CA with production

[jhidding]

Burgess2013 model with only CA and production

[NiklasHohmann]

Please provide some documentation on the contents of the output files. The hdf5 file is currently a large 4d array. From context it is clear to me which dimension corresponds to the facies, time step, and spatial coordinates. However, I think it'd be best of this info is directly associated with the array, so the interpretation of the data independent is not dependent on the contextual knowledge of the examiner

[NiklasHohmann]

I run into an issue while precompiling the dependencies. I get the error

ERROR: The following 1 direct dependency failed to precompile:

LanguageServer [2b0e0bc5-e4fd-59b4-8912-456d1b03d8d7]

Error: Missing source file for LanguageServer [2b0e0bc5-e4fd-59b4-8912-456d1b03d8d7

(CarboKitten) pkg> resolve
ERROR: expected package `LanguageServer [2b0e0bc5]` to exist at path `\home\johannes\.julia\dev\LanguageServer`

which seems to be due to a hardcoded path in manifest.toml

[jhidding]

I run into an issue while precompiling the dependencies. I get the error

ERROR: The following 1 direct dependency failed to precompile:

LanguageServer [2b0e0bc5-e4fd-59b4-8912-456d1b03d8d7]

Error: Missing source file for LanguageServer [2b0e0bc5-e4fd-59b4-8912-456d1b03d8d7

(CarboKitten) pkg> resolve
ERROR: expected package `LanguageServer [2b0e0bc5]` to exist at path `\home\johannes\.julia\dev\LanguageServer`

which seems to be due to a hardcoded path in manifest.toml

This is so annoying. I'm guessing VS Code is adding this entry

[EmiliaJarochowska]

I had the same but other than giving an error message it doesn't actually interfere with running, at least the examples 🤷‍♀️

[EmiliaJarochowska]

One weird thing that happens to me is if I run:

julia> include("examples/plot-caps-osc.jl")
ERROR: error in method definition: function CaProd.main must be explicitly imported to be extended

and include("src/CaProd.jl") doesn't help, but if I open and run CaProd.jl in VS Code using Julia: Execute active File in REPL, then CaProd.main is imported and I can run include("examples/plot-caps-osc.jl") 🤷‍♀️

[EmiliaJarochowska]

Nice idea, but are the plots the benchmark for comparing the output for different settings of CA? I found the plot very hard to read but maybe I miss something.

[jhidding]

It's just not done yet ;)

[NiklasHohmann]

Adjust README

• use template funding info & author info from template repository in the MtG orga
• add repo structure with brief descriptions of what does what
• correct typo in schlager (there is an h missing in the README)

[NiklasHohmann]

• Add minimum running instructions for ca-with-production. As is, it is not obvious for an outside user how to run the model, and how to modify it
• Include tests that outputs from ca-with-production match outputs from the Bosscher-Schlager model

[EmiliaJarochowska]

I think some of these things we can fix ourselves if @jhidding is comfortable with that?

[jhidding]

Some of these have little to do with this PR. I'll fix those items that do, then we merge into main and move on from there?

[EmiliaJarochowska]

Good for me! I asked Nick and @xyl96 for review this way because I wanted them to confirm that they can run everything. We need a clear yes or no, guys 😉 if you have issues running anything this is the moment to share that 😊

[NiklasHohmann]

I'm not sure what is considered part if this PR @jhidding . What would you usually check as part of a PR? @EmiliaJarochowska if it is about being able to run the model: As is I'm not able to run the model from the provided explanations.

[jhidding]

Hmmm, let's say this PR is purely about merging CA and carbonate production code into main. In an early stage like this we should accept that documentation and unit tests are not yet upto standard, and changes shouldn't stay out of main branch for too long. That being said, you should be able to run the examples or I do need to add more documentation before merging.

[NiklasHohmann]

@jhidding and I did some troubleshooting with the namespaces - no more problems from my side with running it

[xyl96]

All the ca (Burgess) stuff runs here. But After I run the Burgess stuff, the bosser schlager 1992 is not working for some reason (I might did some stupid things or have done sth wrong): ERROR: UndefVarError: plot not defined. Why it's not recognising ''plot'' anymore...

[EmiliaJarochowska]

What is the difference between MODEL1 in Config.jl and Facies in the Input struct:

facies = [
        CaProd.Facies((4, 10), (6, 10), 500.0, 0.8, 300),
        CaProd.Facies((4, 10), (6, 10), 400.0, 0.1, 300),
        CaProd.Facies((4, 10), (6, 10), 100.0, 0.005, 300)
    ],

MODEL1 is used in burgess-2013.jl and in long-term.jl, but other examples have all parameters of Facies in Input. Is MODEL1 only created to reproduce Burgess (2013) and otherwise Facies should be always provided as part of Input?

[jhidding]

MODEL1 is used in burgess-2013.jl and in long-term.jl, but other examples have all parameters of Facies in Input. Is MODEL1 only created to reproduce Burgess (2013) and otherwise Facies should be always provided as part of Input?

Yeah, I want two things: make it easy to reproduce exact figures in BS92 and B13, but also show users how they may go about changing these things.

[EmiliaJarochowska]

[celebrate] Jarochowska, E.B. (Emilia) reacted to your message:

…

________________________________ From: Johannes Hidding ***@***.***> Sent: Tuesday, October 3, 2023 9:51:23 AM To: MindTheGap-ERC/CarboKitten ***@***.***> Cc: Jarochowska, E.B. (Emilia) ***@***.***>; Mention ***@***.***> Subject: Re: [MindTheGap-ERC/CarboKitten] CA with production (PR #8) CAUTION: This email originated from outside of Utrecht University. Do not click links or open attachments unless you recognize the sender and know the content is safe. Merged #8<#8> into main. — Reply to this email directly, view it on GitHub<#8 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AELMSVE6BGIJNKE3EP5RFG3X5PNZXAVCNFSM6AAAAAA5AD6SCSVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJQGUZTMMBRGU3DMMY>. You are receiving this because you were mentioned.Message ID: ***@***.***>