ISISNeutronMuon
[ENHANCEMENT] Uniform converter behaviour
Is your feature request related to a problem? Please describe. There is different amount of information provided about the system by different MD engines, which requires some converters to compensate for the missing bits with additional code. Specifically, some engines assign arbitrary labels to atoms, making it difficult to assign correct chemical elements to objects in the trajectory. The way this is handled should be made uniform between converters.
Describe the solution you'd like Every converter should have the following features:
- give a preview of atom types it will load,
- optionally, guess the atom types based on mass,
- optionally, change the atom types before the conversion,
- scan for molecules/bonding information during conversion.
Describe alternatives you've considered At the moment, two converters (LAMMPS and ImprovedASE) have chemical element recognition based on atom mass, and DL_POLY uses molecules.json for atom type lookup. Other converters rely on accurate input from the MD files.
Additional context The converters will always create trajectories with all the atoms inside the box, at the expense of some molecules not being contiguous. If an analysis type needs contiguous molecules, it needs to contain code that will ensure this condition is met.
