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graciaira

express.jl's Issues

Remove `workdir` parameter in config file

Now we have workdir as a parameter and has it checked. But it does not seem to be necessary. The directory where the config file sits should be considered as workdir, as it is currently used by default. Let's see why:

  1. The templates are still need to be provided paths, and they are not necessarily relative to workdir.
  2. xps command, or using from Julia REPL, has to specify a config file path, and that was supposed could be not in workdir. But now users have to set path for config files, workdirs & templates, that's a lot of complications.
    So I am considering just deprecate the workdir parameter.

How can `_makeinput` take variable arguments?

Phonon.SelfConsistentField depends on the last step results (optimized cells), so it may acquire a variable that takes either a new_structure or output. And Dfpt is even more complicated because it needs input from previous steps. But how to distribute the function on each slice of its arguments? One way is

function f(g, args...; kwargs...)
    map(zip(args...)) do arg
        g(arg...; kwargs...)
    end
end

This is exactly like IterTools.imap.

However, Base.map can do similar things. But it cannot take kwargs, so is IterTools.imap. The most flexible one is the one I wrote above.

Can't run Express

Hi,
I'm one of the referees for your paper. I've received the scripts you sent me through the editor and ran them (I'm using julia1.6 to run your code though). I'm then trying to run an eos calculation shown here:
image

If I run it using xps I get this error:
image

When trying to run it with a julia script I run into a different error:
image
image

Any ideas on how to fix this?

Support writing `StepRange` in config file

The current definitions of Pressures & Volumes support construction from an AbstractVector. This is OK in EOS & phonon workflows, but it is not very handy in the QHA workflow since it requires a lot of temperatures and pressures. So we also need to support config the desired temperatures, volumes, pressures from a simple, step-range like syntax like 1:10:300. The following definition is considered fine:

@option struct Temp4
    values::Union{AbstractVector,String}
    unit::String = "K"
    function Temp4(values, unit)
        if values isa Vector
            return new(values, unit)
        elseif values isa String
            return new(Meta.parse(values) |> eval, unit)
        else
            error("")
        end
    end
end

Support AtomsBase.jl

I'm one of the developers of AtomsBase. I'm SO excited that Express.jl exists, and I'd love to discuss the best way that it could support the AtomsBase interface to further enhance interoperability amongst materials science packages in Julia!

I'd love to set up some time to discuss this, perhaps with some of the other AtomsBase team such as @mfherbst and @jgreener64 โ€“ maybe during JuliaCon?

TagBot trigger issue

This issue is used to trigger TagBot; feel free to unsubscribe.

If you haven't already, you should update your TagBot.yml to include issue comment triggers.
Please see this post on Discourse for instructions and more details.

If you'd like for me to do this for you, comment TagBot fix on this issue.
I'll open a PR within a few hours, please be patient!

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