NeighborKMC.base package

The listed modules are the main part of the NeighborKMC package and should be only touched if one knows what one is doing. All adaptations to specific systems are done in the user files and the main controll file.

NeighborKMC.base.basin module

NeighborKMC.base.events module

Defines the EventBase class.

The EventBase class is defined here as a template-class to derive events that can be stored in user_events.py.

The class defines methods that will throw an error if implemented wrongly, or are not implemented, in the derived classes.

See also

Module

user_events

class NeighborKMC.base.events.EventBase(params={}, name='no-name')

Bases: object

Template class for events.

Stores a list of parameters related to reaction events.

The class is only used as a parent, and is in this sense purely abstract.

params

Parameter dict dumped at the beginning of the log.

Type:

dict

alpha

The slowing down factor that is adsjusted when the reaction is accelerated. This factor is set to 1 upon instantiation and varies periodically during simulation. (See Module: NeighborKMC.base.basin)

Type:

int

diffev

Is the event a diffusion event. This can be used to make special rules for diffusion events.

Type:

bool

do_event(system, site, other_site)

Template method to perform the event.

Method needs to be overridden in user_events.py. Should change system site coverages by changing system.sites[i_site].covered and system.sites[other_site].covered.

Parameters:

• system (System) – The system, which the simulation is performed on.

• i_site (int) – Index of site in the system.sites list.

• i_other (int) – Index of other/neighbor site in the system.sites list.

get_involve_other()

Template method to decide if neighboring atoms are effected by event.

Method needs to be overridden in user_events.py. Should return True if event effects neighboring atoms and False if not (e.g. single atom adsorption).

get_rate(system, site, other_site)

Template method to determine the rate constant.

Method needs to be overridden in user_events.py. Should return the reaction rate on site number i_site, and i_other for multi-site reactions.

Parameters:

• system (System) – The system, which the simulation is performed on.

• i_site (int) – Index of site in the system.sites list.

• i_other (int) – Index of other/neighbor site in the system.sites list.

Returns:

Rate constant of event – The rate-constant given the current occupation patterns around the site-pair i_site and i_other.

Return type:

float

possible(system, site, other_site)

Template method to determine if event is possible.

Method needs to be overridden in user_events.py. Should return True if an event is possible on site number i_site and possible a neighbor site i_other, given the current site occupations.

Parameters:

• system (System) – The system, which the simulation is performed on.

• i_site (int) – Index of site in the system.sites list.

• i_other (int) – Index of other/neighbor site in the system.sites list.

Returns:

possible – True if event is possible on site-pair i_site and i_other. False if event is impossible on site-pair i_site and i_other.

Return type:

bool

NeighborKMC.base.kmc module

NeighborKMC.base.logging module

NeighborKMC.base.sites module

Defines the SiteBase Class.

This class is used as a parent for the Site class defined in user_sites.py.

See also

Module

user_sites

class NeighborKMC.base.sites.SiteBase(stype=0, covered=0, ind=[], lattice_pos=None)

Bases: object

Class that templates site objects.

Assigns a site type (stype) to the site, the species covers the site (covered), atomic indices that constitute the site (ind), and the sites that are nearest-neighbors (neighbors).

stype

The site type. The user must decide what that implies. Example: 0 ~ (111)-facet-ontop, 1 ~ edge-ontop …

Type:

int

covered

The species that covers the site. The user must decide what the integer implies. Example: 0 ~ empty-site, 1 ~ Oxygen covered, 2 ~ CO covered.

Type:

int

ind

The atomic-indices c.f. an ase.Atoms object that constitute the site. This is convenient to define for later visualization purposes.

Type:

list(int)

lattice_pos

The lattice position of the site. Can be used for systems that obey periodic boundary conditions, and to determine neighbor-lists.

Type:

list(int)

NeighborKMC.base.system module

Defines the SystemBase class.

The module defines a class used to template the System class defined in user_system.

See also

Module

sites

Module

user_sites

class NeighborKMC.base.system.SystemBase(sites, atoms=None)

Bases: object

Defines a system class to perform kMC.

Method assigns an ASE.Atoms object (atoms) to the object and assigns a list of sites (sites).

A neighbor list (neighbors) is initialized from the sites, which is checked for inconsistencies by the method verify_nlist().

atoms

Can be passed to connect an ASE atoms object to the system.

Type:

ase.atoms

sites

The list of sites that constitute the system.

Type:

Site

find_nn_recurse(sim, update_sites, recursion=0)

Deep search of first nearest neighbors.

Calculates the first nearest neighbors for a list of site_indices (update_sites).

For example, when passing update_sites = [0,1,2], the method returns [0,1,2,N neighbor 0 of site 0, Neighbor 1 of site 0, …, Neighbor 0 of site 1, …].

The method is calling itself recursively until the lattice is updated, c.f. the locality of nearest neighbor interactions.

Parameters:

• update_sites (list(int)) – The site indices to return neighborlist of.

• recursion (int) – The recursive level of which function was called, because the method calls itself, for example in base.kmc.frm_update().

Returns:

out – An update to the list update_sites where the neighbors to update_sites are added.

Return type:

list(int)

See also

kmc.NeighborKMC.frm_update

get_coverages(N_species)

Gets the site-occupations at the present moment.

Returns:

• cov list(list(float)) (a list of site-occupations for each species)

• and all sites. Thus to find the coverage of species

• i on site number j one calls ret[i][j].

get_ncovs(i_site)

Gets the coverage on nearest neighbor sites.

Retrieves and returns the occupations of the nearest neighbor sites to the site with index i_site in self.sites.

Parameters:

i_site (int) – Index of the site in self.sites.

Returns:

covs – List of species occupying the nearest neighbor sites.

Return type:

list(int)

verify_nlist()

Tests the neighborlist for inconsistency.

The method checks if neighborlists are assymetric: If A is a neighbor to B, then B must also be present in the neighborlist of A.

Raises:

Warning: – If the neighborlist is assymetric.

Module contents

Base classes used to template and run behind the scenes.