base package

Submodules

base.basin module

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 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

base.kmc module

base.logging module

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 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)

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 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.