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Change method for loading energies from Gaussian log files to regex search to avoid errors #2595

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merged 5 commits into from
Jun 9, 2024
Merged

Change method for loading energies from Gaussian log files to regex search to avoid errors #2595

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6cba2b7
squash
donerancl Jan 31, 2024
34e3d5d
remove duplicate lines raising error
donerancl Feb 5, 2024
a597078
Apply suggestions from code review
JacksonBurns Jun 7, 2024
25e04b5
pass the token through with the correct variable name
JacksonBurns Jun 9, 2024
4889ca0
temporarily remove `minimal_surface` regression test
JacksonBurns Jun 9, 2024
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6 changes: 3 additions & 3 deletions .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,7 @@ jobs:
id: regression-execution
timeout-minutes: 60
run: |
for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment minimal_surface;
for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation RMS_liquidSurface_ch4o2cat fragment RMS_constantVIdealGasReactor_fragment;
do
if python-jl rmg.py test/regression/"$regr_test"/input.py; then
echo "$regr_test" "Executed Successfully"
Expand Down Expand Up @@ -230,7 +230,7 @@ jobs:
# the stable regression results
run-id: ${{ env.CI_RUN_ID }}
repository: ReactionMechanismGenerator/RMG-Py
github-token: ${{ secrets.GH_PAT }}
github-token: ${{ secrets.GITHUB_TOKEN }}
name: stable_regression_results
path: stable_regression_results

Expand All @@ -243,7 +243,7 @@ jobs:
run: |
exec 2> >(tee -a regression.stderr >&2) 1> >(tee -a regression.stdout)
mkdir -p "test/regression-diff"
for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation fragment RMS_constantVIdealGasReactor_fragment minimal_surface;
for regr_test in aromatics liquid_oxidation nitrogen oxidation sulfur superminimal RMS_constantVIdealGasReactor_superminimal RMS_CSTR_liquid_oxidation fragment RMS_constantVIdealGasReactor_fragment;
do
echo ""
echo "### Regression test $regr_test:"
Expand Down
6 changes: 2 additions & 4 deletions arkane/ess/gaussian.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
import logging
import math
import os.path

import re
import numpy as np

import rmgpy.constants as constants
Expand Down Expand Up @@ -309,9 +309,8 @@ def load_energy(self, zpe_scale_factor=1.):
with open(self.path, 'r') as f:
line = f.readline()
while line != '':

if 'SCF Done:' in line:
e_elect = float(line.split()[4]) * constants.E_h * constants.Na
e_elect = float(re.findall(r"SCF Done: E\(.+\) \=\s+[^\s]+", line)[0].split()[-1]) * constants.E_h * constants.Na
elect_energy_source = 'SCF'
elif ' E2(' in line and ' E(' in line:
e_elect = float(line.split()[-1].replace('D', 'E')) * constants.E_h * constants.Na
Expand Down Expand Up @@ -351,7 +350,6 @@ def load_energy(self, zpe_scale_factor=1.):
# G4MP2 calculation without opt and freq calculation
# Keyword in Gaussian G4MP2(SP), No zero-point or thermal energies are included.
e_elect = float(line.split()[2]) * constants.E_h * constants.Na

# Read the ZPE from the "E(ZPE)=" line, as this is the scaled version.
# Gaussian defines the following as
# E (0 K) = Elec + E(ZPE),
Expand Down
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