# Add objects:
box = pm.make_object(name='Box', type='CUBE') # default size and position
world.add_object(box)
# Add species:
mol_a = pm.make_species(name='a') # red, Sphere_1, 1e-6, and VOLUME by default
mol_b = pm.make_species(name='b', color=[0, 0, 1]) # blue
mol_c = pm.make_species(name='c', color=[0, 1, 0]) # green
world.add_species(mol_a, mol_b, mol_c)
# Add release patterns:
rel_a_b = pm.make_release_pattern(species_list=[mol_a, mol_b],
release_region=box)
world.add_release_pattern(rel_a_b)
# Add reactions:
react_1 = pm.make_reaction(name='React_1',
reaction='a -> NULL') # 1e3 forward_rate by default
react_2 = pm.make_reaction(name='React_2', reaction='a -> b', forward_rate=1e4)
react_3 = pm.make_reaction(name='React_3',
reaction='a + b -> c',
forward_rate=5e3) # isn't this redundant?
react_4 = pm.make_reaction(name='React_4',
reaction='a + b <-> c',
forward_rate=5e3,
backward_rate=1e8)
world.add_reaction(react_1, react_2, react_3, react_4)
# Run simulations:
sim_1 = pm.make_simulation() # using default iteration and time_step
world.run_simulation(sim_1)
Other Parameters:
reaction
"""
# Example 1:
react_1 = pm.make_reaction(name='a_to_null',
reaction='a -> NULL',
forward_rate=1e6)
world.add_reaction(react_1)
#-----------------------------------#
# Run simulations:
"""
Default Parameters:
name = 'sim_1' # then 'sim_2', ...
iterations = 1000
time_step = 1e-6
Other Parameters:
"""
# Example 1:
sim_1 = pm.make_simulation()
world.run_simulation(sim_1)
#Example 2:
sim_1 = pm.make_simulation(iterations=200, time_step=5e-5)
world.run_simulation(sim_1)
world.modify_species(name='a', new_diffusion_const=1e-4)
world.run_simulation(sim_1) # running modified simulation
world.add_object(box, plane)
# Add species:
mol_a = pm.make_species(name='a') # red, Sphere_1, 1e-6, and VOLUME by default
mol_b = pm.make_species(name='b', color=[0, 0, 1]) # blue
mol_c = pm.make_species(name='c', color=[0, 1, 0]) # green
world.add_species(mol_a, mol_b, mol_c)
# Add release patterns:
rel_a_b = pm.make_release_pattern(species_list=[mol_a, mol_b],
release_region=box)
world.add_release_pattern(rel_a_b)
# Add reactions:
react_a_b = pm.make_reaction(name='react_1', reaction='a + b -> c')
world.add_reaction(react_a_b)
# Run simulations:
iters = 50
t_step = 1e-6
sim_1 = pm.make_simulation(iterations=iters, time_step=t_step)
for i in range(0, iters):
world.run_simulation_step(simulations=[sim_1], step_number=i)
print 'Time: ', i * t_step
print 'mol_a count: ', world.get_species_count(name='a', time=i * t_step)
print 'mol_b count: ', world.get_species_count(name='b', time=i * t_step)
print 'mol_c count: ', world.get_species_count(name='c', time=i * t_step)
print 'Reaction a+b->c count: ', world.get_reaction_count(name='react_1',
time=i * t_step)
# ... and so on ... world.get_what_you_want_count()
[ 1, 4, 5 ],
[ 2, 4, 0 ],
[ 7, 1, 5 ],
[ 3, 2, 0 ],
[ 7, 6, 2 ],
[ 5, 4, 6 ],
[ 1, 0, 4 ],
[ 2, 6, 4 ],
[ 7, 3, 1 ] ]
"""
funky_shape = pm.make_object(name='Polyhedron',
type='POLYHEDRON',
vertices=verts_list,
faces=faces_list)
world.add_object(funky_shape)
# Add species:
mol_a = pm.make_species(name='a') # red, Sphere_1, 1e-6, and VOLUME by default
world.add_species(mol_a)
# Add release patterns:
rel_a = pm.make_release_pattern(species_list=[mol_a],
release_region=funky_shape)
world.add_release_pattern(rel_a)
# Add reactions:
# Run simulations:
sim_1 = pm.make_simulation(
time_step=1e-5) # using default iteration and custom time_step
world.run_simulation(sim_1)
Unbounded diffusion
"""
import pymcell as pm
# Make worlds:
world = pm.make_world()
# Add species:
mol_a = pm.make_species(name='a', diffusion_const=1e-6, type='VOLUME')
world.add_species(mol_a)
# Add release patterns:
rel_a = pm.make_release_pattern(species_list=[mol_a],
location=[0, 0, 0],
shape='SPHERICAL',
probablity=1,
quantity=1000)
world.add_release_pattern(rel_a)
# Add reactions:
react_1 = pm.make_reaction(name='React_1',
reaction='a -> NULL',
forward_rate=1e6)
world.add_reaction(react_1)
# Run simulations:
sim_1 = pm.make_simulation(iterations=1000,
time_step=1e-6) # these are the default parameters
world.run_simulation(sim_1)
molecules=[mol_a])
world_trans.add_surface_class(surface_classes=[trans_surf],
objects=[box],
faces=[[0, 2, 4], [3, 4, 7]])
world_abs.add_surface_class(surface_classes=[abs_surf],
objects=[box],
faces=[[1, 3, 5], [2, 5, 6]])
world_clamp_abs.add_surface_class(surface_classes=[clamp_surf],
objects=[box],
faces=[[0, 2, 4], [3, 4, 7]])
world_clamp_abs.add_surface_class(surface_classes=[abs_surf],
objects=[box],
faces=[[1, 3, 5], [2, 5, 6]])
# Add release patterns:
rel_a = pm.make_release_pattern(species_list=[mol_a], release_region=box)
world_trans.add_release_pattern(rel_a)
world_abs.add_release_pattern(rel_a)
# assuming CLAMP_CONCENTRATION allows for diffusion, so we don't need to add an additional release in to world_clamp_abs
# Add reactions:
# nada que hacer aqui
# Run simulations:
sim_long = pm.make_simulation(
iterations=200) # using custom iterations and default time_step
sim_short = pm.make_simulation(
iterations=1500) # using custom iterations and default time_step
world_trans.run_simulation(sim_short)
world_abs.run_simulation(sim_short)
world_clamp_abs.run_simulation(sim_long)
