Deepmd-kit

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

DeePMD-kit v3: Multiple-backend Framework, DPA-2 Large Atomic Model, and Plugin Mechanisms

We are excited to present the first release candidate of DeePMD-kit v3, an advanced version that enables deep potential models with TensorFlow, PyTorch, or JAX backends. Additionally, DeePMD-kit v3 introduces support for the [DPA-2 model](https://arxiv.org/abs/2312.15492), a novel architecture optimized for large atomic models. This release enhances plugin mechanisms, making integrating and developing new models easier.

Highlights

Multiple-backend framework: TensorFlow, PyTorch, and JAX support


DeePMD-kit v3 adds a versatile, pluggable framework providing consistent training and inference experience across multiple backends. Version 3.0.0 includes:

- **TensorFlow backend**: Known for its computational efficiency with a static graph design.
- **PyTorch backend**: A dynamic graph backend that simplifies model extension and development.
- **DP backend**: Built with NumPy and [Array API](https://data-apis.org/array-api/), a reference backend for development without heavy deep-learning frameworks.
- **JAX backend**: Based on the DP backend via Array API, a static graph backend.

| Features |TensorFlow | PyTorch | JAX | DP |
| ------------------------- |----------------- |------------ |------|------|
|Descriptor local frame | ✅ | | | |
|Descriptor se_e2_a | ✅ | ✅ | ✅ | ✅ |
|Descriptor se_e2_r | ✅ | ✅ | ✅ | ✅ |
|Descriptor se_e3 | ✅ | ✅ | ✅ | ✅ |
|Descriptor se_e3_tebd | | ✅ | ✅ | ✅ |
|Descriptor DPA1 | ✅ | ✅ | ✅ | ✅ |
|Descriptor DPA2 | | ✅ | ✅ | ✅ |
|Descriptor Hybrid | ✅ | ✅ | ✅ | ✅ |
|Fitting energy | ✅ | ✅ | ✅ | ✅ |
|Fitting dipole | ✅ | ✅ | ✅ | ✅ |
|Fitting polar | ✅ | ✅ | ✅ | ✅ |
|Fitting DOS | ✅ | ✅ | ✅ | ✅ |
|Fitting property | | ✅ | ✅ | ✅ |
| ZBL | ✅ | ✅ | ✅ | ✅ |
| DPLR | ✅ | | | |
| DPRc | ✅ | ✅ | ✅ | ✅ |
| Spin | ✅ | ✅ | | ✅ |
| Gradient calculation | ✅ | ✅ | ✅ | |
| Model training | ✅ | ✅ | | |
| Model compression | ✅ | ✅ | | |
| Python inference | ✅ | ✅ | ✅ | ✅ |
| C++ inference | ✅ | ✅ | ✅ | |

Critical features of the multiple-backend framework include the ability to:

- Train models using different backends with the same training data and input script, allowing backend switching based on your efficiency or convenience needs.
sh
Training a model using the TensorFlow backend
dp --tf train input.json
dp --tf freeze
dp --tf compress

Training a model using the PyTorch backend
dp --pt train input.json
dp --pt freeze
dp --pt compress


- Convert models between backends using `dp convert-backend`, with backend-specific file extensions (e.g., `.pb` for TensorFlow and `.pth` for PyTorch).
sh
Convert from a TensorFlow model to a PyTorch model
dp convert-backend frozen_model.pb frozen_model.pth
Convert from a PyTorch model to a TensorFlow model
dp convert-backend frozen_model.pth frozen_model.pb
Convert from a PyTorch model to a JAX model
dp convert-backend frozen_model.pth frozen_model.savedmodel
Convert from a PyTorch model to the backend-independent DP format
dp convert-backend frozen_model.pth frozen_model.dp


- Run inference across backends via interfaces like `dp test`, Python/C++/C interfaces, or third-party packages (e.g., dpdata, ASE, LAMMPS, AMBER, Gromacs, i-PI, CP2K, OpenMM, ABACUS, etc.).

sh
In a LAMMPS file:
run LAMMPS with a TensorFlow backend model
pair_style deepmd frozen_model.pb
run LAMMPS with a PyTorch backend model
pair_style deepmd frozen_model.pth
run LAMMPS with a JAX backend model
pair_style deepmd frozen_model.savedmodel
Calculate model deviation using different models
pair_style deepmd frozen_model.pb frozen_model.pth frozen_model.savedmodel out_file md.out out_freq 100


- Add a new backend to DeePMD-kit much more quickly if you want to contribute to DeePMD-kit.

DPA-2 model: Towards a universal large atomic model for molecular and material simulation

The [DPA-2 model](https://arxiv.org/abs/2312.15492) offers a robust architecture for large atomic models (LAM), accurately representing diverse chemical systems for high-quality simulations. In this release, DPA-2 is trainable in the PyTorch backend, with an example configuration available in `examples/water/dpa2`. DPA-2 is available for Python inference in the JAX backend.

The DPA-2 descriptor comprises `repinit` and `repformer`, as shown below.


The PyTorch backend supports training strategies for large atomic models, including:

- **Parallel training**: Train large atomic models on multiple GPUs for efficiency.
sh
torchrun --nproc_per_node=4 --no-python dp --pt train input.json

- **Multi-task training**: For large atomic models trained across a broad range of data calculated on different DFT levels with shared descriptors. An example is given in `examples/water_multi_task/pytorch_example/input_torch.json`.
- **Finetune**: Training a pre-train large atomic model on a smaller, task-specific dataset. The PyTorch backend has supported `--finetune` argument in the `dp --pt train` command line.

Plugin mechanisms for external models

In v3.0.0, plugin capabilities allow you to develop models with TensorFlow, PyTorch, or JAX, leveraging DeePMD-kit's trainer, loss functions, and interfaces. A plugin example is [deepmd-gnn](https://github.com/njzjz/deepmd-gnn), which supports training the MACE and NequIP models in the DeePMD-kit with the familiar commands.

sh
dp --pt train mace.json
dp --pt freeze
dp --pt test -m frozen_model.pth -s ../data/



Other new features

- Descriptor se_e3_tebd. (4066)
- Fitting the property (3867).
- New training parameters: `max_ckpt_keep` (3441), `change_bias_after_training` (3993), and `stat_file`.
- New command line interface: `dp change-bias` (3993) and `dp show` (3796).
- Support generating JSON schema for integration with VSCode (3849).
- The latest LAMMPS version (stable_29Aug2024_update1) is supported. (4088, 4179)

Breaking changes

- Python 3.7 and 3.8 supports are dropped. (3185, 4185)
- We require all model files to have the correct filename extension for all interfaces so a corresponding backend can load them. TensorFlow model files must end with `.pb` extension.
- Bias is removed by default from type embedding. (3958)
- The spin model is refactored, and its usage in the LAMMPS module has been changed. (3301, 4321)
- Multi-task training support is removed from the TensorFlow backend. (3763)
- The `set_prefix` key is deprecated. (3753)
- `dp test` now uses all sets for training and test. In previous versions, only the last set is used as the test set in dp test. (3862)
- The Python module structure is fully refactored. The old `deepmd` module was moved to `deepmd.tf` without other API changes, and `deepmd_utils` was moved to `deepmd` without other API changes. (3177, 3178)
- Python class `DeepTensor` (including `DeepDiople` and `DeepPolar`) now returns atomic tensor in the dimension of `natoms` instead of `nsel_atoms`. (3390)
- C++ 11 support is dropped. (4068)

For other changes, refer to **Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v2.2.11...v3.0.0rc0

Contributors

The PyTorch backend was developed in the [dptech-corp/deepmd-pytorch](https://github.com/dptech-corp/deepmd-pytorch) repository, and then it was fully merged into the deepmd-kit repository in #3180. Contributors to the deepmd-pytorch repository:
- 20171130
- CaRoLZhangxy
- amcadmus
- guolinke
- iProzd
- nahso
- njzjz
- qin2xue3jian4
- shishaochen
- zjgemi

Contributors to the deepmd-kit repository:
* CaRoLZhangxy: 3162 3287 3337 3375 3379 3434 3436 3612 3613 3614 3656 3657 3740 3780 3917 3919 4209 4237
* Chengqian-Zhang: 3615 3796 3828 3840 3867 3912 4120 4145 4280
* ChiahsinChu: 4246 4248
* Cloudac7: 4031
* HydrogenSulfate: 4117
* LiuGroupHNU: 3978
* Mancn-Xu: 3567
* Yi-FanLi: 3822 4013 4084 4283
* anyangml: 3192 3210 3212 3248 3266 3281 3296 3309 3314 3321 3327 3338 3351 3362 3376 3385 3398 3410 3426 3432 3435 3447 3451 3452 3468 3485 3486 3575 3584 3654 3662 3663 3706 3757 3759 3812 3824 3876 3946 3975 4194 4205 4292 4335 4339
* caic99: 3465 4165
* chazeon: 3473 3652 3653 3739
* cherryWangY: 3877 4227 4297 4298 4299 4300
* dependabot: 3231 3312 3446 3487 3777 3882 4045 4127
* hztttt: 3762
* iProzd: 3180 3203 3245 3261 3301 3355 3359 3367 3371 3378 3380 3387 3388 3409 3411 3441 3442 3445 3456 3480 3569 3571 3573 3607 3616 3619 3696 3698 3712 3717 3718 3725 3746 3748 3758 3763 3768 3773 3774 3775 3781 3782 3785 3803 3813 3814 3815 3826 3837 3841 3842 3843 3873 3906 3914 3916 3925 3926 3927 3933 3944 3945 3957 3958 3967 3971 3976 3992 3993 4006 4007 4015 4066 4089 4138 4139 4148 4162 4222 4223 4224 4225 4243 4244 4321 4323 4324 4344 4353 4354
* iid-ccme: 4340
* nahso: 3726 3727
* njzjz: 3164 3167 3169 3170 3171 3172 3173 3174 3175 3176 3177 3178 3179 3181 3185 3186 3187 3191 3193 3194 3195 3196 3198 3200 3201 3204 3205 3206 3207 3213 3217 3220 3221 3222 3223 3226 3228 3229 3237 3238 3239 3243 3244 3247 3249 3250 3253 3254 3257 3258 3263 3267 3271 3275 3276 3283 3284 3285 3286 3288 3290 3292 3293 3294 3303 3304 3306 3307 3308 3310 3313 3315 3316 3318 3323 3325 3326 3330 3331 3332 3333 3335 3339 3342 3343 3346 3348 3349 3350 3356 3358 3360 3361 3364 3365 3366 3369 3370 3373 3374 3377 3381 3382 3383 3384 3386 3390 3393 3394 3395 3396 3397 3399 3402 3403 3404 3405 3415 3418 3419 3421 3422 3423 3424 3425 3431 3437 3438 3443 3444 3449 3450 3453 3461 3462 3464 3484 3519 3570 3572 3574 3580 3581 3583 3600 3601 3605 3610 3617 3618 3620 3621 3624 3625 3631 3632 3633 3636 3651 3658 3671 3676 3682 3685 3686 3687 3688 3694 3695 3701 3709 3711 3714 3715 3716 3721 3737 3753 3767 3776 3784 3787 3792 3793 3794 3798 3800 3801 3810 3811 3816 3820 3829 3832 3834 3835 3836 3838 3845 3846 3849 3851 3855 3856 3857 3861 3862 3870 3872 3874 3875 3878 3880 3888 3889 3890 3891 3893 3894 3895 3896 3897 3918 3921 3922 3930 3956 3964 3965 3972 3973 3977 3980 3981 3982 3985 3987 3989 3995 3996 4001 4002 4005 4009 4010 4012 4021 4024 4025 4027 4028 4032 4038 4047 4049 4059 4067 4068 4070 4071 4073 4074 4075 4079 4081 4083 4088 4095 4100 4106 4110 4111 4113 4131 4134 4136 4144 4146 4147 4152 4153 4155 4156 4160 4172 4176 4178 4179 4180 4185 4187 4190 4196 4199 4200 4204 4212 4213 4214 4217 4218 4219 4220 4221 4226 4228 4230 4236 4238 4239 4240 4242 4247 4251 4252 4254 4256 4257 4258 4259 4260 4261 4263 4264 4269 4271 4274 4275 4278 4284 4285 4286 4287 4288 4289 4290 4293 4294 4301 4304 4307 4309 4313 4315 4318 4319 4320 4325 4326 4327 4329 4330 4331 4336 4338 4341 4342 4343 4345 4350 4351 4352 4355 4356 4357
* njzjz-bot: 3669 3953 3988 4119 4266
* pre-commit-ci: 3163 3236 3264 3305 3454 3489 3599 3634 3659 3675 3700 3720 3754 3779 3825 3850 3863 3883 3900 3938 3955 3983 4003 4048 4053 4065 4080 4097 4115 4130 4159 4173 4192 4235 4268 4310 4337
* robinzyb: 3647
* shiruosong: 3344 3345
* sigbjobo: 4150
* wanghan-iapcm: 3184 3188 3190 3199 3202 3208 3219 3225 3232 3234 3235 3240 3241 3246 3260 3262 3268 3274 3279 3280 3282 3289 3295 3340 3352 3357 3389 3391 3400 3413 3458 3469 3609 3611 3626 3628 3639 3642 3649 3650 3755 3761 4052 4116 4135 4142 4166 4233 4241
* wangzyphysics: 3597 4312

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

What's Changed

Breaking changes

* breaking: drop C++ 11 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4068
* breaking(pt/dp): tune new sub-structures for DPA2 by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/4089
The default values of new options `g1_out_conv` and `g1_out_mlp` are set to `True`. The behaviors in previous versions are `False`.

New features

* feat pt : Support property fitting by Chengqian-Zhang in https://github.com/deepmodeling/deepmd-kit/pull/3867
* feat(pt/dp): support three-body type embedding by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/4066
* feat: load customized OP library in the C++ interface by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4073
* feat: make `dp neighbor-stat --type-map` optional by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4049
* feat: directional nlist by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/4052
* feat(pt): support `eval_typeebd` for `DeepEval` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4110
* feat: `DeepEval.get_model_def_script` and common `dp show` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4131
* chore: support preset bias of atomic model output by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/4116
* feat(jax): support neural networks in https://github.com/deepmodeling/deepmd-kit/pull/4156

Enhancement

* fix: bump LAMMPS to stable_29Aug2024 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4088
* chore(pt): cleanup deadcode by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/4142
* chore(pt): make comm_dict for dpa2 noncompulsory when nghost is 0 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4144
* Set ROCM_ROOT to ROCM_PATH when it exist by sigbjobo in 4150
* chore(pt): move deepmd.pt.infer.deep_eval.eval_model to tests by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4153

Documentation
* docs: improve docs for environment variables by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4070
* docs: dynamically generate command outputs by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4071
* docs: improve error message for inconsistent type maps by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4074
* docs: add multiple packages to `intersphinx_mapping` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4075
* docs: document CMake variables using Sphinx styles by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4079
* docs: update ipi installation command by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4081
* docs: fix the default value of `DP_ENABLE_PYTORCH` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4083
* docs: fix defination of `se_e3` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4113
* docs: update DeepModeling URLs by njzjz-bot in https://github.com/deepmodeling/deepmd-kit/pull/4119
* docs(pt): examples for new dpa2 model by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/4138

Bugfix

* fix: fix PT AutoBatchSize OOM bug and merge execute_all into base by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4047
* fix: replace `datetime.datetime.utcnow` which is deprecated by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4067
* fix:fix LAMMPS MPI tests with mpi4py 4.0.0 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4032
* fix(pt): invalid type_map when multitask training by Cloudac7 in https://github.com/deepmodeling/deepmd-kit/pull/4031
* fix: manage testing models in a standard way by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4028
* fix(pt): fix ValueError when array byte order is not native by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4100
* fix(pt): convert `torch.__version__` to `str` when serializing by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4106
* fix(tests): fix `skip_dp` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4111
* [Fix] Wrap log_path with Path by HydrogenSulfate in https://github.com/deepmodeling/deepmd-kit/pull/4117
* fix: bugs in uts for property fit by Chengqian-Zhang in https://github.com/deepmodeling/deepmd-kit/pull/4120
* fix: type of the preset out bias by wanghan-iapcm in https://github.com/deepmodeling/deepmd-kit/pull/4135
* fix(pt): fix zero inputs for LayerNorm by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4134
* fix(pt/dp): share params of repinit_three_body by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/4139
* fix(pt): move entry point from deepmd.pt.model to deepmd.pt by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4146
* fix: fix DPH5Path.glob for new keys by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4152
* fix(pt): make state_dict safe for weights_only by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/4148
* fix(pt): fix compute_output_stats_global when atomic_output is None by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4155
* fix(pt ut): make separated uts deterministic by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/4162
* fix(pt): finetuning property/dipole/polar/dos fitting with multi-dimensional data causes error by Chengqian-Zhang in https://github.com/deepmodeling/deepmd-kit/pull/4145

Dependency updates
* chore(deps): bump scikit-build-core to 0.9.x by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4038
* build(deps): bump pypa/cibuildwheel from 2.19 to 2.20 by dependabot in https://github.com/deepmodeling/deepmd-kit/pull/4045
* build(deps): bump pypa/cibuildwheel from 2.20 to 2.21 by dependabot in https://github.com/deepmodeling/deepmd-kit/pull/4127

CI/CD
* ci: add `include-hidden-files` to `actions/upload-artifact` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4095
* ci: test Python 3.12 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4059
* CI(codecov): do not notify until all reports are ready by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4136


**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v3.0.0b3...v3.0.0b4

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

What's Changed
Other Changes
* fix: fix nopbc in dpdata driver by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4027


**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v3.0.0b2...v3.0.0b3

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

What's Changed
New features

* feat: add documentation and options for multi-task arguments by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3989
* feat: plain text model format by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4025
* feat: allow model arguments to be registered outside by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3995
* feat: add `get_model` classmethod to `BaseModel` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4002

Enhancement

* add unittest for virial and pe/atom by Yi-FanLi in https://github.com/deepmodeling/deepmd-kit/pull/4013

Documentation
* docs: document `PYTORCH_ROOT` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3981
* docs: Disallow improper capitalization by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3982
* docs: pin sphinx-argparse to < 0.5.0 by njzjz-bot in https://github.com/deepmodeling/deepmd-kit/pull/3988

Bugfixes
* fix(cmake): fix `set_if_higher` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3977
* fix(pt): ensure suffix of `--init_model` and `--restart` is `.pt` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3980
* fix(pt): do not overwrite disp_file when restarting training by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3985
* fix(cc): compile `select_map<int>` when TensorFlow backend is off by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3987
* fix(pt): make 'find_' to be float in get data by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3992
* fix float precision problem of se_atten in line 217 (3961) by LiuGroupHNU in https://github.com/deepmodeling/deepmd-kit/pull/3978
* fix: fix errors for zero atom inputs by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4005
* fix(pt): optimize graph memory usage by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/4006
* fix(pt): fix lammps nlist sort with large sel by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3993
* fix(cc): add `atomic` argument to `DeepPotBase::computew` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3996
* fix(lmp): call model deviation interface without atomic properties when they are not requested by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4012
* fix(c): call C++ interface without atomic properties when they are not requested by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4010
* fix(pt): fix `get_dim` for `DescrptDPA1Compat` by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/4007
* fix(cc): fix message passing when nloc is 0 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4021
* fix(pt): use user seed in `DpLoaderSet` by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/4015

Code style
* style: require explicit device and dtype by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4001
* style: enable N804 and N805 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4024

CI/CD
* ci: pin PT to 2.3.1 when using CUDA by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/4009

**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v3.0.0b1...v3.0.0b2

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

What's Changed

Breaking Changes
* breaking(pt/tf/dp): disable bias in type embedding by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3958
This change may make PyTorch checkpoints generated by v3.0.0b0 cannot be used in v3.0.0b1.

New features
* feat: add plugin entry point for PT by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3965
* feat(tf): improve the activation setting in tebd by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3971

Bugfix
* fix: remove ref-names from .git_archival.txt by njzjz-bot in https://github.com/deepmodeling/deepmd-kit/pull/3953
* fix(dp): fix dp seed in dpa2 descriptor by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3957
* fix(pt): add `finetune_head` to argcheck by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3967
* fix(cmake): fix USE_PT_PYTHON_LIBS by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3972
* fix(cmake): set C++ standard according to the PyTorch version by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3973
* Fix: tf dipole atomic key by anyangml in https://github.com/deepmodeling/deepmd-kit/pull/3975
* fix(pt/tf/dp): normalize the econf by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3976

CI/CD
* ci(deps): bump uv to 0.2.24 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3964
* style: enable B904 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3956

**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v3.0.0b0...v3.0.0b1

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

What's Changed

Compared to [v3.0.0a0](https://github.com/deepmodeling/deepmd-kit/releases/tag/v3.0.0a0), v3.0.0b0 contains all changes in [v2.2.10](https://github.com/deepmodeling/deepmd-kit/releases/tag/v2.2.10) and [v2.2.11](https://github.com/deepmodeling/deepmd-kit/releases/tag/v2.2.11), as well as:

Breaking changes
* breaking: remove multi-task support in tf by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3763
* breaking: deprecate `set_prefix` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3753
* breaking: use all sets for training and test by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3862. In previous versions, only the last set is used as the test set in `dp test`.
* PyTorch models trained in v3.0.0a0 cannot be used in v3.0.0b0 due to several changes. As mentioned in the release note of v3.0.0a0, we didn't promise backward compatibility for v3.0.0a0.
* The DPA-2 configurations have been changed by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3768. The old format in v3.0.0a0 is no longer supported.

Major new features

- Latest supported features in the PyTorch and DP backend, which are consistent with the TensorFlow backend if possible:
- Descriptor: `se_e2_a`, `se_e2_r`, `se_e3`, `se_atten`, `se_atten_v2`, `dpa2`, `hybrid`;
- Fitting: `energy`, `dipole`, `polar`, `dos`, `fparam`/`apram` support
- Model: standard, DPRc, `frozen`, ZBL, Spin
- Python inference interface
- PyTorch only: C++ inference interface for energy only
- PyTorch only: TensorBoard
- Support using the DPA-2 model in the LAMMPS by CaRoLZhangxy in https://github.com/deepmodeling/deepmd-kit/pull/3657. If you install the Python interface from the source, you must set the environment variable `DP_ENABLE_PYTORCH=1` to build the PyTorch customized OPs.
- New command line options `dp show` by Chengqian-Zhang in https://github.com/deepmodeling/deepmd-kit/pull/3796 and `dp change-bias` by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3933.
- New training options `max_ckpt_keep` by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3441 and `change_bias_after_training` by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3933. Several training options now take effect in the PyTorch backend, such as `seed` by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3773, `disp_training` and `time_training` by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3775, and `profiling` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3897.
- Performance improvement of the PyTorch backend by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3422, https://github.com/deepmodeling/deepmd-kit/pull/3424, https://github.com/deepmodeling/deepmd-kit/pull/3425 and by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/3826
- Support generating JSON schema for integration with VSCode by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/3849

Minor enhancements and code refactoring are listed at https://github.com/deepmodeling/deepmd-kit/compare/v3.0.0a0...v3.0.0b0.

Contributors

- CaRoLZhangxy: 3434, 3436, 3612, 3613, 3614, 3656, 3657, 3740, 3780, 3917, 3919
- Chengqian-Zhang: 3615, 3796, 3828, 3840, 3912
- Mancn-Xu: 3567
- Yi-FanLi: 3822
- anyangml: 3398, 3410, 3426, 3432, 3435, 3447, 3451, 3452, 3468, 3485, 3486, 3575, 3584, 3654, 3662, 3663, 3706, 3757, 3759, 3812, 3824, 3876
- caic99: 3465
- chazeon: 3473, 3652, 3653, 3739
- cherryWangY: 3877
- dependabot: 3446, 3487, 3777, 3882
- hztttt: 3762
- iProzd: 3301, 3409, 3411, 3441, 3442, 3445, 3456, 3480, 3569, 3571, 3573, 3607, 3616, 3619, 3696, 3698, 3712, 3717, 3718, 3725, 3746, 3748, 3758, 3763, 3768, 3773, 3774, 3775, 3781, 3782, 3785, 3803, 3813, 3814, 3815, 3826, 3837, 3841, 3842, 3843, 3873, 3906, 3914, 3916, 3925, 3926, 3927, 3933, 3944, 3945
- nahso: 3726, 3727
- njzjz: 3393, 3402, 3403, 3404, 3405, 3415, 3418, 3419, 3421, 3422, 3423, 3424, 3425, 3431, 3437, 3438, 3443, 3444, 3449, 3450, 3453, 3461, 3462, 3464, 3484, 3519, 3570, 3572, 3574, 3580, 3581, 3583, 3600, 3601, 3605, 3610, 3617, 3618, 3620, 3621, 3624, 3625, 3631, 3632, 3633, 3636, 3651, 3658, 3671, 3676, 3682, 3685, 3686, 3687, 3688, 3694, 3695, 3701, 3709, 3711, 3714, 3715, 3716, 3721, 3737, 3753, 3767, 3776, 3784, 3787, 3792, 3793, 3794, 3798, 3800, 3801, 3810, 3811, 3816, 3820, 3829, 3832, 3834, 3835, 3836, 3838, 3845, 3846, 3849, 3851, 3855, 3856, 3857, 3861, 3862, 3870, 3872, 3874, 3875, 3878, 3880, 3888, 3889, 3890, 3891, 3893, 3894, 3895, 3896, 3897, 3918, 3921, 3922, 3930
- njzjz-bot: 3669
- pre-commit-ci: 3454, 3489, 3599, 3634, 3659, 3675, 3700, 3720, 3754, 3779, 3825, 3850, 3863, 3883, 3900, 3938
- robinzyb: 3647
- wanghan-iapcm: 3413, 3458, 3469, 3609, 3611, 3626, 3628, 3639, 3642, 3649, 3650, 3755, 3761
- wangzyphysics: 3597

New Contributors
* wangzyphysics made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/3597
* robinzyb made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/3647
* Mancn-Xu made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/3567
* njzjz-bot made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/3669
* cherryWangY made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/3877

**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v3.0.0a0...v3.0.0b0

For discussion of v3, please go to https://github.com/deepmodeling/deepmd-kit/discussions/3401