4.4. graph_2.py

This module contains the basic graph components of atomic graphs.

class graph_2.Vertex(index, im_coor_x, im_coor_y, r, scale, zeta=0, advanced_species='Un_1', n=3, atomic_species='Un', void=False, parent_graph=None)

A vertex is object is an atomic graph component.

A vertex contains a lot of the local information of the parent atomic graph.

Variables

parent_graph (graph_2.AtomicGraph) – A reference to the AtomicGraph object that the vertex belongs to.

Parameters

  • index (int) – Index of the vertex. Must be unique.

  • im_coor_x (float) – x-coordinate of the center of the column in the image which the vertex represents.

  • im_coor_y (float) – y-coordinate of the center of the column in the image which the vertex represents.

  • r (int) – The “approximate atomic radii” in pixels.

  • scale (float) – The scale of the HAADF-STEM image in pm/pixel

  • zeta (int) – (Optional) The initial zeta value of the vertex (0 or 1). Defaults to 0.

  • advanced_species (str) – (Optional) The initial “advanced species category” of the vertex. Defaults to 'Un_1'.

  • atomic_species (str) – (Optional) The initial “atomic species category” of the vertex. Defaults to 'Un'.

  • void (bool) – (Optional) Whether the vertex is void or not. Defaults to False.

  • parent_graph (graph_2.AtomicGraph) – (Optional) A reference to the graph object that the vertex belongs to. Defaults to None.

determine_species_from_probability_vector()

Set the atomic species of the vertex based on the advanced probability vector

First determine the advanced species from the advanced probability vector, and then set the atomic species of the vertex based on which atomic species the advanced species maps to. Also set the symmetry number ‘n’.

im_pos()

Returns a triple with the image coordinates of the vertex.

Returns

(x, y, z), where x, y and z are the image coordinates of the vertex.

Return type

(float, float, float)

report()

Create a report summarizing the contents of the vertex instance and return it as a string

Returns

A vertex summary

Return type

str

reset_probability_vector(bias='Un_1')

Reset the probability vector with a certain bias

This method will set all the atomic species probabilities equal to each other. If an advanced species bias is given, then that advanced species will be slightly larger than the others. The bias defaults to ‘Un_1’ if no bias is given.

Parameters

bias (string) – Default to this advanced species (optional, default=’Un_1’)

set_probability_from_advanced()

Set atomic species probability vector by summarizing the probabilities of the every advanced species.

If, for instance, the advanced probability vector is:

advanced_species

advanced probability

Si_1

0.01

Si_2

0.2

Al_1

0.09

Al_2

0.7

Then the probability vector will be set to:

Atomic species

probability

Si

0.2 + 0.01 = 0.21

Al

0.09 + 0.7 = 0.79
spatial_pos()

Returns a triple with the spatial coordinates of the vertex.

Returns

(x, y, z), where x, y and z are the spatial coordinates of the vertex.

Return type

(float, float, float)