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ElliottKasoar
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Thanks for this! I need to test is properly, but from a first pass of the code it looks great!
I know they're relatively small, but are you happy for me to upload the data start files to the S3 bucket, just to slim things down?
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I think the plot titles/axes aren't quite working. Since the plots are unique to each model, it would also be nice to include the model name somewhere in the title, if possible. 
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PKourtis
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…ation function - edited to remove unecessary data files
Co-authored-by: Elliott Kasoar <45317199+ElliottKasoar@users.noreply.github.com>
…tor and edited the analysis script accordingly
… skipped if the MD trajs are not present
…e form of outputs / model / {salt}-traj.extxyz
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ElliottKasoar
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Thanks again for this, @PKourtis!
I've rebased and tidied up a little, plus less a couple of suggestions, mainly
| for salt in IRON_SALTS: | ||
| struct_path = data_path / f"{salt}_start.xyz" | ||
| struct = read(struct_path, "0") | ||
| struct.calc = calc |
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| struct.calc = calc | |
| struct.calc = calc | |
| struct.info["charge"] = int(struct.info["charge"]) | |
| struct.info["spin"] = int(struct.info["spin"]) |
Unfortunately when these are read in, ASE seems to set them to numpy.int64, which causes Orb-omol to raise errors
| npt.run() | ||
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| @pytest.mark.parametrize("mlip", MODELS.items()) |
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I think you can just do "model_name", MODELS if you just want the names
ElliottKasoar
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Just wanted to flag that I get warning:
NPT: Setting the center-of-mass momentum to zero (was 8.8567 -10.9324 6.12114)
I think this is unavoidable with the standard ASE NPT (now known as MelchionnaNPT in ASE, although still referred to just as NPT in janus-core).
This seems to have been around for a while (since at least ASE 3.22), so I don't think the behaviour should be too unexpected, just wanted to check in case there's a reason the input has a non-zero momentum before this.
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Summary
Benchmarks how well models capture the different oxidation states of Iron.
Main tests compares the O-Fe RDFs of Fe+2 and Fe+3 by running 20ps NVT MD for Fe 2Cl and Fe 3Cl ions in water.
Linked issue
Resolves #264
Progress
Testing
Tested on mp0-b3, currently running omol-0 MD.
New decorators/callbacks
Added new option to the plot_scatter decorator to remove markers from the plots.