Merge pull request #154 from ReactionMechanismGenerator/new_interface

New interfaces & fix Outlet jacobiany for several domains

Author: mjohnson541

.DS_Store

@@ -2,18 +2,18 @@ name: CI
 on:
   pull_request:
     branches:
-      - master
+      - main
   push:
     branches:
-      - master
+      - main
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
-          version: 1.5
+          version: 1.6
       - uses: actions/cache@v1
         env:
           cache-name: cache-artifacts
@@ -30,7 +30,7 @@ jobs:
             julia -e 'ENV["PYTHON"]="/home/runner/.julia/conda/3/bin/python"; using Pkg; Pkg.add("PyCall"); Pkg.build("PyCall")'
       - name: Build
         run: |
-            julia -e 'using Pkg; Pkg.add(PackageSpec(name="StochasticDiffEq",version="6.36.0")); Pkg.develop(PackageSpec(path="../ReactionMechanismSimulator.jl"));'
+            julia -e 'using Pkg; Pkg.add(PackageSpec(name="StochasticDiffEq",version="6.36.0")); Pkg.develop(PackageSpec(path="../ReactionMechanismSimulator.jl")); Pkg.build("ReactionMechanismSimulator");'
       - name: Run tests
         run: |
             julia -e 'using Pkg; Pkg.test("ReactionMechanismSimulator";coverage=true)'

.github/workflows/CI.yml

@@ -3,7 +3,7 @@ name: Documentation
 on:
   push:
     branches:
-      - master
+      - main
     tags: '*'
   pull_request:
 

.github/workflows/documentation.yml

@@ -2,3 +2,4 @@
 *.png
 *.dot
 docs/build/
+.DS_Store

.gitignore

@@ -43,7 +43,7 @@ Calculus = "0.4,0.5"
 Colors = "0.11,0.12"
 Conda = "1"
 DiffEqBase = "6"
-DiffEqSensitivity = "6.22.0"
+DiffEqSensitivity = "6"
 ForwardDiff = "0.10"
 Images = "0.23"
 IterTools = "1.3.0"
@@ -64,4 +64,4 @@ Tracker = "0.2"
 Unitful = "1.3.0"
 YAML = "0.4"
 Zygote = "0.5,0.6"
-julia = "1.4"
+julia = "1.6"

Project.toml

@@ -389,14 +389,14 @@ Generate a string report from the analysis objects
 function getrxnanalysisstring(sim,ra;branchingcutoff=1e-2,radbranchfract=0.01)
     spcname = sim.names[ra.spcind]
     rstr = getrxnstr(sim.domain.phase.reactions[ra.rxnind])
-    sens = ra.sens
+    sens = round(ra.sens,sigdigits=6)
     s = "Analyzing $spcname sensitivity to $rstr at a value of $sens \n"
     s *= "\n"
     for branch in ra.branchings
         sname = sim.names[branch.spcind]
         s *= "Key branching for $sname \n"
         for i = 1:length(branch.rxninds)+1
-            br = branch.branchingratios[i]
+            br = round(branch.branchingratios[i],sigdigits=6)
             if br < branchingcutoff
                 break
             else
@@ -414,22 +414,22 @@ function getrxnanalysisstring(sim,ra;branchingcutoff=1e-2,radbranchfract=0.01)
             s *= "Associated key reaction path in $spname loss direction \n"
             for i = 1:length(rp.rxninds)
                 rstr = getrxnstr(sim.reactions[rp.rxninds[i]])
-                br = rp.branchfracts[i]
+                br = round(rp.branchfracts[i],sigdigits=6)
                 s *= "$rstr at path branching of $br \n"
             end
         else
             s *= "Associated key reaction path in $spname production direction \n"
             revinds = reverse(rp.rxninds)
             for i = 1:length(rp.rxninds)
                 rstr = getrxnstr(sim.reactions[revinds[i]])
-                br = rp.branchfracts[i]
+                br = round(rp.branchfracts[i],sigdigits=6)
                 s *= "$rstr at path step branching of $br \n"
             end
         end
         s *= "\n"
     end
     if abs(ra.radprodlossfract) > radbranchfract
-        radfract = abs(ra.radprodlossfract)
+        radfract = round(abs(ra.radprodlossfract),sigdigits=6)
         if ra.radprodlossfract > 0
             s *= "Reaction accounts for $radfract of the net radical production \n"
         else

src/AutomaticMechanismAnalysis.jl

@@ -0,0 +1,49 @@
+using Parameters
+
+abstract type AbstractHenryLawConstant end
+export AbstractHenryLawConstant
+
+struct EmptyHenryLawConstant <: AbstractHenryLawConstant end
+(eh::EmptyHenryLawConstant)(;T::N) where {N<:Number} = Inf
+export EmptyHenryLawConstant
+
+@with_kw struct ConstantHenryLawConstant{N<:Number} <: AbstractHenryLawConstant
+    kH::N
+end
+(ch::ConstantHenryLawConstant)(;T::N) where {N<:Number} = ch.kH
+export ConstantHenryLawConstant
+
+struct TemperatureDependentHenryLawConstant{N<:Function} <: AbstractHenryLawConstant
+    kH::N
+end
+
+function TemperatureDependentHenryLawConstant(;Ts::N1,kHs::N2) where {N1<:AbstractArray,N2<:AbstractArray}
+    return TemperatureDependentHenryLawConstant(getspline(Ts,kHs))
+end
+
+(th::TemperatureDependentHenryLawConstant)(;T::N) where {N<:Number} = th.kH(T)
+export TemperatureDependentHenryLawConstant
+
+abstract type AbstractLiquidVolumetricMassTransferCoefficient end
+export AbstractLiquidVolumetricMassTransferCoefficient
+
+struct EmptyLiquidVolumetricMassTransferCoefficient <: AbstractLiquidVolumetricMassTransferCoefficient end
+(eh::EmptyLiquidVolumetricMassTransferCoefficient)(;T::N) where {N<:Number} = 0
+export EmptyLiquidVolumetricMassTransferCoefficient
+
+@with_kw struct ConstantLiquidVolumetricMassTransferCoefficient{N<:Number} <: AbstractLiquidVolumetricMassTransferCoefficient
+    kLA::N
+end
+(cv::ConstantLiquidVolumetricMassTransferCoefficient)(;T::N) where {N<:Number} = cv.kLA
+export ConstantLiquidVolumetricMassTransferCoefficient
+
+struct TemperatureDependentLiquidVolumetricMassTransferCoefficient{N<:Function} <: AbstractLiquidVolumetricMassTransferCoefficient 
+    kLA::N
+end
+
+function TemperatureDependentLiquidVolumetricMassTransferCoefficient(;Ts::N1,kLAs::N2) where {N1<:AbstractArray,N2<:AbstractArray}
+    return TemperatureDependentLiquidVolumetricMassTransferCoefficient(getspline(Ts,kLAs)) 
+end
+
+(tv::TemperatureDependentLiquidVolumetricMassTransferCoefficient)(;T::N) where {N<:Number} = tv.kLA(T)
+export TemperatureDependentLiquidVolumetricMassTransferCoefficient