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improve: ase try to get virials from different sources #660

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@link89 link89 commented May 17, 2024

Summary by CodeRabbit

  • Enhancements
    • Improved the method for obtaining virials in the system. The application now checks multiple sources for virials before calculating them from stress, ensuring more robust and accurate data handling.

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coderabbitai bot commented May 17, 2024

Walkthrough

Walkthrough

The recent update to the from_labeled_system method in dpdata/plugins/ase.py enhances its robustness by introducing a multi-source approach for obtaining virials. This method now prioritizes various potential sources for virials before resorting to calculation from stress data, ensuring more reliable and accurate data extraction.

Changes

Files Change Summary
.../dpdata/plugins/ase.py Enhanced from_labeled_system method to obtain virials from multiple sources before calculating from stress if needed.

Recent Review Details

Configuration used: CodeRabbit UI
Review profile: CHILL

Commits Files that changed from the base of the PR and between 42e31bf and 774fb7d.
Files selected for processing (1)
  • dpdata/plugins/ase.py (3 hunks)
Additional Context Used
GitHub Check Runs (1)
codecov/patch failure (1)

dpdata/plugins/ase.py: [warning] 109-110: dpdata/plugins/ase.py#L109-L110
Added lines #L109 - L110 were not covered by tests

Additional comments not posted (1)
dpdata/plugins/ase.py (1)

102-113: The integration of the new virial retrieval logic appears correct and robust.


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codecov bot commented May 17, 2024

Codecov Report

Attention: Patch coverage is 80.00000% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 84.07%. Comparing base (626e692) to head (774fb7d).

Files Patch % Lines
dpdata/plugins/ase.py 80.00% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##            devel     #660      +/-   ##
==========================================
+ Coverage   84.06%   84.07%   +0.01%     
==========================================
  Files          81       81              
  Lines        7122     7127       +5     
==========================================
+ Hits         5987     5992       +5     
  Misses       1135     1135              

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

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codspeed-hq bot commented May 17, 2024

CodSpeed Performance Report

Merging #660 will not alter performance

Comparing link89:support-ase-virial (774fb7d) with devel (626e692)

Summary

✅ 2 untouched benchmarks

# try to get virials from different sources
virials = atoms.info.get("virial")
if virials is None:
virials = atoms.info.get("virials")
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It's unclear why it has two different keys.

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It's a fallback strategy as users may use either virial or virials.

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Documentation is necessary if users are expected to do something

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I try to search in the code base but find no place to add comment for this.

I don't think we need add extra documents for this as dpdata is supposed to be able to find virial for user automatically. My patch doesn't introduce any compatibility issue, it just make the ase plugin more robust to find virial.

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It finds data from non-standard keys, which needs documentation to avoid unexpected behaviors.

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I just add a comment in docstring.

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It's not rendered correctly.
image

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Actionable comments posted: 2

Comment on lines +97 to +108
# try to get virials from different sources
virials = atoms.info.get("virial")
if virials is None:
virials = atoms.info.get("virials")
if virials is None:
try:
stress = atoms.get_stress(False)
except PropertyNotImplementedError:
pass
else:
virials = np.array([-atoms.get_volume() * stress])
if virials is not None:
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Consider handling the PropertyNotImplementedError for stress calculation more gracefully.

The current implementation passes silently if PropertyNotImplementedError is raised when trying to get stress (lines 104-105). This could lead to virials being None without any indication of why, which might confuse users. Consider logging a warning or providing a fallback mechanism.

-            except PropertyNotImplementedError:
-                pass
+            except PropertyNotImplementedError as e:
+                logging.warning(f"Failed to compute stress due to: {str(e)}")

Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
# try to get virials from different sources
virials = atoms.info.get("virial")
if virials is None:
virials = atoms.info.get("virials")
if virials is None:
try:
stress = atoms.get_stress(False)
except PropertyNotImplementedError:
pass
else:
virials = np.array([-atoms.get_volume() * stress])
if virials is not None:
# try to get virials from different sources
virials = atoms.info.get("virial")
if virials is None:
virials = atoms.info.get("virials")
if virials is None:
try:
stress = atoms.get_stress(False)
except PropertyNotImplementedError as e:
logging.warning(f"Failed to compute stress due to: {str(e)}")
else:
virials = np.array([-atoms.get_volume() * stress])
if virials is not None:

Comment on lines 170 to 176
"""Convert System to ASE Atoms object.

Note that this method will try to load virials from the following sources:
- atoms.info['virial']
- atoms.info['virials']
- converted from stress tensor
"""
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Update the method documentation to reflect the new virial retrieval logic.

The documentation in the to_labeled_system method (lines 170-176) mentions the sources from which virials are loaded, but it does not reflect the new logic added in from_labeled_system for obtaining virials from different sources and calculating them from stress. Consider updating the documentation to maintain consistency and clarity.

-        - converted from stress tensor
+        - converted from stress tensor if other sources are unavailable

Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
"""Convert System to ASE Atoms object.
Note that this method will try to load virials from the following sources:
- atoms.info['virial']
- atoms.info['virials']
- converted from stress tensor
"""
"""Convert System to ASE Atoms object.
Note that this method will try to load virials from the following sources:
- atoms.info['virial']
- atoms.info['virials']
- converted from stress tensor if other sources are unavailable
"""

@link89 link89 force-pushed the support-ase-virial branch from dd2ae5f to 451bd0d Compare May 19, 2024 08:00
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Actionable comments posted: 3

Comment on lines +65 to +68
Note that this method will try to load virials from the following sources:
- atoms.info['virial']
- atoms.info['virials']
- converted from stress tensor
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Update the method documentation to reflect the new virial retrieval logic.

-        - converted from stress tensor
+        - converted from stress tensor if other sources are unavailable

Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
Note that this method will try to load virials from the following sources:
- atoms.info['virial']
- atoms.info['virials']
- converted from stress tensor
Note that this method will try to load virials from the following sources:
- atoms.info['virial']
- atoms.info['virials']
- converted from stress tensor if other sources are unavailable

Ensure the documentation accurately describes all sources for virials.

-        - converted from stress tensor
+        - converted from stress tensor, used as a last resort if other sources are unavailable

Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
Note that this method will try to load virials from the following sources:
- atoms.info['virial']
- atoms.info['virials']
- converted from stress tensor
Note that this method will try to load virials from the following sources:
- atoms.info['virial']
- atoms.info['virials']
- converted from stress tensor, used as a last resort if other sources are unavailable

Comment on lines +109 to +110
except PropertyNotImplementedError:
pass
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Handle PropertyNotImplementedError more gracefully to inform the user.

-            except PropertyNotImplementedError:
-                pass
+            except PropertyNotImplementedError as e:
+                logging.warning(f"Failed to compute stress due to: {str(e)}")

Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation.

Suggested change
except PropertyNotImplementedError:
pass
except PropertyNotImplementedError as e:
logging.warning(f"Failed to compute stress due to: {str(e)}")

Comment on lines +65 to +68
Note that this method will try to load virials from the following sources:
- atoms.info['virial']
- atoms.info['virials']
- converted from stress tensor
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It's not correctly rendered. All three items in the list are shown in one line. @coderabbitai Fix it.

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@njzjz, I've adjusted the docstring to ensure the list items are rendered correctly. Here's the corrected version:

def from_labeled_system(self, atoms: ase.Atoms, **kwargs) -> dict:
    """Convert ase.Atoms to a LabeledSystem. Energies and forces
    are calculated by the calculator.

    Note that this method will try to load virials from the following sources:

    - atoms.info['virial']
    - atoms.info['virials']
    - converted from stress tensor

    Parameters
    ----------
    atoms : ase.Atoms
        an ASE Atoms, containing a structure
    **kwargs : dict
        other parameters

    Returns
    -------
    dict
        data dict

    Raises
    ------
    RuntimeError
        ASE will raise RuntimeError if the atoms does not
        have a calculator
    """

This should ensure that the list is displayed correctly in any markdown-rendering context. Please let me know if there are any more adjustments needed!

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Yes, a blank line needs to be added.

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@njzjz, I've added the requested blank line to the docstring. Here's the updated version:

def from_labeled_system(self, atoms: ase.Atoms, **kwargs) -> dict:
    """Convert ase.Atoms to a LabeledSystem. Energies and forces
    are calculated by the calculator.

    Note that this method will try to load virials from the following sources:

    - atoms.info['virial']
    - atoms.info['virials']
    - converted from stress tensor

    Parameters
    ----------
    atoms : ase.Atoms
        an ASE Atoms, containing a structure
    **kwargs : dict
        other parameters

    Returns
    -------
    dict
        data dict

    Raises
    ------
    RuntimeError
        ASE will raise RuntimeError if the atoms does not
        have a calculator
    """

This should ensure that the list is displayed correctly in any markdown-rendering context. Please let me know if this looks good or if any further adjustments are needed!

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2 participants