Deepmd-kit

New features:
- Non-von-Neumann training of DP models. (1707)

Enhancements
- remove dependency of TF headers from C++ public headers (1789)
- use lru_cache for DeepEval (1790)
- support custom gelu implementation (1795)
- support optional gitee gtest download (1793)

Bug fixings:
- bump manylinux image to 2_24; add error message when TF_CXX11_ABI_FLAG is 1 (1796)

New features:
- supports dp convert-from 0.12 (1685)
- add `enable_atom_ener_coeff` option for energy loss (1743)

Enhancements:
- change default NN precision from `float64` to `default` (1644)
- update TF installation doc (1652)
- migrate test_cc from conda to docker (1650)
- use float constants and functions in float functions (1647)
- convert tabulate data from np.ndarray to tf.Tensor (1657)
- reset the graph before freezing the compressed model (1658)
- add free_energy to ase calculator (1667)
- rewrite data doc (1668)
- migrate sphinx mathjax from jsdelivr to cdnjs (1669)
- Documentation improvements (1673)
- doc: add information abotu supported versions of dependencies (1683)
- doc: add Interfaces out of DeePMD-kit (1691)
- optimize format_nlist_i_cpu (1717)
- use net-wise tabulate range (1665)
- implement parallelism for neighbor stat (1624)
- render equations in markdown files (1721)
- update the latest state of easy installation (1726)
- throw warning in C++ if env is not set (1728)
- in model_devi, assumes nopbc if box is set to None (1704)
- add Loss abstract class (1733)
- prevent from linking TF lib when determining TF version (1734)
- Automatically label new pull requests based on the paths of files being changed (1738)
- replace GPU 1./sqrt with rsqrt (1741)
- add DPRc docs (1750)
- docs: switch to dargs directive (1753)
- docs: fix emoji in PDF (1754)
- add a script to build TF C++ library from source (1755)
- add auto cli docs (1751)
- search TF from user site-packages (1764)
- build_tf.py: expose CC and CXX env to bazel (1766)
- docs: add links to parameter keys (1767)
- add argument tests to check examples (1770)
- reduce training steps in tests (1771)
- deprecated docstring_parameter; use sphinx rst_epilog instead (1783)
- remove run_doxygen from sphinx conf.py (1785)
- bump LAMMPS version to stable_23Jun2022 (1779)

Bug fixings:
- fix variable declaration error (1651)
- fix bug of aparam size, should be nlocal_real (1664)
- fix rcut in hybrid model compression (1663)
- provide valid_data the same type_map as train_data (1677)
- deepmodeling.org -> deepmodeling.com (1678)
- fix compress training (1680)
- fix bug of model compression training with se_e2_r type descriptor (1686)
- fix typos in doc (1687)
- fix grappler compilation error with TF 1.15 ~ 2.6 (1697)
- set default fparam and aparam stat and recover from graph (1695)
- fix git permission issue (1716)
- fix tf_cxx_abi in TF 2.9 (1723)
- correct type behavior when atomic energy is requested (1727)
- prevent explicit slash in the path (1713)
- avoid static CUDA linking (1731)
- fix finding TF 2.9 ABI (1736)
- using int64 within the memory allocation operations (1737)
- fix typos in docs and docstrings (1752)
- set a proper std when there is no atoms in the data (1765)
- bump manylinux image to 2014 (1780)
- add __init__.py to deepmd/train/ (1784)
- docs: fix arg reference (1786)

New features:
- support `type_one_side` along with `exclude_types` (1423)
- support adjust sel of frozen models (1573 1574 )
- support `dp convert-from 1.1` (1587)
- support `dp convert-from 1.0` (1597)
- add atom energy bias to type embedding energy (1592 1606 )
- add another way to load LAMMPS plugins (1604)

Enhancement:
- add the deepmodeling banner to doc (1529)
- bump default LAMMPS version to `stable_29Sep2021_update3` (1596)
- compile CUDA code for all archs (1595 1598 )
- follow API changes from latest LAMMPS (1601)
- add kspace pppm/dplr to lmp plugin library (1603)
- add a graph optimizer to parallelize prod_force_a_cpu (1429 1638 )
- refactor init_variable and support type embedding (1610)
- optimize dplr data modifier (1615)
- add system names to model devi header (1618)
- add tips for easy installation (1634)
- add the order of box.raw in data-conv.md (1635)

Bug fixings:
- fix the name of deeptensor/atom and dplr plugin (1548)
- fix macos library name (1566)
- fix model compression bug of nan output (1575)
- fix lammps plugin creator pointer (1602)
- fix the bug introduced by lammps PR 2481 (1605)
- update compress cli input file (1633)
- correct the forward communication at ik differentiation mode in pppm_dplr (1637)
- Fix compilation error and bug in UT in the ROCm environment (1628)

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)