Add a hydrogel builder #103
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adding hydrogel feature pyMBE.py - not sure why it was left out
pm-blanco
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…drogel-feature-branch
pm-blanco
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Jan 10, 2025
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In general, I really like the shape this feature is taking. Currently, it is restricted to only diamond lattice topologies. However, this implementation already allows to build many interesting systems, so I think that we can keep it like this for this PR and work to generalize in further steps. I have several minor comments in specific lines and some other more conceptual ones that we can discuss during our dev meeting. Thank you for your work @1234somesh!
pm-blanco
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Jan 17, 2025
pm-blanco
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Feb 14, 2025
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@1234somesh I think that we are getting closer to merging this PR. Apart from the remaining changes that I commented on above, we only need to:
- Finish the functional test and try to optimize it so it runs as fast as possible
- Fix the issue with the read and write from the pmb.df
Point number 2 can be done in a different PR if you finish number 1 before we are able to solve the issue.
… changes in attributes of the lattice builder library
…x docs, make pylint happy
pm-blanco
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Mar 21, 2025
pm-blanco
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May 9, 2025
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The new feature is now fully functional and meeting our coding standards. Further developments will be addressed in specific PRs. @jngrad @paobtorres @kosovan just to notify you that this PR is now merged.
pm-blanco
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May 9, 2025
1234somesh
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May 21, 2025
* hydrogel feature in pyMBE.py adding hydrogel feature pyMBE.py - not sure why it was left out * hydrogels-feature refactored * removed unused variables * lattice_builder.py - new testsuite WIP * lattice_builder modified * new testuites for hydrogel builder * Fix R installation issue in testsuite.yml * removed unused variables in hydrogel_builder.py * refactoring hydrogel builder testsuite for code coverage * refactoring hydrogel builder testsuite for code coverage * refactoringhydrogel builder testsuite for code coverage * refactoringhydrogel builder testsuite for code coverage * chain_labels and node_labels to identify chains and nodes * chain_labels and node_labels to identify chains and nodes * benchmarking Landsgessel's result * benchmarking Landsgessel's result * separated analysis and plot scripts * separated analysis and plot scripts * remove time series, solve issues during merging * clean-up unit test, get rid of numpy deprecation warnings * clean up, add missing refs, start organizing data * add support to standarize Landsgesell2022 data, small fixes in weak gel * clean up alpha vs pH plotting script * clean up Landsgesell scripts and data * avoid repeated reference data for monovalent salt solution, simply parsing of data * reorder scripts in samples to comply with the current structure * improve docs for the reference data, fix issues with new paths, small changes in attributes of the lattice builder library * improve documentation, finish refactoring the script * update changelog * small fixes * modify points to simulate exactly at the same conditions as Landsgesell * functional tests * fix broken line in compaction of the hydrogel * update code for current routines in main, remove print statements, fix docs, make pylint happy * functional test refactored * fix coverage issues, smooth hydrogel compresion in sample * substitute deprecated np.testing.assert by standard assert * change method names for clarity * remove excesive equilibration in hydrogel sample, functional test now runs in 35 min * update readme to advertise hydrogels --------- Co-authored-by: Pablo M. Blanco <75744061+pm-blanco@users.noreply.github.com>
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Added
samples/Landsgesell2022/run_simulations.pyandsamples/Landsgesell2022/plot_pH_vs_alpha.pyandsamples/Landsgesell2022/plot_P_vs_V.pysamples/build_hydrogel.pyandsamples/weak_polyacid_hydrogel_grxmc.pypmb.define_hydrogel,pmb.create_hydrogel,pmb.initialize_lattice_builder,pmb.create_chain,pmb.create_node.