diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..3753c66
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,30 @@
+.ipynb_checkpoints
+**/species/*.png
+*:Zone.Identifier
+**/chemkin/*
+**/seed/*
+**/*.jld2
+
+CO2RR_RMS/Cu/CO2RR_Cu.ipynb
+CO2RR_RMS/Ag/CO2RR_RMS.ipynb
+CO2RR_RMS/Ag/CO2RR_RMS_Diffusion_Interface.ipynb
+CO2RR_RMS/Ag/CO2RR_RMS_3.ipynb
+CO2RR_RMS/Ag/CO2RR_RMS_Diffusion_Interface_1.ipynb
+CO2RR_RMS/Ag/CO2RR_RMS_2.ipynb
+CO2RR_RMS/Ag/CO2RR_RMS_AIChE.ipynb
+CO2RR_RMS/Ag/CO2RR_RMS_Diffusion_Interface_Matt.ipynb
+CO2_Reduction_Ag/CO2RR_RMS.ipynb
+CO2_Reduction_Ag/CO2RR_RMS_Diffusion_Interface.ipynb
+CO2_Reduction_Ag/CO2RR_RMS_3.ipynb
+CO2_Reduction_Ag/CO2RR_RMS_Diffusion_Interface_1.ipynb
+CO2_Reduction_Ag/CO2RR_RMS_2.ipynb
+CO2_Reduction_Ag/CO2RR_RMS_AIChE.ipynb
+CO2_Reduction_Ag/CO2RR_RMS_4.ipynb
+CO2_Reduction_Ag/CO2RR_RMS_Diffusion_Interface_Matt.ipynb
+CO2_Reduction_Cu/CO2RR_Cu.ipynb
+AIChE_2025/Plot_FE.ipynb
+AIChE_2025/CO2RR_RMS_Diffusion.ipynb
+CO2_Reduction_Cu3Sn/CO2RR_RMS_Diffusion_Interface_Cu3Sn.ipynb
+CO2_Reduction_Ag/HER-Data/Validation/HER-Val-Data.ipynb
+CO2_Reduction_Ag/HER-Data/Validation/CO2RR_RMS_Sensitivity.ipynb
+setup.ipynb
\ No newline at end of file
diff --git a/AIChE_2025/CO2RR_RMS_Diffusion.ipynb b/AIChE_2025/CO2RR_RMS_Diffusion.ipynb
deleted file mode 100644
index e1a33b0..0000000
--- a/AIChE_2025/CO2RR_RMS_Diffusion.ipynb
+++ /dev/null
@@ -1,1013 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": 257,
- "id": "8a590634",
- "metadata": {},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "\u001b[32m\u001b[1m Activating\u001b[22m\u001b[39m project at `~/mambaforge/envs/rmg_electrocat_2/julia_env`\n"
- ]
- }
- ],
- "source": [
- "using Pkg\n",
- "Pkg.activate(ENV[\"PYTHON_JULIAPKG_PROJECT\"])\n",
- "using ReactionMechanismSimulator"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 258,
- "id": "82245f05",
- "metadata": {},
- "outputs": [],
- "source": [
- "using PythonPlot\n",
- "using DifferentialEquations\n",
- "using Sundials\n",
- "using SciMLBase\n",
- "using QuadGK\n",
- "using CSV, DataFrames"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 259,
- "id": "e941d4fb",
- "metadata": {},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "[00:33:06] WARNING: not removing hydrogen atom without neighbors\n",
- "[00:33:06] WARNING: not removing hydrogen atom without neighbors\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species vacantX\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CO2X\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CHO2X\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CO2HX\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species OCX\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species OX\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CH2O2X\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CHOX\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CH2OX\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species HOX\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C([Pt])C(=O)[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species HX\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species H2OX\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=CC(=O)[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CX\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=O.[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C=C=O.[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species OC#[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C([Pt])C#[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CH2X\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C([Pt])C[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species [Pt]CO[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C([Pt])OC[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species C=C=O.[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C(C[Pt])O[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C([Pt])C=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species [Pt]OC=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C=C=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CHX\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C([Pt])CO[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species [Pt]OCO[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C=C[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species [Pt]COO[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C=CO[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species OO[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C([Pt])C(O)=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species OC(=[Pt])O[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species OC=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species OC([Pt])O[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C([Pt])C(O)[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C=CO.[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C=C([Pt])O[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CO[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species COC(=O)[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CC(=O)[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CC(=O)O[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CH3X\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species OC[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C([Pt])CO\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species OCO[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C([Pt])OC=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species COO[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species [H][H].[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C(C=[Pt])O[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CO.[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C(C#[Pt])O[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C=C(O)[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species OC(O)[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species OC(O)=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CC(=O)O.[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C(O)C[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C(O)C=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=C(O)C#[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CC(O)=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species [Pt]=C=C=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CC(O)([Pt])O[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CC(=[Pt])O[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species CC#[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species [Pt]C#CO[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species [Pt]OC#CO[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species COC=O.[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=COC[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=COC=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species O=COC#[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species [Pt]C=C=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n",
- "┌ Warning: failed to generate StokesDiffusivity model for species [Pt]=CC=[Pt]\n",
- "└ @ ReactionMechanismSimulator /home/ssun30/RMG-electrocat/ReactionMechanismSimulator.jl/src/Parse.jl:352\n"
- ]
- },
- {
- "data": {
- "text/plain": [
- "Dict{Any, Any} with 4 entries:\n",
- " \"Solvents\" => Solvent[Solvent(\"water\", RiedelViscosity{Float64}(…\n",
- " Set([\"gas\", \"surface\"]) => Dict{Any, Any}(\"Reactions\"=>ElementaryReaction[pro…\n",
- " \"gas\" => Dict{Any, Any}(\"Species\"=>Species[Species{NASA{Emp…\n",
- " \"surface\" => Dict{Any, Any}(\"Species\"=>Species[Species{NASA{Emp…"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "outdict = readinput(\"Ag_C2_042925.rms\")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 260,
- "id": "fe2767e9",
- "metadata": {},
- "outputs": [],
- "source": [
- "boundarylayerspcs = outdict[\"gas\"][\"Species\"]\n",
- "boundarylayerrxns = outdict[\"gas\"][\"Reactions\"]\n",
- "surfspcs = outdict[\"surface\"][\"Species\"]\n",
- "surfrxns = outdict[\"surface\"][\"Reactions\"]\n",
- "interfacerxns = outdict[Set([\"surface\", \"gas\"])][\"Reactions\"]\n",
- "solv = outdict[\"Solvents\"][1];"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 261,
- "id": "c54ee65e",
- "metadata": {},
- "outputs": [],
- "source": [
- "sitedensity = 2.294e-5; # Ag111 site density is 2.294e-9 mol/cm^2 or 2.294e-5 mol/m^2\n",
- "boundarylayer = IdealDiluteSolution(boundarylayerspcs,boundarylayerrxns,solv,name=\"boundarylayeruid\",diffusionlimited=true);\n",
- "surf = IdealSurface(surfspcs,surfrxns,sitedensity,name=\"surface\");"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 262,
- "id": "138a067e",
- "metadata": {},
- "outputs": [],
- "source": [
- "phi = -(1.37 + 0.414);"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 263,
- "id": "8894c84d",
- "metadata": {},
- "outputs": [],
- "source": [
- "# Reservoir is a 100 mL (100e-6 m^3) cell\n",
- "# Proton concentration is 10^-7 mol/L (10^-4 mol/m^3)\n",
- "# CO2 concentration is 0.01 mol/L (10 mol/m^3), saturation solubility ~0.03 mol/L\n",
- "# AVratio in experiments is 36 m^-1 but is measured by surface area/reservoir volume\n",
- "# Area of the electrode is therefore 3.6e1 m^-1 * 1e2 * 1e-6 m^3 = 3.6e-3 m^2 = 36 cm^2\n",
- "# Assume boundary layer thickness d_bl = 1 mm or 1e-3 m\n",
- "# Volume of the boundary layer V_bl = 3.6e-3 m^2 * 1e-3 m = 3.6e-6 m^3\n",
- "# Actual AVratio is therefore 3.6e-3 m^2 / 3.6e-6 m^3 = 1e3 m^-1 (reciprocal of d_bl)\n",
- "# Amount of sites is 2.943e-5 mol/m^2 * 3.6e-3 m^2 = 10.595e-8 mol\n",
- "\n",
- "# For earlier simulations, a 100x linear scale factor is applied,\n",
- "# so volume becomes 100e-6 m^3 * (1e2)^3 = 100 m^3,\n",
- "# electrode area becomes 3.6e-3 * (1e2) ^2 = 3.6e1 m^2,\n",
- "# AVratio becomes 3.6e1 m^2 / 1e2 m^3 = 0.36 m^-1\n",
- "# Volume of the boundary layer becomes 3.6e1 m^2 * 1e-3 m = 3.6e-2 m^3\n",
- "\n",
- "C_proton = 1e-7*1e3;\n",
- "C_co2 = 1e-2*1e3;\n",
- "C_default = 1e-12;\n",
- "V_res = 1e3;\n",
- "layer_thickness = 1e-5;\n",
- "AVratio = 36;\n",
- "A_surf = V_res*AVratio;\n",
- "V_bl = A_surf*layer_thickness;\n",
- "# V_bl = V_res;\n",
- "sites = sitedensity*A_surf;\n",
- "\n",
- "# The initial conditions for individual species are moles not concentration, so we need to multiply concentration by boundary layer volume\n",
- "initialcondsboundarylayer = Dict([\"proton\"=>C_proton*V_bl,\n",
- " \"CO2\"=>C_co2*V_bl,\n",
- " # \"H2\"=>C_default*10*V_bl,\n",
- " # \"O=CO\"=>C_default*V_bl,\n",
- " \"V\"=>V_bl,\"T\"=>300,\"Phi\"=>0.0,\"d\"=>0.0]);\n",
- "initialcondsreservoir = Dict([\"proton\"=>C_proton,\n",
- " \"CO2\"=>C_co2,\n",
- " \"V\"=>V_res,\"T\"=>300]);\n",
- "\n",
- "\n",
- "# Assume voltage is -1.0 V vs. R.H.E. which equates to -1.414 V vs. S.H.E. at pH=7\n",
- "initialcondssurf = Dict([\"CO2X\"=>0.4*sites,\n",
- " # \"CHO2X\"=>0.1*sites,\n",
- " # \"CO2HX\"=>0.1*sites,\n",
- " # \"OX\"=>0.1*sites,\n",
- " # \"OCX\"=>0.1*sites,\n",
- " \"vacantX\"=>0.6*sites,\n",
- " # \"CH2O2X\"=>0.05*sites,\n",
- " # \"CHOX\"=>0.04*sites,\n",
- " # \"CH2OX\"=>0.01*sites,\n",
- " \"A\"=>A_surf,\"T\"=>300,\"Phi\"=>phi]);"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 264,
- "id": "ddb39b3d",
- "metadata": {
- "scrolled": false
- },
- "outputs": [],
- "source": [
- "domainboundarylayer, y0boundarylayer, pboundarylayer = ConstantTVDomain(phase=boundarylayer, initialconds=initialcondsboundarylayer);\n",
- "domaincat,y0cat,pcat = ConstantTAPhiDomain(phase=surf,\n",
- " initialconds=initialcondssurf);"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 265,
- "id": "d3aaf802",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "9.32e-9"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "# Set proton diffusivity to a higher value than calculated from Stokes Einstein equation\n",
- "# The values are taken from DOI: 10.1039/C8SC01253A\n",
- "# Values calculated from MD is 1.015 A^2/ps, experimental values are 0.932 A^2/ps.\n",
- "# 1 A^2/ps = 1e-8 m^2/s\n",
- "domainboundarylayer.diffusivity[6] = 0.932e-8"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 266,
- "id": "ed49d2b4",
- "metadata": {},
- "outputs": [],
- "source": [
- "inter,pinter = ReactiveInternalInterfaceConstantTPhi(domainboundarylayer,\n",
- " domaincat,interfacerxns,298.15,A_surf);"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 267,
- "id": "dee14906",
- "metadata": {},
- "outputs": [],
- "source": [
- "# start with 1mm layer thickness\n",
- "diffusionlayer = ConstantReservoirDiffusion(domainboundarylayer, initialcondsreservoir, A_surf, layer_thickness);"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 268,
- "id": "e70ac4b0",
- "metadata": {},
- "outputs": [],
- "source": [
- "interfaces = [inter, diffusionlayer];"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 269,
- "id": "244f0912",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- " 0.003601 seconds (8.47 k allocations: 7.894 MiB)\n"
- ]
- }
- ],
- "source": [
- "@time react,y0,p = Reactor((domainboundarylayer,domaincat), (y0boundarylayer,y0cat), (0.0, 1.8e3), interfaces, (pboundarylayer,pcat,pinter));"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 270,
- "id": "962f838c",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- " 0.211123 seconds (487.07 k allocations: 364.304 MiB, 6.12% gc time)\n",
- "1800.0\n",
- "Success\n"
- ]
- }
- ],
- "source": [
- "@time sol = solve(react.ode,Sundials.CVODE_BDF(),abstol=1e-22,reltol=1e-8);\n",
- "println(sol.t[end]);\n",
- "println(sol.retcode);"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 271,
- "id": "6667bb5a",
- "metadata": {},
- "outputs": [],
- "source": [
- "ssys = SystemSimulation(sol,(domainboundarylayer,domaincat,), interfaces,p);"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 272,
- "id": "d4939a87",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "get_reservoir_concentration"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "\"\"\"\n",
- "diffusive flux to the reservoir\n",
- "\"\"\"\n",
- "function flux_to_reservoir(sim,t,reservoirinterface)\n",
- " cs = concentrations(sim,t)\n",
- " return reservoirinterface.A .* sim.domain.diffusivity .* (cs - reservoirinterface.c) / reservoirinterface.layer_thickness\n",
- "end\n",
- "\n",
- "\"\"\"\n",
- "Integrates the flux to the reservoir and computes the concentration assuming\n",
- "there is no prior concentration of that species in the reservoir\n",
- "\"\"\"\n",
- "function get_reservoir_concentration(sim,t,reservoirinterface,Vres,C0)\n",
- " intg,err = quadgk(x -> flux_to_reservoir(sim,x,reservoirinterface), 0, t);\n",
- " intg[5] = 0;\n",
- " intg[6] = 0;\n",
- " return C0 + intg./Vres\n",
- "end"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 273,
- "id": "411d79d6",
- "metadata": {},
- "outputs": [],
- "source": [
- "# Logarithmic time scale\n",
- "t_vals = 10 .^ range(-12, stop=3, length=160);\n",
- "\n",
- "# Compute reservoir concentrations\n",
- "flux_vals = [flux_to_reservoir(ssys.sims[1], t, diffusionlayer) for t in t_vals]\n",
- "\n",
- "conc_vals_bl = [concentrations(ssys.sims[1], t) for t in t_vals]\n",
- "flux_matrix = hcat(flux_vals...);\n",
- "conc_matrix_bl = hcat(conc_vals_bl...);\n"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 274,
- "id": "1b8bc2d2",
- "metadata": {},
- "outputs": [],
- "source": [
- "conc_0 = concentrations(ssys.sims[1], 0)\n",
- "t_vals_2 = 10 .^ range(-9, stop=3, length=130);\n",
- "conc_vals = [get_reservoir_concentration(ssys.sims[1], t, diffusionlayer, V_res, conc_0) for t in t_vals_2]\n",
- "conc_matrix = hcat(conc_vals...);"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 275,
- "id": "543fe758",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "plotC_Reservoir (generic function with 1 method)"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "function plotC_Reservoir(sim, cs, tvals, tol, exclude)\n",
- " clf()\n",
- " xs = cs\n",
- " maxes = maximum(xs, dims=2)\n",
- "\n",
- " time_filtered = tvals\n",
- " xs_filtered = xs\n",
- "\n",
- " # Custom species order and their corresponding names and color\n",
- " species_order = [\"CO2\", \"proton\", \"H2\", \"O=CO\", \"C=O\", \"CO-2\", \"CCO\", \"CH4\", \"OCO\", \"COC\", \"COCO\", \"CC(=O)O\", \"OCCO\"]\n",
- " color_map = Dict(\"CO2\" => \"black\", \"proton\" => \"grey\", \"H2\" => \"green\",\n",
- " \"O=CO\" => \"red\", \"C=O\" => \"brown\", \"CO-2\" => \"blue\", \"CCO\" => \"magenta\",\n",
- " \"CH4\" => \"brown\", \"OCO\" => \"orange\", \"COC\" => \"teal\", \"COCO\" => \"lime\", \"CC(=O)O\" => \"teal\", \"OCCO\" => \"lime\")\n",
- " # Replacement map for species labels\n",
- " replacement_map = Dict(\"CO-2\" => \"CH3OH\", \"O=CO\" => \"HCOOH\", \"C=O\" => \"HCHO\",\n",
- " \"CCO\" => \"C2H5OH\", \"OCO\" => \"CH2(OH)2\", \"COC\" => \"CH3OCH3\", \"COCO\" => \"CH3OCH2OH\", \"CC(=O)O\" => \"CH3COOH\", \"OCCO\" => \"OHCH2CH2OH\")\n",
- "\n",
- " # Build a map of species names to indices\n",
- " name_to_index = Dict(sim.domain.phase.species[i].name => i for i in 1:length(sim.domain.phase.species))\n",
- " # Keep track of whether the species is plotted, used for later checks\n",
- " plotted = falses(length(sim.domain.phase.species))\n",
- "\n",
- " # Plot species from the custom species dictionary\n",
- " for species_name in species_order\n",
- " if species_name in exclude\n",
- " continue\n",
- " end\n",
- "\n",
- " if haskey(name_to_index, species_name)\n",
- " i = name_to_index[species_name]\n",
- "\n",
- " if (maxes[i] > tol) || (species_name == \"proton\") || (species_name == \"CCO\") # Always plot proton and ethanol\n",
- " plot_label = get(replacement_map, species_name, species_name)\n",
- " plot_color = color_map[species_name]\n",
- "\n",
- " plot(time_filtered, xs_filtered[i, :]/1000, label=plot_label, color=plot_color)\n",
- " plotted[i] = true # Mark as plotted\n",
- " end\n",
- " end\n",
- " end\n",
- "\n",
- " # Plot any remaining species that passed tolerance but were not in species_order\n",
- " for i in 1:length(sim.domain.phase.species)\n",
- " if plotted[i] || sim.domain.phase.species[i].name in exclude\n",
- " continue\n",
- " end\n",
- "\n",
- " if maxes[i] > tol\n",
- " species_name = sim.domain.phase.species[i].name\n",
- " plot(time_filtered, xs_filtered[i, :]/1000, label=species_name) # Default color\n",
- " end\n",
- " end\n",
- "\n",
- " xlabel(\"Time (s)\", fontsize=14)\n",
- " ylabel(\"Bulk Concentration (mol/L)\", fontsize=14)\n",
- " xticks(fontsize=14)\n",
- " yticks(fontsize=14)\n",
- " legend(loc=\"upper left\", bbox_to_anchor=(0, 0.9), fontsize=12, ncol=2)\n",
- "end"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 276,
- "id": "1a6e5f63",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "export_final_molefractions! (generic function with 1 method)"
- ]
- },
- "metadata": {},
- "output_type": "display_data"
- }
- ],
- "source": [
- "function export_final_molefractions!(conc_matrix, ssys, phi; filename=\"final_molefractions.csv\")\n",
- " # species of interest\n",
- " species_list = [\"O=CO\", \"H2\", \"CO\", \"CO-2\", \"C=O\", \"CC(=O)O\"]\n",
- "\n",
- " # map species name → index\n",
- " name_to_index = Dict(ssys.sims[1].domain.phase.species[i].name => i\n",
- " for i in 1:length(ssys.sims[1].domain.phase.species))\n",
- "\n",
- " # extract final concentrations and normalize\n",
- " final_concs = [conc_matrix[name_to_index[sp], end] for sp in species_list]\n",
- " molefracs = final_concs ./ sum(final_concs)\n",
- "\n",
- " phi_label = round(phi + 0.414; digits=2);\n",
- " col_name = string(phi_label)\n",
- "\n",
- " # create or update CSV\n",
- " if isfile(filename)\n",
- " df = CSV.read(filename, DataFrame)\n",
- " else\n",
- " df = DataFrame(Species = species_list)\n",
- " end\n",
- "\n",
- " # insert or update the new column labeled by φ\n",
- " df[!, col_name] = molefracs;\n",
- "\n",
- " CSV.write(filename, df)\n",
- " println(\"✅ Appended mole fractions for φ = $(phi) V to $(filename)\")\n",
- " return df\n",
- "end\n"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 277,
- "id": "9078fcd8",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "✅ Appended mole fractions for φ = -1.784 V to final_molefractions.csv\n"
- ]
- },
- {
- "data": {
- "text/html": [
- "| Row | Species | -0.77 | -0.97 | -1.17 | -1.37 |
|---|
| String7 | Float64 | Float64 | Float64 | Float64 |
|---|
| 1 | O=CO | 0.992779 | 0.949798 | 0.304264 | 0.00858474 |
| 2 | H2 | 0.000156093 | 0.0368266 | 0.694185 | 0.991415 |
| 3 | CO | 6.64579e-19 | 5.57168e-19 | 1.81049e-19 | 1.39735e-21 |
| 4 | CO-2 | 1.55232e-7 | 1.38659e-5 | 0.000232847 | 1.86322e-7 |
| 5 | C=O | 0.00701882 | 0.0127002 | 0.0012945 | 2.93285e-7 |
| 6 | CC(=O)O | 4.58797e-5 | 0.000661208 | 2.38637e-5 | 1.49172e-10 |
| Row | Species | -0.77 | -0.97 | -1.17 | -1.37 |
|---|
| String7 | Float64 | Float64 | Float64 | Float64 |
|---|
| 1 | O=CO | 0.992779 | 0.949798 | 0.304264 | 0.00858474 |
| 2 | H2 | 0.000156093 | 0.0368266 | 0.694185 | 0.991415 |
| 3 | CO | 6.65e-19 | 5.57e-19 | 1.81e-19 | 1.4e-21 |
| 4 | CO-2 | 1.55e-7 | 1.39e-5 | 0.000232847 | 1.86e-7 |
| 5 | CCO | 0.0 | 0.0 | 0.0 | 0.0 |
| 6 | C=O | 0.00701882 | 0.0127002 | 0.00129451 | 2.93e-7 |
| 7 | O=CO | 0.0129667 | 0.0488 | 0.0374667 | 0.012 |
| 8 | H2 | 0.5892 | 0.431465 | 0.780133 | 0.925637 |
| 9 | CO | 0.248133 | 0.383089 | 0.179367 | 0.0159759 |
| 10 | CO-2 | 0.0036 | 0.0 | 0.00146667 | 0.0 |
| 11 | CCO | 0.0 | 0.0 | 0.0134333 | 0.0 |
| 12 | C=O | 0.0 | 0.0 | 0.0 | 0.0 |