v2.2.0-beta.0

New features

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

Enhancements

Python

• dp test output files: energy per atom, virial per atom by @likefallwind in #2029
• log HIP_VISIBLE_DEVICES for ROCm by @njzjz in #2032
• move run_config.ini into the root directory by @njzjz in #2098
• skip get_gpus subprocess when TF is cpu only by @njzjz in #2135
• add Optional to type hints when default is None by @njzjz in #2139
• optimize FioBin.save by @njzjz in #2143
• open the graph file only once in compress by @njzjz in #2144
• refactor enable_compression by @njzjz in #2147
• store energy bias with interface precision by @njzjz in #2174

Core

• dynamically load CUDA runtime library by @njzjz in #2082

C++

• uncouple model precision and interface precision by @njzjz in #2031
• merge double and float cc library by @njzjz in #2033
• add shuffle_exclude_empty to DeepPot.compute(nlist, atomic) by @njzjz in #2111

OP

• remove OP_LIB from op_abi by @njzjz in #2150

LAMMPS

• lmp: throw errors when 6-element atomic virial requested by @njzjz in #1983
• enable ttm without a patch by @njzjz in #2055
• bump lammps to stable_23Jun2022_update2 by @njzjz in #2053

Build and release

• CMake
  • use CPP_CXX_ABI for Python libraries by @njzjz in #1960
  • find protobuf headers in an automatic way by @njzjz in #1975
  • search TF deps from LD_LIBRARY_PATH; eliminate errors by @njzjz in #1976
  • CMake config
    • export c++ library to cmake config by @njzjz in #2049
    • export C library to cmake config by @njzjz in #2059
  • refactor USE_TF_PYTHON_LIBS by @njzjz in #2177
  • add an option to enable native compilation optimization by @njzjz in #2151
• Python and wheel building
  • migrate cibuildwheel configs to pyproject.toml and add tests by @njzjz in #2000
  • migrate from setup.cfg to pyproject.toml by @njzjz in #2011
  • migrate to PEP 517 and PEP 621 by @njzjz in #2035
  • store TF version in the wheel's extras_require by @njzjz in #2084
  • fix win64 builds and add win64 wheels by @njzjz in #2085
  • enable CUDA for linux-64 wheels by @njzjz in #2087
  • add macos-64 wheels by @njzjz in #2088
  • pin manylinux image to a specific tag for GCC 11 by @njzjz in #2137
  • retag wheels to py37-none-<platform> by @njzjz in #2180
  • build wheels for Linux ARM64 by @njzjz in #2179
  • pip install lammps module by @njzjz in #2186
• build_tf.py
  • build_tf.py: support ROCm; bump to TF 2.10 by @njzjz in #2030
  • build_tf.py: export LD_LIBRARY_PATH when executing configure by @njzjz in #2185
• build, package, and release C library by @njzjz in #2072
• perceive LAMMPS version for built-in mode by @njzjz in #1950

Test

• enable gcov for Python tests by @njzjz in #1969
• add unittests for LAMMPS pair deepmd by @njzjz in #1977
• c++: add clang tests and fix clang errors by @njzjz in #1992
• refactor: merge tests into the main cmake project by @njzjz in #2102
• merge double and float cc tests by @njzjz in #2108
• add ut for dp convert-from by @njzjz in #2175
• speed up the UTs
  • print out the time of each Python unit test by @njzjz in #2116
  • speed up test_neighbor_stat by @njzjz in #2120
  • speed up tests with CLI by @njzjz in #2121
• CI
  • upgrade ubuntu-18.04 by @njzjz in #2096
  • add pass step to GitHub Actions by @njzjz in #2141
  • give pass actions different names by @njzjz in #2142

Code cleanup

• clean deprecated codes by @njzjz in #2140

Documents

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

Bug fixings

• fix gcov coverage by @njzjz in #1951
• Fix typo of radisu by @kmu in #1954
• fix compatible with importlib_metadata 5.0.0 and Python 3.12 by @njzjz in #1961
• fix googletest download by @njzjz in #1949
• fix typo in the doc of loc_frame by @amcadmus in #1963
• replace : by ; from LD_LIBRARY_PATH in cmake by @njzjz in #1982
• CVE-2007-4559 Patch by @TrellixVulnTeam in #1984
• use float/double constants for spline5_switch by @njzjz in #1985
• remove duplicated convert_13_to_21 by @njzjz in #1986
• resolve macos clang errors by @njzjz in #1993
• fix Findtensorflow when LD_LIBRARY_PATH is empty by @njzjz in #2010
• fix OP_CXX_ABI for TF>=2.9 by @njzjz in #2013
• Fix compatibility with ROCm>=3.5.1; fix typo in hip neighbor_list by @nj...

v2.1.5

New features:

• Attention based model DPA-1 (#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)

v2.1.4

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)

v2.1.3

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)

v2.1.2

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)

v2.1.1

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)

v2.1.0

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 (PDF·Epub)

v2.0.3

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

v2.0.2

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)

v2.0.1

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)