bfflearn 0.1.0.dev1__py3-none-any.whl

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Files changed (55) hide show
  1. bff/__init__.py +30 -0
  2. bff/bayes/__init__.py +11 -0
  3. bff/bayes/gaussian_process.py +285 -0
  4. bff/bayes/kernels.py +71 -0
  5. bff/bayes/learning.py +484 -0
  6. bff/bayes/likelihoods.py +142 -0
  7. bff/bayes/posterior.py +62 -0
  8. bff/bayes/priors.py +179 -0
  9. bff/bayes/results.py +327 -0
  10. bff/bayes/utils.py +333 -0
  11. bff/cli.py +254 -0
  12. bff/data.py +93 -0
  13. bff/domain/__init__.py +12 -0
  14. bff/domain/bias.py +149 -0
  15. bff/domain/specs.py +347 -0
  16. bff/domain/trainset.py +201 -0
  17. bff/io/__init__.py +12 -0
  18. bff/io/colvars.py +186 -0
  19. bff/io/commands.py +20 -0
  20. bff/io/cp2k.py +330 -0
  21. bff/io/logs.py +213 -0
  22. bff/io/mdp.py +98 -0
  23. bff/io/plumed.py +184 -0
  24. bff/io/progress.py +74 -0
  25. bff/io/schedulers.py +118 -0
  26. bff/io/utils.py +208 -0
  27. bff/mcmc/__init__.py +3 -0
  28. bff/mcmc/convergence.py +168 -0
  29. bff/mcmc/proposal.py +254 -0
  30. bff/mcmc/sampler.py +481 -0
  31. bff/plotting.py +362 -0
  32. bff/qoi/__init__.py +9 -0
  33. bff/qoi/analysis.py +209 -0
  34. bff/qoi/data.py +169 -0
  35. bff/qoi/hbonds.py +255 -0
  36. bff/qoi/rdf.py +108 -0
  37. bff/qoi/routines.py +272 -0
  38. bff/tools.py +168 -0
  39. bff/topology.py +581 -0
  40. bff/workflows/__init__.py +0 -0
  41. bff/workflows/configs.py +1147 -0
  42. bff/workflows/learn.py +77 -0
  43. bff/workflows/md.py +326 -0
  44. bff/workflows/prepare.py +788 -0
  45. bff/workflows/qoi.py +260 -0
  46. bff/workflows/runsims.py +620 -0
  47. bff/workflows/simulate.py +28 -0
  48. bff/workflows/train.py +69 -0
  49. bff/workflows/validate.py +29 -0
  50. bfflearn-0.1.0.dev1.dist-info/METADATA +913 -0
  51. bfflearn-0.1.0.dev1.dist-info/RECORD +55 -0
  52. bfflearn-0.1.0.dev1.dist-info/WHEEL +5 -0
  53. bfflearn-0.1.0.dev1.dist-info/entry_points.txt +2 -0
  54. bfflearn-0.1.0.dev1.dist-info/licenses/LICENSE +674 -0
  55. bfflearn-0.1.0.dev1.dist-info/top_level.txt +1 -0
bff/workflows/train.py ADDED
@@ -0,0 +1,69 @@
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+ """Workflow entry point for surrogate training."""
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+
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+ import sys
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+ from pathlib import Path
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+ from typing import Union
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+
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+ from ..io.logs import Logger
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+ from ..qoi.data import QoIDataset
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+ from .configs import TrainConfig
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+
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+ PathLike = Union[str, Path]
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+
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+
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+ def _load_datasets(config: TrainConfig) -> tuple[QoIDataset, ...]:
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+ datasets: list[QoIDataset] = []
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+ for dataset_config in config.datasets:
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+ dataset = QoIDataset.load(dataset_config.fn_data)
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+ dataset.nuisance = dataset_config.nuisance
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+ datasets.append(dataset)
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+ return tuple(datasets)
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+
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+
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+ def _dataset_options(
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+ config: TrainConfig,
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+ ) -> tuple[dict[str, Path | None], dict[str, object], dict[str, float]]:
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+ model_paths = {dataset.name: dataset.fn_model for dataset in config.datasets}
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+ y_means = {dataset.name: dataset.mean for dataset in config.datasets}
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+ observation_scales = {
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+ dataset.name: dataset.observation_scale for dataset in config.datasets
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+ }
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+ return model_paths, y_means, observation_scales
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+
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+
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+ def main(fn_config: PathLike) -> None:
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+ try:
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+ from ..bayes.learning import train_surrogates
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+ except ModuleNotFoundError as exc:
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+ if exc.name == "torch":
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+ raise RuntimeError(
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+ "PyTorch is required for 'bff train'. Install a CPU or CUDA "
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+ "build of PyTorch first."
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+ ) from exc
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+ raise
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+
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+ config = TrainConfig.load(fn_config)
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+ logger = Logger("BFF", str(config.log), mode="w")
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+ datasets = _load_datasets(config)
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+ model_paths, y_means, observation_scales = _dataset_options(config)
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+
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+ config.training.model_dir.mkdir(parents=True, exist_ok=True)
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+
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+ train_surrogates(
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+ datasets,
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+ y_means=y_means,
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+ observation_scales=observation_scales,
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+ model_paths=model_paths,
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+ reuse_models=config.training.reuse_models,
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+ n_hyper_max=config.training.n_hyper_max,
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+ committee_size=config.training.committee_size,
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+ test_fraction=config.training.test_fraction,
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+ device=config.training.device,
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+ logger=logger,
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+ **config.training.opt_kwargs,
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+ )
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+
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+
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+ if __name__ == "__main__":
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+ fn_config = sys.argv[1]
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+ main(fn_config)
@@ -0,0 +1,29 @@
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+ """Workflow entry point for posterior-sample validation campaigns."""
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+
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+ from ..io.logs import Logger
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+ from .configs import ValidateConfig
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+ from .runsims import (
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+ load_parameter_samples,
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+ print_validate_summary,
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+ run_campaign,
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+ stage_campaign,
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+ )
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+
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+
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+ def main(fn_config: str) -> None:
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+ """Run a validation campaign for provided force-field parameter samples."""
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+ config = ValidateConfig.load(fn_config)
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+ parameter_samples = load_parameter_samples(config.parameters, config.specs)
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+
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+ fn_specs, systems = stage_campaign(config, fn_specs=config.specs)
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+ assert fn_specs is not None
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+
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+ logger = Logger("validate")
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+ print_validate_summary(config, fn_specs, len(parameter_samples), logger)
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+ run_campaign(
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+ config=config,
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+ fn_specs=fn_specs,
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+ systems=systems,
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+ parameter_samples=parameter_samples,
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+ logger=logger,
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+ )