mdsuite.calculators.potential_of_mean_force 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 computation of the potential of mean force (PMF). The PMF can be used to better understand effective bond strength between species of a system.

class mdsuite.calculators.potential_of_mean_force.Args(savgol_order: int, savgol_window_length: int, number_of_bins: int, number_of_configurations: int, cutoff: float, number_of_shells: int)[source]¶

Bases: object

Data class for the saved properties.

cutoff: float¶

number_of_bins: int¶

number_of_configurations: int¶

number_of_shells: int¶

savgol_order: int¶

savgol_window_length: int¶

class mdsuite.calculators.potential_of_mean_force.PotentialOfMeanForce(**kwargs)[source]¶

Bases: Calculator

Class for the calculation of the potential of mean-force.

The potential of mean-force is a measure of the binding strength between atomic species in a experiment.

experiment¶

Class object of the experiment.

Type:: class object

data_range¶

Range over which the property should be evaluated. This is not applicable to the current analysis as the full rdf will be calculated.

Type:: int (default=500)

x_label¶

How to label the x axis of the saved plot.

Type:: str

y_label¶

How to label the y axis of the saved plot.

Type:: str

analysis_name¶

Name of the analysis. used in saving of the tensor_values and figure.

Type:: str

file_to_study¶

The tensor_values file corresponding to the rdf being studied.

Type:: str

data_files¶

list of files to be analyzed.

Type:: list

rdf = None

rdf tensor_values being studied.

Type:: list

radii = None

radii tensor_values corresponding to the rdf.

Type:: list

selected_species¶

A list of species combinations being studied.

Type:: list