENERGY'] = Decimal(mobj.group(1)) + \
Decimal(mobj.group(2)) + Decimal(mobj.group(3))
psivar['MP2 TOTAL ENERGY'] = mobj.group(5)
mobj = re.search(
r'^\s+' + r'(?:E2\(AA\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:E2\(BB\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:E2\(AB\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:E2\(SINGLE\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:E2\(TOT\))' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'(?:Total MP2 energy)' + r'\s+=\s+' + NUMBER + r'\s+a.u.\s*$',
outtext, re.MULTILINE)
if mobj:
print('matched mp2ro')
psivar['MP2 SAME-SPIN CORRELATION ENERGY'] = Decimal(mobj.group(1)) + Decimal(mobj.group(2))
psivar['MP2 OPPOSITE-SPIN CORRELATION ENERGY'] = mobj.group(3)
psivar['MP2 SINGLES ENERGY'] = mobj.group(4)
psivar['MP2 CORRELATION ENERGY'] = Decimal(mobj.group(1)) + \
Decimal(mobj.group(2)) + Decimal(mobj.group(3)) + Decimal(mobj.group(4))
psivar['MP2 TOTAL ENERGY'] = mobj.group(6)
# Process MP3
mobj = re.search(
r'^\s+' + r'(?:D-MBPT\(2\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:D-MBPT\(3\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
print('matched mp3r')
dmp2 = Decimal(mobj.group(1))
dmp3 = Decimal(mobj.group(3))
psivar['MP2 CORRELATION ENERGY'] = dmp2
psivar['MP2 TOTAL ENERGY'] = mobj.group(2)
psivar['MP3 CORRELATION ENERGY'] = dmp2 + dmp3
psivar['MP3 TOTAL ENERGY'] = mobj.group(4)
psivar['MP2.5 CORRELATION ENERGY'] = dmp2 + Decimal('0.500000000000') * dmp3
psivar['MP2.5 TOTAL ENERGY'] = psivar['MP2.5 CORRELATION ENERGY'] + psivar['SCF TOTAL ENERGY']
mobj = re.search(
r'^\s+' + r'(?:S-MBPT\(2\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:D-MBPT\(2\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:S-MBPT\(3\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:D-MBPT\(3\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
print('matched mp3ro')
dmp2 = Decimal(mobj.group(1)) + Decimal(mobj.group(3))
dmp3 = Decimal(mobj.group(5)) + Decimal(mobj.group(7))
psivar['MP3 CORRELATION ENERGY'] = dmp2 + dmp3
psivar['MP3 TOTAL ENERGY'] = mobj.group(8)
psivar['MP2.5 CORRELATION ENERGY'] = dmp2 + Decimal('0.500000000000') * dmp3
psivar['MP2.5 TOTAL ENERGY'] = psivar['MP2.5 CORRELATION ENERGY'] + psivar['SCF TOTAL ENERGY']
# Process MP4
mobj = re.search(
r'^\s+' + r'(?:D-MBPT\(2\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:D-MBPT\(3\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:D-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:Q-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:S-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
print('matched mp4r')
dmp2 = Decimal(mobj.group(1))
dmp3 = Decimal(mobj.group(3))
dmp4sdq = Decimal(mobj.group(5)) + Decimal(mobj.group(7)) + Decimal(mobj.group(9))
psivar['MP2 CORRELATION ENERGY'] = dmp2
psivar['MP2 TOTAL ENERGY'] = mobj.group(2)
psivar['MP3 CORRELATION ENERGY'] = dmp2 + dmp3
psivar['MP3 TOTAL ENERGY'] = mobj.group(4)
psivar['MP2.5 CORRELATION ENERGY'] = dmp2 + Decimal('0.500000000000') * dmp3
psivar['MP2.5 TOTAL ENERGY'] = psivar['MP2.5 CORRELATION ENERGY'] + psivar['SCF TOTAL ENERGY']
psivar['MP4(SDQ) CORRELATION ENERGY'] = dmp2 + dmp3 + dmp4sdq
psivar['MP4(SDQ) TOTAL ENERGY'] = mobj.group(10)
mobj = re.search(
r'^\s+' + r'(?:S-MBPT\(2\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:D-MBPT\(2\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:S-MBPT\(3\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:D-MBPT\(3\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:L-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:NL-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
print('matched mp4ro')
dmp2 = Decimal(mobj.group(1)) + Decimal(mobj.group(3))
dmp3 = Decimal(mobj.group(5)) + Decimal(mobj.group(7))
dmp4sdq = Decimal(mobj.group(9)) + Decimal(mobj.group(11))
psivar['MP2 CORRELATION ENERGY'] = dmp2
psivar['MP2 TOTAL ENERGY'] = mobj.group(4)
psivar['MP3 CORRELATION ENERGY'] = dmp2 + dmp3
psivar['MP3 TOTAL ENERGY'] = mobj.group(8)
psivar['MP2.5 CORRELATION ENERGY'] = dmp2 + Decimal('0.500000000000') * dmp3
psivar['MP2.5 TOTAL ENERGY'] = psivar['MP2.5 CORRELATION ENERGY'] + psivar['SCF TOTAL ENERGY']
psivar['MP4(SDQ) CORRELATION ENERGY'] = dmp2 + dmp3 + dmp4sdq
psivar['MP4(SDQ) TOTAL ENERGY'] = mobj.group(12)
mobj = re.search(
r'^\s+' + r'(?:D-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:Q-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:S-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:T-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
print('matched mp4tr')
dmp4sdq = Decimal(mobj.group(1)) + Decimal(mobj.group(3)) + Decimal(mobj.group(5))
dmp4t = Decimal(mobj.group(7))
psivar['MP4(SDQ) CORRELATION ENERGY'] = psivar['MP3 CORRELATION ENERGY'] + dmp4sdq
psivar['MP4(SDQ) TOTAL ENERGY'] = mobj.group(6)
psivar['MP4(T) CORRECTION ENERGY'] = dmp4t
psivar['MP4(SDTQ) CORRELATION ENERGY'] = psivar['MP3 CORRELATION ENERGY'] + dmp4sdq + dmp4t
psivar['MP4(SDTQ) TOTAL ENERGY'] = mobj.group(8)
psivar['MP4 CORRELATION ENERGY'] = psivar['MP4(SDTQ) CORRELATION ENERGY']
psivar['MP4 TOTAL ENERGY'] = psivar['MP4(SDTQ) TOTAL ENERGY']
mobj = re.search(
r'^\s+' + r'(?:L-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:NL-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:WT12-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*' +
r'^\s+' + r'(?:T-MBPT\(4\))' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
print('matched mp4tro')
dmp4sdq = Decimal(mobj.group(1)) + Decimal(mobj.group(3))
dmp4t = Decimal(mobj.group(5)) + Decimal(mobj.group(7)) # TODO: WT12 with T, not SDQ?
psivar['MP4(SDQ) CORRELATION ENERGY'] = psivar['MP3 CORRELATION ENERGY'] + dmp4sdq
psivar['MP4(SDQ) TOTAL ENERGY'] = mobj.group(4)
psivar['MP4(T) CORRECTION ENERGY'] = dmp4t
psivar['MP4(SDTQ) CORRELATION ENERGY'] = psivar['MP3 CORRELATION ENERGY'] + dmp4sdq + dmp4t
psivar['MP4(SDTQ) TOTAL ENERGY'] = mobj.group(8)
psivar['MP4 CORRELATION ENERGY'] = psivar['MP4(SDTQ) CORRELATION ENERGY']
psivar['MP4 TOTAL ENERGY'] = psivar['MP4(SDTQ) TOTAL ENERGY']
# Process CC Iterations
mobj = re.search(
r'^\s+' + r'(?P<fullCC>(?P<iterCC>CC(?:\w+))(?:\(T\))?)' + r'\s+(?:energy will be calculated.)\s*' +
r'(?:.*?)' +
r'^\s+' + r'(?:\d+)' + r'\s+' + NUMBER + r'\s+' + NUMBER + r'\s+DIIS\s*' +
r'^\s*(?:-+)\s*' +
r'^\s*(?:A miracle (?:has come|come) to pass. The CC iterations have converged.)\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
print('matched cc with full %s iterating %s' % (mobj.group('fullCC'), mobj.group('iterCC')))
psivar['%s CORRELATION ENERGY' % (mobj.group('iterCC'))] = mobj.group(3)
psivar['%s TOTAL ENERGY' % (mobj.group('iterCC'))] = mobj.group(4)
# Process CC(T)
mobj = re.search(
r'^\s+' + r'(?:E\(SCF\))' + r'\s+=\s+' + NUMBER + r'\s+a\.u\.\s*' +
r'(?:.*?)' +
r'^\s+' + r'(?:E\(CCSD\))' + r'\s+=\s+' + NUMBER + r'\s*' +
r'(?:.*?)' +
r'^\s+' + r'(?:E\(CCSD\(T\)\))' + r'\s+=\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
print('matched ccsd(t) vcc')
psivar['SCF TOTAL ENERGY'] = mobj.group(1)
psivar['CCSD TOTAL ENERGY'] = mobj.group(2)
psivar['(T) CORRECTION ENERGY'] = Decimal(mobj.group(3)) - Decimal(mobj.group(2))
psivar['CCSD(T) CORRELATION ENERGY'] = Decimal(mobj.group(3)) - Decimal(mobj.group(1))
psivar['CCSD(T) TOTAL ENERGY'] = mobj.group(3)
mobj = re.search(
r'^\s+' + r'(?:E\(SCF\))' + r'\s+=\s+' + NUMBER + r'\s+a\.u\.\s*' +
r'(?:.*?)' +
r'^\s+' + r'(?:CCSD energy)' + r'\s+' + NUMBER + r'\s*' +
r'(?:.*?)' +
r'^\s+' + r'(?:Total perturbative triples energy:)' + r'\s+' + NUMBER + r'\s*' +
r'^\s*(?:-+)\s*' +
r'^\s+' + r'(?:CCSD\(T\) energy)' + r'\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
print('matched ccsd(t) ecc')
psivar['SCF TOTAL ENERGY'] = mobj.group(1)
psivar['CCSD TOTAL ENERGY'] = mobj.group(2)
psivar['(T) CORRECTION ENERGY'] = mobj.group(3)
psivar['CCSD(T) CORRELATION ENERGY'] = Decimal(mobj.group(4)) - Decimal(mobj.group(2))
psivar['CCSD(T) TOTAL ENERGY'] = mobj.group(4)
mobj = re.search(
r'^\s+' + r'(?:CCSD energy)' + r'\s+' + NUMBER + r'\s*' +
r'^\s*(?:-+)\s*' +
r'^\s+' + r'(?:CCSD\(T\) energy)' + r'\s+' + NUMBER + r'\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj:
print('matched ccsd(t) lamb')
psivar['CCSD TOTAL ENERGY'] = mobj.group(1)
psivar['(T) CORRECTION ENERGY'] = Decimal(mobj.group(2)) - Decimal(mobj.group(1))
psivar['CCSD(T) CORRELATION ENERGY'] = Decimal(mobj.group(2)) - psivar['SCF TOTAL ENERGY']
psivar['CCSD(T) TOTAL ENERGY'] = mobj.group(2)
# Process SCS-CC
mobj = re.search(
r'^\s+' + r'(?P<fullCC>(?P<iterCC>CC(?:\w+))(?:\(T\))?)' + r'\s+(?:energy will be calculated.)\s*' +
r'(?:.*?)' +
r'^\s*' + r'(?:@CCENRG-I, Correlation energies.)' + r'\s+(?:ECCAA)\s+' + NUMBER + r'\s*' +
r'^\s+(?:ECCBB)\s+' + NUMBER + '\s*' +
r'^\s+(?:ECCAB)\s+' + NUMBER + '\s*' +
r'^\s+(?:Total)\s+' + NUMBER + '\s*',
outtext, re.MULTILINE | re.DOTALL)
if mobj: # PRINT=2 to get SCS-CC components
print('matched scscc')
psivar['%s SAME-SPIN CORRELATION ENERGY' % (mobj.group('iterCC'))] = Decimal(mobj.group(3)) + Decimal(mobj.group(4))
psivar['%s OPPOSITE-SPIN CORRELATION ENERGY' % (mobj.group('iterCC'))] = mobj.group(5)
psivar['%s CORRELATION ENERGY' % (mobj.group('iterCC'))] = mobj.group(6)
mobj = re.search(
r'^\s+' + r'(?P<fullCC>(?P<iterCC>CC(?:\w+))(?:\(T\))?)' + r'\s+(?:energy will be calculated.)\s*' +
r'(?:.*?)' +
r'^\s+' + r'Amplitude equations converged in' + r'\s*\d+\s*' + r'iterations.\s*' +
r'^\s+' + r'The AA contribution to the correlation energy is:\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'The BB contribution to the correlation energy is:\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'The AB contribution to the correlation energy is:\s+' + NUMBER + r'\s+a.u.\s*' +
r'^\s+' + r'The total correlation energy is\s+' + NUMBER + r'\s+a.u.\s*' +
r'(?:.*?)' +
#r'^\s+' + r'The CC iterations have converged.' + r'\s*$',
r'^\s+' + r'(?:A miracle come to pass. )?' + r'The CC iterations have converged.' + r'\s*$',
outtext, re.MULTILINE | re.DOTALL)
if mobj: # PRINT=2 to get SCS components
print('matched scscc2')
psivar['%s SAME-SPIN CORRELATION ENERGY' % (mobj.group('iterCC'))] = Decimal(mobj.group(3)) + Decimal(mobj.group(4))
psivar['%s OPPOSITE-SPIN CORRELATION ENERGY' % (mobj.group('iterCC'))] = mobj.group(5)
psivar['%s CORRELATION ENERGY' % (mobj.group('iterCC'))] = mobj.group(6)
# Process gradient
mobj = re.search(
r'\s+' + r'Molecular gradient' + r'\s*' +
r'\s+' + r'------------------' + r'\s*' +
r'\s+' + r'\n' +
r'(?:(?:\s+[A-Z]+\s*#\d+\s+[xyz]\s+[-+]?\d+\.\d+\s*\n)+)' + # optional, it seems
r'\n\n' + # optional, it seems
r'((?:\s+[A-Z]+\s*#\d+\s+\d?\s+[-+]?\d+\.\d+\s+[-+]?\d+\.\d+\s+[-+]?\d+\.\d+\s*\n)+)' +
r'\n\n' +
r'\s+' + 'Molecular gradient norm',
outtext, re.MULTILINE)
if mobj:
print('matched molgrad')
atoms = []
psivar_grad = []
for line in mobj.group(1).splitlines():
lline = line.split()
atoms.append(lline[0])
#psivar_gradient.append([Decimal(lline[-3]), Decimal(lline[-2]), Decimal(lline[-1])])
psivar_grad.append([float(lline[-3]), float(lline[-2]), float(lline[-1])])
# Process geometry
mobj = re.search(
# r'\s+(?:-+)\s*' +
# r'^\s+' + r'Z-matrix Atomic Coordinates (in bohr)' + r'\s*' +
r'^\s+' + r'Symbol Number X Y Z' + r'\s*' +
r'^\s+(?:-+)\s*' +
r'((?:\s+[A-Z]+\s+[0-9]+\s+[-+]?\d+\.\d+\s+[-+]?\d+\.\d+\s+[-+]?\d+\.\d+\s*\n)+)' +
r'^\s+(?:-+)\s*',
outtext, re.MULTILINE)
if mobj:
print('matched geom')
molxyz = '%d bohr\n\n' % len(mobj.group(1).splitlines())
for line in mobj.group(1).splitlines():
lline = line.split()
molxyz += '%s %16s %16s %16s\n' % (lline[0], lline[-3], lline[-2], lline[-1])
# Rather a dinky Molecule as no ghost, charge, or multiplicity
psivar_coord = Molecule.init_with_xyz(molxyz, no_com=True, no_reorient=True, contentsNotFilename=True)
# Process atom geometry
mobj = re.search(
r'^\s+' + r'@GETXYZ-I, 1 atoms read from ZMAT.' + r'\s*' +
r'^\s+' + r'[0-9]+\s+([A-Z]+)\s+[0-9]+\s+' + NUMBER + r'\s*',
outtext, re.MULTILINE)
if mobj:
print('matched atom')
# Dinky Molecule
molxyz = '1 bohr\n\n%s 0.0 0.0 0.0\n' % (mobj.group(1))
psivar_coord = Molecule.init_with_xyz(molxyz, no_com=True, no_reorient=True, contentsNotFilename=True)
# Process error codes
mobj = re.search(
r'^\s*' + r'--executable ' + r'(\w+)' + r' finished with status' + r'\s+' + r'([1-9][0-9]*)',
outtext, re.MULTILINE)
if mobj:
print('matched error')
psivar['CFOUR ERROR CODE'] = mobj.group(2)
# Process CURRENT energies (TODO: needs better way)
if 'SCF TOTAL ENERGY' in psivar:
psivar['CURRENT REFERENCE ENERGY'] = psivar['SCF TOTAL ENERGY']
psivar['CURRENT ENERGY'] = psivar['SCF TOTAL ENERGY']
if 'MP2 TOTAL ENERGY' in psivar and 'MP2 CORRELATION ENERGY' in psivar:
psivar['CURRENT CORRELATION ENERGY'] = psivar['MP2 CORRELATION ENERGY']
psivar['CURRENT ENERGY'] = psivar['MP2 TOTAL ENERGY']
if 'MP3 TOTAL ENERGY' in psivar and 'MP3 CORRELATION ENERGY' in psivar:
psivar['CURRENT CORRELATION ENERGY'] = psivar['MP3 CORRELATION ENERGY']
psivar['CURRENT ENERGY'] = psivar['MP3 TOTAL ENERGY']
if 'MP4 TOTAL ENERGY' in psivar and 'MP4 CORRELATION ENERGY' in psivar:
psivar['CURRENT CORRELATION ENERGY'] = psivar['MP4 CORRELATION ENERGY']
psivar['CURRENT ENERGY'] = psivar['MP4 TOTAL ENERGY']
# if ('%s TOTAL ENERGY' % (mobj.group('fullCC')) in psivar) and \
# ('%s CORRELATION ENERGY' % (mobj.group('fullCC')) in psivar):
# psivar['CURRENT CORRELATION ENERGY'] = psivar['%s CORRELATION ENERGY' % (mobj.group('fullCC')]
# psivar['CURRENT ENERGY'] = psivar['%s TOTAL ENERGY' % (mobj.group('fullCC')]
if 'CC2 TOTAL ENERGY' in psivar and 'CC2 CORRELATION ENERGY' in psivar:
psivar['CURRENT CORRELATION ENERGY'] = psivar['CC2 CORRELATION ENERGY']
psivar['CURRENT ENERGY'] = psivar['CC2 TOTAL ENERGY']
if 'CCSD TOTAL ENERGY' in psivar and 'CCSD CORRELATION ENERGY' in psivar:
psivar['CURRENT CORRELATION ENERGY'] = psivar['CCSD CORRELATION ENERGY']
psivar['CURRENT ENERGY'] = psivar['CCSD TOTAL ENERGY']
if 'CCSD(T) TOTAL ENERGY' in psivar and 'CCSD(T) CORRELATION ENERGY' in psivar:
psivar['CURRENT CORRELATION ENERGY'] = psivar['CCSD(T) CORRELATION ENERGY']
psivar['CURRENT ENERGY'] = psivar['CCSD(T) TOTAL ENERGY']
if 'CC3 TOTAL ENERGY' in psivar and 'CC3 CORRELATION ENERGY' in psivar:
psivar['CURRENT CORRELATION ENERGY'] = psivar['CC3 CORRELATION ENERGY']
psivar['CURRENT ENERGY'] = psivar['CC3 TOTAL ENERGY']
if 'CCSDT TOTAL ENERGY' in psivar and 'CCSDT CORRELATION ENERGY' in psivar:
psivar['CURRENT CORRELATION ENERGY'] = psivar['CCSDT CORRELATION ENERGY']
psivar['CURRENT ENERGY'] = psivar['CCSDT TOTAL ENERGY']
return psivar, psivar_coord, psivar_grad