In [1]:

    

%matplotlib inline
from ecell4.core import *
from ecell4.util import *
from ecell4 import lattice, egfrd
viz.init_ipynb()


    

In [2]:

    

with species_attributes():
    A | B | C | {"D": "1", "radius": "0.005"}

with reaction_rules():
    A + B == C | (0.01, 0.3)

m = get_model(False)


    

In [3]:

    

# factory = egfrd.EGFRDFactory(Integer3(4, 4, 4))
factory = lattice.LatticeFactory(0.005)


    

In [4]:

    

w = factory.create_world(Real3(1, 1, 1))
w.bind_to(m)


    

In [5]:

    

w.add_molecules(Species("A"), 60, AABB(Real3(0, 0, 0), Real3(0.5, 1, 1)))
w.add_molecules(Species("B"), 60, AABB(Real3(0.5, 0, 0), Real3(1, 1, 1)))


    

In [6]:

    

sim = factory.create_simulator(w)
# obs1 = FixedIntervalHDF5Observer(0.02, "test%03d.h5")
obs2 = NumberObserver(("A", "C"))
# sim.run(1.0, [obs1, obs2])
sim.run(1.0, [obs2])


    

In [7]:

    

# viz.plot_movie([factory.create_world("test%03d.h5" % _) for _ in xrange(51)], radius=0.005, grid=False, species_list=("A", "B", "C"))


    

In [8]:

    

viz.plot_number_observer(obs2, 'o-', markeredgewidth=0)