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I think it would be good to have a ff file and then create symlinks to it for the tests and examples. This way the tests would work directly.
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Hey,
I'm currently implementing the HAT reaction (without rates). I don't need plumed for that but the config reader is very peculiar when not using plumed. Here are different options on what to writ…
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https://github.com/hits-mbm-dev/kimmdy/blob/4cde37430db18b4c6e680ec84471efec2725647c/src/kimmdy/changemanager.py#L29-L33
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Hey,
I was just wondering why it is not possible to pass arguments from command line to kimmdy. With the current code in main.py it would always take the default arguments because of this line:
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The way I treated the working directory should be reworked to be state of the art and more compatible with a modular approach
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Make sure our top parser works with fixed-width formatting and long numbers.
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The current implementation assumes just one ReactionRecipe where the RunManager stores results and the decision strategy picks one conversion to perform based on the rates from this recipe, which brea…
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https://github.com/hits-mbm-dev/kimmdy/blob/e83cf0fd6a168325761a50095cbe6f0bc5eede7c/functions.py#L103-L109