Merge pull request #196 from ReactionMechanismGenerator/transitoryedge

Transitory Edge Analysis

Author: mjohnson541

.github/workflows/CI.yml

@@ -24,10 +24,15 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - uses: julia-actions/julia-buildpkg@v1
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          environment-file: environment.yml
+          python-version: 3.7
+          activate-environment: rms_env
       - name: Fix PyCall linking
         run: |
-            julia -e 'ENV["PYTHON"]="/home/runner/.julia/conda/3/bin/python"; using Pkg; Pkg.add("PyCall"); Pkg.build("PyCall")'
+            julia -e 'ENV["PYTHON"]=ENV["CONDA"] * "/envs/rms_env/bin/python"; using Pkg; Pkg.add("PyCall"); Pkg.build("PyCall")'
+      - uses: julia-actions/julia-buildpkg@v1
       - name: Build
         run: |
             julia -e 'using Pkg; Pkg.add(PackageSpec(name="StochasticDiffEq",version="6.36.0")); Pkg.develop(PackageSpec(path="../ReactionMechanismSimulator.jl")); Pkg.build("ReactionMechanismSimulator");'

.github/workflows/documentation.yml

@@ -15,15 +15,14 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: 1.6
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          environment-file: environment.yml
+          python-version: 3.7
+          activate-environment: rms_env
       - name: Install dependencies
         run: |
-            wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-            bash miniconda.sh -b -p $HOME/miniconda
-            export PATH=$HOME/miniconda/bin:$PATH
-            conda create -n conda_jl --yes python=3.7 conda
-            source activate conda_jl
-            conda install -c rmg --yes rmg
-            conda update --yes conda
+            julia -e 'ENV["PYTHON"]=ENV["CONDA"] * "/envs/rms_env/bin/python"; using Pkg; Pkg.add("PyCall"); Pkg.build("PyCall")'
             julia --project=docs/ -e 'using Pkg; Pkg.add(PackageSpec(name="StochasticDiffEq",version="6.36.0")); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate();'
       - name: Build and deploy
         env:

environment.yml

@@ -0,0 +1,9 @@
+name: rms_env
+channels:
+  - defaults
+  - rmg
+dependencies:
+  - rdkit
+  - rmg
+  - pydot
+  - yaml

src/EdgeAnalysis.jl

@@ -44,13 +44,13 @@ function IdealGas(species,reactions; name="",diffusionlimited=false)
     echangevec = getfield.(rxns,:electronchange)
     if all(echangevec .== 0)
         electronchange = nothing
-    else 
+    else
         electronchange = convert(echangevec,Array{Float64,1})
     end
     reversibility = getfield.(rxns,:reversible)
     return IdealGas(species=species,reactions=rxns,name=name,
-        spcdict=Dict([sp.name=>i for (i,sp) in enumerate(species)]),stoichmatrix=M,Nrp=Nrp,rxnarray=rxnarray,veckinetics=vectuple, 
-        veckineticsinds=posinds, vecthermo=therm, otherreactions=otherrxns, electronchange=electronchange, 
+        spcdict=Dict([sp.name=>i for (i,sp) in enumerate(species)]),stoichmatrix=M,Nrp=Nrp,rxnarray=rxnarray,veckinetics=vectuple,
+        veckineticsinds=posinds, vecthermo=therm, otherreactions=otherrxns, electronchange=electronchange,
         reversibility=reversibility,diffusionlimited=diffusionlimited,)
 end
 export IdealGas
@@ -84,7 +84,7 @@ function IdealDiluteSolution(species,reactions,solvent; name="",diffusionlimited
     echangevec = getfield.(rxns,:electronchange)
     if all(echangevec .== 0)
         electronchange = nothing
-    else 
+    else
         electronchange = convert(echangevec,Array{Float64,1})
     end
     reversibility = getfield.(rxns,:reversible)
@@ -125,7 +125,7 @@ function IdealSurface(species,reactions,sitedensity;name="",diffusionlimited=fal
     echangevec = getfield.(rxns,:electronchange).*F
     if all(echangevec .== 0)
         electronchange = nothing
-    else 
+    else
         electronchange = convert(typeof(Nrp),echangevec)
     end
     reversibility = getfield.(rxns,:reversible)
@@ -209,7 +209,7 @@ function getveckinetics(rxns)
             push!(fs,x)
             if posinds == Array{Int64,1}()
                 push!(posinds,length(rinds))
-            else 
+            else
                 push!(posinds,length(rinds)+posinds[end])
             end
         end
@@ -277,7 +277,9 @@ function getreactionindices(spcs,rxns) where {Q<:AbstractPhase}
             end
             for (key,val) in rxn.kinetics.nameefficiencies
                 ind = findfirst(isequal(key),names)
-                rxn.kinetics.efficiencies[ind] = val
+                if !(ind === nothing)
+                    rxn.kinetics.efficiencies[ind] = val
+                end
             end
         end
     end

src/Phase.jl

@@ -17,8 +17,8 @@ module ReactionMechanismSimulator
     const yaml = PyNULL()
     const os = PyNULL()
     function __init__()
-        copy!(Chem,pyimport_conda("rdkit.Chem","rdkit","rdkit"))
-        copy!(Desc,pyimport_conda("rdkit.Chem.Descriptors","rdkit","rdkit"))
+        copy!(Chem,pyimport_conda("rdkit.Chem","rdkit","rmg"))
+        copy!(Desc,pyimport_conda("rdkit.Chem.Descriptors","rdkit","rmg"))
         copy!(molecule,pyimport_conda("rmgpy.molecule","rmg","rmg"))
         copy!(pydot,pyimport_conda("pydot","pydot"))
         copy!(chemkin,pyimport_conda("rmgpy.chemkin","rmg","rmg"))

src/ReactionMechanismSimulator.jl

@@ -52,11 +52,10 @@ using Sundials
     coredomain,y0,corep = ConstantTPDomain(phase=coregas,initialconds=initialconds);
     react = Reactor(coredomain,y0,(0.0,1e6);p=corep);
     coreedgedomain,coreedgey0,coreedgep = ConstantTPDomain(phase=coreedgegas,initialconds=initialconds);
-    
+    reactedge = Reactor(coreedgedomain,coreedgey0,(0.0,1e6);p=coreedgep);
     (terminated,resurrected,invalidobjects,unimolecularthreshold,bimolecularthreshold,
-    trimolecularthreshold,maxedgespeciesrateratios) = selectobjects(react,coreedgedomain,[],coredomain,
-        [],corep,coreedgep,0.03,0.03,false,true,5,0.005,1.0,1.0,true,termination,1.0e8)
-        
+    trimolecularthreshold,maxedgespeciesrateratios) = selectobjects(react,reactedge,coreedgedomain,[],coredomain,
+        [],corep,coreedgep,0.03,0.03,false,true,5,0.005,1.0,1.0,true,termination,1.0e8,Dict(),20)
     @test terminated == false
     @test invalidobjects[1].name == "[CH2]CCC"
     @test unimolecularthreshold[5] == true