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Implementation of se_a_mask op #2313

Merged
merged 15 commits into from
Feb 14, 2023
Merged

Implementation of se_a_mask op #2313

merged 15 commits into from
Feb 14, 2023

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dingye18
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  • Implement se_a_mask op. Training and inference (c++ interface) are tested. Unit test files are required.

  • Fix bug in atom pref setting for forces.

  • Add the unit test for descrpt se_a_mask

  • Remove the unit test for dp mask model

  • Update dp mask system path for unit test

@dingye18
Implementation of se_a_mask op. (#3)
415ac43 
* Implement se_a_mask op. Training and inference (c++ interface) are tested. Unit test files are required.

* Fix bug in atom pref setting for forces.

* Add the unit test for descrpt se_a_mask

* Remove the unit test for dp mask model

* Update dp mask system path for unit test
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codecov-commenter commented Feb 11, 2023 •
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Codecov Report

Base: 74.89% // Head: 74.80% // Decreases project coverage by -0.10% ⚠️

Coverage data is based on head (1be2702) compared to base (96d3a1d).
Patch coverage: 75.56% of modified lines in pull request are covered.

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Additional details and impacted files 
@@            Coverage Diff             @@
##            devel    #2313      +/-   ##
==========================================
- Coverage   74.89%   74.80%   -0.10%     
==========================================
  Files         217      222       +5     
  Lines       21613    22168     +555     
  Branches     1586     1627      +41     
==========================================
+ Hits        16187    16582     +395     
- Misses       4401     4532     +131     
- Partials     1025     1054      +29
Impacted Files Coverage Δ
source/op/prod_force_se_a_mask_grad.cc 13.09% <13.09%> (ø)
source/op/_prod_force_se_a_mask_grad.py 71.42% <71.42%> (ø)
deepmd/loss/ener.py 63.21% <76.66%> (-2.24%) ⬇️
deepmd/descriptor/se_a_mask.py 86.20% <86.20%> (ø)
source/op/descrpt_se_a_mask.cc 87.50% <87.50%> (ø)
source/op/prod_force_se_a_mask.cc 89.77% <89.77%> (ø)
deepmd/descriptor/__init__.py 100.00% <100.00%> (ø)
deepmd/fit/ener.py 89.36% <100.00%> (+0.06%) ⬆️
deepmd/utils/argcheck.py 90.66% <100.00%> (+0.29%) ⬆️
deepmd/utils/weight_avg.py 19.04% <0.00%> (-0.96%) ⬇️
... and 9 more

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@njzjz njzjz changed the title Implementation of se_a_mask op. (#3) Implementation of se_a_mask op Feb 11, 2023
njzjz
njzjz requested changes Feb 11, 2023
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deepmd/utils/argcheck.py Outdated Show resolved Hide resolved
deepmd/descriptor/se_a_mask.py Outdated Show resolved Hide resolved
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dingye18 and others added 5 commits February 12, 2023 16:19
@dingye18
Remove total atom num in input for se_a_mask. Make python class Descr…
d575563 
…ptSeAMask Inherit from DescrptSeA (#4)

* Implement se_a_mask op. Training and inference (c++ interface) are tested. Unit test files are required.

* Fix bug in atom pref setting for forces.

* Add the unit test for descrpt se_a_mask

* Remove the unit test for dp mask model

* Update dp mask system path for unit test

* Remove total_atom_num dependency in se_a_mask. Fetch total atom num through natoms vector.

* Merge devel to dp_mask
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
816a209 
for more information, see https://pre-commit.ci
@dingye18
Dp mask (#5)
44cd591 
* Implement se_a_mask op. Training and inference (c++ interface) are tested. Unit test files are required.

* Fix bug in atom pref setting for forces.

* Add the unit test for descrpt se_a_mask

* Remove the unit test for dp mask model

* Update dp mask system path for unit test

* Remove total_atom_num dependency in se_a_mask. Fetch total atom num through natoms vector.

* Merge devel to dp_mask

* Fix issue in argcheck.
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
dcef8c2 
for more information, see https://pre-commit.ci
@dingye18
Fix format issue in op
18e615d
njzjz
njzjz reviewed Feb 12, 2023
View reviewed changes
deepmd/utils/argcheck.py Outdated Show resolved Hide resolved
deepmd/descriptor/se_a_mask.py Show resolved Hide resolved
wanghan-iapcm
wanghan-iapcm requested changes Feb 13, 2023
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  • please add to the doc how to use the se_a_mask and provide an example
  • I do not see the necessity of the changes in the deepmd/loss/ener.py.

@dingye18
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  • please add to the doc how to use the se_a_mask and provide an example
  • I do not see the necessity of the changes in the deepmd/loss/ener.py.
  • The doc for se_a_mask is added. Example input and data system are put into examples/zinc_protein directory.
  • The changes in deepmd/loss/ener.py is necessary. Since the return virial tensor is set to be None in se_a_mask and energy.npy is not provided by default. The previous version will throw an error when doing tf.reshape(virial, [-1]) and trying to find energy.npy for l2_ener_loss calculation.

@wanghan-iapcm wanghan-iapcm merged commit 4eb753e into deepmodeling:devel Feb 14, 2023
dingye18 added a commit to dingye18/deepmd-kit that referenced this pull request Feb 17, 2023
@dingye18 @njzjz
@pre-commit-ci @iProzd @caic99 @Yi-FanLi
Devel (#6)
0738f70 
* print MAE for `dp test` (deepmodeling#2310)

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>

* Fix bug deepmodeling#2311 when using FP32 in se_atten (deepmodeling#2312)

Fix bug deepmodeling#2311 when using FP32 in se_atten

* support multiple frames DeepPot in C/hpp API (deepmodeling#2309)

* Add DeepPot C API v2 to support multiple frames. Also, preserve the
arguments for fparam and aparam for future use (planned in deepmodeling#2236). V1 is
kept for API and ABI compatibility.
* Support multiple frames for DeepPot hpp API. The API compatibility is
kept. Add tests for new situation.

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

* Implementation of se_a_mask op (deepmodeling#2313)

* Implement se_a_mask op. Training and inference (c++ interface) are
tested. Unit test files are required.

* Fix bug in atom pref setting for forces.

* Add the unit test for descrpt se_a_mask

* Remove the unit test for dp mask model

* Update dp mask system path for unit test

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* support exclude_types for se_atten (deepmodeling#2315)

Fix deepmodeling#2232.

Also, clean old useless codes for `exclude_types`.

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

* fix restarting from the original model (deepmodeling#2317)

deepmodeling#2253 supports restarting from the compressed model but breaks the
original model. This PR fixes the error by detecting the model type
first.

```
FAILED_PRECONDITION: Attempting to use uninitialized value
```

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

* package dp_ipi in the PyPI wheels (deepmodeling#2320)

Fix deepmodeling#2282.

In addition, change the return code of `dp_ipi` (without any arguments)
from 1 to 0.

---------

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>

* build Docker images for each push (deepmodeling#2324)

and push the image to the GitHub container.

Also, provide the pypi CUDA support for pypi LAMMPS.

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

* Fix typo in install docs (deepmodeling#2325)

Signed-off-by: Chun Cai <amoycaic@gmail.com>

* Add a script to detect model version (deepmodeling#2318)

This PR adds a script in deepmd/utils to detect the version of a Deep
Potential model.

---------

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>
Signed-off-by: Chun Cai <amoycaic@gmail.com>
Co-authored-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: Duo <50307526+iProzd@users.noreply.github.com>
Co-authored-by: Chun Cai <amoycaic@gmail.com>
Co-authored-by: Yifan Li李一帆 <yifanl0716@gmail.com>
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@njzjz njzjz njzjz approved these changes

@wanghan-iapcm wanghan-iapcm wanghan-iapcm approved these changes

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@dingye18 @codecov-commenter @njzjz @wanghan-iapcm