# ---- Cube ----
Cube_vertex_list = [[-0.25, -0.25, -0.25], [-0.25, -0.25, 0.25],
[-0.25, 0.25, -0.25], [-0.25, 0.25, 0.25],
[0.25, -0.25, -0.25], [0.25, -0.25, 0.25],
[0.25, 0.25, -0.25], [0.25, 0.25,
0.25]] # Cube_vertex_list
Cube_wall_list = [[1, 2, 0], [3, 6, 2], [7, 4, 6], [5, 0, 4], [6, 0, 2],
[3, 5, 7], [1, 3, 2], [3, 7, 6], [7, 5, 4], [5, 1, 0],
[6, 4, 0], [3, 1, 5]] # Cube_wall_list
Cube_left_side_wall_indices = [3, 9] #Cube_left_side_wall_indices
Cube_left_side = m.SurfaceRegion(name='left_side',
wall_indices=Cube_left_side_wall_indices,
initial_color=color_green)
Cube_right_side_wall_indices = [1, 7] #Cube_right_side_wall_indices
Cube_right_side = m.SurfaceRegion(name='right_side',
wall_indices=Cube_right_side_wall_indices,
initial_color=color_red)
Cube = m.GeometryObject(name='Cube',
vertex_list=Cube_vertex_list,
wall_list=Cube_wall_list,
surface_regions=[Cube_left_side, Cube_right_side],
initial_color=color_default)
# ^^^^ Cube ^^^^
# WARNING: This is an automatically generated file and will be overwritten
# by CellBlender on the next model export.
import mcell as m
# ---- Cube ----
Cube_vertex_list = [[-0.05, -0.05, -0.05], [-0.05, -0.05, 0.05],
[-0.05, 0.05, -0.05], [-0.05, 0.05, 0.05],
[0.05, -0.05, -0.05], [0.05, -0.05, 0.05],
[0.05, 0.05, -0.05], [0.05, 0.05,
0.05]] # Cube_vertex_list
Cube_wall_list = [[1, 2, 0], [3, 6, 2], [7, 4, 6], [5, 0, 4], [6, 0, 2],
[3, 5, 7], [1, 3, 2], [3, 7, 6], [7, 5, 4], [5, 1, 0],
[6, 4, 0], [3, 1, 5]] # Cube_wall_list
Cube_membrane_wall_indices = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11] #Cube_membrane_wall_indices
Cube_membrane = m.SurfaceRegion(name='membrane',
wall_indices=Cube_membrane_wall_indices)
Cube = m.GeometryObject(name='Cube',
vertex_list=Cube_vertex_list,
wall_list=Cube_wall_list,
surface_regions=[Cube_membrane])
# ^^^^ Cube ^^^^
import mcell as m
# ---- Cube1 ----
Cube1_vertex_list = [[-0.1, -0.1, -0.1], [-0.1, -0.1, 0.1], [-0.1, 0.1, -0.1],
[-0.1, 0.1, 0.1], [0.1, -0.1, -0.1], [0.1, -0.1, 0.1],
[0.1, 0.1, -0.1], [0.1, 0.1, 0.1]] # Cube1_vertex_list
Cube1_wall_list = [[1, 2, 0], [3, 6, 2], [7, 4, 6], [5, 0, 4], [6, 0, 2],
[3, 5, 7], [1, 3, 2], [3, 7, 6], [7, 5, 4], [5, 1, 0],
[6, 4, 0], [3, 1, 5]] # Cube1_wall_list
Cube1 = m.GeometryObject(name='Cube1',
vertex_list=Cube1_vertex_list,
wall_list=Cube1_wall_list,
surface_regions=[])
# ^^^^ Cube1 ^^^^
# ---- Cube2 ----
Cube2_vertex_list = [[-0.2, -0.2, -0.2], [-0.2, -0.2, 0.2], [-0.2, 0.2, -0.2],
[-0.2, 0.2, 0.2], [0.2, -0.2, -0.2], [0.2, -0.2, 0.2],
[0.2, 0.2, -0.2], [0.2, 0.2, 0.2]] # Cube2_vertex_list
Cube2_wall_list = [[1, 2, 0], [3, 6, 2], [7, 4, 6], [5, 0, 4], [6, 0, 2],
[3, 5, 7], [1, 3, 2], [3, 7, 6], [7, 5, 4], [5, 1, 0],
[6, 4, 0], [3, 1, 5]] # Cube2_wall_list
Cube2 = m.GeometryObject(name='Cube2',
vertex_list=Cube2_vertex_list,
wall_list=Cube2_wall_list,
surface_regions=[])
# ^^^^ Cube2 ^^^^
import os
MCELL_PATH = os.environ.get('MCELL_PATH', '')
if MCELL_PATH:
sys.path.append(os.path.join(MCELL_PATH, 'lib'))
else:
print(
"Error: variable MCELL_PATH that is used to find the mcell library was not set."
)
sys.exit(1)
import mcell as m
model = m.Model()
a = m.Species('a', diffusion_constant_3d=1e-6)
rs = m.ReleaseSite('rel_a', a, location=(0, 0, 0), number_to_release=1)
model.add_release_site(rs)
s1 = model.find_release_site('rel_a')
assert s1 is not None and s1.name == 'rel_a'
s2 = model.find_release_site('rel_b')
assert s2 is None
g = m.GeometryObject('g', [[0, 0, 0], [1, 1, 1], [0, 0, 1]], [[0, 1, 2]])
model.add_geometry_object(g)
g1 = model.find_geometry_object('g')
assert g1 is not None and g1.name == 'g'
g2 = model.find_geometry_object('qx')
assert g2 is None
import mcell as m
# ---- Compartment ----
Compartment_vertex_list = [[0, 0, 0.02], [0.02, 0,
-0.01], [-0.01, 0.02, -0.01],
[-0.01, -0.02, -0.01]] # Compartment_vertex_list
Compartment_wall_list = [[0, 1, 2], [0, 2, 3], [0, 3, 1],
[1, 3, 2]] # Compartment_wall_list
Compartment = m.GeometryObject(name='Compartment',
vertex_list=Compartment_vertex_list,
wall_list=Compartment_wall_list,
surface_regions=[])
# ^^^^ Compartment ^^^^
[-0.300000071525574, 0.100000023841858, -0.100000023841858],
[-0.300000071525574, 0.100000023841858, 0.100000023841858],
[0.300000071525574, -0.100000023841858, -0.100000023841858],
[0.300000071525574, -0.100000023841858, 0.100000023841858],
[0.300000071525574, 0.100000023841858, -0.100000023841858],
[0.300000071525574, 0.100000023841858, 0.100000023841858]
] # box1_vertex_list
box1_wall_list = [[1, 2, 0], [3, 6, 2], [7, 4, 6], [5, 0, 4], [6, 0, 2],
[3, 5, 7], [1, 3, 2], [3, 7, 6], [7, 5, 4], [5, 1, 0],
[6, 4, 0], [3, 1, 5]] # box1_wall_list
sr1 = m.SurfaceRegion(name='sr1', wall_indices=[0, 1, 2, 3])
box1 = m.GeometryObject(name='box1',
vertex_list=box1_vertex_list,
wall_list=box1_wall_list,
surface_regions=[sr1])
# ^^^^ box1 ^^^^
# ---- box2 ----
box2_vertex_list = [
[-0.150000035762787, -0.150000035762787, -0.150000035762787],
[-0.150000035762787, -0.150000035762787, 0.150000035762787],
[-0.150000035762787, 0.150000035762787, -0.150000035762787],
[-0.150000035762787, 0.150000035762787, 0.150000035762787],
[0.150000035762787, -0.150000035762787, -0.150000035762787],
[0.150000035762787, -0.150000035762787, 0.150000035762787],
[0.150000035762787, 0.150000035762787, -0.150000035762787],
[0.150000035762787, 0.150000035762787, 0.150000035762787]
] # box2_vertex_list
# WARNING: This is an automatically generated file and will be overwritten
# by CellBlender on the next model export.
import mcell as m
# ---- box ----
box_vertex_list = [[-0.234999999403954, -0.234999999403954, -2.5],
[-0.234999999403954, -0.234999999403954, 2.5],
[-0.234999999403954, 0.234999999403954, -2.5],
[-0.234999999403954, 0.234999999403954, 2.5],
[0.234999999403954, -0.234999999403954, -2.5],
[0.234999999403954, -0.234999999403954, 2.5],
[0.234999999403954, 0.234999999403954, -2.5],
[0.234999999403954, 0.234999999403954,
2.5]] # box_vertex_list
box_wall_list = [[1, 2, 0], [3, 6, 2], [7, 4, 6], [5, 0, 4], [6, 0, 2],
[3, 5, 7], [1, 3, 2], [3, 7, 6], [7, 5, 4], [5, 1, 0],
[6, 4, 0], [3, 1, 5]] # box_wall_list
box_bottom_wall_indices = [4, 10] #box_bottom_wall_indices
box_bottom = m.SurfaceRegion(name='bottom',
wall_indices=box_bottom_wall_indices)
box = m.GeometryObject(name='box',
vertex_list=box_vertex_list,
wall_list=box_wall_list,
surface_regions=[box_bottom])
# ^^^^ box ^^^^
[3, 6, 2],
[7, 4, 6],
[5, 0, 4],
[6, 0, 2],
[3, 5, 7],
[1, 3, 2],
[3, 7, 6],
[7, 5, 4],
[5, 1, 0],
[6, 4, 0],
[3, 1, 5]
] # up_wall_list
up = m.GeometryObject(
name = 'up',
vertex_list = up_vertex_list,
wall_list = up_wall_list,
surface_regions = []
)
# ^^^^ up ^^^^
# ---- bottom ----
bottom_vertex_list = [
[-0.199999988079071, -0.199999988079071, -0.02],
[-0.199999988079071, -0.199999988079071, 0.018], # the gap is 2nm
[-0.199999988079071, 0.199999988079071, -0.02],
[-0.199999988079071, 0.199999988079071, 0.018],
[0.199999988079071, -0.199999988079071, -0.02],
[0.199999988079071, -0.199999988079071, 0.018],
[0.199999988079071, 0.199999988079071, -0.02],
[0.199999988079071, 0.199999988079071, 0.018]
import mcell as m
# ---- Cube ----
Cube_vertex_list = [[-0.25, -0.25, -0.25], [-0.25, -0.25, 0.25],
[-0.25, 0.25, -0.25], [-0.25, 0.25, 0.25],
[0.25, -0.25, -0.25], [0.25, -0.25, 0.25],
[0.25, 0.25, -0.25], [0.25, 0.25,
0.25]] # Cube_vertex_list
Cube_wall_list = [[1, 2, 0], [3, 6, 2], [7, 4, 6], [5, 0, 4], [6, 0, 2],
[3, 5, 7], [1, 3, 2], [3, 7, 6], [7, 5, 4], [5, 1, 0],
[6, 4, 0], [3, 1, 5]] # Cube_wall_list
Cube_left_side_wall_indices = [3, 9] #Cube_left_side_wall_indices
Cube_left_side = m.SurfaceRegion(name='left_side',
wall_indices=Cube_left_side_wall_indices)
Cube_right_side_wall_indices = [1, 7] #Cube_right_side_wall_indices
Cube_right_side = m.SurfaceRegion(name='right_side',
wall_indices=Cube_right_side_wall_indices)
Cube = m.GeometryObject(name='Cube',
vertex_list=Cube_vertex_list,
wall_list=Cube_wall_list,
surface_regions=[Cube_left_side, Cube_right_side])
# ^^^^ Cube ^^^^
[6, 0, 2],
[3, 5, 7],
[1, 3, 2],
[3, 7, 6],
[7, 5, 4],
[5, 1, 0],
[6, 4, 0],
[3, 1, 5]
]
"""
0010-3)
We use the previously defined list of vertices and walls
to create an object of class GeometryObject.
"""
box = m.GeometryObject(name='box',
vertex_list=box_vertex_list,
wall_list=box_wall_list)
#0000-7)
model = m.Model()
model.add_species(species_a)
model.add_release_site(release_site_a)
model.add_viz_output(viz_output)
"""
0010-4)
In addition to the previous components, we also add our box
to the model.
"""
model.add_geometry_object(box)
#0000-8)
[-0.0625, 0.0625, -0.0625],
[-0.0625, 0.0625, 0.0625],
[0.0625, -0.0625, -0.0625],
[0.0625, -0.0625, 0.0625],
[0.0625, 0.0625, -0.0625],
[0.0625, 0.0625,
0.0625]] # default_compartment_vertex_list
default_compartment_wall_list = [[1, 2, 0], [3, 6, 2], [7, 4, 6], [5, 0, 4],
[6, 0, 2], [3, 5, 7], [1, 3, 2], [3, 7, 6],
[7, 5, 4], [5, 1, 0], [6, 4, 0],
[3, 1, 5]] # default_compartment_wall_list
default_compartment = m.GeometryObject(
name='DEFAULT',
vertex_list=default_compartment_vertex_list,
wall_list=default_compartment_wall_list,
surface_regions=[])
# ^^^^ default_compartment ^^^^
# ---- EC ----
EC_vertex_list = [[-0.25, -0.25, -0.25], [-0.25, -0.25, 0.25],
[-0.25, 0.25, -0.25], [-0.25, 0.25, 0.25],
[0.25, -0.25, -0.25], [0.25, -0.25, 0.25],
[0.25, 0.25, -0.25], [0.25, 0.25, 0.25]] # EC_vertex_list
EC_wall_list = [[1, 2, 0], [3, 6, 2], [7, 4, 6], [5, 0, 4], [6, 0,
2], [3, 5, 7],
[1, 3, 2], [3, 7, 6], [7, 5, 4], [5, 1, 0], [6, 4, 0],
[3, 1, 5]] # EC_wall_list
# WARNING: This is an automatically generated file and will be overwritten
# by CellBlender on the next model export.
import mcell as m
# ---- Plane ----
Plane_vertex_list = [[-1.10000002384186, -1.10000002384186, 0],
[1.10000002384186, -1.10000002384186, 0],
[-1.10000002384186, 1.10000002384186, 0],
[1.10000002384186, 1.10000002384186,
0]] # Plane_vertex_list
Plane_wall_list = [[1, 2, 0], [1, 3, 2]] # Plane_wall_list
Plane = m.GeometryObject(name='Plane',
vertex_list=Plane_vertex_list,
wall_list=Plane_wall_list,
surface_regions=[])
# ^^^^ Plane ^^^^
# ---- Cube ----
Cube_vertex_list = [[-1, -1, -1], [-1, -1, 1], [-1, 1, -1], [-1, 1, 1],
[1, -1, -1], [1, -1, 1], [1, 1, -1],
[1, 1, 1]] # Cube_vertex_list
Cube_wall_list = [[1, 2, 0], [3, 6, 2], [7, 4, 6], [5, 0, 4], [6, 0, 2],
[3, 5, 7], [1, 3, 2], [3, 7, 6], [7, 5, 4], [5, 1, 0],
[6, 4, 0], [3, 1, 5]] # Cube_wall_list
Cube = m.GeometryObject(name='Cube',
vertex_list=Cube_vertex_list,
wall_list=Cube_wall_list,
import mcell as m
# ---- Tetrahedron ----
Tetrahedron_vertex_list = [[0, 0, 0.02], [0.02, 0,
-0.01], [-0.01, 0.02, -0.01],
[-0.01, -0.02, -0.01]] # Tetrahedron_vertex_list
Tetrahedron_wall_list = [[0, 1, 2], [0, 2, 3], [0, 3, 1],
[1, 3, 2]] # Tetrahedron_wall_list
Tetrahedron = m.GeometryObject(name='Tetrahedron',
vertex_list=Tetrahedron_vertex_list,
wall_list=Tetrahedron_wall_list,
surface_regions=[])
# ^^^^ Tetrahedron ^^^^