def main():
model_name = str(__file__[+0:-3]).replace(
"__build", ""
) # This line automatically names the model based on the python file’s name. The brackets cut off zero characters from the beginning and three character from the end (".py"). The replace command removes the ‘__build’ part of the string. If you want to override this automatic naming, just set the variable ‘model_name’ equal to the string that you would like to use.
kmc_model = kmcos.create_kmc_model(model_name)
# Meta
kmc_model.meta.author = 'Max J. Hoffmann'
kmc_model.meta.email = '*****@*****.**'
kmc_model.meta.model_name = 'AB_no_diffusion'
kmc_model.meta.model_dimension = 2
kmc_model.meta.debug = 0
# add species
kmc_model.add_species(name='empty')
kmc_model.add_species(name='A', representation="Atoms('O')")
kmc_model.add_species(name='B',
representation="Atoms('CO', [[0,0,0],[0,0,1.2]])")
# add sites/layer
layer = Layer(name='default')
layer.sites.append(Site(name='a'))
kmc_model.add_layer(layer)
kmc_model.species_list.default_species = 'empty'
# add parameter
parameters = {}
parameters['p_COgas'] = {
'value': 1.,
'adjustable': True,
'min': 1.e-13,
'max': 1.e2,
'scale': 'log'
}
parameters['p_O2gas'] = {
'value': 1.,
'adjustable': True,
'min': 1.e-13,
'max': 1.e2,
'scale': 'log'
}
parameters['T'] = {'value': 600}
parameters['A'] = {'value': 1.552e-19}
parameters['E_bind_O2'] = {'value': -2.138}
parameters['E_bind_CO'] = {'value': -1.9}
parameters['E_react'] = {'value': 0.9}
for key, value in parameters.items():
kmc_model.add_parameter(name=key, **value)
coord = kmc_model.lattice.generate_coord('a.(0,0,0).default')
up = kmc_model.lattice.generate_coord('a.(0,1,0).default')
right = kmc_model.lattice.generate_coord('a.(1,0,0).default')
down = kmc_model.lattice.generate_coord('a.(0,-1,0).default')
left = kmc_model.lattice.generate_coord('a.(-1,0,0).default')
kmc_model.add_process(
name='A_adsorption',
rate_constant='p_O2gas*bar*A/sqrt(2*pi*m_O2*umass/beta)',
condition_list=[Condition(coord=coord, species='empty')],
action_list=[Action(coord=coord, species='A')],
)
kmc_model.add_process(
name='A_desorption',
rate_constant=
'p_O2gas*bar*A/sqrt(2*pi*m_O2*umass/beta)*exp(beta*(E_bind_O2-mu_O2gas)*eV)',
condition_list=[Condition(coord=coord, species='A')],
action_list=[Action(coord=coord, species='empty')],
)
kmc_model.add_process(
name='B_adsorption',
rate_constant='p_COgas*bar*A/sqrt(2*pi*m_CO*umass/beta)',
condition_list=[Condition(coord=coord, species='empty')],
action_list=[Action(coord=coord, species='B')],
)
kmc_model.add_process(
name='B_desorption',
rate_constant=
'p_COgas*bar*A/sqrt(2*pi*m_CO*umass/beta)*exp(beta*(E_bind_CO-mu_COgas)*eV)',
condition_list=[Condition(coord=coord, species='B')],
action_list=[Condition(coord=coord, species='empty')],
)
for neighbor, name in [(right, 'right'), (left, 'left'), (up, 'up'),
(down, 'down')]:
kmc_model.add_process(name='AB_react_%s' % name,
rate_constant='1/(beta*h)*exp(-beta*E_react*eV)',
condition_list=[
Condition(coord=coord, species='A'),
Condition(coord=neighbor, species='B')
],
action_list=[
Action(coord=coord, species='empty'),
Action(coord=neighbor, species='empty')
],
tof_count={'TOF': 1})
return kmc_model
#!/usr/bin/env python
import kmcos
from kmcos.types import *
from itertools import product
import numpy as np
model_name = str(__file__[+0:-3]).replace(
"__build", ""
) # This line automatically names the model based on the python file’s name. The brackets cut off zero characters from the beginning and three character from the end (".py"). The replace command removes the ‘__build’ part of the string. If you want to override this automatic naming, just set the variable ‘model_name’ equal to the string that you would like to use.
kmc_model = kmcos.create_kmc_model(model_name)
kmc_model.set_meta(author='Juan M. Lorenzi',
email='*****@*****.**',
model_name=model_name,
model_dimension=2)
layer = kmc_model.add_layer(name='simplecubic_2d')
layer.add_site(name='a')
kmc_model.add_species(name='empty', color='#ffffff')
kmc_model.add_species(
name='O',
color='#ff0000',
representation="Atoms('O')",
)
kmc_model.add_species(name='CO',
color='#000000',
representation="Atoms('CO',[[0,0,0],[0,0,1.2]])",
tags='carbon')
kmc_model.add_parameter(name='E_CO', value=-1, adjustable=True, min=-2, max=0)
kmc_model.add_parameter(name='E_CO_nn',
value=.2,
adjustable=True,
def main():
kmc_model = kmcos.create_kmc_model(model_name)
# Meta
kmc_model.meta.author = 'Max J. Hoffmann'
kmc_model.meta.email = '*****@*****.**'
kmc_model.meta.model_name = 'AB_no_diffusion'
kmc_model.meta.model_dimension = 2
kmc_model.meta.debug = 0
# add species
kmc_model.add_species(name='empty')
kmc_model.add_species(name='A', representation="Atoms('O')")
kmc_model.add_species(name='B',
representation="Atoms('CO', [[0,0,0],[0,0,1.2]])")
# add sites/layer
layer = Layer(name='default')
layer.sites.append(Site(name='a'))
kmc_model.add_layer(layer)
kmc_model.species_list.default_species = 'empty'
# add parameter
parameters = {}
parameters['p_COgas'] = {
'value': 1.,
'adjustable': True,
'min': 1.e-13,
'max': 1.e2,
'scale': 'log'
}
parameters['p_O2gas'] = {
'value': 1.,
'adjustable': True,
'min': 1.e-13,
'max': 1.e2,
'scale': 'log'
}
parameters['T'] = {'value': 600}
parameters['A'] = {'value': 1.552e-19}
parameters['E_bind_O2'] = {'value': -2.138}
parameters['E_bind_CO'] = {'value': -1.9}
parameters['E_react'] = {'value': 0.9}
for key, value in parameters.items():
kmc_model.add_parameter(name=key, **value)
coord = kmc_model.lattice.generate_coord('a.(0,0,0).default')
up = kmc_model.lattice.generate_coord('a.(0,1,0).default')
right = kmc_model.lattice.generate_coord('a.(1,0,0).default')
down = kmc_model.lattice.generate_coord('a.(0,-1,0).default')
left = kmc_model.lattice.generate_coord('a.(-1,0,0).default')
kmc_model.add_process(
name='A_adsorption',
rate_constant='p_O2gas*bar*A/sqrt(2*pi*m_O2*umass/beta)',
condition_list=[Condition(coord=coord, species='empty')],
action_list=[Action(coord=coord, species='A')],
)
kmc_model.add_process(
name='A_desorption',
rate_constant=
'p_O2gas*bar*A/sqrt(2*pi*m_O2*umass/beta)*exp(beta*(E_bind_O2-mu_O2gas)*eV)',
condition_list=[Condition(coord=coord, species='A')],
action_list=[Action(coord=coord, species='empty')],
)
kmc_model.add_process(
name='B_adsorption',
rate_constant='p_COgas*bar*A/sqrt(2*pi*m_CO*umass/beta)',
condition_list=[Condition(coord=coord, species='empty')],
action_list=[Action(coord=coord, species='B')],
)
kmc_model.add_process(
name='B_desorption',
rate_constant=
'p_COgas*bar*A/sqrt(2*pi*m_CO*umass/beta)*exp(beta*(E_bind_CO-mu_COgas)*eV)',
condition_list=[Condition(coord=coord, species='B')],
action_list=[Condition(coord=coord, species='empty')],
)
for neighbor, name in [(right, 'right'), (left, 'left'), (up, 'up'),
(down, 'down')]:
kmc_model.add_process(name='AB_react_%s' % name,
rate_constant='1/(beta*h)*exp(-beta*E_react*eV)',
condition_list=[
Condition(coord=coord, species='A'),
Condition(coord=neighbor, species='B')
],
action_list=[
Action(coord=coord, species='empty'),
Action(coord=neighbor, species='empty')
],
tof_count={'TOF': 1})
return kmc_model
