def generate_model():
import kmos
from kmos.types import \
ConditionAction, \
Coord, \
Layer, \
Parameter, \
Process,\
Project,\
Site, \
Species
project = Project()
# set meta information
model_name = 'test_cli_generated_model'
project.meta.author = 'Max J. Hoffmann'
project.meta.email = '*****@*****.**'
project.meta.model_dimension = '2'
project.meta.debug = 0
project.meta.model_name = model_name
# add layer
project.add_layer(
Layer(name='default', sites=[Site(name='cus', pos='0 0.5 0.5')]))
project.layer_list.default_layer = 'default'
# add species
project.add_species(Species(name='oxygen', color='#ff0000'))
project.add_species(Species(name='CO', color='#000000'))
project.add_species(Species(name='empty', color='#ffffff'))
project.species_list.default_species = 'empty'
# add parameters
project.add_parameter(Parameter(name='p_CO', value=0.2, scale='log'))
project.add_parameter(Parameter(name='T', value=500, adjustable=True))
project.add_parameter(Parameter(name='p_O2', value=1.0, adjustable=True))
# add processes
cus = Coord(name='cus', layer='default')
p = Process(name='CO_adsorption', rate_constant='1000.')
p.add_condition(ConditionAction(species='empty', coord=cus))
p.add_action(ConditionAction(species='CO', coord=cus))
project.add_process(p)
p = Process(name='CO_desorption', rate_constant='1000.')
p.add_condition(ConditionAction(species='CO', coord=cus))
p.add_action(ConditionAction(species='empty', coord=cus))
project.add_process(p)
return project
def __init__(self, parent, menubar):
self.project_data = ObjectTree([
Column('name', use_markup=True, data_type=str, sorted=True),
Column('info')
])
self.project_data.connect('row-activated', self.on_row_activated)
self.model_tree = Project()
self._set_treeview_hooks()
self.menubar = menubar
self.set_parent(parent)
self.filename = ''
self.undo_stack = UndoStack(self.model_tree.__repr__,
self.import_xml_file,
self.project_data.select, menubar,
self.meta, 'Initialization')
SlaveDelegate.__init__(self, toplevel=self.project_data)
#!/usr/bin/env python
from kmos.types import Project, Condition, Action
import numpy as np
pt = Project()
pt.set_meta(author='StangenMensch',
email='*****@*****.**',
model_dimension=1,
model_name='hopping_model')
pt.add_species(
name='empty',
color='#ffffff',
)
pt.add_species(name='C',
representation="Atoms('C',[[0,0,0]])",
color='#000000')
pt.layer_list.cell = np.diag([1., 1., 1.])
pt.add_layer(name='default', color='#ffffff')
pt.add_site(layer='default', pos='0 0 0', name='a')
coord = pt.layer_list.generate_coord
pt.add_process(name='ads',
rate_constant='10**6',
conditions=[Condition(species='empty', coord=coord('a'))],
actions=[Action(species='C', coord=coord('a'))],
tof_count={'adsorption': 1})
