- Add feature to calculate local WCP parameter.
- Remove NEP model output.
- Add feature to Minimizer class for optimizing the box.
- Add many options for calculating SteinhardtBondOrientation, including the Voronoi neighbor, weighted by Voronoi face area and average version.
- Fix a bug for reading xyz format with multi space.
- Upgrade the minimum polars to the latest version 1.8.0, so many code changes have been done.
- Update doc.
- Add a new feature to calculate the distribution of bond length and bond angle.
- Fix a typo bug for LammpsPotential.
- Add test script for lammps interface.
- 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.
- Improve the performance for split_dump and split_xyz method.
- 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.
- 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.
- Update NEP interface to V1.3, compatible with GPUMD 3.9.5.
- Updated some documentations.
- Fix a bug for create_polycrystalline module.
- Fix a bug for reading xyz.
- 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.
- Rewrite the plot_dispersion function to make users custom figures easily.
- 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.
- Fix a typo bug in DFT2NEPXYZ class.
- 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.
- 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
- 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.
- Significantly optimize the performance of Neighbor class.
- Add label for colorbar while visualizing in jupyter.
- Provide a GUI interface based on the polyscope.
- Provide a GUI software for Windows platform.
- Fix a bug when generating System from array with velocity.
- Modify repr of System to print entire DataFrame.
- Fix a bug in pair_distribution class.
- Fix a bug when loading dump file.
- Fix a bug in PTM module.
- Update polars version to 0.20.0
- Updated README.
- Make mdapy support polars>=0.19.17
- Make mdapy support taichi>=1.7.0
- Fix a bug in void_distribution class
- Fix a bug when system with small size
- Change the display when system pos changed
- Rewrite the pltset and add a set_figure feature, which makes plotting easier.
- We can use elemental list to calculate the atomic temperature now.
- Fix a bug when loading xyz file.
- Update support for Polars>=0.19.14.
- Prepared to support Python 3.12.
- Remove the SciencePlots and pyfnntw as optional dependency for concise.
- Update support for Polars>=0.19.13
- Support clustering with multi cutoff distance for different elemental pairs.
- Add species clustering feature.
- Let k3d be an optional dependency. One can install it only if you need visualize the System in Jupyter environment.
- Experimentally support Visualizing System (only in Jupyter environment).
- Add k3d as a dependency.
- Add jupyter as a dependency.
- One can explicitly assign the type number when writing to data file.
- Support load/save POSCAR format.
- Support load/save XYZ format.
- Fix the documentations.
- Add a dynamic logo.
- Improve the memory use for System class.
- Improve the README.
- Add plot for 3D spatial binning.
- Remove dependency for Pandas and Pyarrow. mdapy uses Polars to be the newer DataFrame structure.
- Updated Documentation.
- Improve the importing speed.
- Minor improvement on compilation speed.
- Support generating special crystalline orientations for FCC and BCC lattice.
- Fix bug for warpping positions.
- Fix bug for write dump.
- Fix bug for generate System class from np.ndarray.
- Update an example to calculate the Generalized Stacking Fault Energy (GSFE).
- Fix capacity of cross-platform.
- Updated doc.
- Add Polars as dependency package. Now we still use pandas, but mdapy maybe move to polars in the future.
- Optimize the performance of reading and saving Dump and Data file.
- Support loading/saving compressed Dump file (such as sample.dump.gz).
- Support the lowest python version to 3.8.0.
- Add pyproject.toml.
- Support triclinic box now!!!
- Add Select feature.
- Rewrite the load and save module.
- Make many method suitable for small system.
- Fix some bugs.
- Fix installation in python 3.11.5.
- Fix memory leak in SpatialBinning class, not the correct issue.
- Fix bug in SteinhardtBondOrientation class.
- Fix bug in read data.
- Fix bug in spatial_binning.
- Updated the IdentifySFTBinFCC class to identify the twinning and extrinsic stacking fault.
- Updated Taichi to 1.6.0, which decreases the import time and supports Python 3.11.
- Fix bug in read data.
- Updated mdapy citation. We are pleased that our article for mdapy has been accepted by Computer Physics Communications.
- Add repr for System class.
- Add Replicate class.
- Improve the performance of reading/writing DATA file with pyarrow.
- Improve the performance of building Voronoi diagram with new version voro++.
- Compile it on MAC OS with M1. Now mdapy is fully cross-platform.
- Obviously improve the performance of reading/writing DUMP with pyarrow.
- Add pyarrow as a dependency package.
- Fix bug of create_polycrystalline module. One can give box with any number, the old version only works for positive float.
- Fix bug of spatial_binning module for empty region.
- Let tqdm as an Optional dependency.
- Optimize Pair Distribution module.
- Optimize Neighbor module.
- Update many Benchmark cases.
- Make Polyhedral Template Mathing parallel.
- Fix bugs of unwrap positions.
- Fix a typo error in msd.
- Add Steinhardt Bondorder Parameter method, which can be used to identify the lattice structure and distinguish the solid/liquid phase during melting process.
- Add Polyhedral Template Mathing method.
- Add IdentifySFsTBs method to identify the stacking faults (SFs) and twinning boundary (TBs) in FCC lattice.
- Add Ackland Jones Analysis (AJA) method.
- Add Common Neighbor Parameter (CNP) method.
- Update the nearest neighbor search in CSP method.
- Fix bug of create_polycrystalline module in Linux.
- Update TaiChi version to 1.4.0.
- Set SciencePlots as a optional package.
- Fix bug in create_polycrystalline.