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Extend model system #58

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Extend model system #58

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92785b9
- Add first implementation of bond length calculation + tests
Apr 18, 2024
e60bceb
Fix typos
Apr 19, 2024
6ddc77c
Fix typos
Apr 19, 2024
a1cd476
Improve pbc default system\
Apr 19, 2024
68b5d32
- Accomodate schema for hosting interatomic distances
Apr 23, 2024
8e3e859
- Add angles
Apr 23, 2024
c05e46e
- Fix shape issue with `elemental`s
Apr 24, 2024
12246f1
- Restructure functionalities into a chain of factory classes
Apr 26, 2024
e63c987
Fix some mistakes
Apr 26, 2024
479725a
- Work out distance and angle values tests for ethane
Apr 26, 2024
d0506a3
Add test for `DistributionFactory`
Apr 28, 2024
81b3ece
- Add tests for `DistributionHistogram`
Apr 28, 2024
897ccb6
Improve `analyze_geometry` check
Apr 28, 2024
5440b4d
Apply reviewer feedback
May 13, 2024
fd1bff9
Rename `GeometryDistribution.elements` to `GeometryDistribution.atom_…
May 13, 2024
1539c15
- Split out `GeometryDistribution` in to subcases (resolving reviewer…
May 13, 2024
333f15c
Correct typing (mypy)
May 13, 2024
45e12aa
- Merge branch 'develop' into `extend_model_system`
May 17, 2024
e8f59f8
Fix indentation error `AtomicCell.to_ase_atoms()`
May 17, 2024
208c2ba
Move `bond_list` from `Cell` ro `AtomicCell` upon reviewer request
May 17, 2024
a398857
Reapply `@check_attributes` to `to_ase_atoms`
May 17, 2024
7265b53
- Remove `positions` and `velocities` from `AtomicCell`, in favor of …
May 17, 2024
4333a53
Add test for `GeometryDistribution` (instantiation and normalization)
May 17, 2024
2b9c287
- Add test case to `test_distribution_histogram`
May 17, 2024
a3ac6a3
Change `GeometricDistribution` units for angles from degrees to radian
May 17, 2024
9023837
- Add documentation
May 17, 2024
4da9060
Fix mypy typing nameclash (gosh, mypy sucks)
May 17, 2024
6a6305a
- Build in non-stored default for bins in archive storage
ndaelman May 23, 2024
4c2bf8c
- Remove `check_attrributes`
ndaelman May 27, 2024
b498bd7
- add bin units in pipeline classes
ndaelman May 27, 2024
4e92474
- Fix `mypy` errors
ndaelman May 27, 2024
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