Deepmd-kit

New features
* support C API by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1098
* add get cutoff, numb_types, and type_map to C API by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2061
* c: support neighbor list input in the C API by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2106
* c: support DeepPot model deviation in the C API by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2112
* c: fix `ComputeNlist` -> `ComputeNList` in the C API by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2119
* c: fix bug in hpp float interface and add tests by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2128
* c: DeepTensor by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2184
* add a header-only C++ DeepPot class based on C library by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2079
* support the multi-task training api by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/2093
* support the finetune api by iProzd in https://github.com/deepmodeling/deepmd-kit/pull/1946
* supports left hands volume by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1956
* support bfloat16 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1970
* support DPRc + type embedding by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2166

Enhancements
Python
* dp test output files: energy per atom, virial per atom by likefallwind in https://github.com/deepmodeling/deepmd-kit/pull/2029
* log HIP_VISIBLE_DEVICES for ROCm by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2032
* move run_config.ini into the root directory by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2098
* skip `get_gpus` subprocess when TF is cpu only by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2135
* add Optional to type hints when default is None by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2139
* optimize FioBin.save by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2143
* open the graph file only once in compress by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2144
* refactor enable_compression by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2147
* store energy bias with interface precision by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2174
Core
* dynamically load CUDA runtime library by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2082
C++
* uncouple model precision and interface precision by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2031
* merge double and float cc library by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2033
* add shuffle_exclude_empty to DeepPot.compute(nlist, atomic) by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2111
OP
* remove OP_LIB from op_abi by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2150
LAMMPS
* lmp: throw errors when 6-element atomic virial requested by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1983
* enable ttm without a patch by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2055
* bump lammps to stable_23Jun2022_update2 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2053
Build and release
* CMake
* use CPP_CXX_ABI for Python libraries by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1960
* find protobuf headers in an automatic way by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1975
* search TF deps from LD_LIBRARY_PATH; eliminate errors by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1976
* CMake config
* export c++ library to cmake config by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2049
* export C library to cmake config by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2059
* refactor `USE_TF_PYTHON_LIBS` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2177
* add an option to enable native compilation optimization by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2151
* Python and wheel building
* migrate cibuildwheel configs to pyproject.toml and add tests by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2000
* migrate from setup.cfg to pyproject.toml by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2011
* migrate to PEP 517 and PEP 621 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2035
* store TF version in the wheel's extras_require by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2084
* fix win64 builds and add win64 wheels by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2085
* enable CUDA for linux-64 wheels by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2087
* add macos-64 wheels by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2088
* pin manylinux image to a specific tag for GCC 11 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2137
* retag wheels to `py37-none-<platform>` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2180
* build wheels for Linux ARM64 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2179
* pip install lammps module by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2186
* build_tf.py
* build_tf.py: support ROCm; bump to TF 2.10 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2030
* build_tf.py: export `LD_LIBRARY_PATH` when executing `configure` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2185
* build, package, and release C library by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2072
* perceive LAMMPS version for built-in mode by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1950
Test
* enable gcov for Python tests by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1969
* add unittests for LAMMPS pair deepmd by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1977
* c++: add clang tests and fix clang errors by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1992
* refactor: merge tests into the main cmake project by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2102
* merge double and float cc tests by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2108
* add ut for dp convert-from by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2175
* speed up the UTs
* print out the time of each Python unit test by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2116
* speed up test_neighbor_stat by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2120
* speed up tests with CLI by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2121
* CI
* upgrade ubuntu-18.04 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2096
* add pass step to GitHub Actions by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2141
* give pass actions different names by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2142
Code cleanup
* clean deprecated codes by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2140

Documents
* docs: document lammps keyword `relative_v`, `aparam`, and `ttm` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2060
* add dp test help doc by likefallwind in https://github.com/deepmodeling/deepmd-kit/pull/2038
* docs: fix HDF5 path by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2076
* docs: document pip install by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2091
* docs: document the conda-forge channel by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2095
* docs: fix spellings and grammars by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2114
* docs: rewrite docs for parallelism by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2099
* docs: add a FAQ about precision by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2115
* docs: add a note about lammps runpath by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2156
* the se-2 descriptor is multi-body by amcadmus in https://github.com/deepmodeling/deepmd-kit/pull/2069
* add header only library example by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2083
* Update python.md by LiangWenshuo1118 in https://github.com/deepmodeling/deepmd-kit/pull/2158

Bug fixings
* fix gcov coverage by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1951
* Fix typo of radisu by kmu in https://github.com/deepmodeling/deepmd-kit/pull/1954
* fix compatible with importlib_metadata 5.0.0 and Python 3.12 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1961
* fix googletest download by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1949
* fix typo in the doc of `loc_frame` by amcadmus in https://github.com/deepmodeling/deepmd-kit/pull/1963
* replace `:` by `;` from `LD_LIBRARY_PATH` in cmake by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1982
* CVE-2007-4559 Patch by TrellixVulnTeam in https://github.com/deepmodeling/deepmd-kit/pull/1984
* use float/double constants for spline5_switch by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1985
* remove duplicated `convert_13_to_21` by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1986
* resolve macos clang errors by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/1993
* fix Findtensorflow when LD_LIBRARY_PATH is empty by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2010
* fix OP_CXX_ABI for TF>=2.9 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2013
* Fix compatibility with ROCm>=3.5.1; fix typo in hip neighbor_list by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2012
* fix python inference on windows by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2054
* cmake: set TensorFlow as import libraries by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2056
* build_tf.py: mirror fixes by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2057
* build_tf.py: roll back TF version to 2.9 by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2065
* fix type hints errors by Angel-Jia in https://github.com/deepmodeling/deepmd-kit/pull/2070
* improve building wheel workflow by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2074
* skip checking `_GLIBCXX_USE_CXX11_ABI` on windows or osx by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2075
* fix codecov by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2097
* fix TF compile warnings about Status::OK by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2109
* Fix version 0.12 model conversion by Yi-FanLi in https://github.com/deepmodeling/deepmd-kit/pull/2110
* fix invalid escape sequence in strings by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2122
* add precompile headers by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2123
* fix the missing header in api_c tests by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2131
* do not apply automatic batch size on CPUs by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2148
* pass user defined CUDA_NVCC_FLAGS and HIP_HIPCC_FLAGS by njzjz in https://github.com/deepmodeling/deepmd-kit/pull/2168

New Contributors
* kmu made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/1954
* TrellixVulnTeam made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/1984
* Angel-Jia made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/2070
* LiangWenshuo1118 made their first contribution in https://github.com/deepmodeling/deepmd-kit/pull/2158

**Full Changelog**: https://github.com/deepmodeling/deepmd-kit/compare/v2.1.5...v2.2.0.b0

New features:
- Attention based model [DPA-1](https://arxiv.org/abs/2208.08236) (#1866 1886 1923 1943)

Enhancements:
- remove white space from train_attr/training_script (1870)
- replace FastGFile with GFile. FastGFile throws a deprecated warning. (1874)
- docs: make warnings more prominent (1879)
- add examples to cli help (1887)
- remove `get_platform` in setup.py (1897)
- bump to C++ 17 for TF 2.10 (1898)
- compare converted lr with almost equal (1901)
- add tutorial and publication links to docs (1904)
- LAMMPS: Use of “override” instead of “virtual” (1915)
- highlight LAMMPS codes in doc (1921)

Bug fixings:
- support initilize parameters from a fitting with suffix (1885)
- fix DeprecationWarning of imp (1896)
- find protobuf headers from extra paths (1910)
- Fix bugs when init_frz_model using tebd. (1891)
- Use GeluCustom as operator name (1918)
- handle float point error in sys_probs (1919)
- fix model conversion of 0.12 (1941)

Enhancements:
- add core api docs (1800)
- add op docs (1804)
- There's no need for building libtensorflow_cc.so anymore (1744)
- improve conda installation in the documentation (1808)
- merge CMake test codes via `add_subdirectory` (1814)
- avoid multiple sessions in DeepEval (1829)
- bump default lammps version to stable_23Jun2022_update1 (1847)
- error if LAMMPS_VERSION_NUMBER is not defined (1849)
- add variant info to output message (1851)
- generate author list from git (1854)
- lammps plugin: replace v2.0 with actual version (1863)

Bug fixings:
- fix OMP bugs in `prod_force` and `prod_virial` triggered when the cell is smaller than 2rc. (revert prod_force OMP in 1360) (1862)
- fix typo in hip assert error message (1802)
- fix memory leaking of GraphDef (1811)
- add the missing sstream header (1817)
- fix grappler compilation error with TF 1.15 (1821)
- docs: fix shape of virial (1824)
- fix build and running issues on Windows (1830)
- comment unused session in DPTabulate (1834)
- fix deprecated bare `pair_coeff` (1838)

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)