def main():
a = m.Species("a", dc=1e-6)
reg = m.Region("tube_reg", tube.reg_indices)
tube_obj = m.MeshObject("tube", tube.verts, tube.faces, [reg])
mesh_objs = [tube_obj]
sim = m.Simulation(dt=1e-6, meshes=mesh_objs)
sim.create_molecules_reg(a, reg, 100)
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
plane_top = m.create_plane("top", 1.0, (0, 0, 0.1))
plane_bottom = m.create_plane("bottom", 1.0, (0, 0, -0.1))
mesh_objs = [plane_top, plane_bottom]
sim = m.Simulation(dt=1e-6, meshes=mesh_objs)
for i in range(-10, 11):
sim.create_molecule(a, (i*0.1, 0, 0))
sim.run_iterations(100)
def main():
a = m.Species("a", volume=False, dc=1e-6)
box = m.create_box("box", 1.0, (0, 0, 0))
sim = m.Simulation(dt=1e-6, meshes=[box])
sim.create_molecules_reg(a,
box.regions["top"],
100,
conc_dens=True,
orient=m.Orient.up)
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
b = m.Species("b", volume=False, dc=1e-6)
c = m.Species("c", volume=False, dc=1e-6)
a_mix = (a, m.Orient.mix)
b_up = (b, m.Orient.up)
c_up = (c, m.Orient.up)
bimol_irrev = m.Reaction([a_mix, b_up], [c_up], rate=1e4)
box = m.import_obj(Path("./box.obj"))
sim = m.Simulation(dt=1e-6, meshes=[box], reactions=[bimol_irrev])
sim.create_molecules_obj(a, box, 100)
sim.create_molecules_obj(b, box, 100)
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
a_up = (a, m.Orient.up)
a_down = (a, m.Orient.down)
transp_a = m.SurfaceProperty("transp_a", m.SP.transp, a_down)
absorb_a = m.SurfaceProperty("absorb_a", m.SP.absorb, a_down)
clamp_a = m.SurfaceProperty("clamp_a", m.SP.clamp, a_up, clamp_val=1e-8)
box = m.create_box("box", 1.0, (0, 0, 0))
box.add_surface_property(transp_a, box.regions["left"])
box.add_surface_property(absorb_a, box.regions["right"])
box.add_surface_property(clamp_a, box.regions["top"])
box.add_surface_property(absorb_a, box.regions["top"])
sim = m.Simulation(dt=1e-6, meshes=[box])
sim.create_molecules_obj(a, box, 100)
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
b = m.Species("b", dc=1e-6)
c = m.Species("c", dc=1e-6)
a_mix = (a, m.Orient.mix)
b_mix = (b, m.Orient.mix)
c_mix = (c, m.Orient.mix)
bimol_irrev = m.Reaction([a_mix, b_mix], [c_mix], rate=0)
box = m.create_box("box", 1.0, (0, 0, 0))
sim = m.Simulation(dt=1e-6, meshes=[box], reactions=[bimol_irrev])
sim.create_molecules_obj(a, box, 100)
sim.create_molecules_obj(b, box, 100)
for i in range(100):
offs = 1e6
bimol_irrev.rate = math.sin(i * 0.1) * offs + offs
sim.run_iteration()
def main():
a = m.Species("a", dc=1e-6)
b = m.Species("b", dc=1e-6)
c = m.Species("c", dc=1e-6)
a_mix = (a, m.Orient.mix)
b_mix = (b, m.Orient.mix)
c_mix = (c, m.Orient.mix)
unimol1 = m.Reaction([a_mix], [b_mix], rate=1e4)
unimol2 = m.Reaction([a_mix], rate=1e4)
bimol_irrev = m.Reaction([a_mix, b_mix], [c_mix], rate=1e4)
bimol_rev = m.Reaction([a_mix, b_mix], [c_mix], reversible=True, rate=1e4)
rxns = [unimol1, unimol2, bimol_irrev, bimol_rev]
box = m.import_obj(Path("./box.obj"))
sim = m.Simulation(dt=1e-6, meshes=[box], reactions=rxns)
sim.create_molecules_obj(a, box, 100)
sim.create_molecules_obj(b, box, 100)
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
b = m.Species("b", dc=1e-6)
c = m.Species("c", dc=1e-6)
a_mix = (a, m.Orient.mix)
b_mix = (b, m.Orient.mix)
c_mix = (c, m.Orient.mix)
bimol_irrev = m.Reaction([a_mix, b_mix], [c_mix], rate=1e4, name="rxn")
box = m.create_box("box", 1.0, (0, 0, 0))
count_a_box = m.CountMolecules(a, box)
count_a_rxn = m.CountReaction(bimol_irrev, box)
sim_counts = [count_a_box, count_a_rxn]
sim = m.Simulation(dt=1e-6,
meshes=[box],
reactions=[bimol_irrev],
counts=sim_counts)
sim.create_molecules_obj(a, box, 100)
sim.create_molecules_obj(b, box, 100)
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
sim = m.Simulation(dt=1e-6)
sim.create_molecules_shape(a, 100, (0, 0, 0))
sim.run_iterations(100)
def main():
a = m.Species("a", dc=1e-6)
box = m.create_box("box", 1.0, (0, 0, 0))
sim = m.Simulation(dt=1e-6)
sim.create_molecules_obj(a, box, 100)
sim.run_iterations(100)