Feature decouple somd 3 #29
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…class _engine_runner_config. Write out the A3FE version, and make the output logs more concise and suitable for debugging
| self._stream_log_level = stream_log_level | ||
| self._set_up_logging() | ||
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| def _set_up_logging(self) -> None: |
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Can remove logging as it's not used. Thanks
| config = self.get_config() | ||
| with open(file_path, "w") as f: | ||
| _yaml.safe_dump(config, f, default_flow_style=False) | ||
| self._logger.info(f"Configuration dumped to {file_path}") |
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Can probably remove, thanks
| """ | ||
| pass | ||
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| def __eq__(self, other: object) -> bool: |
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No need to define if this derived from pdyantic base model.
| from ..run._logging_formatters import _A3feStreamFormatter | ||
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| class EngineRunnerConfig(ABC): |
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Inherit from base model please.
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| from ._engine_runner_config import EngineRunnerConfig as _EngineRunnerConfig | ||
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Probably shift the base class into the same file - have a think about it - up to you!
| @@ -191,8 +192,8 @@ three replicates. Note that this is expected to produce an erroneously favourabl | |||
| cfg.runtime_npt = 50 # ps | |||
| cfg.ensemble_equilibration_time = 100 # ps | |||
| calc = a3.Calculation(ensemble_size = 3) | |||
| calc_set.setup(bound_leg_sysprep_config = cfg, free_leg_sysprep_config = cfg) | |||
| calc_set.run(adaptive = False, runtime=0.1) # ns | |||
| calc.setup(bound_leg_sysprep_config = cfg, free_leg_sysprep_config = cfg) | |||
| @@ -140,7 +141,7 @@ Individual Simulation settings | |||
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| To customise the specifics of how each lambda window is run (e.g. timestep), you can use the ``set_simfile_option`` method. For example, to set the timestep to 2 fs, run | |||
| ``calc.set_simfile_option("timestep", "2 * femtosecond")``. This will change parameters from the defaults given in ``template_config.cfg`` in the ``input`` directory, and warn | |||
| ``calc.set_simfile_option("timestep", "2 * femtosecond")``. This will change parameters from the defaults generated by ``engine_config``, and warn | |||
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We need to update this entire function to update the configs for all sub-simulation runners. Please rename it to something more appropriate e.g. set_config_option and test that it updates all configs.
| @@ -304,12 +305,12 @@ You can run sets of calculations using the :class:`a3fe.run.CalcSet` class. To d | |||
| ABFE with Charged Ligands | |||
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| Since A3FE 0.2.0, ABFE calculations with charged ligands are supported using a co-alchemical ion approach. The charge of the ligand will be automatically detected, assuming that this is correctly specified in the input sdf. The only change in the input required is that the use of PME, rather than reaction field electrostatics, should be specified in ``template_config.cfg`` as e.g.: | |||
| Since A3FE 0.2.0, ABFE calculations with charged ligands are supported using a co-alchemical ion approach. The charge of the ligand will be automatically detected, assuming that this is correctly specified in the input sdf. The only change in the input required is that the use of PME, rather than reaction field electrostatics, should be specified in ``somd_config.cfg`` as e.g.: | |||
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Please change to SomdEngineConfig (or whatever it was). Thanks
| The default `somd_config.cfg` uses reaction field instead of PME. This is faster (around twice as fast for some of our systems) and has been shown to give equivalent results for neutral ligands in RBFE calculations - see https://pubs.acs.org/doi/full/10.1021/acs.jcim.0c01424 . |
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Please also change to point to the the config class rather than the template. Thanks!
| @@ -338,19 +338,6 @@ def run(self, runtime: float = 2.5) -> None: | |||
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| None | |||
| """ | |||
| # Need to make sure that runtime is a multiple of the time per cycle | |||
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Please ensure that the somd.cfg file is written out before here, to ensure that the most up-to-date options are written out before the simulation is run.
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Hi Finlay, I hope you're doing well! So far, the template_config.cfg has been replaced with a Pydantic SomdConfig class, which can now be generated automatically when the simulation requires it. Additionally, we aim to avoid writing the somd.cfg file until it’s ready to be submitted to Slurm. The only place where the file should be written is in the run method of the simulation.py file. The workflow should only interact with the somd_config object, avoiding read from file. Information should flow one way: from the Pydantic classes to the files, without reading data back from files. To support this, I have removed all read_simfile_option calls and definitions, as well as the write_simfile_option function. However, the generated somd.cfg file is still missing some extended parameters, such as morph, top, crdFiles, and restraints. Perhaps in our next meeting, we can discuss this part in detail and explore potential solutions. I’d appreciate any advice you have. Thanks a lot for your support! Best regards |
Description
Replace template_config.cfg with Pydantic config
Todos
Remove the template_config.cfg and replace with a Pydantic SomdConfig class (which derived from a general EngineConfig class which can be configured in the code, or else read from a yaml/json file if not supplied.