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)
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',
class GTKProject(SlaveDelegate):
"""A facade of kmos.types.Project so that
pygtk can display in a TreeView.
"""
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)
def _set_treeview_hooks(self):
"""Fudge function to import to access function to kmos.types.Project
to kmos.gui.GTKProject.
"""
self.project_data.clear()
# Meta
self.meta = self.project_data.append(None, self.model_tree.meta)
self.model_tree.meta = self.meta
# Layer List
self.model_tree.add_layer = self.add_layer
self.layer_list = self.project_data.append(None,
self.model_tree.layer_list)
self.get_layers = lambda :\
sorted(self.project_data.get_descendants(self.layer_list),
key=lambda x: x.name)
self.model_tree.get_layers = self.get_layers
self.lattice = self.layer_list
# Parameter List
self.parameter_list = self.project_data.append(
None, self.model_tree.parameter_list)
self.add_parameter = lambda parameter :\
self.project_data.append(self.parameter_list, parameter)
self.model_tree.add_parameter = self.add_parameter
self.get_parameters = lambda :\
sorted(self.project_data.get_descendants(self.parameter_list),
key=lambda x: x.name)
self.model_tree.get_parameters = self.get_parameters
# Species List
self.species_list = self.project_data.append(
None, self.model_tree.species_list)
self.add_species = lambda species :\
self.project_data.append(self.species_list, species)
self.model_tree.add_species = self.add_species
self.get_speciess = lambda :\
sorted(self.project_data.get_descendants(self.species_list),
key=lambda x: x.name)
self.model_tree.get_speciess = self.get_speciess
# Process List
self.process_list = self.project_data.append(
None, self.model_tree.process_list)
self.add_process = lambda process:\
self.project_data.append(self.process_list, process)
self.model_tree.add_process = self.add_process
self.get_processes = lambda :\
sorted(self.project_data.get_descendants(self.process_list),
key=lambda x: x.name)
self.model_tree.get_processes = self.get_processes
# Output List
self.output_list = self.project_data.append(
None, self.model_tree.output_list)
self.add_output = lambda output:\
self.project_data.append(self.output_list, output)
self.model_tree.add_output = self.add_output
self.get_outputs = lambda : \
sorted(self.project_data.get_descendants(self.output_list),
key=lambda x: x.name)
self.model_tree.get_outputs = self.get_outputs
def add_layer(self, layer):
self.project_data.append(self.layer_list, layer)
if len(self.get_layers()) == 1:
self.set_default_layer(layer.name)
self.set_substrate_layer(layer.name)
def set_default_species(self, species):
self.model_tree.species_list.default_species = species
def set_substrate_layer(self, layer):
self.model_tree.layer_list.substrate_layer = layer
def set_default_layer(self, layer):
self.model_tree.layer_list.default_layer = layer
def update(self, model):
self.project_data.update(model)
def on_row_activated(self, tree, data):
if isinstance(data, Layer):
data.active = not data.active
def get_name(self):
if self.filename:
return os.path.basename(self.filename)
else:
return 'Untitled'
def __repr__(self):
return str(self.model_tree)
def import_xml_file(self, filename):
self.model_tree.import_xml_file(filename)
self.expand_all()
def expand_all(self):
"""Expand all list of the project tree
"""
self.project_data.expand(self.species_list)
self.project_data.expand(self.layer_list)
self.project_data.expand(self.parameter_list)
self.project_data.expand(self.process_list)
self.project_data.expand(self.output_list)
def on_key_press(self, _, event):
"""When the user hits the keyboard focusing the treeview
this event is triggered. Right now the only supported function
is to deleted the selected item
"""
selection = self.project_data.get_selected()
if gtk.gdk.keyval_name(event.keyval) == 'Delete':
if (isinstance(selection, Species)
or isinstance(selection, Process)
or isinstance(selection, Parameter)
or isinstance(selection, Layer)):
if kiwi.ui.dialogs.yesno(
"Do you really want to delete '%s'?" \
% selection.name) == gtk.RESPONSE_YES:
self.project_data.remove(selection)
def on_project_data__selection_changed(self, _, elem):
"""When a new item is selected in the treeview this function
loads the main area of the window with the corresponding form
and data.
"""
slave = self.get_parent().get_slave('workarea')
if slave:
self.get_parent().detach_slave('workarea')
if isinstance(elem, Layer):
if self.meta.model_dimension in [1, 3]:
self.get_parent().toast('Only 2d supported')
return
self.undo_stack.start_new_action('Edit Layer %s' % elem.name, elem)
form = LayerEditor(elem, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, Meta):
self.undo_stack.start_new_action('Edit Meta', elem)
meta_form = MetaForm(self.meta, self)
self.get_parent().attach_slave('workarea', meta_form)
meta_form.focus_toplevel()
meta_form.focus_topmost()
elif isinstance(elem, OutputList):
self.undo_stack.start_new_action('Edit Output', elem)
form = OutputForm(self.output_list, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, Parameter):
self.undo_stack.start_new_action('Edit Parameter %s' % elem.name,
elem)
form = ParameterForm(elem, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, Process):
if self.meta.model_dimension in [1, 3]:
self.get_parent().toast('Only 2d supported')
return
self.undo_stack.start_new_action('Edit Process %s' % elem.name,
elem)
form = ProcessForm(elem, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, ProcessList):
if self.meta.model_dimension in [1, 3]:
self.get_parent().toast('Only 2d supported')
return
self.undo_stack.start_new_action('Batch process editing', elem)
form = BatchProcessForm(self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, Species):
self.undo_stack.start_new_action('Edit species', elem)
form = SpeciesForm(elem, self.project_data)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, SpeciesList):
self.undo_stack.start_new_action('Edit default species', elem)
form = SpeciesListForm(elem, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, LayerList):
self.undo_stack.start_new_action('Edit lattice', elem)
dimension = self.meta.model_dimension
form = LatticeForm(elem, dimension, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
else:
self.get_parent().toast('Not implemented, yet(%s).' % type(elem))
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 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
#!/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})
from itertools import product
from kmos.cli import main as cli_main
from kmos.types import Action, Condition, Layer, Project, Site, Species
# Project
pt = Project()
pt.set_meta(
author='Michael Seibt',
email='*****@*****.**',
model_name='LGD_lateral',
model_dimension=2
)
# Species
pt.add_species(
Species(name='empty', color='#d3d3d3'),
Species(name='ion', color='#0000ff', representation="Atoms('Si')"),
Species(name='source', color='#00ff00', representation="Atoms('Au')"),
Species(name='drain', color='#ff0000', representation="Atoms('Ag')")
)
pt.species_list.default_species = 'empty'
# Layer and Coordinates
layer = Layer(name='simple_cubic')
layer.add_site(Site(name='hollow', pos='0.5 0.5 0.5'))
pt.add_layer(layer)
center = pt.lattice.generate_coord('hollow')
bottom = pt.lattice.generate_coord('hollow.(0,-1,0)')
#!/usr/bin/env python
import numpy as np
from kmos.types import Project, Site, Condition, Action
pt = Project()
pt.set_meta(author="LotkaVolterra",
email='*****@*****.**',
model_name='lotka_volterra_model',
model_dimension=2)
pt.add_species(name='empty')
pt.add_species(name='A', representation="Atoms('O')")
pt.add_species(name='B', representation="Atoms('C')")
layer = pt.add_layer(name='sc')
pt.lattice.cell = np.diag([3.5, 3.5, 10])
layer.sites.append(Site(name='site', pos='.5 .5 .5'))
pt.add_parameter(name='k1', value='1000000.', adjustable=True, min=0., max=100.)
pt.add_parameter(name='k2', value=3.65, adjustable=True, min=0., max=100.)
pt.add_parameter(name='k3', value=1.1, adjustable=True, min=0., max=100.)
pt.add_parameter(name='zeta', value='0.06', adjustable=True, min=0., max=1.)
class GTKProject(SlaveDelegate):
"""A facade of kmos.types.Project so that
pygtk can display in a TreeView.
"""
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)
def _set_treeview_hooks(self):
"""Fudge function to import to access function to kmos.types.Project
to kmos.gui.GTKProject.
"""
self.project_data.clear()
# Meta
self.meta = self.project_data.append(None, self.model_tree.meta)
self.model_tree.meta = self.meta
# Layer List
self.model_tree.add_layer = self.add_layer
self.layer_list = self.project_data.append(None,
self.model_tree.layer_list)
self.get_layers = lambda :\
sorted(self.project_data.get_descendants(self.layer_list),
key=lambda x: x.name)
self.model_tree.get_layers = self.get_layers
self.lattice = self.layer_list
# Parameter List
self.parameter_list = self.project_data.append(None,
self.model_tree.parameter_list)
self.add_parameter = lambda parameter :\
self.project_data.append(self.parameter_list, parameter)
self.model_tree.add_parameter = self.add_parameter
self.get_parameters = lambda :\
sorted(self.project_data.get_descendants(self.parameter_list),
key=lambda x: x.name)
self.model_tree.get_parameters = self.get_parameters
# Species List
self.species_list = self.project_data.append(None,
self.model_tree.species_list)
self.add_species = lambda species :\
self.project_data.append(self.species_list, species)
self.model_tree.add_species = self.add_species
self.get_speciess = lambda :\
sorted(self.project_data.get_descendants(self.species_list),
key=lambda x: x.name)
self.model_tree.get_speciess = self.get_speciess
# Process List
self.process_list = self.project_data.append(None,
self.model_tree.process_list)
self.add_process = lambda process:\
self.project_data.append(self.process_list, process)
self.model_tree.add_process = self.add_process
self.get_processes = lambda :\
sorted(self.project_data.get_descendants(self.process_list),
key=lambda x: x.name)
self.model_tree.get_processes = self.get_processes
# Output List
self.output_list = self.project_data.append(None,
self.model_tree.output_list)
self.add_output = lambda output:\
self.project_data.append(self.output_list, output)
self.model_tree.add_output = self.add_output
self.get_outputs = lambda : \
sorted(self.project_data.get_descendants(self.output_list),
key=lambda x: x.name)
self.model_tree.get_outputs = self.get_outputs
def add_layer(self, layer):
self.project_data.append(self.layer_list, layer)
if len(self.get_layers()) == 1 :
self.set_default_layer(layer.name)
self.set_substrate_layer(layer.name)
def set_default_species(self, species):
self.model_tree.species_list.default_species = species
def set_substrate_layer(self, layer):
self.model_tree.layer_list.substrate_layer = layer
def set_default_layer(self, layer):
self.model_tree.layer_list.default_layer = layer
def update(self, model):
self.project_data.update(model)
def on_row_activated(self, tree, data):
if isinstance(data, Layer):
data.active = not data.active
def get_name(self):
if self.filename:
return os.path.basename(self.filename)
else:
return 'Untitled'
def __repr__(self):
return str(self.model_tree)
def import_xml_file(self, filename):
self.model_tree.import_xml_file(filename)
self.expand_all()
def expand_all(self):
"""Expand all list of the project tree
"""
self.project_data.expand(self.species_list)
self.project_data.expand(self.layer_list)
self.project_data.expand(self.parameter_list)
self.project_data.expand(self.process_list)
self.project_data.expand(self.output_list)
def on_key_press(self, _, event):
"""When the user hits the keyboard focusing the treeview
this event is triggered. Right now the only supported function
is to deleted the selected item
"""
selection = self.project_data.get_selected()
if gtk.gdk.keyval_name(event.keyval) == 'Delete':
if(isinstance(selection, Species)
or isinstance(selection, Process)
or isinstance(selection, Parameter)
or isinstance(selection, Layer)):
if kiwi.ui.dialogs.yesno(
"Do you really want to delete '%s'?" \
% selection.name) == gtk.RESPONSE_YES:
self.project_data.remove(selection)
def on_project_data__selection_changed(self, _, elem):
"""When a new item is selected in the treeview this function
loads the main area of the window with the corresponding form
and data.
"""
slave = self.get_parent().get_slave('workarea')
if slave:
self.get_parent().detach_slave('workarea')
if isinstance(elem, Layer):
if self.meta.model_dimension in [1, 3]:
self.get_parent().toast('Only 2d supported')
return
self.undo_stack.start_new_action('Edit Layer %s' % elem.name,
elem)
form = LayerEditor(elem, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, Meta):
self.undo_stack.start_new_action('Edit Meta', elem)
meta_form = MetaForm(self.meta, self)
self.get_parent().attach_slave('workarea', meta_form)
meta_form.focus_toplevel()
meta_form.focus_topmost()
elif isinstance(elem, OutputList):
self.undo_stack.start_new_action('Edit Output', elem)
form = OutputForm(self.output_list, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, Parameter):
self.undo_stack.start_new_action('Edit Parameter %s' % elem.name,
elem)
form = ParameterForm(elem, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, Process):
if self.meta.model_dimension in [1, 3]:
self.get_parent().toast('Only 2d supported')
return
self.undo_stack.start_new_action('Edit Process %s' % elem.name,
elem)
form = ProcessForm(elem, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, ProcessList):
if self.meta.model_dimension in [1, 3]:
self.get_parent().toast('Only 2d supported')
return
self.undo_stack.start_new_action('Batch process editing', elem)
form = BatchProcessForm(self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, Species):
self.undo_stack.start_new_action('Edit species', elem)
form = SpeciesForm(elem, self.project_data)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, SpeciesList):
self.undo_stack.start_new_action('Edit default species', elem)
form = SpeciesListForm(elem, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
elif isinstance(elem, LayerList):
self.undo_stack.start_new_action('Edit lattice', elem)
dimension = self.meta.model_dimension
form = LatticeForm(elem, dimension, self)
self.get_parent().attach_slave('workarea', form)
form.focus_topmost()
else:
self.get_parent().toast('Not implemented, yet(%s).' % type(elem))
#!/usr/bin/env python
import numpy as np
from kmos.types import Project, Site, Condition, Action
pt = Project()
pt.set_meta(author="Ziff,Gulari,Barshad",
email='*****@*****.**',
model_name='zgb_model',
model_dimension=2)
pt.add_species(name='empty', color='#ffffff')
pt.add_species(name='CO', representation="Atoms('C')", color='#000000')
pt.add_species(name='O', representation="Atoms('O')", color='#ff0000')
layer = pt.add_layer(name='sc')
pt.lattice.cell = np.diag([3.5, 3.5, 10])
layer.sites.append(Site(name='site', pos='.5 .5 .5'))
pt.add_parameter(name='yCO', value='0.45', adjustable=True, min=0., max=1.)
pt.parse_and_add_process('CO_adsorption; empty@site -> CO@site; yCO')
pt.parse_and_add_process('O2_adsorption1; empty@site + empty@site.(1, 0, 0) -> O@site + O@site.(1,0,0); (1 - yCO)/2.')
pt.parse_and_add_process('O2_adsorption2; empty@site + empty@site.(0, 1, 0) -> O@site + O@site.(0,1,0); (1 - yCO)/2.')
pt.parse_and_add_process('CO_oxidation1; CO@site + O@site.(1, 0, 0) -> empty@site + empty@site.(1,0,0); 10**10')
#!/usr/bin/env python
import numpy as np
from kmos.types import Project, Site, Condition, Action
pt = Project()
pt.set_meta(author="Ziff,Gulari,Barshad",
email='*****@*****.**',
model_name='zgb_model',
model_dimension=2)
pt.add_species(name='empty', color='#ffffff')
pt.add_species(name='CO', representation="Atoms('C')", color='#000000')
pt.add_species(name='O', representation="Atoms('O')", color='#ff0000')
layer = pt.add_layer(name='sc')
pt.lattice.cell = np.diag([3.5, 3.5, 10])
layer.sites.append(Site(name='site', pos='.5 .5 .5'))
pt.add_parameter(name='yCO', value='0.45', adjustable=True, min=0., max=1.)
pt.parse_and_add_process('CO_adsorption; empty@site -> CO@site; yCO')
pt.parse_and_add_process(
'O2_adsorption1; empty@site + empty@site.(1, 0, 0) -> O@site + O@site.(1,0,0); (1 - yCO)/2.'
)
pt.parse_and_add_process(
'O2_adsorption2; empty@site + empty@site.(0, 1, 0) -> O@site + O@site.(0,1,0); (1 - yCO)/2.'
#!/usr/bin/env python
import numpy as np
from kmos.types import Project, Site, Condition, Action
pt = Project()
pt.set_meta(author="LotkaVolterra",
email='*****@*****.**',
model_name='lotka_volterra_model',
model_dimension=2)
pt.add_species(name='empty')
pt.add_species(name='A', representation="Atoms('O')")
pt.add_species(name='B', representation="Atoms('C')")
layer = pt.add_layer(name='sc')
pt.lattice.cell = np.diag([3.5, 3.5, 10])
layer.sites.append(Site(name='site', pos='.5 .5 .5'))
pt.add_parameter(name='k1',
value='1000000.',
adjustable=True,
min=0.,
max=100.)
pt.add_parameter(name='k2', value=3.65, adjustable=True, min=0., max=100.)
pt.add_parameter(name='k3', value=1.1, adjustable=True, min=0., max=100.)
pt.add_parameter(name='zeta', value='0.06', adjustable=True, min=0., max=1.)
from itertools import product
from kmos.cli import main as cli_main
from kmos.types import Action, Condition, Layer, Project, Site, Species
# Project
pt = Project()
pt.set_meta(author='Michael Seibt',
email='*****@*****.**',
model_name='LGD_lateral',
model_dimension=2)
# Species
pt.add_species(
Species(name='empty', color='#d3d3d3'),
Species(name='ion', color='#0000ff', representation="Atoms('Si')"),
Species(name='source', color='#00ff00', representation="Atoms('Au')"),
Species(name='drain', color='#ff0000', representation="Atoms('Ag')"))
pt.species_list.default_species = 'empty'
# Layer and Coordinates
layer = Layer(name='simple_cubic')
layer.add_site(Site(name='hollow', pos='0.5 0.5 0.5'))
pt.add_layer(layer)
center = pt.lattice.generate_coord('hollow')
bottom = pt.lattice.generate_coord('hollow.(0,-1,0)')
top = pt.lattice.generate_coord('hollow.(0,+1,0)')
left = pt.lattice.generate_coord('hollow.(-1,0,0)')
right = pt.lattice.generate_coord('hollow.(+1,0,0)')