♻️ Initialization of the refactoring of the LAMMPS plugin #35
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… files to follow this format.
Added a new more general schema for the base calculation. Minor modifications to the input_generator
Fixing an issue in which the schema did not have the complete list of fixes for the minimization. Renamed the "relax" to "minimize" in the schema for clarity.
Added a function for the generation of the dump block. General improvements for the dosctrings. Added the automatic tag generation as a function. Added the capability of creating groups in the structure generation.
Add the capability of having any of the defined computes in the thermo block so that they are printed in the log file.
Adding a helper routine and file to programatically generate the compute strings for the thermo_style.
Make the generation of printing strings for computes for local and global variables automatic
Adding the extra attributes to tage the potential. Improvements of the dosctrings.
Changes to ensure that the potential can be created via the get_or_create method. Improvement of docstrings. Adding any missing dosctrings.
Added the control, potential, and structure to the validation schema. Several minor format changes.
Adding a new tag to the potential, indicating how the potential was generated. Small changes to the format.
…e velocity can be read and properly parsed. Separated the integration from the fixes so that it is more compatible to the current version of the plugin. Created a function to automatically write the options for the integrations.
Adding a more general way to pass the velocity to the md calculation.
Fix smaller issues in the schema. Add a function for the schema validation.
…with the pre-commit style.
Increasing pylint version to 2.6
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Hello @chrisjsewell ! Should I just handle the PR myself? Or do you want to give it a look? I think after this I'll work in the workflows themselves. If you have time to look at the dynamic namespaces for the potential stuff would be great, if not let me know where I can check an example so I can try to do it on my own. Cheers |
Codecov Report
@@ Coverage Diff @@
## develop #35 +/- ##
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+ Coverage 77.83% 81.89% +4.05%
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Files 37 30 -7
Lines 2369 2336 -33
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+ Hits 1844 1913 +69
+ Misses 525 423 -102
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All sorted @JPchico!
I made a few extra changes 😅:
dropped all the dynaphopy code, moved the tests out of the package, and fixed the documentation build
chrisjsewell
changed the title
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Fantastic @chrisjsewell ! that is very nice news! I'll check it ASAP |
Refactoring the
aiida-lammpsplugin so that it is more flexible and in line with what has been developed for the DFT codes.@chrisjsewell I have created the first PR for the refactoring of the code, I'm pointing it towards the
developmentbranch. In principle what one would need to do to ensure that it can be easily merged is to make a new development branch which is a copy from the master branch.Also, we need to see about taking care of the parts of the plugin which were not maintained before we took over, like the
dynaphopyparts. We probably need to remove those classes or make them functional.