iphasimulator.workflows.md_benchmark

Batch MD benchmark workflow for PHA validation systems.

Attributes

SYSTEMS
CHARGE_METHODS
DEFAULT_REPO_ROOT

Classes

BenchmarkTarget

Input and output paths for one benchmark system.

Functions

discover_targets(→ list[BenchmarkTarget])
selected_system_names(→ tuple[str, ...])
run_benchmark(→ int)
parse_args(→ argparse.Namespace)
main(→ None)

Module Contents

iphasimulator.workflows.md_benchmark.SYSTEMS = ('P3HB_4', 'P3HB_8', 'P3HO_4', 'P3HO_8', 'P3HDD_4', 'P3HDD_8')

iphasimulator.workflows.md_benchmark.CHARGE_METHODS = ('abcg2', 'bcc', 'gas', 'mul')

iphasimulator.workflows.md_benchmark.DEFAULT_REPO_ROOT

class iphasimulator.workflows.md_benchmark.BenchmarkTarget

Input and output paths for one benchmark system.

name: str

sdf_path: pathlib.Path

output_dir: pathlib.Path

property gaff2_dir: pathlib.Path

property prmtop_path: pathlib.Path

property inpcrd_path: pathlib.Path

property openmm_dir: pathlib.Path

property gromacs_dir: pathlib.Path

iphasimulator.workflows.md_benchmark.discover_targets(system_names: tuple[str, ...], *, repo_root: pathlib.Path = DEFAULT_REPO_ROOT) → list[BenchmarkTarget]

iphasimulator.workflows.md_benchmark.selected_system_names(args: argparse.Namespace) → tuple[str, ...]

iphasimulator.workflows.md_benchmark.run_benchmark(args: argparse.Namespace) → int

iphasimulator.workflows.md_benchmark.parse_args(argv: list[str] | None = None) → argparse.Namespace

iphasimulator.workflows.md_benchmark.main(argv: list[str] | None = None) → None