Deepmd-kit

What's Changed

Bugfixes
* cc: fix returning type of sel_types by njzjz in 3181
* fix compile gromacs with precompiled C library by njzjz in 3217
* gmx: fix include directive by njzjz in 3221
* c: fix all memory leaks; add sanitizer checks in 3223

CI/CD
* build macos-arm64 wheel on M1 runners by njzjz in 3206

**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v2.2.8...v2.2.9

<!-- Release notes generated using configuration in .github/release.yml at master -->

What's Changed
Breaking Changes
* breaking(lmp): do not apply scale factor to model deviation by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3036
New Features
* build neighbor list with external Python program by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3046
* nvnmd: init-model feature and 256 neighbors by LiuGroupHNU in https://github.com/deepmodeling/deepmd-kit/pull/3058
* Add pairwise tabulation as an independent model by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3101
Enhancement
* support compressing gelu_tf by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2957
* respect user defined CUDAARCHS by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2979
* lmp: refactor ixnode by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2971
* print system prob using scientific natation by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3008
* remove unused codes in se_a.py by nahso in https://github.com/deepmodeling/deepmd-kit/pull/3049
* print NaN loss when labeled data is not found by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3047
Documentation
* docs: add theory from v2 paper by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2715
* docs: configuring automatically generated release notes by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2975
* docs: use relative links by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2976
* docs: remove lammps.md by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2986
* docs: document horovod on Conda-Forge by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3001
* docs: document external neighbor list by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3056
* docs: update documentation for pre-compiled C library by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3083
* docs: update Amber interface by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3074
* docs: document CP2K interface by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3158
Build and release
* bump scikit-build-core to 0.6 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2981
* bump CUDA version to 12.2 for pre-built packages by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2960
* add cu11 prebuilt packages by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3002
* bump scikit-build-core to 0.7 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3038
* bump LAMMPS to stable_2Aug2023_update2 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3066
Bug fixings
* fix SpecifierSet behavior with prereleases by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2959
* fix restarting from compressed training with type embedding by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2996
* Add the missing initializations for extra embedding variables by nahso in https://github.com/deepmodeling/deepmd-kit/pull/3005
* Fix macro issue with multiple arguments by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3016
* fix se_a_ebd_v2 when nloc != nall by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3037
* fix: invalid read and write when natom grows by Cloudac7 in https://github.com/deepmodeling/deepmd-kit/pull/3031
* fix GPU mapping error for Horovod + finetune by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3048
* lmp: Register styles when using CMake by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3097
* fix segfault in ~Region by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3108
* lmp: fix evflag initialization by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3133
* cmake: fix setting `CMAKE_HIP_FLAGS` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3155
* Fix max nbor size related issues by denghuilu in https://github.com/deepmodeling/deepmd-kit/pull/3157
* Fix possible memory leak in constructors by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3062
* fix memory leaks related to `char*` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3063
* Update the path to training and validation data dir in zinc_se_a_mask.json by dingye18 in https://github.com/deepmodeling/deepmd-kit/pull/3068
* Fix catching by value by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3077
* resolve "Multiplication result converted to larger type" by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3149
* resolve "Multiplication result converted to larger type" by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3159
CI/CD
* move to ruff formatter by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2951
* add unit tests for LAMMPS fparam/aparam keywords by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2998
* fix labeler.yml with actions/labeler v5 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3059
* add CodeQL checks by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3075

Code refactor and enhancement to prepare for upcoming v3
* rename `deepmd_cli` to `deepmd_utils` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2983
* merge prob_sys_size with prob_sys_size;0:nsys:1.0 by CaRoLZhangxy in https://github.com/deepmodeling/deepmd-kit/pull/2963
* add utils for DP native model format by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3064
* rm rcut from DeepmdDataSystem by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3106
* add activation_function and resnet arguments and NumPy implementation to NativeLayer by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3109
* NativeLayer: support None bias. by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3111
* fix native layer concat bug. by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3112
* model format for the embedding net by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3113
* support numerical precision and env_mat by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3114
* Add dp model format sea by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3123
* input order of env_mat changed to be consistent with descriptor by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3125
* doc string for dp model format descriptor se_e2_a by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3124
* add native Networks for mutiple Network classes by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3117
* add definition for the output of fitting and model by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3128
* cc: refactor DeepPotModelDevi, making it framework-independent by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3134
* fix: model check assumes __call__ as the forward method by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3136
* support fitting net by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3137
* refactorize NativeLayer, interface does not rely on the platform by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3138
* refactorize networks, now can be used cross platform by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3141
* move utility to `deepmd_utils` (without modifaction) by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3140
* add cross-platform AutoBatchSize by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3143
* move deepmd.entrypoints.{doc,gui} to deepmd_utils.entrypoints.{doc,gui} by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3144
* cc: refactor DeepPot to support multiple backends by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3142
* cc: refactor DeepTensor for multiple-backend framework by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3151
* cc: refactor DataModifier for multiple-backend framework by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3148
* fix: some issue of the output def by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/3152
* cc: merge `DeepPotBase` and `DeepTensor` member functions by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3145
* move `OutOfMemoryError` from `deepmd` to `deepmd_utils` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3153
* set dpgui entry point to `deepmd_utils` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3161

New Contributors
* Cloudac7 made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/3031

**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v2.2.7...v2.2.8

> [!CAUTION]
> Known critical issues in this version
> - Incorrect results on GPUs.
>
> We suggest all users use a newer version. See https://github.com/deepmodeling/deepmd-kit/issues/2866 for more information.

New features
* add `aparam_from_compute` to `pair deepmd` by ChiahsinChu in https://github.com/deepmodeling/deepmd-kit/pull/2929
* support compressing any neuron structure by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2933
* Support conversion to pbtxt in command line interface by Yi-FanLi in https://github.com/deepmodeling/deepmd-kit/pull/2943

Enhancement
* argcheck: restrict the type of elements in a list by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2945
* reformat func for further merging with pt version by zxysbsbzxy in https://github.com/deepmodeling/deepmd-kit/pull/2946

Build and release
* deploy developed Python packages to GitHub Pages by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2932

Bug fix
* fix py lmp plugin path for editable installation by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2922
* fix se_a compression for just enough sel and symmetrical coordinates by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2924
* fix floating point exception when nloc or nall is zero by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2923
* fix typo about fparam/aparam by ChiahsinChu in https://github.com/deepmodeling/deepmd-kit/pull/2925
* Fix typos by HydrogenSulfate in https://github.com/deepmodeling/deepmd-kit/pull/2930
* only freeze in rank 0 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2937
* fix ase tarball url and testing C library by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2950


New Contributors
* HydrogenSulfate made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/2930
* zxysbsbzxy made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/2946

**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v2.2.6...v2.2.7

> [!CAUTION]
> Known critical issues in this version
> - Incorrect results on GPUs.
>
> We suggest all users use a newer version. See https://github.com/deepmodeling/deepmd-kit/issues/2866 for more information.

New features
* apply compression for se_e2_a_tebd by nahso in https://github.com/deepmodeling/deepmd-kit/pull/2841
* cmake: support LAMMPS in built-in mode; remove kspace requirement by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2891
* support neighbor stat on GPUs by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2897
* Add `dpgui` entry point and `dp gui` CLI by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2904

Enhancement
* forward GPU error message by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2878
* Generate CUDA stubs dynamically by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2884 and https://github.com/deepmodeling/deepmd-kit/pull/2900
* refactor update_sel by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2901
* support combining frozen models into a pairwise DPRc model by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2902

Bugfixes
* `se_atten` and `se_atten_v2`
* Se atten grad grad by nahso in https://github.com/deepmodeling/deepmd-kit/pull/2898 and https://github.com/deepmodeling/deepmd-kit/pull/2903
* fix: make the se attn v2 descriptor energy conservative. by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/2905 and https://github.com/deepmodeling/deepmd-kit/pull/2916
* nvnmd: update doc and fix bug in map_flt_nvnmd.cc by LiuGroupHNU in https://github.com/deepmodeling/deepmd-kit/pull/2831
* cmake: skip executing python when cross compiling by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2876
* set GPU binding in DeepTensor and DataModifier by Yi-FanLi in https://github.com/deepmodeling/deepmd-kit/pull/2886
* fix LAMMPS wheel with CUDA wheels by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2887
* fix TypeError when type_map is not given by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2890
* fix "expression result unused" warnings by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2910

CI/CD

* fix cuda installation for building wheels by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2879
* fix source distribution version in build-wheel.yml by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2883
* run Test CUDA in container by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2892
* fix a typo in tool.cibuildwheel.linux.environment by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2896

Documentation
* docs: update DPRc examples to make it compressible by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2874
* docs: add easy install development version by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2880
* docs: replace relative URLs in PyPI documentation by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2885
* docs: `mpirun --version` to get MPI version by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2915

**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v2.2.5...v2.2.6

> [!CAUTION]
> Known critical issues in this version
> - Incorrect results on GPUs.
> - `se_atten_v2` gives inconsistent energy and forces.
>
> We suggest all users use a newer version. See https://github.com/deepmodeling/deepmd-kit/issues/2866 for more information.

New features
* lmp: support `unit real` by njzjz and Yi-FanLi in https://github.com/deepmodeling/deepmd-kit/pull/2775 https://github.com/deepmodeling/deepmd-kit/pull/2790 https://github.com/deepmodeling/deepmd-kit/pull/2800
* add linear models that are linear combination of DP models by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2781
* support atomic/relative model deviation in CLI by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2801
* make pairwise_dprc model work with MPI by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2818

Merge cuda and rocm code
* merge cuda and rocm files by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2844
* merge CUDA and ROCm codes in op by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2847

Enhancement
* lmp: throw error for traditional installation if dependent packages are not installed by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2777
* lmp: add the header for atomic model deviation by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2778
* check status of allocate_temp by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2782
* do not sort atoms in dp test by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2794
* lmp: `fix_dplr` use the same `type_map` from `pair_deepmd` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2776
* check status of allocate_temp by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2797
* fix np.loadtxt DeprecationWarning by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2802
* `ndarray.tostring` -> `ndarray.tobytes` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2814
* `tf.accumulate_n` -> `tf.add_n` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2815
* `tf.test.TestCase.test_session` -> `tf.test.TestCase.cached_session` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2816
* make the pairwise DPRc model 2x faster by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2833
* prod_env_mat: allocate GPU memory out of frame loop by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2832
* refactor model version convert by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2854
* bump LAMMPS version to stable_2Aug2023_update1 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2859

Documentation
* docs: improve checkpoint description by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2784
* fix grammatical errors by Yi-FanLi in https://github.com/deepmodeling/deepmd-kit/pull/2796
* docs: add doc to install cmake by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2805
* docs: add docs for addtional CMake arguments via pip by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2806
* add citation for fparam by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2821
* add citation for `aparam` by mingzhong15 in https://github.com/deepmodeling/deepmd-kit/pull/2825
* docs: rewrite coding conventions by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2855

Build and release
* migrate Python build backend to scikit-build-core by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2798
* drop old GCC versions in test by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2812
* speed up GitHub Actions by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2822
* improve configurations of Python lint tools by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2823
* fix CTest by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2828
* add tox configutation by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2829
* use parse_version from packaging.version instead of pkg_resources by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2830
* build linux-aarch64 wheel on self-hosted runner by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2851
* add test cuda workflow by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2848
* cmake: use pip to install tensorflow by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2858
* cmake: use modern `HIP` language by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2857
* download cub using CMake FetchContent by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2870

Bug fixing
* fix dp test atomic polar; add UTs for dp test by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2785
* ignore drdq when generalized force loss is not set by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2807
* lmp: let fparam_do_compute not execute by default by Yi-FanLi in https://github.com/deepmodeling/deepmd-kit/pull/2819
* Fix invalid escape sequence by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2820
* fix missing version file with setuptools-scm v8 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2850
* fix compatibility with NumPy 1.26 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2853
* fix finetune RMSE and memory issue by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2860
* fix the issue of applying modifier multiple times when batch set is load only once by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/2864

**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v2.2.4...v2.2.5

> [!CAUTION]
> Known critical issues in this version
> - Incorrect results from DPLR training.
> - `se_atten_v2` gives inconsistent energy and forces.
>
> See https://github.com/deepmodeling/deepmd-kit/issues/2866 for more information.

Breaking changes
* breaking: dp test all data by default by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2756

New features
* support mapping to ghost type by link89 in https://github.com/deepmodeling/deepmd-kit/pull/2732
* Added atomic dipole to test.py by hanao2 in https://github.com/deepmodeling/deepmd-kit/pull/2747
* feat: calculate the real error in dp model-devi by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2757
* feat: add se_atten_v2 descriptor by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/2755

Enhancement
* enable check_json hook by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2760

Bug fixings
* fix documentation url in pyproject.toml by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2742
* fix bug in deepmd.infer.deep_pot.DeepPot by ChiahsinChu in https://github.com/deepmodeling/deepmd-kit/pull/2731
* Use `module.__path__[0]` instead of `module.__file__` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2769

New Contributors
* link89 made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/2732
* hanao2 made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/2747

**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v2.2.3...v2.2.4