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Electronic structure Python package for post analysis and large scale tight-binding DFT/NEGF calculations

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Instead of having a geometry object with similar features, it would be nice to have a vector object which takes into account the basic routines for duplicating stuff, etc. I.e....

feature

Removed all deprecation methods. This means that older code should update their function calls.

**Describe the issue** Documentation in spin_squared, remove velocity etc from Hamiltonian. Check if soc and spin_squared might work by disentangling the up/down stuff.

The correct name is a contamination of the spin states. This change adheres so that it is more correct. @tfrederiksen @sofiasanz could you please review this name change? I think...

This PR addreses #493. Concept and implementation details --- The basic idea is to compute orbital values and store them in a sparse data structure. For now, the orbital values...

If one wants to calculate the `LDOS(E)` from a set of density matrices for different energies, one needs to call `dm.density()` for each energy, which results in the computation of...

**Describe the bug** AtomUnknown instantiation with Z values not being integers etc. Test for all corner cases.

**Describe the feature** Currently only x, y, z axis rotations are being done. But I could imagine that theta, phi rotations can be translated into x, y, z axis rotations...

The neighbor finder got an overhaul to check for PBC and friends. 1. Deleted `pbc` arguments to routines, they now get it from the `geometry` object contained. 2. The `find_all_unique_pairs`...

- [ ] Added tests for new/changed functions? - [x] Ran `isort .` and `black .` [24.2.0] at top-level - [x] Documentation for functionality in `docs/` - [x] Changes documented...