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Method doesn't look clean at the moment, might want to shift some functionality to other parts of KIMMDY
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Ideally, store it in runmng.radical_idxs = []
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when I call kimmdy during tests, it fails without raising an error
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I would like to have a more consistent naming for the reactions in kimmdy/plugins. Currently the package name is dummyreactions and it includes dummyreaction and hat_naive.
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Currently, Kimmdy does not run on python 3.9 due to changes related to typing.
Python3.9 is still supported until 10.2025; Ubuntu 20.04 ships with 3.8 and is also supported until 04.2025
On the …
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`pytest tests/test_changemanager.py -k test_modify_top --pdb` throws error
In FF initialization:
```
atomtypes = get_top_section(top, "atomtypes")
if atomtypes is None:
> …
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Equilibration after a reaction, probably most applicable if the change is small or the coordinates were changed to a reasonable structure right before this equilibration.
All equilibration methods: #…
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* [x] Kimmdy should handle plugins not having a schema.json. Currently, it just exits even if the plugin is not used
* [x] Proper error message if a **used** plugin has issues
* [x] Fallback for rea…
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Currently atom_idx is tuple(int,int) but for the changemanager it typically needs to be tuple(str,str) to compare to topology entries.
Are there any cases when we need tuple(int,int)? Can we change …
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Currently, we are specifying only threads-per-rank `-ntomp`. Sometimes (not always??), gromacs throws fatal errors since `-ntmpi` is missing (but is required when `-ntomp` is set).
Should we even s…