Deepmd-kit

New feature:
- Model compression for se_3, se_r descriptors. Energy and tensor models (1225 1228 1361 )
- Add init-frz-model support for se-t type descriptor (1245)
- Added all activation functions for model compression. (1283)
- Update guidelines for the number of threads (1291)
- Enable mixed precision support for deepmd-kit (1285 1471 )
- Unify C++ errors and pass message to LAMMPS (1326)
- Optimize `DPTabulate._build_lower` method (1323)
- Calculate neighbor statistics from CLI (1476)
- Add an interface to eval descriptors (1483)

Enhancement:
- deprecate `numb_test` in the training script (1249)
- Accelerate model compression (1274)
- Use c++14 for TF 2.7 (1275)
- Add a citation badge (1280)
- Add embedding network dimension check of model compression (1303)
- Provide an option to skip neighbor stat (1313)
- Add an error message to compress/freeze (1319)
- Redirect `print_summary` to LAMMPS log (1324)
- Enable OpenMP for `prod_force` and `prod_virial` (1360)
- Update issue templates (1368)
- Bump LAMMPS version to `stable_29Sep2021_update2` (1279)
- Remove `api_cc/include/custom_op.h` (1405)
- Introduce TensorFlow Profiler (1414)
- Only test/eval fitting properties during training (1416 1419 )
- Remove the dependency on `inputs` from `inputs_zero` (1417)
- Support recursive detection for the systems of model_devi (1424)
- Enable TF remapper optimizer (1418)
- Dynamically load op library in C++ interface (1384)
- Dplr doc and examples (1458)
- Bump the Python version to 3.10 (1465)
- Do some small optimization to ops (avoid concat or add in loops. Instead, append tensors to a list, and concat or accumulate_n after loops) (943)
- Optimizations related to data statistics
- Skip `data_stat` in `init_from_model` and `restart` mode (1463)
- Assign energy shift stats if atomic energies are assigned (1477)
- Recover input stats from frozen models (1482)
- Test: move loading graphs to setUpClass to accelerate tests (1484)
- Run test_python in the pre-built container (1487)

Bug fixings:
- Update and fix typos in doc (1238 1239 1328 1300 1445 1490 1497 1504 1503 1514 )
- Fix compress training bug within the dp train --init-frz-model interface (1233)
- Fix Python bugs of loc_frame descriptor (1253)
- Fix bug of loc_frame descriptor when using lammps (1255)
- Fix single precision error (1212)
- Fix the np.frombuffer in dp transfer (1246)
- Fix SyntaxWarning in graph.py (1278)
- Change googletest from master to main (1292)
- `update_deepmd_input` when compress (1297 1301 )
- Add importlib_metadata as dependency (1308)
- Fix bugs about parameters of memset (1302)
- Fix model compression bug when fparam or aparam is not zero (1306)
- Add space between words in messages (1312)
- Do not print virial error with nopbc data (1314)
- Fix test errors with TensorFlow 2.7 (1315)
- Fix bug of hip model compression (1325)
- Prevents rcut_smth larger than rcut (1354)
- Fix cell and virial transpose bug in dp_ipi (1353)
- Fix bug in DipoleFittingSeA: (1363)
- Fix cxx standard for LAMMPS (1379)
- Explicitly set neighbor request to full in compute deeptensor/atom to fix bug 1381 (1382)
- Fix NameError (1385)
- Fix network precision under specific situation (1391 1394 )
- Initialize input virial vector to zero (1397)
- Make OpenMP an optional dependency (1498)
- Fix nvcc warning when using cuda-11.x toolkit (1401)
- Add UT for se_3 type descriptor (1404)
- Fix github git url (1409)
- Fix gelu grad multi definitions error (1406)
- Fix `cast_precision` breaking docstring (1437)
- Add image link of ROCm version. (1432)
- Pass integer zero to memset (1499)

[Manual](https://docs.deepmodeling.org/projects/deepmd/en/v2.1.0/) ([PDF](https://docs.deepmodeling.org/_/downloads/deepmd/en/v2.1.0/pdf/)·[Epub](https://docs.deepmodeling.org/_/downloads/deepmd/en/v2.1.0/epub/))

Enhancements
- bump default LAMMPS version to `stable_29Sep2021` (1176)
- improved documentation (1184 1191)

Bug fixings
- add `start_pref_pf` and `limit_pref_pf` to `loss` Argument (1200)
- Fix the bug when type_map has only one element (1196)
- failure of hybrid descriptor (1214)
- fix single precision error in the model compression (1212)

[Download manual](https://docs.deepmodeling.org/_/downloads/deepmd/en/v2.0.3/pdf/)

New features:
- support the plugin for GROMACS (1160 1169 )
- support the `init-frz-model` option for `se_r` and `se_t` (1144)
- support data in hdf5 format (1163)
- automatic batch size for the inference of DP (1165 1154 1173 )
- Allow to scale LR in parallel training in different ways. (1167)

Enhancement for developers:
- support descriptor plugin (1118 1143 )
- support lammps 20210831 (1129)

Bug fixings:
- explicitly set lammps' neighbor request to full to fix bug 1109
- Add init-frz-model command support to the frozen model generated by this command (1137)
- Add error message for repeated model compression (1136)
- doc related improvements and bug fixings (1141 1131 1147 1156 1153 1171 )
- Fix freezing error on checkpoint from parallel training. (1166)

New features:
- correct heat flux calculation: interface for deepmd with the centroids atoms, full 3x3 "atomic-virial" (1093).
- Enable init-frz-model support for the original model (1102 1107 )
- support init-frz-model for hybrid descriptor (1112)

Enhancements:
- use `np.testing.assert_almost_equal` for array comparing (1059)
- set `allow_growth` in `default_tf_session_config` (1067)
- Enable parallel training UT in GitHub CI. (1075)
- create cross-references in docstring (1083)
- add ABC for descriptors (1081)
- merge duplicated NeighborStat.get_stat (1103)

Bug fixings:
- fix hybrid descriptor training error (1052)
- bugs and memory issues in UTs (1056 1066 )
- copy `all_virial` for float precision (1069)
- fix building problem on macos (1071)
- use loader_path on macos instead of $ORIGIN (1078)
- Revert "get library extension suffix from built-in method" 1072
- undo reset lcurve.out during the model compression process (1080)
- fix typo: `lcueve.out`->`lcurve.out` (1077)
- create model compression checkpoint, avoid overwriting original checkpoint (1076)
- Fix shape mismatch when type_embedding is enabled and type_one_side is disabled (1074 )
- reduce `rcut` and `sel` in the example of `se_e3` (1082)
- Fix a potential slice bug in se_t descriptor (1087)
- make compress work for hybrid descriptor composed of se_e2_a (1094)
- Fix gradient not averaged when parallel training. (1104)
- fix bug of single precision model compression (1110)
- fix bug of single precision transfer (1111)
- fix LAMMPS_VERSION_NUMBER condition (1116)
- Fix missing `std::numeric_limits` (1113)
- fix data_modifier OOM problem when set size is too large (1117)
- fix bugs of dipole charge modifier: binary str and missing frozen node (1124 )
- fix "Call to method DeepTensor.__init__ with too many arguments" (1125)

New features:
- parallel training (892 905 913) (Bytedance)
- automatically determine the `sel` from the training data. (831)
- build low and high precision at the same time (879)

Performance improvement:
- speedup tabulate cuda kernel by reducing shm using (830) (Bytedance)
- speedup format_nlist_b (832 845)

Enhancements:
- support to specify CUDA/ROCm root in python pkg building (834) (Bytedance)
- use cached Session to speed up py tests (833)
- add message for DecodeError raised when using model compression (839)
- remove cub include for CUDA>=11 (866)
- Add Errcheck after every kernel function runs And merge redundant code (855)
- adapt changes to auditwheel directory in manylinux (889)
- enhance the cli to generate doc json file (891)
- raise warning before training if sel is not enough (914)

Bug fixings:
- fix bug 824 and Synchronize updates to CUDA cod (828)
- Fix the empty neighbor distance array in neighbor_stat.py (882)
- fix `InvalidArgumentError` caused by zero `sel` and optimize zero matrix (900)
- fix 'NoneType' has no len() in `auto_sel` (911)