Description:
"2D diffusion" between two sheets
- initial release in a line source
"""
import pymcell as pm
# 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:
Description:
Box of A & B with reactions:
- A -> 0 decay
- A -> B decay
- A + B -> C irreversible
- A + B <-> C reversible
"""
import pymcell as pm
# Make worlds:
world = pm.make_world()
# 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',
normal_vector = [0,0,1] # the x-y plane
extrude_direction = normal_vector
display = 'SOLID'
triangulate = False
Other Parameters:
type
vertices = []
faces = []
radius
extrude_length
objects = [] # which objects the other parameters (such as "faces") are referencing
etc. (see notebook, p.60)
"""
# Example_1:
box = pm.make_object(name='Box', type='CUBE') # default size and position
world.add_object(box)
# Example_2:
box_surfaces = pm.make_object(name='Surfaces',
type='SURFACE',
objects=[box],
faces=[[0, 1, 2], [0, 2, 3], [4, 5, 6],
[4, 6, 7]])
world.add_object(box_surfaces)
# Exmaple 3:
funky_shape = pm.make_object(name='Polyhedron',
type='POLYHEDRON',
vertices=verts_list,
faces=faces_list)
"""
Description:
2D diffusion on a real 2D surface
- initial release on a patch by either density or Boolean intersection of e.g. a sphere with a plane
"""
import pymcell as pm
# Make worlds:
world = pm.make_world()
# Add objects:
box = pm.make_object(name='Box', type='CUBE')
# could also write: faces = ['BOTTOM']
surface = pm.redefine_object(name='Surface',
type='SURFACE',
objects=[box],
faces=[[0, 1, 2], [0, 2, 3]])
world.add_object(box, surface)
# Add species:
mol_a = pm.make_species(name='a', type='SURFACE', scale_factor=.5)
world.add_species(mol_a)
# Add release patterns:
rel_a = pm.make_release_pattern(species_list=[mol_a], release_region=surface)
world.add_release_pattern(rel_a)
# Run simulations:
sim_1 = pm.make_simulation() # using default iteration and time_step
Description:
Counting statements
- A box (maybe with some region definition) with A+B->C reaction where we count each of the following at each timestep:
+ What: molecule, reaction, event/trigger
+ Where: World, object, region
+ When: frequency of counting
+ How: Front hits/back hits, e.g. on a plane that goes through the box
"""
import pymcell as pm
# Make worlds:
world = pm.make_world()
# Add objects:
box = pm.make_object(type='CUBE') # default size and position
plane = pm.make_object(type='SURFACE',
normal_vector=[0, 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)
Description:
Dynamic changes
- Dynamic geometry: an interface to change the mesh at each timestep
+ Example: An initial box that updates it's geometry at each timestep with some new list of vertices and faces
"""
import pymcell as pm
# Make worlds:
world = pm.make_world()
# Add objects:
x_len = 1
y_len = 1
z_len = 1
dynmc_box = pm.make_object(name = 'Dynamic_box', type = 'CUBE', edge_dimensions = [x_len,y_len,z_len]) # default position
world.add_object(dynmc_box)
# Add species:
diff_const = 1e-6
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 = dynmc_box)
world.add_release_pattern(rel_a)
# Run simulations:
iters = 500
sim_1 = pm.make_simulation(iterations = iters, time_step = 1e-5)
for i in range(0,iters):
faces_list = [
[ 3, 0, 1 ],
[ 7, 2, 3 ],
[ 5, 6, 7 ],
[ 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:
"""
Description:
Dynamic changes:
- Dynamic rate constants: changing the rate constant of a reaction
+ Example: A box with A+B->C that where the rate constant depends on the number of A,B, or C
"""
import pymcell as pm
# Make worlds:
world = pm.make_world()
# Add objects:
box = pm.make_object(type='CUBE') # default name, 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:
dynmc_rate = 1e5
react_dynmc = pm.make_reaction(name='react_1',
reaction='a + b -> c',
"1D diffusion" in a thin tube
- initial release in a plane in the middle
"""
import pymcell as pm
# Make worlds:
world = pm.make_world()
# Add objects:
# 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,