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Merge pull request #2598 for electrochemistry a.k.a. RMG-electrocat
Electrochemistry! (finally) a.k.a. RMG-electrocat This brings in lots of electrochemistry work, both for CO2 reduction and for Lithium SEI work. See https://chemrxiv.org/engage/chemrxiv/article-details/6695ecaf5101a2ffa87f3953 for the Lithium stuff and https://doi.org/10.17760/D20467257}{10.17760/D20467257 for CO2 reduction. Many thanks to @davidfarinajr @mjohnson541 and @ssun30 Requires updated RMG-database at least at commit 0add9cdee2dd2e0677c765086dbcd471d1377cb4
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‎.github/workflows/CI.yml‎

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@@ -175,7 +175,7 @@ jobs:
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timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
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run: |
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python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
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julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
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julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator'
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- name: Install Q2DTor
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run: echo "" | make q2dtor
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export FAILED=Yes
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fi
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echo "" # blank line so next block is interpreted as markdown
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cat "$regr_test-core.log"
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cat "$regr_test-core.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
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echo "</details>"
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echo "<details>"
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if python-jl scripts/checkModels.py \
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export FAILED=Yes
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fi
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echo "" # blank line so next block is interpreted as markdown
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cat "$regr_test-edge.log"
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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")
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echo "</details>"
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# Check for Regression between Reference and Dynamic (skip superminimal)
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with:
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push: true
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tags: reactionmechanismgenerator/rmg:latest
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build-args: |
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RMS_Branch=for_rmg

‎.github/workflows/docs.yml‎

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@@ -64,7 +64,7 @@ jobs:
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timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
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run: |
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python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
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julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
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julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator'
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- name: Checkout gh-pages Branch
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uses: actions/checkout@v2

‎arkane/encorr/ae.py‎

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'Methane',
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'Methyl',
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'Ammonia',
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'Chloromethane'
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'Chloromethane',
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# Lithium species shall be uncommented after we reconcile the difference in AECs and BACs
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# 'Lithium Hydride',
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# 'Lithium Fluoride'
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]
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‎arkane/encorr/bac.py‎

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

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#. Install and Link Julia dependencies: ::
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julia -e 'using Pkg; Pkg.add("PyCall");Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;'
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julia -e 'using Pkg; Pkg.add("PyCall");Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator;'
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python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
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‎examples/rmg/CO2RR/input.py‎

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# Data sources
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database(
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thermoLibraries=['surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo', 'electrocatThermo',
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# 'CO2RR_Adsorbates_Ag111'
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],
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reactionLibraries = [('Surface/CPOX_Pt/Deutschmann2006_adjusted', False)],
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seedMechanisms = [],
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kineticsDepositories = ['training'],
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kineticsFamilies = ['electrochem',
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# 'surface',
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'Surface_Abstraction',
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'Surface_Abstraction_vdW',
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'Surface_Abstraction_Single_vdW',
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'Surface_Abstraction_Beta_double_vdW',
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'Surface_Adsorption_Dissociative',
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'Surface_Adsorption_Dissociative_Double',
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'Surface_Adsorption_vdW',
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'Surface_Dissociation',
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'Surface_Dissociation_Double_vdW',
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'Surface_Dissociation_vdW',
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'Surface_EleyRideal_Addition_Multiple_Bond',
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'Surface_Migration',
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],
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kineticsEstimator = 'rate rules',
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)
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catalystProperties(
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metal = 'Ag111'
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)
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# List of species
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species(
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label='CO2',
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reactive=True,
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structure=adjacencyList(
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"""
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1 O u0 p2 c0 {2,D}
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2 C u0 p0 c0 {1,D} {3,D}
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3 O u0 p2 c0 {2,D}
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"""),
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)
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species(
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label='proton',
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reactive=True,
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structure=adjacencyList(
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"""
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1 H u0 p0 c+1
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"""),
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)
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species(
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label='vacantX',
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reactive=True,
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structure=adjacencyList("1 X u0"),
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)
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species(
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label='H',
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reactive=True,
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structure=adjacencyList(
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"""
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1 H u1 p0 c0
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"""),
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)
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species(
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label='CO2X',
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reactive=True,
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structure=adjacencyList("""
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1 O u0 p2 c0 {3,D}
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2 O u0 p2 c0 {3,D}
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3 C u0 p0 c0 {1,D} {2,D}
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4 X u0 p0 c0
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"""),
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)
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species(
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label='CHO2X',
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reactive=True,
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structure=adjacencyList("""
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1 O u0 p2 c0 {3,S} {5,S}
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2 O u0 p2 c0 {3,D}
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3 C u0 p0 c0 {1,S} {2,D} {4,S}
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4 H u0 p0 c0 {3,S}
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5 X u0 p0 c0 {1,S}
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"""),
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)
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species(
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label='CO2HX',
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reactive=True,
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structure=adjacencyList("""
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1 O u0 p2 c0 {2,S} {4,S}
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2 C u0 p0 c0 {1,S} {3,D} {5,S}
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3 O u0 p2 c0 {2,D}
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4 H u0 p0 c0 {1,S}
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5 X u0 p0 c0 {2,S}
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"""),
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)
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species(
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label='OCX',
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reactive=True,
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structure=adjacencyList("""
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1 O u0 p2 c0 {2,D}
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2 C u0 p0 c0 {1,D} {3,D}
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3 X u0 p0 c0 {2,D}
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"""),
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)
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species(
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label='OX',
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reactive=True,
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structure=adjacencyList("""
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1 O u0 p2 c0 {2,D}
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2 X u0 p0 c0 {1,D}
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"""),
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)
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species(
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label='CH2O2X',
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reactive=True,
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structure=adjacencyList("""
128+
1 O u0 p2 c0 {3,S} {5,S}
129+
2 O u0 p2 c0 {3,D}
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3 C u0 p0 c0 {1,S} {2,D} {4,S}
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4 H u0 p0 c0 {3,S}
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5 H u0 p0 c0 {1,S}
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6 X u0 p0 c0
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"""),
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)
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species(
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label='CHOX',
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reactive=True,
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structure=adjacencyList("""
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1 O u0 p2 c0 {2,D}
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2 C u0 p0 c0 {1,D} {3,S} {4,S}
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3 H u0 p0 c0 {2,S}
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4 X u0 p0 c0 {2,S}
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"""),
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)
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species(
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label='CH2OX',
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reactive=True,
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structure=adjacencyList("""
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1 O u0 p2 c0 {2,D}
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2 C u0 p0 c0 {1,D} {3,S} {4,S}
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3 H u0 p0 c0 {2,S}
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4 H u0 p0 c0 {2,S}
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5 X u0 p0 c0
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"""),
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)
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forbidden(
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label='CO2-bidentate',
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structure=adjacencyList(
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"""
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1 O u0 p2 c0 {2,D}
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2 C u0 p0 c0 {1,D} {3,S} {4,S}
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3 X u0 p0 c0 {2,S}
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4 O u0 p2 c0 {2,S} {5,S}
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5 X u0 p0 c0 {4,S}
170+
"""
171+
)
172+
)
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174+
liquidSurfaceReactor(
175+
temperature=(300,'K'),
176+
liqPotential=(0,'V'),
177+
surfPotential=(-2.0,'V'),
178+
initialConcentrations={
179+
"CO2": (1e-3,'mol/cm^3'),
180+
"proton": (1e-4,'mol/m^3'),
181+
},
182+
initialSurfaceCoverages={
183+
# "HX": 0.5,
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# # "CXO2": 0.0,
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"CHO2X": 0.1,
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"CO2HX": 0.1,
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"vacantX": 0.1,
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"CO2X": 0.4,
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'OX': 0.1,
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'OCX': 0.1,
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'CH2O2X': 0.05,
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'CHOX': 0.04,
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'CH2OX': 0.01
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},
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surfaceVolumeRatio=(1.0e5, 'm^-1'),
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terminationTime=(1.0e3,'sec'),
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# terminationConversion={'CO2': 0.90},
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# constantSpecies=["proton"],
199+
)
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liquidSurfaceReactor(
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temperature=(300,'K'),
203+
liqPotential=(0,'V'),
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surfPotential=(-1.5,'V'),
205+
initialConcentrations={
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"CO2": (1e-3,'mol/cm^3'),
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"proton": (1e-4,'mol/m^3'),
208+
},
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initialSurfaceCoverages={
210+
# "HX": 0.5,
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# # "CXO2": 0.0,
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"CHO2X": 0.1,
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"CO2HX": 0.1,
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"vacantX": 0.1,
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"CO2X": 0.4,
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'OX': 0.1,
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'OCX': 0.1,
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'CH2O2X': 0.05,
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'CHOX': 0.04,
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'CH2OX': 0.01
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},
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surfaceVolumeRatio=(1.0e5, 'm^-1'),
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terminationTime=(1.0e3,'sec'),
224+
# terminationConversion={'CO2': 0.90},
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# constantSpecies=["proton"],
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)
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liquidSurfaceReactor(
229+
temperature=(300,'K'),
230+
liqPotential=(0,'V'),
231+
surfPotential=(-1.0,'V'),
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initialConcentrations={
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"CO2": (1e-3,'mol/cm^3'),
234+
"proton": (1e-4,'mol/m^3'),
235+
},
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initialSurfaceCoverages={
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# "HX": 0.5,
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# # "CXO2": 0.0,
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"CHO2X": 0.1,
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"CO2HX": 0.1,
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"vacantX": 0.1,
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"CO2X": 0.4,
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'OX': 0.1,
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'OCX': 0.1,
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'CH2O2X': 0.05,
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'CHOX': 0.04,
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'CH2OX': 0.01
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},
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surfaceVolumeRatio=(1.0e5, 'm^-1'),
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terminationTime=(1.0e3,'sec'),
251+
# terminationConversion={'CO2': 0.90},
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# constantSpecies=["proton"],
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)
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# liquidSurfaceReactor(
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# temperature=(300,'K'),
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# liqPotential=(0,'V'),
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# surfPotential=(-0.5,'V'),
259+
# initialConcentrations={
260+
# "CO2": (1e-3,'mol/cm^3'),
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# "proton": (1e-4,'mol/m^3'),
262+
# },
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# initialSurfaceCoverages={
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# # "HX": 0.5,
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# # # "CXO2": 0.0,
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# "CHO2X": 0.1,
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# "CO2HX": 0.1,
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# "vacantX": 0.1,
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# "CO2X": 0.4,
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# 'OX': 0.1,
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# 'OCX': 0.1,
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# 'CH2O2X': 0.05,
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# 'CHOX': 0.04,
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# 'CH2OX': 0.01
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# },
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# surfaceVolumeRatio=(1.0e5, 'm^-1'),
277+
# terminationTime=(1.0e3,'sec'),
278+
# # terminationConversion={'CO2': 0.90},
279+
# # constantSpecies=["proton"],
280+
# )
281+
282+
solvation(
283+
solvent='water'
284+
)
285+
286+
simulator(
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atol=1e-16,
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rtol=1e-8,
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)
290+
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model(
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toleranceKeepInEdge=1E-16,
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toleranceMoveToCore=1E-3,
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toleranceRadMoveToCore=1E-6,
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toleranceInterruptSimulation=1E6,
296+
filterReactions=False,
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maximumEdgeSpecies=5000,
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toleranceBranchReactionToCore=1E-6,
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branchingIndex=0.5,
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branchingRatioMax=1.0,
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)
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options(
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units='si',
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generateOutputHTML=True,
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generatePlots=True,
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saveEdgeSpecies=True,
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saveSimulationProfiles=False,
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)
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generatedSpeciesConstraints(
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allowed=['input species','reaction libraries'],
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maximumSurfaceSites=2,
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maximumCarbonAtoms=3,
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maximumOxygenAtoms=2,
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maximumRadicalElectrons=1,
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)

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