# Make worlds:
world = pm.make_world()
# Add objects:
# "CUBE" (perhaps we need a better name?) is defined first by declaring the [x,y,z] edge lendths ("dimensions"), then \
# the normal_vector is given to define it's rotational orientation about the center.
box = pm.make_object(name='Box',
type='CUBE',
center=[0, 0, 0],
edge_dimensions=[10, 10, 0.01])
world.add_object(box)
# Add species:
mol_a = pm.make_species(name='a')
mol_b = pm.make_species(name='b')
mol_c = pm.make_species(name='c')
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 + b -> c')
world.add_reaction(react_1)
# Run simulations:
sim_1 = pm.make_simulation() # using default iteration and time_step
world.run_simulation(sim_1)
# 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)
#-----------------------------------#
# Add reactions:
"""
Default Parameters:
name = 'react_1' # then react_2, ...
forward_rate = 1e6
rate = forward_rate
backward_rate = 1e6
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:
0]) # 1x1 plane created on the x-z plane
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()
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)
# 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:
dynmc_rate = 1e5
react_dynmc = pm.make_reaction(name='react_1',
reaction='a + b -> c',
rate=dynmc_rate)
world.add_reaction(react_dynmc)
# Run simulations:
iters = 1000
t_step = 1e-6
step_len = 10
sim_1 = pm.make_simulation(iterations=iters, time_step=t_step)
for i in range(0, iters, step_len):
world.run_simulation_step(simulations=[sim_1],
step_number=i,
step_duration=t_step(step_len))
dynmc_rate += 1e-6
# "name" is used to ID which object we're changing, then all "new_" parameters update the previous version
world.modify_reaction(name='react_1',
# In make_object(), there are many input parameters, and if you don't include the necessary \
# parameters for the given object type, you'll get default values and perhaps a notification.
cylinder = pm.make_object(name='Cylinder',
type='CYLINDER',
center=[0, 0, 0],
radius=1,
normal_vector=[1, 0, 0],
extrude_length=20)
plane = pm.make_object(name='Plane',
type='PLANE',
center=[0, 0, 0],
normal_vector=[1, 0, 0])
world.add_object(cylinder, plane)
# Add species:
mol_a = pm.make_species(name='a', scale_factor=2)
world.add_species(mol_a)
# Add release patterns:
rel_a = pm.make_release_pattern(species_list=[mol_a],
release_region=plane,
boundary=cylinder)
world.add_release_pattern(rel_a)
# Add reactions:
react_1 = pm.make_reaction(name='React_1', reaction='a -> NULL')
world.add_reaction(react_1)
# Run simulations:
sim_1 = pm.make_simulation() # using default iteration and time_step
world.run_simulation(sim_1)
