Mdapy

- Refactor the code about generating box, supporting all triclinic box now. The previous version only support lammps style triclinic box.
- Add the farthest point sampling method to select the configuration by descriptor.
- Add stress_max parameter for DFT2NEPXYZ class.
- Fix a bug for obtaining descriptor in NEP interface.
- Fix a bug for reading xyz.
- Refactor code of unwraping position.
- Let read/write xyz containing the global information, such as energy, virial and stress.
- Add cutoff_radius and displacement parameter in Phonon class. Fix 4
- Rewrite the plot_dispersion function to make users custom figures easily. Fix 5
- Reading POSCAR dose not need to rotate the box.
- Add MANIFEST.in file.

- Let tqdm as a dependency package.
- Fix frame counter in DFT2NEPXYZ.
- Fix a bug for NEP potential with triclinic box.
- Add write_cp2k method.
- Fix a bug when reading xyz.
- Fix a bug when writing cif.
- Fix a bug for phonon calculation.

- 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