gnrs.descriptor¶

gnrs.descriptor.descriptor_task¶

This module provides the DescriptorEvaluationTask class for evaluating descriptors.

This source code is licensed under the BSD-3-Clause license found in the LICENSE file in the root directory of this source tree.

class gnrs.descriptor.descriptor_task.DescriptorEvaluationTask[source]¶

Bases: TaskABC

Task for evaluating crystal structure descriptors.

Initialize the descriptor evaluation task.

Parameters:

comm – MPI communicator
config – Config dictionary
gnrs_info – Genarris info dictionary
descriptor – Descriptor class name

__init__(comm, config, gnrs_info, descriptor)[source]¶

Initialize the descriptor evaluation task.

Parameters:

comm (mpi4py.MPI.Comm) – MPI communicator
config (dict) – Config dictionary
gnrs_info (dict) – Genarris info dictionary
descriptor (str) – Descriptor class name

Return type:

None

initialize()[source]¶

Initialize the descriptor evaluation task.

Return type:: None

pack_settings()[source]¶

Pack settings needed for descriptor evaluation.

Returns:: Task settings dictionary
Return type:: dict

print_settings(task_set)[source]¶

Print task settings in a formatted table.

Parameters:: task_set (dict) – Task settings dictionary
Return type:: None

create_folders()[source]¶

Create folders needed for the task.

Return type:: None

perform_task(task_set)[source]¶

Execute the descriptor evaluation task.

This method: 1. Computes descriptors for all structures 2. Optionally performs PCA compression

Parameters:: task_set (dict) – Task settings dictionary
Return type:: None

collect_results()[source]¶

Collect and save the results of the task.

Return type:: None

analyze()[source]¶

Analyze the results of the task.

Return type:: None

finalize()[source]¶

Finalize the task and update runtime settings.

Return type:: None

gnrs.descriptor.acsf¶

This module provides the ACSF descriptor implementation.

This source code is licensed under the BSD-3-Clause license found in the LICENSE file in the root directory of this source tree.

class gnrs.descriptor.acsf.ACSFDescriptor[source]¶

Bases: DescriptorABC

Computes Atom-Centered Symmetry Function (ACSF) descriptors.

ACSFs can be used to represent the local environment near an atom by using a fingerprint composed of the output of multiple two- and three-body functions that can be customized to detect specific structural features.

Initialize the ACSF descriptor calculator.

Parameters:

comm – MPI communicator for parallel computation
task_settings – Task settings Dictionary for ACSF descriptor

__init__(comm, task_settings)[source]¶

Initialize the ACSF descriptor calculator.

Parameters:

comm (mpi4py.MPI.Comm) – MPI communicator for parallel computation
task_settings (dict) – Task settings Dictionary for ACSF descriptor

Return type:

None

initialize()[source]¶

Initialization step.

Return type:: None

compute(xtal)[source]¶

Compute ACSF descriptors for the given crystal structure.

Parameters:: xtal (ase.Atoms) – Crystal structure to compute descriptors.
Return type:: None

finalize()[source]¶

Finalization step.

Return type:: None