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Feature decouple somd 3#29

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Roy-Haolin-Du wants to merge 51 commits intomichellab:feature-decouple-somd-3michellab/a3fe:feature-decouple-somd-3from Roy-Haolin-Du:feature-decouple-somd-3Roy-Haolin-Du/a3fe:feature-decouple-somd-3Copy head branch name to clipboard

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Commits on Jan 6, 2025

• Replace template_config.cfg with Pydantic config

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• test and format for removing run_somd.sh and template_config.cfg

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Commits on Jan 8, 2025

• Update engine_config validation, ncycle, runtime and test passed

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• keep partition as default

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Commits on Jan 9, 2025

• Flexibly handle SOMD configuration files and create an abstract base class _engine_runner_config. Write out the A3FE version, and make the output logs more concise and suitable for debugging

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Commits on Jan 12, 2025

• engine_confi and test

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• engine_confi and test

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Commits on Jan 16, 2025

• only consult somd_config object, not read from files

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Commits on Jan 20, 2025

• consult engine_config to update somd.cfg with the necessary configurations

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Commits on Jan 26, 2025

• refactor the lambda array and writing of somd.cfg at diff stages

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• nmoves is a required to be written into somd.cfg

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• Pass self-set runtime and add simulation timestep attribute

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Commits on Jan 28, 2025

• Tweak EngineConfig and refactor system preparation

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Commits on Feb 2, 2025

• save enginetype between loading and dump, job name at pre-stages

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Commits on Feb 3, 2025

• pass lambda parameters

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• EnsEnsure first ensemble equilibration restraint is used for all runs

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• Fix incorrect stage setter in Leg

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• Move system prep config attribute descriptions to the fields

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• Make get_file_name a static method

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• Make load function ignorant of derived classes

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• Fix order of decorators

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• Supply lambda values to engine config

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• Import dicts of engine type to config maps in __init__

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• Ensure lambda value information is passed to simulation configs

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Commits on Feb 4, 2025

• check if need restraint at bound/free leg or not

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Commits on Feb 5, 2025

• make sure write path for top,crd,mor files in somd.cfg

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• Only restrain stage need turn on rep-lig on

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Commits on Feb 6, 2025

• pass timestep and nrg_freq to simulation attribute and correct crd top files

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• ruff check for removing unsed func

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Commits on Feb 9, 2025

• add test for update_engine_config_option and modify engine_config test file

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• Delete redundant comments

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• change for importng new SomdSystemPreparationConfig

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• add test for the update_engine_config_option functio

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Commits on Feb 10, 2025

• Only bound state need restraints

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• self.engine_config.timestep/nrg_freq - make sure the information is stored only in one place

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• import SomdSystemPreparationConfig instead of Systemprepconfig used before

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Commits on Feb 14, 2025

• self.engine_config.timestep etc - this means the information is stored only in one place

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• Make new test files for testing

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• Make new test files for testing

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• self.engine_config.timestep etc - this means the information is stored only in one place

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• copy restraint file into stage input and output folders

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• If read lambda from cfg file, make sure pass lambda to lambda_values

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• New test files

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Commits on Feb 19, 2025

• Make required stages a property of the sysprep config

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• Move enums to configuration

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• In progress... store engine config info in EngineType enum

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• Merge branch 'feature-decouple-somd-3' of https://github.com/Roy-Haolin-Du/a3fe into feature-decouple-somd-3

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Commits on Feb 24, 2025

• changed the EngineType enum,removed the mapping dictionaries

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• making new test data for usage of testing

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• making sure somd.cfg is written in the correct place and lambda values are only stored in one place.

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• New test files for removing mapping, correct somd.cfg writen and lambda stored in right place

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