Feature decouple somd 3 to main#68

Merged

Roy-Haolin-Du merged 107 commits intomainfrom

feature-decouple-somd-3

Oct 8, 2025

Commits on Dec 31, 2024

Move SystemPreparationConfig to configuration module
finlayclark
committed
Update SystemPreparationConfig to avoid deprecation warnings
finlayclark
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Serialise SystemPreparationConfig to YAML
finlayclark
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Improve naming of sysprep config module
finlayclark
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Commits on Jan 3, 2025

Improve the error message for attempted analysis when data is unequilibrated
finlayclark
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Merge branch 'michellab:feature-decouple-somd-2' into feature-decouple-somd-2
fjclark
authored

Commits on Jan 4, 2025

Commits on Jan 5, 2025

Merge pull request #25 from fjclark/feature-decouple-somd-2
Roy-Haolin-Du
authored

Commits on Jan 6, 2025

Commits on Jan 8, 2025

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
Roy-Haolin-Du
committed

Commits on Jan 12, 2025

Commits on Jan 16, 2025

only consult somd_config object, not read from files
Roy-Haolin-Du
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Commits on Jan 20, 2025

consult engine_config to update somd.cfg with the necessary configurations
Roy-Haolin-Du
committed

Commits on Jan 26, 2025

Commits on Jan 28, 2025

Tweak EngineConfig and refactor system preparation
finlayclark
committed

Commits on Feb 2, 2025

save enginetype between loading and dump, job name at pre-stages
Roy-Haolin-Du
committed

Commits on Feb 3, 2025

pass lambda parameters
Roy-Haolin-Du
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EnsEnsure first ensemble equilibration restraint is used for all runs
finlayclark
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Fix incorrect stage setter in Leg
finlayclark
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Move system prep config attribute descriptions to the fields
finlayclark
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Make get_file_name a static method
finlayclark
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Make load function ignorant of derived classes
finlayclark
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Fix order of decorators
finlayclark
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Supply lambda values to engine config
finlayclark
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Import dicts of engine type to config maps in __init__
finlayclark
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Ensure lambda value information is passed to simulation configs
finlayclark
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Commits on Feb 4, 2025

check if need restraint at bound/free leg or not
Roy-Haolin-Du
committed

Commits on Feb 5, 2025

Commits on Feb 6, 2025

Commits on Feb 10, 2025

Commits on Feb 19, 2025

Make required stages a property of the sysprep config
finlayclark
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Move enums to configuration
finlayclark
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In progress... store engine config info in EngineType enum
finlayclark
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Merge branch 'feature-decouple-somd-3' of https://github.com/Roy-Haolin-Du/a3fe into feature-decouple-somd-3
finlayclark
committed

Commits on Feb 27, 2025

Make sure get_result function reads the Scorrect surm output file
Roy-Haolin-Du
committed

Commits on Feb 28, 2025

Merge pull request #29 from Roy-Haolin-Du/feature-decouple-somd-3
Roy-Haolin-Du
authored

Commits on Mar 4, 2025

Commits on Mar 5, 2025

ruff formating for all files
Roy-Haolin-Du
committed

Commits on Mar 13, 2025

Commits on Mar 20, 2025

Some extensive docs on new features. Adding Makefile and pre-commit-config hooks
Roy-Haolin-Du
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Commits on Mar 27, 2025

Simplied env setup in Makefile and CI configuration
Roy-Haolin-Du
committed

Commits on Apr 11, 2025

Commits on Apr 12, 2025

check the exact expected equil time is found in adaptive test
Roy-Haolin-Du
committed

Commits on Apr 14, 2025

Using a small system integration test convenient
Roy-Haolin-Du
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Commits on Jun 10, 2025

Adding python version support to make env and removing mike deployment
Roy-Haolin-Du
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Commits on Jun 22, 2025

Commits on Jun 23, 2025

Commits on Aug 11, 2025

Changed the copyright notice to 2023-2025 and include Roy
Roy-Haolin-Du
committed

Commits on Sep 23, 2025

Merge pull request #40 from Roy-Haolin-Du/feature-decouple-somd-3
Roy-Haolin-Du
authored

Commits on Oct 6, 2025

Commits on Oct 8, 2025

Added SLURM queue check intervals into SlurmConfig class Fixes #70
Roy-Haolin-Du
committed