Mdapy

- Add phonon calculation feature based on the phonopy, supporting any kind of potential format.
- Add atomic virial computation for eam/alloy potential.
- Fix a bug for NEP interface.
- Fix a bug for read_data.
- Add feature of cell_opt, using lammps as calculation backend.
- Add phonopy and lammps as optional package.
- Add force_max and mode parameter for DFT2NEPXYZ class.
- Support taichi>=1.7.1.
- Support polars>=0.20.22.
- Update readme.
- No updating on GUI mode at this release.

- Fix a typo bug in DFT2NEPXYZ class.
- **No updating on GUI mode at this release.**

- Refactor the code structure. Delete calculator file. Remove timer into tool_function file.
- Support [NEP](https://gpumd.org/potentials/nep.html) model to evaluate the energy, force and virial.
- Add feature for generating initial geometry model with perturbation, which is helpful to prepare the initial database for deep learning. The function is similar to init_bulk and init_surf in [dpgen](https://github.com/deepmodeling/dpgen).
- Add feature for converge cp2k output to xyz format for [NEP](https://gpumd.org/potentials/nep.html) trainning.
- Add feature to split dump/xyz containing multi frames into seperate frames.
- Optimize timer decorators.
- Fix bug when writing cif and POSCAR.
- Fix bug for create_polycrystalline when input wrong box, and optimize the performance of deleting overlap atoms.
- Make mdapy support polars>=0.20.19.
- **No updating on GUI mode at this release.**

- Add feature for plotting phonon dispersion based on the data generated by [phonopy](https://phonopy.github.io/phonopy).
- Fix bug for writing xyz.
- Make mdapy support polars>=0.20.15

- Fix bug when read/write POSCAR with reduced positions.
- Fix bug when read data file with multi space.
- Fix bug when read dump with reduced positions.
- Add support for write data with type name list.
- Support read/write simple [Crystallographic Information File cif](https://www.iucr.org/resources/cif/spec/version1.1/cifsyntax) format.

- Significantly optimize the performance of Neighbor class.
- Add label for colorbar while visualizing in jupyter.