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* implement descriptor plugin; pass params to `Descriptor` * avoid class name conflict * add ArgsPlugin * fix lint warning * revert changes to DescrptSeAR * remove descrpt_se_ar which is replaced by hybrid
* support lammps 20210831 * fix typo Co-authored-by: Han Wang <amcadmus@gmail.com> Co-authored-by: Han Wang <amcadmus@gmail.com>
This commit fixes a typo in Eq. of se_a.
* add error message for replicated model compression * fix typo
* add doc: create a model * use another reference style
* bump doxygen and sphinx version on RTD This fixes #847. The idea comes fom readthedocs/readthedocs.org#8151 (comment). * use version 2 * add other dependencies * fix error * fix path * got a memory error... * 3.9 is not supported * Revert "3.9 is not supported" This reverts commit 3732e62. * Revert "got a memory error..." This reverts commit cb596f1.
* support init-frz-model for se_r and se_t I just copied several codes from se_a, which can also be applied to se_r and se_t. * add a base class for smooth descriptors * clean other changes * modify `embedding_net_pattern` to support se_e3 * fix typo in `embedding_net_pattern`
as now easy installation also contains horovod, so we may want to discuss separately
* Update parallel-training.md * Fix typo * Update parallel training description Trying to be more specific in the parallel training description * Update parallel-training.md
* Add .idea to .gitignore * Add doc for models in model deviation. * Update doc/third-party/lammps-command.md Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: Han Wang <amcadmus@gmail.com> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
* Add gromacs examples * Add doc for gmx/dp plugin * Add gmx plugin in README.md * Add gmx/dp plugin code * Upgrade json.hpp to 3.9.1 * Update doc of installing gromacs * Change the min gcc version to 4.8 * Compile TENSORFLOW_ROOT and DEEPMD_ROOT in dp_gmx_patch * Remove extra files * Update doc to use gcc version 4.8 * Resolve inconsistency in gcc version
* make a draft * add support for hdf5 * fix error with old python * fix rglobal * fix tests_path * fix tests * Update test_deepmd_data.py * use `visit` instead of `visititems` * cache file keys to prevent performance issues * improve performance
* automatic batch size for `dp test` Resolves #1149. We start nbatch * natoms from 1024 (or we can set a different number), and iteratively multiply it by 2 until catching the OOM error. A small issue is that it's a bit slow to catch the TF OOM error. It's a problem of TF and I don't know how to resolve it. Luckily we only need to catch once. * replace `execuate` with `execute` * add unittest; bugfix
* Add entry of install gromacs in README.md
/examples/water/gmx/rdf.png -- 167.16kb -> 141.24kb (15.5%) Signed-off-by: ImgBotApp <ImgBotHelp@gmail.com> Co-authored-by: ImgBotApp <ImgBotHelp@gmail.com>
* generate sphinx doc on the fly for training parameters Sometimes we will forget re-generating train-input-auto.rst, so we may want to regenerate it when running sphinx. This will not affect that file on the GitHub. * get string * remove JSON file
Codecov Report
@@ Coverage Diff @@
## master #1177 +/- ##
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+ Coverage 75.47% 76.04% +0.56%
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Files 88 91 +3
Lines 7043 7258 +215
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+ Hits 5316 5519 +203
- Misses 1727 1739 +12
Continue to review full report at Codecov.
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njzjz
approved these changes
Sep 29, 2021
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