Solvent radial distribution

class mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionBenchmark(force_field: ForceField | Calculator, data_input_dir: str | PathLike = './data', run_mode: RunMode | Literal['dev', 'fast', 'standard'] = RunMode.STANDARD)

Benchmark for solvent radial distribution function.

name

The unique benchmark name that should be used to run the benchmark from the CLI and that will determine the output folder name for the result file. The name is solvent_radial_distribution.

Type:

str

category

A string that describes the category of the benchmark, used for example, in the UI app for grouping. Default, if not overridden, is “General”. This benchmark’s category is “Molecular Liquids”.

Type:

str

result_class

A reference to the type of BenchmarkResult that will determine the return type of self.analyze(). The result class type is SolventRadialDistributionResult.

Type:

type[mlipaudit.benchmark.BenchmarkResult] | None

model_output_class

A reference to the SolventRadialDistributionModelOutput class.

Type:

type[mlipaudit.benchmark.ModelOutput] | None

required_elements

The set of atomic element types that are present in the benchmark’s input files.

Type:

set[str] | None

skip_if_elements_missing

Whether the benchmark should be skipped entirely if there are some atomic element types that the model cannot handle. If False, the benchmark must have its own custom logic to handle missing atomic element types. For this benchmark, the attribute is set to True.

Type:

bool

__init__(force_field: ForceField | Calculator, data_input_dir: str | PathLike = './data', run_mode: RunMode | Literal['dev', 'fast', 'standard'] = RunMode.STANDARD) → None

Initializes the benchmark.

Parameters:

• force_field – The force field model to be benchmarked.

• data_input_dir – The local input data directory. Defaults to “./data”. If the subdirectory “{data_input_dir}/{benchmark_name}” exists, the benchmark expects the relevant data to be in there, otherwise it will download it from HuggingFace.

• run_mode – Whether to run the standard benchmark length, a faster version, or a very fast development version. Subclasses should ensure that when RunMode.DEV, their benchmark runs in a much shorter timeframe, by running on a reduced number of test cases, for instance. Implementing RunMode.FAST being different from RunMode.STANDARD is optional and only recommended for very long-running benchmarks. This argument can also be passed as a string “dev”, “fast”, or “standard”.

Raises:

• ChemicalElementsMissingError – If initialization is attempted with a force field that cannot perform inference on the required elements.

• ValueError – If force field type is not compatible.

run_model() → None

Run an MD simulation for each structure. The MD simulation is performed using the JAX MD engine and starts from the reference structure. NOTE: This benchmark runs a simulation in the NVT ensemble, which is not recommended for a water RDF calculation.

analyze() → SolventRadialDistributionResult

Calculate how much the radial distribution deviates from the reference.

Returns:

A SolventRadialDistributionResult object.

Raises:

RuntimeError – If called before run_model().

class mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionResult(*, failed: bool = False, score: Annotated[float | None, Ge(ge=0), Le(le=1)] = None, structure_names: list[str], structures: list[SolventRadialDistributionStructureResult], avg_peak_deviation: Annotated[float, Ge(ge=0)] | None = None)

Result object for the solvent radial distribution benchmark.

structure_names

The names of the structures.

Type:

list[str]

structures

List of per structure results.

Type:

list[mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionStructureResult]

avg_peak_deviation

The average deviation across all structures.

Type:

float | None

failed

Whether all the simulations failed and no analysis could be performed. Defaults to False.

Type:

bool

score

The final score for the benchmark between 0 and 1.

Type:

float | None

class mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionStructureResult(*, structure_name: str, radii: list[float] | None = None, rdf: list[float] | None = None, first_solvent_peak: float | None = None, peak_deviation: Annotated[float, Ge(ge=0)] | None = None, failed: bool = False, score: float = 0.0)

Stores the result for a single structure.

structure_name

The structure name.

Type:

str

radii

The radii values in Angstrom.

Type:

list[float] | None

rdf

The radial distribution function values at the radii.

Type:

list[float] | None

first_solvent_peak

The first solvent peak, i.e. the radius at which the rdf is the maximum.

Type:

float | None

peak_deviation

The deviation of the first solvent peak from the reference.

Type:

float | None

failed

Whether the simulation was successful. If unsuccessful, the other attributes will be not be set.

Type:

bool

score

The score for the molecule.

Type:

float

class mlipaudit.benchmarks.solvent_radial_distribution.solvent_radial_distribution.SolventRadialDistributionModelOutput(*, structure_names: list[str], simulation_states: list[SimulationState | None])

Model output containing the final simulation states for each structure.

structure_names

The names of the structures.

Type:

list[str]

simulation_states

SimulationState or None object for each structure in the same order as the structure names. None if the simulation failed.

Type:

list[mlip.simulation.state.SimulationState | None]