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Processing monoatomic species in Arkane/molpro #1521

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merged 2 commits into from
Jan 3, 2019
Merged

Processing monoatomic species in Arkane/molpro #1521

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ad7cf09
Read geometry of monoatomic species from Molpro sp jobs
alongd Dec 14, 2018
bf04302
Don't look for ZPE for monoatomic molecules
alongd Dec 14, 2018
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7 changes: 4 additions & 3 deletions arkane/molpro.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ def getNumberOfAtoms(self):
# Automatically determine the number of atoms
if 'ATOMIC COORDINATES' in line and Natoms == 0:
for i in range(4): line = f.readline()
while 'Bond lengths' not in line:
while 'Bond lengths' not in line and 'nuclear charge' not in line.lower():
Natoms += 1
line = f.readline()
line = f.readline()
Expand Down Expand Up @@ -137,12 +137,13 @@ def loadGeometry(self):
# Close file when finished
f.close()

#If no optimized coordinates were found, uses the input geometry (for example if reading the geometry from a frequency file
# If no optimized coordinates were found, uses the input geometry
# (for example if reading the geometry from a frequency file)
if coord == []:
f = open(self.path, 'r')
line = f.readline()
while line != '':
if 'Atomic Coordinates' in line:
if 'atomic coordinates' in line.lower():
symbol = []; coord = []
for i in range(4):
line = f.readline()
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6 changes: 5 additions & 1 deletion arkane/statmech.py
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Expand Up @@ -394,7 +394,11 @@ def load(self):
atomEnergies=self.atomEnergies,
applyAtomEnergyCorrections=self.applyAtomEnergyCorrections,
applyBondEnergyCorrections=self.applyBondEnergyCorrections)
ZPE = statmechLog.loadZeroPointEnergy() * self.frequencyScaleFactor
if len(number) > 1:
ZPE = statmechLog.loadZeroPointEnergy() * self.frequencyScaleFactor
else:
# Monoatomic species don't have frequencies
ZPE = 0.0
logging.debug('Corrected minimum energy is {0} J/mol'.format(E0))
# The E0_withZPE at this stage contains the ZPE
E0_withZPE = E0 + ZPE
Expand Down