pass element_num to sparam in hti_liq #81
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## devel #81 +/- ##
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Coverage 0.00% 0.00%
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Files 24 24
Lines 5913 5914 +1
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- Misses 5913 5914 +1 ☔ View full report in Codecov by Sentry. |
📝 WalkthroughWalkthroughThe changes in the pull request focus on the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant HTI_LIQ
participant Sigma_Params
User->>HTI_LIQ: Call _make_tasks()
HTI_LIQ->>HTI_LIQ: Calculate element_num from mass_map
HTI_LIQ->>Sigma_Params: Validate sigma parameters in sparam
Sigma_Params-->>HTI_LIQ: Return validation result
HTI_LIQ->>User: Complete task generation
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
dpti/hti_liq.py (1)
267-267: Add test coverage for the new element_num assignment.The static analysis indicates that this new line is not covered by tests. Since this is a critical part of the fix for handling multiple atom types, it should be tested.
Would you like me to help create a test case that verifies the correct handling of element_num with multiple atom types?
🧰 Tools
🪛 GitHub Check: codecov/patch
[warning] 267-267: dpti/hti_liq.py#L267
Added line #L267 was not covered by tests
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Review profile: CHILL
📒 Files selected for processing (1)
dpti/hti_liq.py(1 hunks)
🧰 Additional context used
🪛 GitHub Check: codecov/patch
dpti/hti_liq.py
[warning] 267-267: dpti/hti_liq.py#L267
Added line #L267 was not covered by tests
🔇 Additional comments (1)
dpti/hti_liq.py (1)
267-268: LGTM! The element_num assignment is correctly placed.
The addition of element_num to sparam based on mass_map length is well-positioned, as it's used immediately after in the sigma key validation logic. This change properly addresses the issue where pair_coeff for lj/cut/soft pair potentials fails in systems with multiple atom types.
Let's verify the usage of element_num in pair_coeff assignments:
✅ Verification successful
Let me analyze the search results. The output shows that lj/cut/soft pair coefficients are used extensively in test files and implementation files. Most importantly, I can see that in dpti/hti_liq.py, the pair coefficients are generated in a loop over atom types using the format:
ret += "pair_coeff {} {} lj/cut/soft ${{EPSILON}} {:f} {:f}\n".format(
i + 1,
j + 1,
sparam["sigma_" + str(i) + "_" + str(j)],
...
)This confirms that the code correctly handles multiple atom types by generating pair coefficients for each pair of atom types (i,j) using the sigma values stored in sparam. The addition of element_num to sparam is used to determine how many such pairs need to be processed.
Let me verify the validation logic around this by checking how these sigma parameters are validated:
The search results show the validation logic that checks for the existence of all required sigma parameters in sparam. Let me verify how sigma_key_index is constructed to ensure it covers all atom type pairs:
I can now generate the final response based on the comprehensive evidence gathered. The code shows that:
element_numis correctly set frommass_maplengthsigma_key_indexgenerates all required (i,j) pairs for atom types usingelement_num- The code validates that all required sigma parameters exist in
sparam - The pair coefficients are correctly generated for each atom type pair
The element_num assignment is correctly implemented and properly used.
The addition of element_num to sparam based on mass_map length is well-integrated with the existing code:
- It's used to generate all required (i,j) pairs for atom types
- These pairs are used to validate the presence of all required sigma parameters
- The validated parameters are then used to generate the correct pair coefficients for LAMMPS
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Search for pair_coeff usage in lj/cut/soft contexts
rg -A 3 "pair_coeff.*lj/cut/soft"
Length of output: 24702
Script:
#!/bin/bash
# Search for sigma parameter validation in hti_liq.py
rg -A 10 "sigma.*str.*str" dpti/hti_liq.py
Length of output: 1831
Script:
#!/bin/bash
# Search for sigma_key_index construction
rg -B 5 -A 5 "sigma_key_index" dpti/hti_liq.py
Length of output: 2389
🧰 Tools
🪛 GitHub Check: codecov/patch
[warning] 267-267: dpti/hti_liq.py#L267
Added line #L267 was not covered by tests
For a system with multiple types of atoms, the hti_liquid will miss pair_coeff for lj/cut/soft pair potentials since the element_num inferred from the length of mass_type is not clearly passed. See Issue #80.
This PR fixes #80.
Summary by CodeRabbit
New Features
Bug Fixes