core.components.calculate

Copyright (c) Meta Platforms, Inc. and affiliates.

This source code is licensed under the MIT license found in the LICENSE file in the root directory of this source tree.

Submodules

• core.components.calculate.adsorbml_runner
• core.components.calculate.adsorption_runner
• core.components.calculate.adsorption_singlepoint_runner
• core.components.calculate.calculate_runner
• core.components.calculate.elasticity_runner
• core.components.calculate.kappa_runner
• core.components.calculate.nve_md_runner
• core.components.calculate.pairwise_ct_runner
• core.components.calculate.phonon_runner
• core.components.calculate.recipes
• core.components.calculate.relaxation_runner
• core.components.calculate.singlepoint_runner

Classes

CalculateRunner	Runner to run calculations/predictions using an ASE-like calculator and save results to file.
ElasticityRunner	Calculate elastic tensor for a set of structures.
RelaxationRunner	Relax a sequence of several structures/molecules.

Package Contents

class core.components.calculate.CalculateRunner(calculator: ase.calculators.Calculator, input_data: collections.abc.Sequence)

Bases: fairchem.core.components.runner.Runner

Runner to run calculations/predictions using an ASE-like calculator and save results to file.

Note

When running with the fairchemv2 cli, the job_config and attribute is set at runtime to those given in the config file.

See the Runner interface class for implementation details.

job_config

a managed attribute that gives access to the job config

Type:

DictConfig

result_glob_pattern

glob pattern of results written to file

Type:

str

result_glob_pattern: ClassVar[str] = '*'

_calculator

_input_data

property calculator: ase.calculators.Calculator

Get the calculator instance.

Returns:

The ASE-like calculator used for calculations

Return type:

Calculator

property input_data: collections.abc.Sequence

Get the input data.

Returns:

The input data to be processed

Return type:

Sequence

abstract calculate(job_num: int = 0, num_jobs: int = 1) → R

Run any calculation using an ASE like Calculator.

Parameters:

• job_num (int, optional) – Current job number in array job. Defaults to 0.

• num_jobs (int, optional) – Total number of jobs in array. Defaults to 1.

Returns:

Results of the calculation

Return type:

R

abstract write_results(results: R, results_dir: str, job_num: int = 0, num_jobs: int = 1) → None

Write results to file in results_dir.

Parameters:

• results (R) – Results from the calculation

• results_dir (str) – Directory to write results to

• job_num (int, optional) – Current job number in array job. Defaults to 0.

• num_jobs (int, optional) – Total number of jobs in array. Defaults to 1.

abstract save_state(checkpoint_location: str, is_preemption: bool = False) → bool

Save the current state of the calculation to a checkpoint.

Parameters:

• checkpoint_location (str) – Location to save the checkpoint

• is_preemption (bool, optional) – Whether this save is due to preemption. Defaults to False.

Returns:

True if state was successfully saved, False otherwise

Return type:

bool

abstract load_state(checkpoint_location: str | None) → None

Load a previously saved state from a checkpoint.

Parameters:

checkpoint_location (str | None) – Location of the checkpoint to load, or None if no checkpoint

run()

Run the actual calculation and save results.

Creates the results directory if it doesn’t exist, runs the calculation, and writes the results to the specified directory.

Note

Re-implementing this method in derived classes is discouraged.

class core.components.calculate.ElasticityRunner(calculator: ase.calculators.calculator.Calculator, input_data: fairchem.core.datasets.AseDBDataset)

Bases: fairchem.core.components.calculate.CalculateRunner

Calculate elastic tensor for a set of structures.

result_glob_pattern: ClassVar[str] = 'elasticity_*-*.json.gz'

calculate(job_num: int = 0, num_jobs: int = 1) → list[dict[str, Any]]

Calculate elastic properties for a batch of structures.

Parameters:

• job_num (int, optional) – Current job number in array job. Defaults to 0.

• num_jobs (int, optional) – Total number of jobs in array. Defaults to 1.

Returns:

List of dictionaries containing elastic properties for each structure

write_results(results: list[dict[str, Any]], results_dir: str, job_num: int = 0, num_jobs: int = 1) → None

Write calculation results to a compressed JSON file.

Parameters:

• results – List of dictionaries containing elastic properties

• results_dir – Directory path where results will be saved

• job_num – Index of the current job

• num_jobs – Total number of jobs

save_state(checkpoint_location: str, is_preemption: bool = False) → bool

Save the current state of the calculation to a checkpoint.

Parameters:

• checkpoint_location (str) – Location to save the checkpoint

• is_preemption (bool, optional) – Whether this save is due to preemption. Defaults to False.

Returns:

True if state was successfully saved, False otherwise

Return type:

bool

load_state(checkpoint_location: str | None) → None

Load a previously saved state from a checkpoint.

Parameters:

checkpoint_location (str | None) – Location of the checkpoint to load, or None if no checkpoint

class core.components.calculate.RelaxationRunner(calculator: ase.calculators.calculator.Calculator, input_data: fairchem.core.datasets.AseDBDataset, calculate_properties: collections.abc.Sequence[str], save_relaxed_atoms: bool = True, normalize_properties_by: dict[str, str] | None = None, save_target_properties: collections.abc.Sequence[str] | None = None, **relax_kwargs)

Bases: fairchem.core.components.calculate.CalculateRunner

Relax a sequence of several structures/molecules.

This class handles the relaxation of atomic structures using a specified calculator, processes the input data in chunks, and saves the results.

result_glob_pattern: ClassVar[str] = 'relaxation_*-*.json.gz'

_calculate_properties

_save_relaxed_atoms

_normalize_properties_by

_save_target_properties

_relax_kwargs

calculate(job_num: int = 0, num_jobs: int = 1) → list[dict[str, Any]]

Perform relaxation calculations on a subset of structures.

Splits the input data into chunks and processes the chunk corresponding to job_num.

Parameters:

• job_num (int, optional) – Current job number in array job. Defaults to 0.

• num_jobs (int, optional) – Total number of jobs in array. Defaults to 1.

Returns:

list[dict[str, Any]] - List of dictionaries containing calculation results

write_results(results: list[dict[str, Any]], results_dir: str, job_num: int = 0, num_jobs: int = 1) → None

Write calculation results to a compressed JSON file.

Parameters:

• results – List of dictionaries containing elastic properties

• results_dir – Directory path where results will be saved

• job_num – Index of the current job

• num_jobs – Total number of jobs

save_state(checkpoint_location: str, is_preemption: bool = False) → bool

Save the current state of the calculation to a checkpoint.

Parameters:

• checkpoint_location (str) – Location to save the checkpoint

• is_preemption (bool, optional) – Whether this save is due to preemption. Defaults to False.

Returns:

True if state was successfully saved, False otherwise

Return type:

bool

load_state(checkpoint_location: str | None) → None

Load a previously saved state from a checkpoint.

Parameters:

checkpoint_location (str | None) – Location of the checkpoint to load, or None if no checkpoint