mdsuite.calculators.spatial_distribution_function module

MDSuite: A Zincwarecode package.

License

This program and the accompanying materials are made available under the terms of the Eclipse Public License v2.0 which accompanies this distribution, and is available at https://www.eclipse.org/legal/epl-v20.html

SPDX-License-Identifier: EPL-2.0

Copyright Contributors to the Zincwarecode Project.

Contact Information

email: zincwarecode@gmail.com github: https://github.com/zincware web: https://zincwarecode.com/

Citation

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Summary

Module for the spatial distribution function calculator.

class mdsuite.calculators.spatial_distribution_function.Args(number_of_configurations: int, data_range: int, correlation_time: int, atom_selection: np.s_, molecules: bool, species: list, r_min: float, r_max: float, n_bins: int)

Bases: object

Data class for the saved properties.

atom_selection: np.s_

correlation_time: int

data_range: int

molecules: bool

n_bins: int

number_of_configurations: int

r_max: float

r_min: float

species: list

class mdsuite.calculators.spatial_distribution_function.SpatialDistributionFunction(experiment: Experiment, experiments=None)

Bases: TrajectoryCalculator

Spatial Distribution Function Calculator based on the r_ij matrix.

r_ij_to_bins(r_ij) → Tensor

Compute the 2D histogram in spherical coordinates while projecting all values of r to a unit sphere.

Parameters:

r_ij (tf.Tensor) – any r_ij matrix with shape (…, 3)

Returns:

bins with shape (n_bins, n_bins)

Return type:

tf.Tensor

run_calculator()

Run the computation.