Update molecule mapping

[SamTov]

The idea in this PR is that I wanted to add an analysis of water as a test and example and in doing so, go through MDSuite functionality and identify bugs and repair them such that the study can continue. I will keep adding small notes on what has changed to aid in the review. It is nothing large just small bug fixes that arise when trying to use the software together. Along with the fixes, I am also writing specific tests to avoid these things from breaking in the future.

Summary of additions and changes

Anything Bold-fonted is now included to some extent in a test. To the extent that a test will fail if something that was fixed in this PR is violated in the future.

• Allowed for building molecule from arbitrary species, i.e. one can now write {'HW1': 1, 'OW': 1, 'HW2': 1} and it will build water molecules with these species. This makes it easier to work with GROMACS where typically species are given as a ligand name or simple a numbered species based on its location in a molecule.
• Removed molecules from the experiment species dict and updated transformations to look through both species and molecules dicts when performing transformation
• Fixed bug in batching for angular distribution function that resulted in errors. This is resolved by setting the default mini batch in the ADF to -1 rather than 50 but I have also added a check in the get_triplets method to completely avoid this issue from occurring.
• Adjust ADF such that it can work with molecules
• Update transformations so that they work with molecules.
• Add integration test to rigorously check that the correct water molecules are built from a GROMACS simulation
• Add Functional test to check that MDSuite runs with and without molecules for several calculators
• Adjusted length of some tqdm bars so that they remain at 70 columns
• Added tutorial notebook for mapping molecules.
• Adapted ADF to work with selected atoms
• Started adapting RDF to work with selected atoms, see notes below.
• Fix indexing error for molecule mapping that resulted in a false reference. This was visible, notably, in the centre molecule of the SDF.
• Fix critical bug in the ensemble generation for remainders and for system-wide properties
• Move Graph related operations to the graph module
• Changed default chemfiles positions property to positions rather that unwrapped positions.
• Removed indices from molecules, I believe closing Check missing indicies #432
• Allowed for molecule pbc from gromacs

How to test this pull request

Tests will be added along with a notebook discussing the different methods for building molecules and how they work which can also go into the documentation.

Notes

Reviews are welcomed at any point in the PR as well as ideas for improving the mapping module as I go through it. I have some changes planned in terms of its overall functionality so perhaps it is better to wait for that but the choice is yours.

TODO

• Fix issue in RDF for atom-selection. I think it has something to do with one entry having only a single atom as the distance tensor is computed correctly but the masking fails.
• Resolve issue with chemfiles return. Update, see here
• Include more tests for the graph module and update functional test with real data
• Add proper data to DataHub and enforce stricter checks to ensure same bugs don't occur again. This is done but the tests not written as the coordination numbers are broken. TBF in another PR.

Problem with RDF

The RDF seems to return all zeros when trying to use selected atoms to compute it. The distance tensor is correct but during the binning method all values in the tensors are set to zero even if in the distance tensor they are within the cutoff.

[PythonFZ]

Because this is still a draft, I don't really know what to review

[PythonFZ]

The Example Notebook fails on Binder for the ADF calculation due to memory issues. This is not related to this PR, but I want to leave the link here so you can test out the changes in a clean environment

[SamTov]

The Example Notebook fails on Binder for the ADF calculation due to memory issues. This is not related to this PR, but I want to leave the link here so you can test out the changes in a clean environment

This is however related to #476

[PythonFZ]

I'm still struggeling with the dataclass tests but besides them looking forward to merge it.

[SamTov]

I'm still struggeling with the dataclass tests but besides them looking forward to merge it.

The data class that you are referring to is the issue that you agreed to handle at a separate time and is open in #477. The initial points for which you wanted a data class are now a data class in the tests and in the code.

[christophlohrmann]

this PR should have really been squashed before merge with all the back and forth + format litter

[PythonFZ]

this PR should have really been squashed before merge with all the back and forth + format litter

I would propose to almost always use squash and merge