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Merge pull request #273 from ReactionMechanismGenerator/rmg_new
Integrating Bugfixes and Improvements from the for_rmg branch
2 parents 539956e + ba722b1 commit 74e04f2

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‎.github/workflows/CI.yml‎

Lines changed: 7 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -11,20 +11,15 @@ jobs:
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runs-on: ubuntu-latest
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steps:
1313
- uses: actions/checkout@v4
14-
- uses: julia-actions/setup-julia@v1
14+
- name: Setup Juliaup
15+
uses: julia-actions/install-juliaup@v2
1516
with:
16-
version: '1.10'
17-
- uses: actions/cache@v1
18-
env:
19-
cache-name: cache-artifacts
20-
with:
21-
path: ~/.julia/artifacts
22-
key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
23-
restore-keys: |
24-
${{ runner.os }}-test-${{ env.cache-name }}-
25-
${{ runner.os }}-test-
26-
${{ runner.os }}-
17+
channel: '1.10'
18+
19+
- uses: julia-actions/cache@v2
20+
2721
- uses: julia-actions/julia-buildpkg@v1
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- name: Build
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run: |
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current_path=${{ github.workspace }}

‎.github/workflows/documentation.yml‎

Lines changed: 9 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -13,10 +13,16 @@ jobs:
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contents: write
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
17-
- uses: julia-actions/setup-julia@latest
16+
- uses: actions/checkout@v4
17+
- name: Setup Juliaup
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uses: julia-actions/install-juliaup@v2
1819
with:
19-
version: '1.10'
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channel: '1.10'
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22+
- uses: julia-actions/cache@v2
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24+
- uses: julia-actions/julia-buildpkg@v1
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- name: Install dependencies
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run: |
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current_path=${{ github.workspace }}

‎src/EdgeAnalysis.jl‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1037,8 +1037,10 @@ function selectobjects(react,edgereact,coreedgedomains,coreedgeinters,domains,in
10371037
dydt,rts,frts,rrts,cs,corespeciesrates,charrate,edgespeciesrates,edgereactionrates,edgerxnradrateratios,
10381038
corespeciesrateratios,edgespeciesrateratios,corereactionrates,corespeciesconcentrations,
10391039
corespeciesproductionrates,corespeciesconsumptionrates = processfluxes(sim,corespcsinds,corerxninds,edgespcsinds,edgerxninds)
1040-
@inbounds ind = edgespcsinds[argmax(edgespeciesrates)]
1041-
@inbounds invalidobjects = [sim.species[ind]]
1040+
if !isempty(edgespeciesrates)
1041+
@inbounds ind = edgespcsinds[argmax(edgespeciesrates)]
1042+
@inbounds invalidobjects = [sim.species[ind]]
1043+
end
10421044
return (terminated,true,invalidobjects,unimolecularthreshold,
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bimolecularthreshold,trimolecularthreshold,maxedgespeciesrateratios,t,conversion)
10441046
end

‎src/Initialization.jl‎

Lines changed: 54 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,54 @@
1+
using PythonCall
2+
using CondaPkg
3+
4+
function checkmolecule()
5+
has_rmgpy = try; PythonCall.pyimport("rmgpy"); true; catch e; false; end
6+
has_rmgmolecule = try; PythonCall.pyimport("molecule"); true; catch e; false; end
7+
return has_rmgpy,has_rmgmolecule
8+
end
9+
10+
function installmolecule()
11+
if !(v"3.7" <= PythonCall.C.python_version() && PythonCall.C.python_version() <= v"3.9")
12+
@info "python version was not in 3.7-3.9 changing python version"
13+
CondaPkg.add("python"; version=">=3.9",resolve=false)
14+
end
15+
16+
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
17+
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
18+
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
19+
CondaPkg.add("pydot", channel="conda-forge",resolve=false,version=">=2.0")
20+
CondaPkg.resolve()
21+
end
22+
23+
function loadsubmodules()
24+
include("Constants.jl")
25+
include("Tools.jl")
26+
include("Calculators/RateUncertainty.jl")
27+
include("Calculators/ThermoUncertainty.jl")
28+
include("Calculators/Thermo.jl")
29+
include("Calculators/Diffusion.jl")
30+
include("Calculators/Rate.jl")
31+
include("Calculators/Viscosity.jl")
32+
include("Calculators/Thermovec.jl")
33+
include("Calculators/Ratevec.jl")
34+
include("Calculators/kLAkH.jl")
35+
include("Species.jl")
36+
include("Solvent.jl")
37+
include("Reaction.jl")
38+
include("Phase.jl")
39+
include("PhaseState.jl")
40+
include("Interface.jl")
41+
include("Domain.jl")
42+
include("yml.jl")
43+
include("Parse.jl")
44+
include("ModelReduction.jl")
45+
include("Reactor.jl")
46+
include("ThreadedSensitivities.jl")
47+
include("Simulation.jl")
48+
include("TransitorySensitivities.jl")
49+
include("AutomaticMechanismAnalysis.jl")
50+
include("EdgeAnalysis.jl")
51+
include("Debugging.jl")
52+
include("Plotting.jl")
53+
include("fluxdiagrams.jl")
54+
end

‎src/ReactionMechanismSimulator.jl‎

Lines changed: 8 additions & 53 deletions
Original file line numberDiff line numberDiff line change
@@ -1,31 +1,15 @@
11
module ReactionMechanismSimulator
2-
ENV["JULIA_CONDAPKG_BACKEND"] = "MicroMamba"
32
using CondaPkg
43
using Logging
5-
packages = keys(CondaPkg.current_packages())
4+
using PythonCall
5+
6+
include("Initialization.jl")
7+
8+
has_rmgpy,has_rmgmolecule = checkmolecule()
69

7-
if !("rmg" in packages) && !("rmgmolecule" in packages)
10+
if !has_rmgpy && !has_rmgmolecule
811
@info "missing rmg and rmgmolecule installing rmgmolecule..."
9-
if "python" in packages
10-
py_version = VersionNumber(CondaPkg.current_packages()["python"][:version])
11-
else
12-
py_version = nothing
13-
end
14-
if py_version === nothing || !(v"3.7" <= py_version && py_version <= v"3.9")
15-
@info "python version was not in 3.7-3.9 changing python version"
16-
CondaPkg.add("python"; version="3.9",resolve=false)
17-
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
18-
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
19-
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
20-
CondaPkg.add("pydot", channel="conda-forge",resolve=false,version=">=2.0")
21-
CondaPkg.resolve()
22-
else
23-
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
24-
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
25-
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
26-
CondaPkg.add("pydot", channel="conda-forge",resolve=false,version=">=2.0")
27-
CondaPkg.resolve()
28-
end
12+
installmolecule()
2913
end
3014

3115
using PythonCall
@@ -74,34 +58,5 @@ function __init__()
7458
end
7559
PythonCall.pycopy!(pydot, pyimport("pydot"))
7660
end
77-
include("Constants.jl")
78-
include("Tools.jl")
79-
include("Calculators/RateUncertainty.jl")
80-
include("Calculators/ThermoUncertainty.jl")
81-
include("Calculators/Thermo.jl")
82-
include("Calculators/Diffusion.jl")
83-
include("Calculators/Rate.jl")
84-
include("Calculators/Viscosity.jl")
85-
include("Calculators/Thermovec.jl")
86-
include("Calculators/Ratevec.jl")
87-
include("Calculators/kLAkH.jl")
88-
include("Species.jl")
89-
include("Solvent.jl")
90-
include("Reaction.jl")
91-
include("Phase.jl")
92-
include("PhaseState.jl")
93-
include("Interface.jl")
94-
include("Domain.jl")
95-
include("yml.jl")
96-
include("Parse.jl")
97-
include("ModelReduction.jl")
98-
include("Reactor.jl")
99-
include("ThreadedSensitivities.jl")
100-
include("Simulation.jl")
101-
include("TransitorySensitivities.jl")
102-
include("AutomaticMechanismAnalysis.jl")
103-
include("EdgeAnalysis.jl")
104-
include("Debugging.jl")
105-
include("Plotting.jl")
106-
include("fluxdiagrams.jl")
61+
loadsubmodules()
10762
end

‎src/rmstest.jl‎

Lines changed: 13 additions & 58 deletions
Original file line numberDiff line numberDiff line change
@@ -1,75 +1,30 @@
11
import Logging
22
Logging.disable_logging(Logging.Warn)
3-
ENV["JULIA_CONDAPKG_BACKEND"] = "MicroMamba"
43
using CondaPkg
4+
using PythonCall
5+
6+
include("Initialization.jl")
57

6-
packages = keys(CondaPkg.current_packages())
8+
has_rmgpy,has_rmgmolecule = checkmolecule()
79

8-
if !("rmg" in packages) && !("rmgmolecule" in packages)
10+
if !has_rmgpy && !has_rmgmolecule
911
@info "missing rmg and rmgmolecule installing rmgmolecule..."
10-
if "python" in packages
11-
py_version = VersionNumber(CondaPkg.current_packages()["python"][:version])
12-
else
13-
py_version = nothing
14-
end
15-
if py_version === nothing || !(v"3.7" <= py_version && py_version <= v"3.9")
16-
@info "python version was not in 3.7-3.9 changing python version"
17-
CondaPkg.add("python"; version="3.9",resolve=false)
18-
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
19-
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
20-
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
21-
CondaPkg.add("pydot", channel="conda-forge",resolve=false,version=">=2.0")
22-
CondaPkg.resolve()
23-
else
24-
CondaPkg.add("rmgmolecule"; version=">=0.3.0", channel="mjohnson541",resolve=false)
25-
CondaPkg.add("matplotlib", channel="conda-forge",resolve=false)
26-
CondaPkg.add("rdkit", channel="conda-forge",resolve=false)
27-
CondaPkg.add("pydot", channel="conda-forge",resolve=false,version=">=2.0")
28-
CondaPkg.resolve()
29-
end
12+
installmolecule()
3013
end
3114

32-
using PythonCall
33-
3415
const Chem = PythonCall.pynew()
3516
const molecule = PythonCall.pynew()
3617
const fragment = PythonCall.pynew()
3718
const pydot = PythonCall.pynew()
3819

39-
PythonCall.pycopy!(Chem, pyimport("rdkit.Chem"))
20+
PythonCall.pycopy!(Chem, PythonCall.pyimport("rdkit.Chem"))
4021
try
41-
PythonCall.pycopy!(molecule, pyimport("rmgpy.molecule"))
42-
PythonCall.pycopy!(fragment, pyimport("rmgpy.molecule.fragment"))
22+
PythonCall.pycopy!(molecule, PythonCall.pyimport("rmgpy.molecule"))
23+
PythonCall.pycopy!(fragment, PythonCall.pyimport("rmgpy.molecule.fragment"))
4324
catch e
44-
PythonCall.pycopy!(molecule, pyimport("molecule.molecule"))
45-
PythonCall.pycopy!(fragment, pyimport("molecule.molecule.fragment"))
25+
PythonCall.pycopy!(molecule, PythonCall.pyimport("molecule.molecule"))
26+
PythonCall.pycopy!(fragment, PythonCall.pyimport("molecule.molecule.fragment"))
4627
end
47-
PythonCall.pycopy!(pydot, pyimport("pydot"))
28+
PythonCall.pycopy!(pydot, PythonCall.pyimport("pydot"))
4829

49-
include("Constants.jl")
50-
include("Tools.jl")
51-
include("Calculators/RateUncertainty.jl")
52-
include("Calculators/ThermoUncertainty.jl")
53-
include("Calculators/Thermo.jl")
54-
include("Calculators/Diffusion.jl")
55-
include("Calculators/Rate.jl")
56-
include("Calculators/Viscosity.jl")
57-
include("Calculators/kLAkH.jl")
58-
include("Species.jl")
59-
include("Solvent.jl")
60-
include("Reaction.jl")
61-
include("Phase.jl")
62-
include("PhaseState.jl")
63-
include("Interface.jl")
64-
include("Domain.jl")
65-
include("Parse.jl")
66-
include("ModelReduction.jl")
67-
include("Reactor.jl")
68-
include("ThreadedSensitivities.jl")
69-
include("Simulation.jl")
70-
include("TransitorySensitivities.jl")
71-
include("AutomaticMechanismAnalysis.jl")
72-
include("Debugging.jl")
73-
include("EdgeAnalysis.jl")
74-
include("Plotting.jl")
75-
include("fluxdiagrams.jl")
30+
loadsubmodules()

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