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Add initial examples#1

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alinelena merged 98 commits into
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add-example
Sep 19, 2025
Merged

Add initial examples#1
alinelena merged 98 commits into
mainfrom
add-example

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@ElliottKasoar

@ElliottKasoar ElliottKasoar commented Jul 21, 2025

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Adds example benchmarks for OC157 and Li diffusion barriers (NEB).

To do:

  • Fix callback for Li diffusion atom visualisation
  • Fix sorting/order of models/storage of data (use dictionary rather than list)
  • Add benchmark with multiple tables

@ElliottKasoar ElliottKasoar changed the title Add OC157 example Add initial examples Aug 18, 2025
@ElliottKasoar ElliottKasoar added the enhancement New feature or request label Aug 19, 2025
@ElliottKasoar ElliottKasoar force-pushed the add-example branch 2 times, most recently from c1d558b to 7b855a5 Compare August 20, 2025 16:29
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@ElliottKasoar ElliottKasoar mentioned this pull request Sep 4, 2025
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@ElliottKasoar ElliottKasoar force-pushed the add-example branch 2 times, most recently from 7e050e9 to c855ae4 Compare September 5, 2025 16:20
@ThomasWarford

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Hi,

the bug I noticed was that points in the parity plots for S24 are given the wrong labels

The following XYZ (found at mlip_testing/app/data/surfaces/S24/mace_mp_0b3/C48H24O26Zn8-H2..csv) has ref adsorption energy of -0.1.

NOTE: I save it as csv because GitHub won't let me upload xyz, change the file extension if you want.
<img width="198" he
C48H24O26Zn8-H2..csv

The point with label C48H24O26Zn8-H2 has very different energy.
ight="73" alt="image" src="https://github.com/user-attachments/assets/103528b8-181f-49c5-806a-801dcbbc9363" />

I fixed this on my branch by changing the get_system_names function in mlip_testing/analysis/surfaces/S24/analyse_S24.py

def system_names() -> list:
    """
    Get list of system names.

    Returns
    -------
    list
        List of all system names.
    """
    # NOTE: The parity plot associates hover data with points in the
    # order the data arrays are provided. In `adsorption_energies` the
    # systems are iterated with `sorted((CALC_PATH / model_name).glob("*.xyz"))`.
    # Originally this function used the unsorted `.glob()` ordering,
    # which can differ from the sorted order, leading to mismatched
    # (mislabelled) hover labels (system names) in the output JSON.
    # We therefore reproduce the exact ordering used in the data
    # collection step by applying the same `sorted(...)` here.
    system_names_list = []
    for model_name in MODELS:
        for system_path in sorted((CALC_PATH / model_name).glob("*.xyz")):
            system_names_list.append(system_path.stem)
        break  # only need the first model to list available systems
    return system_names_list
    ```

@ThomasWarford

ThomasWarford commented Sep 10, 2025

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I have not confirmed this fix for S24, but I did for the branch I made, which copied this code, maybe the function should be moved into another file without the global variable dependence.

@ElliottKasoar ElliottKasoar linked an issue Sep 11, 2025 that may be closed by this pull request
@ElliottKasoar ElliottKasoar force-pushed the add-example branch 2 times, most recently from 6d8aa91 to 6a67624 Compare September 16, 2025 15:57
@alinelena alinelena merged commit 9f3baf9 into main Sep 19, 2025
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@alinelena alinelena deleted the add-example branch September 19, 2025 10:34
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Error handling for missing files Finalise run options Add initial examples and repo structure

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