Oxygen reduction reaction

Created on Fri May 26 13:41:45 2017

@author: mpnun

class Cat_structure.cat_structure(met_name=None, facet=None, dim1=None, dim2=None)

Catalyst structure with defects

copy_data()

Create a new individual with identical essential data

eval_current_density(atom_graph=None, normalize=True)

Normalized: current density [mA/cm^2] Not normalized: current [mA]

eval_surface_energy(atom_graph=None, normalize=True)

Normalized: surface energy [J/m^2] Not normalized: formation energy [eV]

flip_atom(ind)

If atom number ind is present in the defected graph, remove it. If it is not present, add it and all edges to adjacent atoms.

get_Nnn()

For each active atom, print the number of nearest neighbors that are also active

get_defected_mols()

Use defected graph and template atoms object to generate the atoms object for the defected structure

load_from_file(ftoread, d_cut=0.001)

Determine which atoms in the template are missing in the defected structure d_cut: distance cutoff in angstroms

randomize(coverage=None)

Randomize the occupancies in the top layer

show(x=None, n_struc=1, fmat='picture')

Print image of surface

Created on Fri May 26 14:39:12 2017

@author: mpnun

ORR.ORR_rate(delEads_OH, delEads_OOH)

Compute ORR rate from OH and OOH binding energies Follows the method and data in S.1 of F. Calle-Vallejo et al., Science 350(6257), 185 (2015). Also see J. K. Nørskov et al., The Journal of Physical Chemistry B 108(46), 17886 (2004). for method on how to convert binding energies to activity

Returns:Current

Created on Fri May 26 13:26:51 2017

@author: mpnun

Created on Fri May 26 15:36:16 2017

@author: mpnun

class graph_theory.Graph(graph_dict=None)

Adapted from http://www.python-course.eu/graphs_python.php

add_edge(edge)

assumes that edge is of type set, tuple or list; between two vertices can be multiple edges!

add_vertex(vertex)

If the vertex “vertex” is not in self.__graph_dict, a key “vertex” with an empty list as a value is added to the dictionary. Otherwise nothing has to be done.

copy_data()

returns a copy of the graph with the same dictionary

edges()

returns the edges of a graph

get_coordination_number(vertex)

The degree of a vertex is the number of edges connecting it, i.e. the number of adjacent vertices. Loops are counted double, i.e. every occurence of vertex in the list of adjacent vertices.

get_generalized_coordination_number(vertex, CN_max)

Compute the GCN of a vertex

remove_vertex(vertex)

Delete a node from the graph

vertices()

returns the vertices of a graph