Feature decouple somd 3 to main #68
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Also create YamlSerialisableEnum to allow serialisation of enums.
Feature decouple somd 2-Implement stage 1
This includes updates to the docs and a purge of run_somd.sh from all the example directories. Note that a3fe/tests/test_sys_prep_configuration.py::test_config_dump_and_load seems to be flaky - failing when run with all the tests, but fine when run individually.
…feature-decouple-somd-2
Replace run_somd.sh with Pydantic configuration class
…class _engine_runner_config. Write out the A3FE version, and make the output logs more concise and suitable for debugging
Removed lots of code duplication.
…alidation to setup()
…nput validation to setup()
Decoupled SOMD engine from a3fe calculation and removed run_somd.sh and template_config.cfg, replacing them with a3fe.configuration.slurm_config.SlurmConfig and a3fe.configuration.engine_config.SomdConfig. - SystemPreparationConfigs saved as readable yaml file, rather than as a pickle. - Separated system preparation configuration from system preparation and configured SOMD with a3fe.configuration.system_prep_config.SomdSystemPreparationConfig. - Streamlined the installation process with a Makefile.
merge conflicts for Feature decouple somd 3
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Merge into main and test everything
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