merge devel into master#1942
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Merge master into devel
deepmodeling#921 discussed that the tensors are compressed in the graph file. But it looks no... So at least we remove white space.
FastGFile throws a deprecated warning. See https://github.com/tensorflow/tensorflow/blob/d8ce9f9c301d021a69953134185ab728c1c248d3/tensorflow/python/platform/gfile.py#L128 Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Here I upload the implementation of attention based model (DPA-1), see details in paper: https://arxiv.org/abs/2208.08236. The changes can mainly be listed as following: 1. Add a new descriptor '**se_atten**', using attention schemes and type embeddings (deepmd/descriptor/se_atten.py); 2. Add a new custom op '**ProdEnvMatAMix**', mixing atoms with different types in the sorting, which is only suitable for descriptor using type embeddings (source/op/prod_env_mat_multi_device.cc and other sub files, here I try the best to reuse the previous codes); 3. Other changes to match the newly added descriptor, such as 'sel' supporting 'int' type as input (deepmd/entrypoints/train.py ) and type embedding with padding (deepmd/utils/type_embed.py); 4. **Mixed_type**: a new format of DeepmdData to put different systems sharing the same 'nloc' (instead of same fingerprints) together. (deepmd/utils/data.py & data_system.py) Note that this is only the training code on this new format of data. The generation code of this new format will soon be uploaded in _dpdata_. 5. An example of DPA-1 on water system (examples/water/se_atten/input.json); 6. The unittests on both C++&CUDA&ROCM and python interface of newly added apis(source/lib/tests & source/tests). Unittests passed individually for these newly added features. Thanks for reviewing and disccusions are welcome.
Make warnings shown on the web page more prominent.
…#1885) Note: commonly there is no suffix for a fitting. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
 Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
> deepmd/env.py:8: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses See also https://docs.python.org/3/library/imp.html#imp.reload Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
It is not used anymore. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Also, (1) replace `GREATER_EQUAL` by `VERSION_GREATER_EQUAL`. `GREATER_EQUAL` does not work with `2.10`; (2) upgrade manylinux to 2_28 to have a newer compiler that supports C++ 17. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Fix bugs when init_frz_model using tebd. Add init_variables for attention variables. Fix precision of self.t_bias_atom_e in se_atten.py. Change the default values in argcheck for se_atten (typos). Improve the name scope in se_atten.py. Delete some redundant variables in se_atten.py. Move tf.constant from se_a.__init__() into build. Add UTs for init_frz_model. Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
This should avoid the conflicts related to the custom `Gelu` and Tensorflow's `Gelu`. Also Fix deepmodeling#1913.
enforce type_map change when mixed_type. add out_of_bound check for 'real_atom_types.npy'.
Fix deepmodeling#1934. Add `descrpt_attr/rcut`, `descrpt_attr/ntypes`, `fitting_attr/dfparam`, `model_type`, `o_energy`, `o_force`, `o_virial`, `o_atom_energy`, `o_atom_virial`. Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Codecov ReportBase: 76.98% // Head: 78.16% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## master #1942 +/- ##
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+ Coverage 76.98% 78.16% +1.18%
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Files 117 118 +1
Lines 9417 9876 +459
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+ Hits 7250 7720 +470
+ Misses 2167 2156 -11
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fix bugs in type_idx_map using np.searchsorted
njzjz
approved these changes
Sep 23, 2022
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