Reconciling Electrochem Branch with main

.github/workflows/CI.yml

@@ -2,7 +2,7 @@
 # This file contains the script used by GitHub actions to execute the Continuous Integration (CI)
 # for RMG-Py. This includes building RMG and its dependencies, executing the unit tests,
 # functional tests, database tests, and regression tests.
-# 
+#
 # This will run automatically on any push to any branch, but will only run one instance of
 # itself at a time per branch (to avoid spawning tons of runners, which prevents them from
 # executing).
@@ -14,7 +14,7 @@
 #
 #
 # Changelog:
-# 2023-04    - Jackson Burns - Added this header, regression tests, cleanup of action in 
+# 2023-04    - Jackson Burns - Added this header, regression tests, cleanup of action in
 #              in general, and documentation throughout the file.
 # 2023-05    - added Docker build steps
 # 2023-05-12 - added changes to allow running on forks
@@ -46,14 +46,19 @@ concurrency:
 env:
   # if running on RMG-Py but requiring changes on an un-merged branch of RMG-database, replace
   # main with the name of the branch
-  RMG_DATABASE_BRANCH: main
+  RMG_DATABASE_BRANCH: lithium
 
 
 jobs:
   build-osx:
     runs-on: macos-latest
     # skip scheduled runs from forks
     if: ${{ !( github.repository != 'ReactionMechanismGenerator/RMG-Py' && github.event_name == 'schedule' ) }}
+    env:
+      # Update this if needed to match a pull request on the RMG-database:
+      RMG_DATABASE_BRANCH: lithium
+      # This is true only if this is a reference case for the regression testing:
+      REFERENCE_JOB: ${{ github.ref == 'refs/heads/main' && matrix.os =='ubuntu-latest' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
     defaults:
       run:
         shell: bash -l {0}
@@ -272,7 +277,7 @@ jobs:
               export FAILED=Yes
             fi
             echo "" # blank line so next block is interpreted as markdown
-            cat "$regr_test-core.log"
+            cat "$regr_test-core.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
             echo "</details>"
             echo "<details>"
             if python-jl scripts/checkModels.py \
@@ -289,7 +294,7 @@ jobs:
               export FAILED=Yes
             fi
             echo "" # blank line so next block is interpreted as markdown
-            cat "$regr_test-edge.log"
+            cat "$regr_test-edge.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
             echo "</details>"
 
             # Check for Regression between Reference and Dynamic (skip superminimal)

arkane/encorr/ae.py

@@ -73,7 +73,9 @@
     'Methane',
     'Methyl',
     'Ammonia',
-    'Chloromethane'
+    'Chloromethane',
+    'Lithium Hydride',
+    'Lithium Fluoride'
 ]
 
 

arkane/encorr/bac.py

@@ -241,7 +241,7 @@ class BAC:
     ref_databases = {}
     atom_spins = {
         'H': 0.5, 'C': 1.0, 'N': 1.5, 'O': 1.0, 'F': 0.5,
-        'Si': 1.0, 'P': 1.5, 'S': 1.0, 'Cl': 0.5, 'Br': 0.5, 'I': 0.5
+        'Si': 1.0, 'P': 1.5, 'S': 1.0, 'Cl': 0.5, 'Br': 0.5, 'I': 0.5, 'Li': 0.5,
     }
     exp_coeff = 3.0  # Melius-type parameter (Angstrom^-1)
 

examples/rmg/SEI_pure_ACN/input.py

@@ -0,0 +1,181 @@
+# Data sources
+database(
+    thermoLibraries=['LithiumSurface','electrocatLiThermo','primaryThermoLibrary', 'LithiumPrimaryThermo', 'LithiumAdditionalThermo', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo'], # 'surfaceThermoPt' is the default. Thermo data is derived using bindingEnergies for other metals
+    reactionLibraries = ['LithiumPrimaryKinetics',"LithiumSurface"], # when Ni is used change the library to Surface/Deutschmann_Ni
+    seedMechanisms = [],
+    kineticsDepositories = ['training'],
+    kineticsFamilies = ['surface',
+			'1+2_Cycloaddition',
+    'Surface_Carbonate_Deposition',
+    'Surface_Carbonate_F_CO_Decomposition',
+    'Surface_Carbonate_2F_Decomposition',
+    'Surface_Carbonate_CO_Decomposition',
+    '1,2_Elimination_LiR',
+    '1,2_Intra_Elimination_LiR',
+    'Li_Addition_MultipleBond',
+    'Li_NO_Substitution',
+    'Li_NO_Ring_Opening',
+    'Li_Abstraction',
+    'R_Addition_MultipleBond_Disprop',
+    'Cation_R_Recombination',
+    'Cation_Addition_MultipleBond',
+    '1,2-Birad_to_alkene',
+    '1,2_Insertion_CO',
+    '1,2_Insertion_carbene',
+    '1,2_shiftS',
+    '1,3_Insertion_CO2',
+    '1,3_Insertion_ROR',
+    '1,3_Insertion_RSR',
+    '1,4_Cyclic_birad_scission',
+    '1,4_Linear_birad_scission',
+    '2+2_cycloaddition',
+    'Birad_recombination',
+    'CO_Disproportionation',
+    'Birad_R_Recombination',
+    'Cyclic_Ether_Formation',
+    'Cyclic_Thioether_Formation',
+    'Diels_alder_addition',
+    'Diels_alder_addition_Aromatic',
+    #'Disproportionation',
+    'HO2_Elimination_from_PeroxyRadical',
+    'H_Abstraction',
+    'Intra_Retro_Diels_alder_bicyclic',
+    'Intra_Disproportionation',
+    'Intra_R_Add_Endocyclic',
+    'Intra_R_Add_Exocyclic',
+    'R_Addition_COm',
+    'R_Addition_MultipleBond',
+    'R_Recombination',
+    'intra_H_migration',
+    'intra_NO2_ONO_conversion',
+    'intra_OH_migration',
+    'intra_substitutionCS_cyclization',
+    'intra_substitutionCS_isomerization',
+    'intra_substitutionS_cyclization',
+    'intra_substitutionS_isomerization',
+    #'ketoenol',
+    'Singlet_Carbene_Intra_Disproportionation',
+    'Singlet_Val6_to_triplet',
+    'Intra_5_membered_conjugated_C=C_C=C_addition',
+    'Intra_Diels_alder_monocyclic',
+    'Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH',
+    'Intra_2+2_cycloaddition_Cd',
+    'Intra_ene_reaction',
+    'Cyclopentadiene_scission',
+    '6_membered_central_C-C_shift',
+    'Intra_R_Add_Exo_scission',
+    '1,2_shiftC',
+    '1,2_NH3_elimination',
+    '1,3_NH3_elimination',
+    'Retroene',],
+    kineticsEstimator = 'rate rules',
+    adsorptionGroups='adsorptionLi',
+)
+
+catalystProperties(
+    metal = 'Li110',
+)
+
+# List of species
+species(
+    label="Lip",
+    reactive=True,
+    structure=SMILES("[Li+]"),
+)
+
+species(
+    label='ACN',
+    reactive=True,
+    structure=SMILES("CC#N"),
+)
+
+species(
+    label='vacantX',
+    reactive=True,
+    structure=adjacencyList("1 X u0"),
+)
+
+liquidSurfaceReactor(
+    temperature=(298.15,'K'),
+    distance=(10.0e-10,"m"),
+    viscosity=(5e7,"Pa*s"),
+    liqPotential=(0.3,'V'),
+    surfPotential=(0.0,'V'),
+    initialConcentrations={
+        "ACN": (0.019146,'mol/cm^3'),
+        "Lip": (15.0,'mol/m^3'),
+    },
+	initialSurfaceCoverages={
+       "vacantX": 1.0, 
+    },
+    surfaceVolumeRatio=(1.0e-5, 'm^-1'),
+    terminationTime=(1e3,'sec'),
+	constantSpecies=["ACN","Lip"],
+)
+
+liquidSurfaceReactor(
+    temperature=(298.15,'K'),
+    distance=(0.0,"m"),
+    liqPotential=(0.0,'V'),
+    surfPotential=(0.0,'V'),
+    initialConcentrations={
+        "ACN": (0.019146,'mol/cm^3'),
+        "Lip": (15.0,'mol/m^3'),
+    },
+	initialSurfaceCoverages={
+        "vacantX": 1.0, 
+    },
+    surfaceVolumeRatio=(1.0e5, 'm^-1'),
+    terminationTime=(1e3,'sec'),
+	constantSpecies=["ACN","Lip"],
+)
+
+solvation(
+	solvent='acetonitrile'
+)
+
+simulator(
+    atol=1e-16,
+    rtol=1e-6,
+)
+
+model(
+    toleranceKeepInEdge=1E-20,
+    toleranceMoveToCore=0.1,
+    toleranceRadMoveToCore=0.1,
+    toleranceInterruptSimulation=1e10,
+    maximumEdgeSpecies=100000,
+    filterReactions=False,
+    maxNumObjsPerIter=1,
+    terminateAtMaxObjects=True,
+    toleranceBranchReactionToCore=0.001,
+    branchingIndex=0.5,
+    branchingRatioMax=1.0,
+)
+
+options(
+    units='si',
+    saveEdgeSpecies=False,
+)
+
+forbidden(
+    label='vacancies',
+    structure=adjacencyListGroup("""
+1 Xv u0 p0 c0
+"""),
+)
+
+forbidden(
+    label='Li2',
+    structure=adjacencyList("""
+1 Li u0 p0 c0 {2,S}
+2 Li u0 p0 c0 {1,S}"""),
+)
+
+generatedSpeciesConstraints(
+    allowed=['input species','reaction libraries'],
+    maximumSurfaceSites=1,
+    maximumCarbonAtoms=7,
+    maximumOxygenAtoms=4,
+    maximumRadicalElectrons=1,
+)