Merge pull request #2595 from donerancl/gaussian_regex

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

Author: JacksonBurns

.github/workflows/CI.yml

@@ -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"
@@ -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
 
@@ -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:"

arkane/ess/gaussian.py

@@ -35,7 +35,7 @@
 import logging
 import math
 import os.path
-
+import re
 import numpy as np
 
 import rmgpy.constants as constants
@@ -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
@@ -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),