Improve function pert_scaled
#1563
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Simplify API version validation (deepmodeling#1556)
WalkthroughWalkthroughRecent changes to Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant pert_scaled
participant Systems
participant Scales
participant Command
User ->> pert_scaled: Call pert_scaled()
pert_scaled ->> Systems: Iterate over systems
loop for each system
Systems ->> pert_scaled: Process system
pert_scaled ->> Scales: Iterate over scales
loop for each scale
Scales ->> pert_scaled: Process scale
alt Initialization Style: VASP
pert_scaled ->> Command: Construct VASP pert_cmd
else Initialization Style: ABACUS
pert_scaled ->> Command: Construct ABACUS pert_cmd
end
pert_scaled ->> Command: Handle perturbation
end
end
pert_scaled -->> User: Return results
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Files skipped from review as they are similar to previous changes (2)
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #1563 +/- ##
==========================================
- Coverage 49.56% 49.55% -0.01%
==========================================
Files 83 83
Lines 14860 14850 -10
==========================================
- Hits 7365 7359 -6
+ Misses 7495 7491 -4 ☔ View full report in Codecov by Sentry. |
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Actionable comments posted: 2
Outside diff range and nitpick comments (1)
dpgen/data/gen.py (1)
Line range hint
729-842: The implementation of thepert_scaledfunction has been significantly refactored to accommodate different initialization styles and to handle perturbations more flexibly. However, there are a couple of points that need attention:
Error Handling: The use of
assertstatements (e.g., line 746) for checking if directories exist is generally not recommended for production code as it can cause the program to crash without a graceful recovery option. Consider using if-statements with proper exceptions or error messages.Command Injection Risk: The construction of the
pert_cmdcommand string (lines 764-769) directly incorporates user input (pert_box,fp_style,poscar_name,pert_numb,pert_atom) which could potentially lead to command injection if not properly sanitized. Ensure that these inputs are validated or sanitized before being used in command line contexts.File Handling: The function modifies the current working directory frequently (e.g., lines 746, 775, 779). This can lead to hard-to-track bugs and is generally not a good practice in a multi-threaded environment where the current directory is shared among all threads. Consider using absolute paths and avoid changing the global state.
Resource Management: The function uses
os.remove(pos_in)inside a loop (line 811) which might lead to errors if the file does not exist or has already been removed in a previous iteration. Adding checks before attempting to delete can prevent runtime errors.Overall, the function's logic appears sound, but these improvements could enhance robustness and security.
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@Liu-RX could you take a review? Thanks! |
Sorry for the late reply!!! |
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Actionable comments posted: 2
Outside diff range, codebase verification and nitpick comments (2)
dpgen/data/gen.py (2)
Line range hint
782-813: Avoid repeated code for file handling.The code for handling files based on
fp_styleis repeated. Consider refactoring to reduce duplication.
Line range hint
814-844: Clarify the purpose of the special case handling.The handling of the special case (unperturbed) is not clearly documented. Consider adding comments to explain its purpose.
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Improve function `pert_scaled` (deepmodeling#1563)
My suggestion:
Summary by CodeRabbit
New Features
pert_scaledfunction to support different initialization styles ("VASP" or "ABACUS").Refactor
make_vasp_relaxandmake_scalefunctions for improved readability and clarity.pert_scaledfunction.