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", 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)
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)
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 create_reactions_from_dm(
data_model: Dict[str, Any],
species: Dict[str, m.Species]) -> List[m.Reaction]:
""" Create a dictionary of Reactions from a CB data model """
logging.info("Creating reactions from data model")
rxn_dm_list = data_model['mcell']['define_reactions']['reaction_list']
rxn_list = []
for rxn_dm in rxn_dm_list:
# rxn_name = rxn_dm['rxn_name']
fwd_rate = float(rxn_dm['fwd_rate'])
# try:
# bkwd_rate = float(rxn_dm['bkwd_rate'])
# except ValueError:
# pass
reactants_str_list = rxn_dm['reactants'].split(" + ")
products_str_list = rxn_dm['products'].split(" + ")
r_list = make_spec_orient_list(reactants_str_list, species)
p_list = make_spec_orient_list(products_str_list, species)
# rxn_type = rxn_dm['rxn_type']
rxn_dm = m.Reaction(r_list, p_list, fwd_rate)
rxn_list.append(rxn_dm)
return rxn_list
def test_vm1sm1_to_vm2(self):
rxn = m.Reaction((self.vm1.down(), self.sm1.up()), self.vm2.down(),
1e8)
def test_vm1_to_vm2(self):
rxn = m.Reaction(self.vm1, self.vm2, 1e8)
def test_vm1_to_null(self):
rxn = m.Reaction(self.vm1.down(), None, 1e8)
def main():
world = m.MCellSim(seed=1)
world.set_time_step(time_step=1e-5)
world.set_iterations(iterations=1000)
world.enable_logging()
world.silence_notifications()
world.set_output_freq(1)
slow_dc = 1e-9
fast_dc = 1e-5
# define species
vm1 = m.Species("vm1", fast_dc)
vm2 = m.Species("vm2", fast_dc)
vm3 = m.Species("vm3", slow_dc)
sm_list = []
for i in range(1, 11):
sm_list.append(m.Species("sm{}".format(i), fast_dc, surface=True))
sm1 = sm_list[0]
sm2 = sm_list[1]
spec_orient_list = [sm.up() for sm in sm_list]
all_mols = sm_list + [vm1, vm2, vm3]
world.add_species(all_mols)
# define reaction
rxn = m.Reaction(sm1.up(), sm2.down(), 1e3, name="create_sm2")
world.add_reaction(rxn)
# create torus object
torus_obj = m.MeshObj(
"Torus", t.vert_list, t.face_list, translation=(0, 0, 0))
torus_reg = m.SurfaceRegion(torus_obj, 'half', t.surf_reg_face_list)
world.add_geometry(torus_obj)
# create box object
box_obj = m.MeshObj(
"Box", b.vert_list, b.face_list, translation=(0, 0, 0))
box_reg = m.SurfaceRegion(box_obj, 'top', b.surf_reg_face_list)
world.add_geometry(box_obj)
# create surface class to absorb vm1
# sc = m.SurfaceClass(SC.absorb, sm1.mix())
# world.assign_surf_class(sc, torus_reg)
# world.assign_surf_class_to_all_surface_mols("abs_all_surfs", SC.absorb, torus_reg)
world.assign_surface_property_to_all_mols(
"abs_all_vols", SC.absorb, torus_reg, moltype=MolType.surface_mols)
# release vm1, vm2, and sm1 molecules into/onto torus
vm1_torus_rel = m.ObjectRelease(vm1, number=1000, mesh_obj=torus_obj)
world.release(vm1_torus_rel)
vm2_torus_rel = m.ObjectRelease(vm2, number=1000, mesh_obj=torus_obj)
world.release(vm2_torus_rel)
sm1_torus_rel = m.ObjectRelease(sm1.up(), number=1000, region=torus_reg)
world.release(sm1_torus_rel)
# release vm3 molecules in a line (list based release)
vm3_pos = [(x*0.01, 0, 0) for x in range(-5, 5)]
vm3_list_release = m.ListRelease(vm3, vm3_pos)
world.release(vm3_list_release)
# release sm molecules in a line on top of box (list based release)
sm_pos = [(x*0.01, 0, 0.1) for x in range(-5, 5)]
sm_list_release = m.ListRelease(spec_orient_list, sm_pos)
world.release(sm_list_release)
# pos_vec3 = m.Vector3()
# diam_vec3 = m.Vector3(0.015, 0.015, 0.015)
# world.create_release_site(vm1, 100, "spherical", diam_vec3=diam_vec3)
# viz and reaction data
world.add_viz(all_mols)
world.add_count(vm1, torus_obj)
world.add_count(vm2, torus_obj)
world.add_count(sm1, torus_obj)
# set partitions
world.add_partitions('x', -1.3, 1.3, 0.05)
world.add_partitions('y', -1.3, 1.3, 0.05)
world.add_partitions('z', -0.275, 0.275, 0.05)
# run the simulation! :)
# for i in range(iterations+1):
# vm3_count = world.get_species_count(vm3, torus_obj)
# if (vm3_count > 50):
# world.modify_rate_constant(rxn, 1e12)
# world.run_iteration()
world.run_sim()
world.end_sim()