No method matching species error

[vkeerth]

While trying to run the simulation for Steam methane reforming (examples/rmg/catalysis/methane_steam) example of RMG software using RMS in Jupyter notebook (Julia 1.6.0), the following error always pops up for the code;

Code: phaseDict = readinput("rms/chem76.rms")

Error: MethodError: no method matching Species(; index=23, name="site", adjlist="1 X u0 p0 c0\n\n", radicalelectrons=0, thermo=NASA{EmptyThermoUncertainty} polys: Array{NASApolynomial}((2,)) unc: EmptyThermoUncertainty EmptyThermoUncertainty() , smiles="[Pt]")

I have attached the word document of the rms file. Can someone guide me? Chem76 file: chem76.docx

[mjohnson541]

Sorry, I must've missed when this got posted. Is this still an issue? Can you send the full error trace?

[vkeerth]

Yes, thanks for getting back. Please find the pdf file attached. Untitled1_using_Julia.pdf

[mjohnson541]

Hmm...I'm having difficulty reproducing this issue. What versions of RMS and RMG are you on? Can you send me the exact .rms file (not pasted into a docx)?

[vkeerth]

RMG version: 3.1.0 pyrms downloaded from: https://github.com/ReactionMechanismGenerator/pyrms

I have attached all the rms files of methane_steam into the zip file below. RMS.zip

[mjohnson541]

Hmm...I'm not getting this issue on RMS master and I don't think you should be getting this on the latest release v0.4.0 so I suspect the RMS version your pyrms has installed is too old. Try running in the command line:

julia -e 'using Pkg; Pkg.update("ReactionMechanismSimulator")'

[vkeerth]

When I run this command, 5 of the files do not get compiled (including ReactionMechanismSimulator). So when I run the code in jupyter notebook I get the following error:

Failed to precompile DifferentialEquations [0c46a032-eb83-5123-abaf-570d42b7fbaa] to /home/keerths/anaconda3/envs/rms_env/share/julia/site/compiled/v1.6/DifferentialEquations/jl_0LEqoK.

Stacktrace: [1] error(s::String) @ Base ./error.jl:33 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IJulia.IJuliaStdio{Base.PipeEndpoint}, internal_stdout::IJulia.IJuliaStdio{Base.PipeEndpoint}) @ Base ./loading.jl:1360 [3] compilecache(pkg::Base.PkgId, path::String) @ Base ./loading.jl:1306 [4] _require(pkg::Base.PkgId) @ Base ./loading.jl:1021 [5] require(uuidkey::Base.PkgId) @ Base ./loading.jl:914 [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:901 [7] eval @ ./boot.jl:360 [inlined] [8] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String) @ Base ./loading.jl:1094

I have attached the jupyter notebook file for your reference. jupyter file.zip

Could you please guide me. Thank you.

[mjohnson541]

Try opening the julia repl with julia and then running ]add StochasticDiffEq@6.36.0