Source code for base.system
"""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
"""
[docs]class SystemBase:
"""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().
Attributes
-----------
atoms: ase.atoms
Can be passed to connect an ASE atoms object to the system.
sites: Site
The list of sites that constitute the system.
"""
def __init__(self, sites, atoms=None):
self.sites = sites
self.Nsites = len(self.sites)
self.neighbors = [s.neighbors for s in sites]
self.verify_nlist()
self.atoms = atoms
[docs] def verify_nlist(self):
"""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.
"""
for i, s in enumerate(self.neighbors):
for nn in s:
if i not in self.neighbors[nn]:
raise Warning("Site " + str(i) + " is a neighbor to site " +
str(nn) + " but not vice-versa")
[docs] def get_ncovs(self, 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(int)
List of species occupying the nearest neighbor sites.
"""
covs = [self.sites[n].covered for n in self.neighbors[i_site]]
return covs
[docs] def get_coverages(self, 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].
"""
cov = []
for species in range(N_species + 1):
cspec = [self.sites[i].covered for i \
in range(self.Nsites) if \
self.sites[i].covered == species]
cov.append(float(len(cspec)) / float(self.Nsites))
return cov
[docs] def find_nn_recurse(self, 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: list(int)
An update to the list update_sites where the neighbors to update_sites
are added.
See Also
---------
kmc.NeighborKMC.frm_update()
"""
out = [n for n in update_sites]
for s in update_sites:
out.extend(self.neighbors[s])
out = list(set(out))
if recursion < sim.nninter - 1:
out = self.find_nn_recurse(sim, out, recursion + 1)
return out
