Fabian Zills

Plot Energies/Forces/... over time

5

**What feature would you like to see added?** For the investigation of ML based trajectories it can be interesting to be able to look at properties such as energy, forces,...

Use Poetry for development

9

Using setuptools has many downsides described elsewhere in much detail. Many of them can be solved by using [Poetry](https://github.com/python-poetry/poetry). Therefore, I propose changing MDSuite to use poetry as well. This...

Documentation - Read numpy data

1

Add: How to use numpy input data to the documentation Working solution can be found: https://github.com/zincware/MDSuite/blob/0d4837c730364034fe9e04af17ab368fd1353eaa/CI/unit_tests/database/test_file_read.py#L83-L116

https://github.com/zincware/MDSuite/blob/0d4837c730364034fe9e04af17ab368fd1353eaa/mdsuite/database/scheme.py#L266

RDF issue that occasionally happens in the CI

1

``` traj_file = '/tmp/pytest-of-runner/pytest-0/NaCl_gk_i_q.lammpstraj' true_values = {'Cl_Cl': {'left': 0.2372193090684762, 'min_pomf': 5.4953035102048034e-11, 'pomf': [inf, inf, inf, inf, inf, inf, ...]...20018507094386176, 0.0030027760641579263, 0.004003701418877235, 0.005004626773596544, 0.006005552128315853, ...], ...}} tmp_path = PosixPath('/tmp/pytest-of-runner/pytest-0/test_experiment1') def test_experiment(traj_file,...

fix StructureFactor calculator

15

just fix StructureFactor calculator

Remove legacy code

4

I actually think several meta functions are now legacy and can be removed. I will leave this for a future PR. _Originally posted by @SamTov in https://github.com/zincware/MDSuite/pull/475#discussion_r795618398_

Species handling struggles with `_`

3

**Describe the bug** This is just one example https://github.com/zincware/MDSuite/blob/6ed32d47a62b3719c96f0dc6cbc7fb61d21f9099/mdsuite/calculators/radial_distribution_function.py#L313 that failes if the species contain `_` e.g. `Na_1` also a bit related to #486

Add tests for transformations

4

Thanks to @christophlohrmann most of the Transformations are now tested. # Still Missing tests / bad coverage - [ ] integrated_heat_current - [ ] kinaci_interaged_heat_current - [ ] map_molecules -...

**Describe the bug** Currently there is `adf_data["O_H_H"]` to give access to an ADF with the central atom being `O` and two neighbouring `H`. Maybe rename it `"O_(H_H)"` to highlight the...