import pymcell as m
# Make a world
world = m.make_mcell_world()
# Set timestep
world.dt = 0.1
###
# Box
###
# Create a box
box = m.create_simple_object(name="My box",
type="CUBE",
center=[0, 0, 0],
radius=[1, 1, 1])
# Add it to the mcell world
world.obj_list.append(box)
###
# Species
###
mol_A = m.create_species(name="A", dc=1)
world.species_list.append(mol_A)
mol_B = m.create_species(name="B", dc=1)
world.species_list.append(mol_B)
surf_class_a = m.create_surface_class(name="Absorptive",
molecules=[mol_A],
type="ABSORPTIVE")
# Create a clamp surface class
surf_class_c = m.create_surface_class(name="Clamp",
molecules=[mol_A],
type="CLAMP",
clamp_value=1)
##########
# Transparency
##########
# Make a world
world_t = m.make_mcell_world()
# Set timestep
world_t.dt = 0.1
# Add the box to the world
world_t.obj_list.append(box)
# Add the surface classes to the world
world_t.reg_list.append(surf_reg_1)
world_t.reg_list.append(surf_reg_2)
# Add the molecule to the world
world_t.species_list.append(mol_A)
# Assign the surface class to the regions