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* 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
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