ENH: support tpx 134 (GMX 2024.4) #4866
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* Fixes MDAnalysisgh-4855. * Add support for reading topology data from `.tpr` files produced by GROMACS 2024.4, corresponding to tpx version `134`. * My approach was similar to the one I used in MDAnalysisgh-4523, except for two things: 1) I retrieved the current generation (`28`) from a `print` in our own binary parser rather than rebuilding GMX from source with added `printf`, and more importantly 2) I had to add some shims because the `.tpr` format has changed. * With regard to the additional field data now stored in the `.tpr` format, I was involved in reviewing it upstream at: https://gitlab.com/gromacs/gromacs/-/merge_requests/4544. You can see that the changes related to the MARTINI functional form made it into the `v2024.4` tag i.e., here: https://gitlab.com/gromacs/gromacs/-/blob/v2024.4/src/gromacs/gmxpreprocess/convparm.cpp?ref_type=tags#L372
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Hello @tylerjereddy! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2024-12-27 17:25:12 UTC |
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hmacdope
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Tiny typo but thanks for doing this!
tanishy7777
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I was going through this PR and I am not able to understand why u added an elif for fver>=134. I am a bit new to this repo.
* Remove the periods (`.`) from Tyler's identifier in the `CHANGELOG` to satisfy reviewer comments.
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* Add support for GROMACS `2025.0` `.tpr` version 137, which mostly involves accounting for the new PyTorch neural network potential field, `F_ENNPOT`. Most of the other changes are similar to the approach I previously used for bumping `.tpr` version support in MDAnalysisgh-4866. * Some other `.tpr` additions are noted at MDAnalysis#4888, but we don't appear to need to use those within the context of our current `.tpr` parsing tests. It may be sensible to occasionally generate `.tpr` test files that use those extra bells and whistles to see how we fare, though as a first pass here the full testsuite passes for us if we simply do the usual `gmx convert-tpr` at the latest stable GROMACS release tag `v2025.0` and propagate our current TPR testing to additionally use the converted files.
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* ENH: support tpx 134 (GMX 2024.4) * Fixes MDAnalysisgh-4855. * Add support for reading topology data from `.tpr` files produced by GROMACS 2024.4, corresponding to tpx version `134`. * My approach was similar to the one I used in MDAnalysisgh-4523, except for two things: 1) I retrieved the current generation (`28`) from a `print` in our own binary parser rather than rebuilding GMX from source with added `printf`, and more importantly 2) I had to add some shims because the `.tpr` format has changed. * With regard to the additional field data now stored in the `.tpr` format, I was involved in reviewing it upstream at: https://gitlab.com/gromacs/gromacs/-/merge_requests/4544. You can see that the changes related to the MARTINI functional form made it into the `v2024.4` tag i.e., here: https://gitlab.com/gromacs/gromacs/-/blob/v2024.4/src/gromacs/gmxpreprocess/convparm.cpp?ref_type=tags#L372 * DOC: PR 4866 revisions * Remove the periods (`.`) from Tyler's identifier in the `CHANGELOG` to satisfy reviewer comments.
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* Add support for GROMACS `2025.0` `.tpr` version 137, which mostly involves accounting for the new PyTorch neural network potential field, `F_ENNPOT`. Most of the other changes are similar to the approach I previously used for bumping `.tpr` version support in MDAnalysisgh-4866. * Some other `.tpr` additions are noted at MDAnalysis#4888, but we don't appear to need to use those within the context of our current `.tpr` parsing tests. It may be sensible to occasionally generate `.tpr` test files that use those extra bells and whistles to see how we fare, though as a first pass here the full testsuite passes for us if we simply do the usual `gmx convert-tpr` at the latest stable GROMACS release tag `v2025.0` and propagate our current TPR testing to additionally use the converted files.
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* ENH: tpx 137 support * Add support for GROMACS `2025.0` `.tpr` version 137, which mostly involves accounting for the new PyTorch neural network potential field, `F_ENNPOT`. Most of the other changes are similar to the approach I previously used for bumping `.tpr` version support in gh-4866. * Some other `.tpr` additions are noted at #4888, but we don't appear to need to use those within the context of our current `.tpr` parsing tests. It may be sensible to occasionally generate `.tpr` test files that use those extra bells and whistles to see how we fare, though as a first pass here the full testsuite passes for us if we simply do the usual `gmx convert-tpr` at the latest stable GROMACS release tag `v2025.0` and propagate our current TPR testing to additionally use the converted files. * TST: Add GROMACS 2025.0 TPR with NNpot * Generated input file with random set of features enabled Using inputs from gromacs/src/testutils/simulationdatabase/ `gmx grompp -f tt6710474.mdp -c ala.gro -n ala.ndx -p ala.top -o ala_nnpot_gmx_2025_0.tpr` * Add Andrey to `CHANGELOG` * Apply suggestions from code review --------- Co-authored-by: Andrey Alekseenko <al42and@gmail.com>
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* ENH: tpx 137 support * Add support for GROMACS `2025.0` `.tpr` version 137, which mostly involves accounting for the new PyTorch neural network potential field, `F_ENNPOT`. Most of the other changes are similar to the approach I previously used for bumping `.tpr` version support in MDAnalysisgh-4866. * Some other `.tpr` additions are noted at MDAnalysis#4888, but we don't appear to need to use those within the context of our current `.tpr` parsing tests. It may be sensible to occasionally generate `.tpr` test files that use those extra bells and whistles to see how we fare, though as a first pass here the full testsuite passes for us if we simply do the usual `gmx convert-tpr` at the latest stable GROMACS release tag `v2025.0` and propagate our current TPR testing to additionally use the converted files. * TST: Add GROMACS 2025.0 TPR with NNpot * Generated input file with random set of features enabled Using inputs from gromacs/src/testutils/simulationdatabase/ `gmx grompp -f tt6710474.mdp -c ala.gro -n ala.ndx -p ala.top -o ala_nnpot_gmx_2025_0.tpr` * Add Andrey to `CHANGELOG` * Apply suggestions from code review --------- Co-authored-by: Andrey Alekseenko <al42and@gmail.com>
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Fixes Error: Your tpx version is 134, which this parser does not support, yet #4855.
Add support for reading topology data from
.tprfiles produced by GROMACS 2024.4, corresponding to tpx version134.My approach was similar to the one I used in ENH: support tpx 133 (GMX 2024.1) #4523, except for two things: 1) I retrieved the current generation (
28) from aprintin our own binary parser rather than rebuilding GMX from source with addedprintf, and more importantly 2) I had to add some shims because the.tprformat has changed.With regard to the additional field data now stored in the
.tprformat, I was involved in reviewing it upstream at: https://gitlab.com/gromacs/gromacs/-/merge_requests/4544. You can see that the changes related to the MARTINI functional form made it into thev2024.4tag i.e., here:https://gitlab.com/gromacs/gromacs/-/blob/v2024.4/src/gromacs/gmxpreprocess/convparm.cpp?ref_type=tags#L372
The new
.tprbinary assets added here were produced usinggmx convert-tpras I did for previous adjustments of this type, and I did confirm that the tests failed before adding the source code shims inutils.py.PR Checklist
Developers certificate of origin
📚 Documentation preview 📚: https://mdanalysis--4866.org.readthedocs.build/en/4866/