Add HPHT_CH4_H2O free energy profile of proton hopping benchmark

[ThomasThevenet]

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Summary

"HPHT_CH4_H2O" is a new benchmark of the "Molecular Reactions" category which tests the free energy profile of proton hopping reaction in CH4/H2O liquid from molecular dynamics simulations at 3000 K and 22-69 GPa. The associated analysis performs a molecular recognition algorithm to collect reaction coordinate values and compute the free energy profile associated to the reaction : H3O+ + CH4 = H2O + CH5+. Reference profiles were computed at the DFT (GGA) level (PBE+D3).
Currently three metrics are available :

1. Global MAE of predicted profiles with respect to reference ones.
2. MAE on free energy of reaction (F[product] - F[reactant])
3. MAE on foward free energy barrier (F[transition state] - F[reactant])

The application displays parity plot for MAE of both free energy of reaction and barrier. Interaction of the user with parity plots dynamically displays the predicted and reference free energy profiles of the selected structure.

Linked issue

None.

Progress

• Calculations
• Analysis
• Application
• Documentation

to do:

• Prepare reference data

• Upload reference data to S3 bucket

• Write documentation

• Talk about the full pipeline test

• Testing

Analysis and application components have been tested locally from precomputed molecular dynamics trajectories. Full MD-based pipeline is not manageable with local ressources and has not been tested.

New decorators/callbacks

No new decorators were introduced. A new Dash callback leveraging clickData was implemented to enable interactive visualization of free energy profiles. Selecting a point in the parity plot dynamically displays the corresponding structure's profiles for all MLIP models.