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Release Notes

Mdapy 0.11.1 (September 19, 2024)

🏆 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 (June 22, 2024)

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

V0.10.9 (June 20, 2024)

  • 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.

V0.10.8 (May 17, 2024)

  • 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 (April 25, 2024)

  • 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.

V0.10.6 (April 13, 2024)

  • Fix a typo bug in DFT2NEPXYZ class.

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.

V0.10.4 (March 12, 2024)

  • 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 (January 30, 2024)

  • 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 (January 8, 2024)

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

V0.10.1 (December 18, 2023)

  • 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.

V0.10.0 (November 28, 2023)

  • 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

V0.9.9 (November 21, 2023)

  • 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.

V0.9.8 (November 13, 2023)

  • 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.

V0.9.7 (11/5/2023)

  • Experimentally support Visualizing System (only in Jupyter environment).
  • Add k3d as a dependency.
  • Add jupyter as a dependency.

V0.9.6 (11/2/2023)

  • One can explicitly assign the type number when writing to data file.
  • Support load/save POSCAR format.
  • Support load/save XYZ format.

V0.9.5 (10/24/2023)

  • Fix the documentations.
  • Add a dynamic logo.
  • Improve the memory use for System class.
  • Improve the README.
  • Add plot for 3D spatial binning.

V0.9.4 (10/20/2023)

  • 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.

V0.9.3 (10/19/2023)

  • 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).

V0.9.2 (10/12/2023)

  • Fix capacity of cross-platform.
  • Updated doc.

V0.9.1 (10/11/2023)

  • 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.

V0.9.0 (9/23/2023)

  • Support triclinic box now!!!
  • Add Select feature.
  • Rewrite the load and save module.
  • Make many method suitable for small system.
  • Fix some bugs.

V0.8.9 (9/5/2023)

  • Fix installation in python 3.11.5.

V0.8.8 (8/24/2023)

  • 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.

V0.8.7 (5/25/2023)

  • 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.

V0.8.6 (4/22/2023)

  • 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++.

V0.8.5 (4/9/2023)

  • 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.

V0.8.4 (3/30/2023)

  • Optimize Pair Distribution module.
  • Optimize Neighbor module.
  • Update many Benchmark cases.

V0.8.3 (3/20/2023)

  • Make Polyhedral Template Mathing parallel.

V0.8.2

  • Fix bugs of unwrap positions.
  • Fix a typo error in msd.

V0.8.1

  • 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.

V0.8.0

  • Add Ackland Jones Analysis (AJA) method.
  • Add Common Neighbor Parameter (CNP) method.
  • Update the nearest neighbor search in CSP method.

V0.7.9

  • Fix bug of create_polycrystalline module in Linux.

V0.7.8

  • Update TaiChi version to 1.4.0.
  • Set SciencePlots as a optional package.
  • Fix bug in create_polycrystalline.