Mdapy 0.11.1

🏆 Highlights

• Refactor the visualization code in Jupyter, make it more beautiful and convinient.
• Add minimizer engine with FIRE method.
• Add a new feature to calculate the atomic shear strain.
• Add OrthogonalBox module to change triclinic box to rectangular box.
• Add adaptive common neighbor analysis method.
• Add IdentifyDiamondStructure method.

🚀 Performance improvements

• Improve the performance for split_dump and split_xyz method.

✨ Enhancements

• Add an example to compute Vacancy Formation energy.
• Make CreatePolycrystalline module can accept any files as matrix.
• Let the max type in LammpsPotential module is determined by given elemental list, enabling more flexible usage.

🐞 Bug fixes

• Fix a bug for cell_opt class.
• Fix a bug for neighbor class.
• Fix a bug for RDF with partial interaction in multi-elemental system.
• Fix a bug for reading cp2k output file with OT method.
• Let GUI model compatible with latest polars.

🛠️ Other improvements

• Update NEP interface to V1.3, compatible with GPUMD 3.9.5.
• Updated some documentations.

v0.11.0

• Fix a bug for create_polycrystalline module.
• Fix a bug for reading xyz.

v0.10.9

• 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.

v0.10.8

• 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.

V0.10.7

• 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.

V0.10.6

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

V0.10.5

V0.10.5 (April 12, 2024)

• Refactor the code structure. Delete calculator file. Remove timer into tool_function file.
• Support NEP 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.
• Add feature for converge cp2k output to xyz format for NEP 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.

v0.10.4

• Add feature for plotting phonon dispersion based on the data generated by phonopy.
• Fix bug for writing xyz.
• Make mdapy support polars>=0.20.15

V0.10.3

• 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 format.

v0.10.2

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