chore(lmp): add LAMMPS DPA-2 nopbc tests #4220
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Signed-off-by: Jinzhe Zeng <[email protected]>
Signed-off-by: Jinzhe Zeng <[email protected]>
Signed-off-by: Jinzhe Zeng <[email protected]>
Signed-off-by: Jinzhe Zeng <[email protected]>
📝 WalkthroughWalkthroughThe changes introduce a new command-line argument Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Script
participant LAMMPS
User->>Script: Run with --nopbc
Script->>LAMMPS: Set boundary conditions to "f f f"
Script->>LAMMPS: Execute simulation
LAMMPS-->>Script: Return results
Script-->>User: Display results
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (3)
source/lmp/tests/run_mpi_pair_deepmd.py (2)
42-45: LGTM: Boundary conditions set correctly based on--nopbcargument.The implementation correctly uses the new
--nopbcargument to set the boundary conditions. This change allows for testing both periodic and non-periodic boundary conditions, which is crucial for verifying the issues mentioned in PR #4167.Consider adding a comment explaining the meaning of "f f f" and "p p p" for improved clarity:
if args.nopbc: lammps.boundary("f f f") # Set free boundaries in all directions else: lammps.boundary("p p p") # Set periodic boundaries in all directions
Line range hint
1-67: Consider adding error handling and a test case for MPI-related issues.While the changes implemented are correct, the PR description mentions segmentation faults when using MPI. To address this:
- Consider adding error handling around the MPI calls to catch and report any segmentation faults or other errors that might occur during execution.
- It might be beneficial to add a test case that attempts to reproduce the segmentation fault mentioned in the PR description. This could help in identifying and resolving the issue.
Here's a simple example of how you might add some basic error handling:
try: # Your existing MPI code here ... MPI.Finalize() except Exception as e: print(f"Error occurred during MPI execution: {e}") # You might want to log this error or handle it in a way that's appropriate for your testing framework raiseWould you like assistance in implementing more robust error handling or creating a test case to reproduce the segmentation fault?
source/lmp/tests/test_lammps_dpa_pt_nopbc.py (1)
685-691: Remove commented-out code to enhance readabilityThe stack trace comments within the
if balance_args == []:block are unnecessary and can clutter the code. If this information is important for debugging or historical context, consider moving it to a dedicated documentation file or including it in the test's docstring.Apply this diff to clean up the code:
if balance_args == []: - # python:5331 terminated with signal 11 at PC=7f3e940e3806 SP=7ffd5787edc0. Backtrace: - # /home/runner/work/deepmd-kit/deepmd-kit/dp_test/lib/libdeepmd_op_pt.so(+0x95806)[0x7f3e940e3806] - # /home/runner/work/deepmd-kit/deepmd-kit/dp_test/lib/libdeepmd_op_pt.so(+0x8f76e)[0x7f3e940dd76e] - # /home/runner/work/deepmd-kit/deepmd-kit/dp_test/lib/libdeepmd_op_pt.so(+0x9a38a)[0x7f3e940e838a] - # /home/runner/work/deepmd-kit/deepmd-kit/dp_test/lib/libdeepmd_op_pt.so(_Z9border_opRKN2at6TensorES2_S2_S2_S2_S2_S2_S2_S2_+0x8e)[0x7f3e940dda63] - # /home/runner/work/deepmd-kit/deepmd-kit/dp_test/lib/libdeepmd_op_pt.so(+0xaeac3)[0x7f3e940fcac3] pytest.skip(reason="Known segfault, see comments for details")
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📒 Files selected for processing (2)
- source/lmp/tests/run_mpi_pair_deepmd.py (2 hunks)
- source/lmp/tests/test_lammps_dpa_pt_nopbc.py (1 hunks)
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🔇 Additional comments (1)
source/lmp/tests/run_mpi_pair_deepmd.py (1)
24-24: LGTM: New command-line argument added correctly.The addition of the
--nopbcargument as a boolean flag is implemented correctly and aligns with the PR objectives. The argument name is clear and descriptive.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## devel #4220 +/- ##
=======================================
Coverage 83.50% 83.50%
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Files 541 541
Lines 52486 52486
Branches 3043 3047 +4
=======================================
+ Hits 43830 43831 +1
Misses 7708 7708
+ Partials 948 947 -1 ☔ View full report in Codecov by Sentry. |
Adding tests to see whether #4167 is resolved. The answer is no. Segfaults are thrown with MPI. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Introduced a new command-line argument `--nopbc` to modify boundary conditions in LAMMPS simulations. - **Tests** - Added a comprehensive suite of unit tests for the DeepMD potential in LAMMPS, covering various configurations and scenarios to ensure accuracy and reliability. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <[email protected]>
github-merge-queue
bot
removed this pull request from the merge queue due to failed status checks
…4237) fix errors mentioned in following pr: #4220 #4209 #4144 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Enhanced message passing logic in the computation process for improved efficiency. - Added new test functions to evaluate DeepMD model performance under various conditions. - **Bug Fixes** - Improved error handling and assertions in test cases to ensure robustness. - **Refactor** - Streamlined tensor operations in the communication process to enhance clarity and reduce unnecessary computations. - Removed outdated test cases related to neighbor list handling in the DeepPot class. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Adding tests to see whether #4167 is resolved. The answer is no. Segfaults are thrown with MPI.
Summary by CodeRabbit
--nopbcto modify boundary conditions in LAMMPS simulations.