readNeighbors()
Description
readNeighbors() is a function used to read the states (as predicted through Machine Learning) of the neighbors of each molecule to list the state compositions. The neighbors list has to be collected first using the doVoro() function.
Unless specified explicitely, this function should be automatically started by doVoro().
The function will both update the input tessellation and output an array of the neighbor composition as well as a list of the phase names.
Argument, keywords and outputs
Input(s) / Argument(s)
| Name | Flag | Type | Description |
|---|---|---|---|
| Representation | class Tessellation | Instance of the class Tessellation including the representation on the system and its Voronoi tessellation. |
Output(s)
| Name | Type | Description |
|---|---|---|
| Neighbors Phases | np.ndarray | Array of the phases of the neighbors of each molecule. Dimension(s) are in (N frames, N molecules, N phases). |
| Phases List | np.ndarray | Array listing the phases analysed and the order used for the neighbors phases array. |
Examples
Read the local environment and return the composition
The following example will read the local environment in the instance of the Tessellation class named voronoi, and both return the results in the variables phase_array and phase_names; but also store them in the same instance.
import mllpa
phase_array, phase_names = mllpa.readNeighbors(voronoi)
Read the local environment but don’t return anything
The following example will read the local environment in the instance of the Tessellation class named voronoi, and store the output in the same instance.
mllpa.readNeighbors(voronoi)
Related tutorials
The following tutorial(s) detail further the use of the readNeighbors() function: