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feat: descriptor provide get_rcut_smth and get_env_protection #3761

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merged 10 commits into from
May 11, 2024

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@wanghan-iapcm wanghan-iapcm commented May 9, 2024

Summary by CodeRabbit

  • New Features
    • Introduced methods to enhance the calculation of smooth decay radius and environment matrix protection across various descriptor modules. This will improve the precision and reliability of environmental interactions in models.

@wanghan-iapcm wanghan-iapcm requested a review from njzjz May 9, 2024 05:17
@wanghan-iapcm wanghan-iapcm linked an issue May 9, 2024 that may be closed by this pull request
@github-actions github-actions bot added the Python label May 9, 2024
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coderabbitai bot commented May 9, 2024

Walkthrough

Walkthrough

The recent updates in the deepmd library introduce consistency and enhanced functionality by adding get_rcut_smth and get_env_protection methods across various descriptor modules. These additions standardize the handling of neighbor information decay and environment matrix protection, ensuring uniform behavior and improved data processing for molecular dynamics simulations.

Changes

File Path Change Summary
.../descriptor/dpa1.py Added methods get_rcut_smth() and get_env_protection().
.../descriptor/hybrid.py Introduced get_rcut_smth() and get_env_protection(), and added import math.
.../descriptor/se_e2_a.py New methods get_rcut_smth() and get_env_protection() added.
.../descriptor/se_r.py Added get_rcut_smth() and get_env_protection(); updated get_rcut() to get_rcut_smth().
.../pt/model/descriptor/... All files in this path now include get_rcut_smth() and get_env_protection() methods. Adjustments made to class Descriptor.

Recent Review Details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits Files that changed from the base of the PR and between 644addd and 7e5723a.
Files selected for processing (1)
  • source/tests/pt/model/test_dpa2.py (1 hunks)

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Actionable comments posted: 6

Out of diff range and nitpick comments (1)
source/tests/common/dpmodel/test_descriptor_hybrid.py (1)

Line range hint 72-99: Add a TODO comment for implementation.

+        # TODO: Implement the test logic for self-consistency checks

This method currently sets up test data but does not perform any assertions or function calls. It should have a TODO comment indicating that the test logic needs to be implemented.

deepmd/dpmodel/descriptor/hybrid.py Outdated Show resolved Hide resolved
deepmd/dpmodel/descriptor/hybrid.py Outdated Show resolved Hide resolved
deepmd/pt/model/descriptor/hybrid.py Outdated Show resolved Hide resolved
deepmd/pt/model/descriptor/hybrid.py Outdated Show resolved Hide resolved
def test_get_parameters(
self,
):
rng = np.random.default_rng()

Check notice

Code scanning / CodeQL

Unused local variable Note test

Variable rng is not used.
self,
):
rng = np.random.default_rng()
nf, nloc, nnei = self.nlist.shape

Check notice

Code scanning / CodeQL

Unused local variable Note test

Variable nf is not used.
self,
):
rng = np.random.default_rng()
nf, nloc, nnei = self.nlist.shape

Check notice

Code scanning / CodeQL

Unused local variable Note test

Variable nloc is not used.
self,
):
rng = np.random.default_rng()
nf, nloc, nnei = self.nlist.shape

Check notice

Code scanning / CodeQL

Unused local variable Note test

Variable nnei is not used.
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codecov bot commented May 9, 2024

Codecov Report

Attention: Patch coverage is 89.87342% with 8 lines in your changes are missing coverage. Please review.

Project coverage is 82.44%. Comparing base (74dce7f) to head (7e5723a).

Files Patch % Lines
deepmd/dpmodel/descriptor/dpa2.py 50.00% 2 Missing ⚠️
deepmd/dpmodel/descriptor/make_base_descriptor.py 66.66% 2 Missing ⚠️
deepmd/pt/model/descriptor/descriptor.py 66.66% 2 Missing ⚠️
deepmd/pt/model/descriptor/dpa2.py 60.00% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##            devel    #3761      +/-   ##
==========================================
+ Coverage   82.43%   82.44%   +0.01%     
==========================================
  Files         517      517              
  Lines       49185    49264      +79     
  Branches     2979     2982       +3     
==========================================
+ Hits        40547    40618      +71     
- Misses       7727     7735       +8     
  Partials      911      911              

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

Han Wang and others added 5 commits May 9, 2024 13:52
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Han Wang <[email protected]>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Han Wang <[email protected]>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Han Wang <[email protected]>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
Signed-off-by: Han Wang <[email protected]>
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Actionable comments posted: 1

deepmd/dpmodel/descriptor/dpa2.py Outdated Show resolved Hide resolved
@wanghan-iapcm wanghan-iapcm enabled auto-merge May 11, 2024 09:59
@wanghan-iapcm wanghan-iapcm disabled auto-merge May 11, 2024 10:18
@wanghan-iapcm wanghan-iapcm enabled auto-merge May 11, 2024 10:19
@wanghan-iapcm wanghan-iapcm added this pull request to the merge queue May 11, 2024
@github-merge-queue github-merge-queue bot removed this pull request from the merge queue due to failed status checks May 11, 2024
@wanghan-iapcm wanghan-iapcm enabled auto-merge May 11, 2024 12:52
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Actionable comments posted: 2

Out of diff range and nitpick comments (1)
source/tests/pt/model/test_dpa2.py (1)

84-85: Consider refining the comment regarding the adjustment of atol for "float64" precision.

The comment "marginal GPU test cases..." could be expanded to explain why the adjustment is necessary specifically for "float64" precision, which would help maintain clarity and usefulness of the comment for future maintainers or developers.

source/tests/pt/model/test_dpa2.py Show resolved Hide resolved
@wanghan-iapcm wanghan-iapcm added this pull request to the merge queue May 11, 2024
Merged via the queue into deepmodeling:devel with commit 3a6d2c4 May 11, 2024
61 checks passed
@wanghan-iapcm wanghan-iapcm deleted the descrpt-get-rcsmth-ep branch May 11, 2024 14:43
mtaillefumier pushed a commit to mtaillefumier/deepmd-kit that referenced this pull request Sep 18, 2024
…deling#3761)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit


- **New Features**
- Introduced methods to enhance the calculation of smooth decay radius
and environment matrix protection across various descriptor modules.
This will improve the precision and reliability of environmental
interactions in models.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Han Wang <[email protected]>
Co-authored-by: Han Wang <[email protected]>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
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export rcut_smth from DescriptorBlock
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