merge devel to master#535
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wanghan-iapcm merged 41 commits intodeepmodeling:masterfrom Sep 8, 2023
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…deepmodeling#466) Co-authored-by: Jia-Xin Zhu <xmuchiahsin@gmail.com> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
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Before this PR, when using DP models to predict energies and forces, the atom types were changed in the returned system according to the type map in the model. This is not an expected behavior. The changed atom types should only be used for internal inference.
In this commit, the deepmd format reads data types from `dpdata.system.LabeledSystem.DTYPES` and load or dump the corresponding data. One can modify `dpdata.system.LabeledSystem.DTYPES` before using it or in a plugin (see tests), so deepmd format can be extended in this way. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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When using system.to() and convert data to write ABACUS `STRU` file, func `make_unlabeled_stru` won't use `atom_types` in data and miswriting the atom order. For example when using data from gaussian/log and other file using ungrouped atom coordinations,as the `atom_types=[0,1,1,1,2,1]` the func will write wrong coordinations and regard the atom as `atom_types=[0,1,1,1,1,2]` which cause serious problem.
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Follow up deepmodeling#476. `deepmd/npy` and `deepmd/raw` are ok, and only `deepmd/hdf5` has this bug.
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Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
When `sys1.append(sys2)`, we do not hope that `sys2` to be modified in any way. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
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Revert after materialsproject/pymatgen#3166 is fixed.
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
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Reverts deepmodeling#501 Let's see if the error got fixed.
…g#505) Move DataType to an independent module, so register it will be eaiser. No breaking changes are made. --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Sometimes, the shape is unknown and can be any integer. This PR supports this situation. The shape of a dimension can be `-1`. Note: Only one `-1` can be used. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: liaoruihao <liaoruihao@liaoruihaodeMacBook-Pro.local>
Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
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The example is wrong? "driver" should be "Driver"? Signed-off-by: Levi Zhou <31941107+ZhouXY-PKU@users.noreply.github.com>
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unclear what this file is used for
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fix deepmodeling#508, deepmodeling#507 --------- Signed-off-by: link89 <xuweihong.cn@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #535 +/- ##
==========================================
+ Coverage 82.76% 82.97% +0.20%
==========================================
Files 70 73 +3
Lines 6313 6490 +177
==========================================
+ Hits 5225 5385 +160
- Misses 1088 1105 +17
☔ View full report in Codecov by Sentry. |
wanghan-iapcm
approved these changes
Sep 8, 2023
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