breaking(gmx): remove in-tree GROMACS patch integration#5377
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njzjz-bot wants to merge 4 commits intodeepmodeling:masterfrom
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breaking(gmx): remove in-tree GROMACS patch integration#5377njzjz-bot wants to merge 4 commits intodeepmodeling:masterfrom
njzjz-bot wants to merge 4 commits intodeepmodeling:masterfrom
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Remove the obsolete source/gmx tree, drop the related CMake wiring, and replace the old GROMACS documentation with deprecation notices that point users to LAMMPS or the third-party implementation linked from issue deepmodeling#5360. Also remove the bundled GROMACS-only examples and clean up residual references in README, troubleshooting docs, labels, and API comments. Authored by OpenClaw (model: gpt-5.4)
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✅ Files skipped from review due to trivial changes (4)
🚧 Files skipped from review as they are similar to previous changes (1)
📝 WalkthroughWalkthroughRemoves the in-tree GROMACS integration: deletes GROMACS plugin sources, build rules, patches, patching utility, and GROMACS examples; updates docs and configs to deprecate/remove GROMACS references and point users to third‑party or LAMMPS/i-PI alternatives. Changes
Estimated code review effort🎯 4 (Complex) | ⏱️ ~45 minutes Possibly related issues
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Actionable comments posted: 3
🤖 Prompt for all review comments with AI agents
Verify each finding against the current code and only fix it if needed.
Inline comments:
In `@doc/install/install-gromacs.md`:
- Around line 9-10: Replace the deprecated directive token "next release" in the
deprecation block (:::{deprecated} next release) with the explicit target
release version used elsewhere (for example "3.0.0") so the notice matches other
deprecation notices; update the line that begins with :::{deprecated} to use the
chosen semantic version string.
In `@doc/third-party/gromacs.md`:
- Around line 9-10: Replace the ambiguous deprecation directive "{deprecated}
next release" in the GROMACS docs with a concrete version to match other files;
update the directive in the locations referencing GROMACS (the "{deprecated}
next release" occurrences in gromacs.md and install-gromacs.md) to a specific
version string such as "{deprecated} 3.0.0" (or the actual first version where
removal applies) so the deprecation marker is consistent with "{deprecated}
3.0.0" used elsewhere.
In `@source/CMakeLists.txt`:
- Around line 490-492: The status message claiming "use gcc/g++ >= 4.8" is
inconsistent with the actual guard that uses VERSION_GREATER 4.8 for the ipi/
subdirectory (and md/ is commented out), so update the build logic to match the
message: change the ipi/ gate from VERSION_GREATER 4.8 to VERSION_GREATER_EQUAL
4.8 (or alternatively change the message to state "> 4.8"); locate the
VERSION_GREATER check that controls the ipi/ add_subdirectory and make it use
VERSION_GREATER_EQUAL 4.8 so gcc/g++ 4.8 exactly will enable the i-PI driver as
the message promises.
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Configuration used: Repository UI
Review profile: CHILL
Plan: Pro
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⛔ Files ignored due to path filters (1)
examples/water/gmx/rdf.pngis excluded by!**/*.png
📒 Files selected for processing (37)
.github/labeler.ymlAGENTS.mdREADME.mddoc/getting-started/quick_start.ipynbdoc/install/index.rstdoc/install/install-from-c-library.mddoc/install/install-gromacs.mddoc/third-party/gromacs.mddoc/third-party/index.rstdoc/troubleshooting/installation.mdexamples/methane/index.rawexamples/methane/input.jsonexamples/methane/lig_solv.groexamples/methane/md.mdpexamples/methane/methane.itpexamples/methane/run.shexamples/methane/topol.topexamples/methane/type.rawexamples/water/gmx/index.rawexamples/water/gmx/input.jsonexamples/water/gmx/md.mdpexamples/water/gmx/md.shexamples/water/gmx/type.rawexamples/water/gmx/water.groexamples/water/gmx/water.topsource/CMakeLists.txtsource/api_cc/include/DeepPot.hsource/api_cc/include/DeepSpin.hsource/gmx/.gitignoresource/gmx/CMakeLists.txtsource/gmx/dp_gmx_patchsource/gmx/include/gmx_plugin.hsource/gmx/patches/2020.2/CMakeLists.txt.patch.insource/gmx/patches/2020.2/src/gromacs/mdlib/forcerec.cpp.patchsource/gmx/patches/2020.2/src/gromacs/mdlib/forcerec.h.patchsource/gmx/patches/2020.2/src/gromacs/mdlib/sim_util.cpp.patchsource/gmx/src/gmx_plugin.cpp
💤 Files with no reviewable changes (27)
- doc/install/index.rst
- source/gmx/.gitignore
- doc/third-party/index.rst
- examples/methane/index.raw
- examples/methane/input.json
- examples/water/gmx/index.raw
- .github/labeler.yml
- examples/methane/type.raw
- examples/water/gmx/input.json
- examples/water/gmx/type.raw
- examples/methane/lig_solv.gro
- source/gmx/patches/2020.2/src/gromacs/mdlib/forcerec.h.patch
- examples/methane/md.mdp
- examples/methane/run.sh
- examples/methane/methane.itp
- source/gmx/patches/2020.2/CMakeLists.txt.patch.in
- examples/water/gmx/md.mdp
- examples/methane/topol.top
- examples/water/gmx/md.sh
- examples/water/gmx/water.gro
- source/gmx/src/gmx_plugin.cpp
- source/gmx/CMakeLists.txt
- examples/water/gmx/water.top
- source/gmx/patches/2020.2/src/gromacs/mdlib/forcerec.cpp.patch
- source/gmx/patches/2020.2/src/gromacs/mdlib/sim_util.cpp.patch
- source/gmx/include/gmx_plugin.h
- source/gmx/dp_gmx_patch
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Pull request overview
Note
Copilot was unable to run its full agentic suite in this review.
Removes the repository’s in-tree GROMACS patch/plugin integration and updates documentation/examples to reflect deprecation and point users to supported alternatives.
Changes:
- Deletes the
source/gmxbuild/patch implementation and related patch assets. - Removes GROMACS example inputs and updates build system / labeler configuration accordingly.
- Replaces GROMACS install/usage docs with deprecation notices and cleans up remaining references across docs/README/notebooks.
Reviewed changes
Copilot reviewed 37 out of 38 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| source/gmx/src/gmx_plugin.cpp | Removes the GROMACS plugin implementation source file. |
| source/gmx/patches/2020.2/src/gromacs/mdlib/sim_util.cpp.patch | Deletes the bundled GROMACS patch hunk for force/energy integration. |
| source/gmx/patches/2020.2/src/gromacs/mdlib/forcerec.h.patch | Removes patch for Deepmd globals/hooks in GROMACS headers. |
| source/gmx/patches/2020.2/src/gromacs/mdlib/forcerec.cpp.patch | Removes patch for initializing DeePMD integration in GROMACS. |
| source/gmx/patches/2020.2/CMakeLists.txt.patch.in | Removes patch template that injected DeePMD linking into GROMACS CMake. |
| source/gmx/include/gmx_plugin.h | Deletes in-tree public header for the GROMACS plugin. |
| source/gmx/dp_gmx_patch | Removes the helper script used to patch/revert GROMACS sources. |
| source/gmx/CMakeLists.txt | Removes the CMake subproject that built/installed the GROMACS plugin. |
| source/gmx/.gitignore | Removes ignore rule used for generated patch files (no longer needed). |
| source/api_cc/include/DeepSpin.h | Updates API comment to drop GROMACS as a stated consumer. |
| source/api_cc/include/DeepPot.h | Updates API comment to drop GROMACS as a stated consumer. |
| source/CMakeLists.txt | Removes GROMACS plugin build hooks/vars from the main build. |
| examples/water/gmx/water.top | Deletes GROMACS example topology. |
| examples/water/gmx/water.gro | Deletes GROMACS example coordinates. |
| examples/water/gmx/type.raw | Deletes GROMACS example type mapping. |
| examples/water/gmx/md.sh | Deletes GROMACS example run script. |
| examples/water/gmx/md.mdp | Deletes GROMACS example mdp parameters. |
| examples/water/gmx/input.json | Deletes GROMACS example DeePMD input config. |
| examples/water/gmx/index.raw | Deletes GROMACS example atom indices file. |
| examples/methane/type.raw | Deletes methane example type mapping (GROMACS-related). |
| examples/methane/topol.top | Deletes methane GROMACS topology wrapper. |
| examples/methane/run.sh | Deletes methane GROMACS run script. |
| examples/methane/methane.itp | Deletes methane GROMACS itp. |
| examples/methane/md.mdp | Deletes methane GROMACS mdp. |
| examples/methane/lig_solv.gro | Deletes methane GROMACS coordinate file. |
| examples/methane/input.json | Deletes methane DeePMD input config used by GROMACS workflow. |
| examples/methane/index.raw | Deletes methane GROMACS atom indices file. |
| doc/troubleshooting/installation.md | Updates troubleshooting text to remove GROMACS mention. |
| doc/third-party/index.rst | Removes GROMACS page from third-party docs toctree. |
| doc/third-party/gromacs.md | Replaces the GROMACS guide with a deprecation notice page. |
| doc/install/install-gromacs.md | Replaces GROMACS install guide with a deprecation notice page. |
| doc/install/install-from-c-library.md | Removes “GROMACS patch” references; links to deprecation notice for context. |
| doc/install/index.rst | Removes GROMACS install page from install docs toctree. |
| doc/getting-started/quick_start.ipynb | Removes GROMACS mention from the quick start notebook narrative. |
| README.md | Removes GROMACS from the list of integrated MD packages and repo structure. |
| AGENTS.md | Updates project description to remove GROMACS integration mention. |
| .github/labeler.yml | Removes the “Gromacs” label rule tied to source/gmx/**. |
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Adjust the GROMACS deprecation messaging to keep the external support story visible while making it clear that the in-tree patch was removed in v3.2.0. Also restore the third-party GROMACS page in the docs navigation and add a concise overview of the externally maintained GROMACS NNPot-based integration reported in arXiv:2602.02234, including its demonstrated capabilities and current scope limits. Authored by OpenClaw (model: custom-chat-jinzhezeng-group/gpt-5.4)
Do not single out GROMACS as a third-party integration in the README feature list, since several listed interfaces are also maintained outside the DeePMD-kit repository. Authored by OpenClaw (model: custom-chat-jinzhezeng-group/gpt-5.4)
njzjz
changed the title
Refine the GROMACS-related documentation to read like software manual content rather than a paper summary, while keeping the third-party pointer and scope notes useful for users. Also fix the gcc 4.8 boundary inconsistency by aligning the CMake i-PI guard with the documented threshold in troubleshooting. Authored by OpenClaw (model: custom-chat-jinzhezeng-group/gpt-5.4)
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #5377 +/- ##
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- Coverage 82.37% 82.37% -0.01%
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Files 812 812
Lines 83560 83560
Branches 4091 4090 -1
==========================================
- Hits 68832 68829 -3
Misses 13507 13507
- Partials 1221 1224 +3 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Problem
source/gmxintegration, install guides, and examples that make the removed workflow look officially supported.Change
Notes
git diff --check, and JSON validation ofdoc/getting-started/quick_start.ipynb.Authored by OpenClaw (model: gpt-5.4)
Summary by CodeRabbit