def test_constructor(self):
# Create a Simulator object
v = pystospa.Voxel([10], 1.0)
v.add_reaction(pystospa.Reaction(1.5, lambda x, y: x[0], [-1]))
s = pystospa.Simulator([v])
# Check that the Simulator attributes are as expected
self.assertEqual(s.get_time(), 0.0)
self.assertEqual(s.get_voxels()[0].get_molecules()[0], 10)
def test_member_functions(self):
# Create a Simulator object
v = pystospa.Voxel([10], 1.0)
v.add_reaction(pystospa.Reaction(1.5, lambda x, y: x[0], [-1]))
s = pystospa.Simulator([v])
# Check setting seed for generating random number
s.set_seed(153)
self.assertEqual(s.get_seed(), 153)
# Check a single step in SSA works
s.step()
self.assertGreater(s.get_time(), 0)
self.assertEqual(s.get_voxels()[0].get_molecules()[0], 9)
# Check that getting to specific time point works
s.advance(1.0)
self.assertGreater(s.get_time(), 1.0)
initial_num = [100] # number of molecules of species A
domain_size = 10.0 # size of the domain in cm
v = ss.Voxel(initial_num, domain_size)
# Create reaction object.
# Arguments: reaction rate, propensity func, stoichiometry vector
k = 1.0
propensity = lambda num_mols, area: num_mols[0]
stoch = [-1]
r = ss.Reaction(k, propensity, stoch)
# Add a reaction to a voxel
v.add_reaction(r)
# Pass the voxel with the reaction(s) to the simulator object
s = ss.Simulator([v])
# Run the simulation. Arguments: path to output file, time step, number of steps
s.run("cme_example.dat", 0.01, 500)
# Read the file containing the data
data = np.loadtxt("cme_example.dat")
time = data[:, 0] # Time points
num_A = data[:, 1] # Number of molecules of A
# Plot of the data
fig, ax = plt.subplots()
ax.step(time, num_A, label="A")
ax.set_xlabel("Time [s]")
ax.set_ylabel("Number of molecules")
ax.legend()
fig.savefig("cme_example.svg")
domain.append(ss.Voxel([0], voxel_size))
# Create and add the reaction objects
d = 1.0 # diffusion rate
k = 1.0 # decay rate
propensity = lambda num_mols, length : num_mols[0]
stoch = [-1]
for i, vox in enumerate(domain):
# Add diffusion jump to the right from voxel i to voxel i+1 (if one exists)
if i < len(domain)-1: vox.add_reaction(ss.Reaction(d, propensity, stoch, i+1))
# Add diffusion jump to the left from voxel i+1 to voxel i (if one exists)
if i > 0: vox.add_reaction(ss.Reaction(d, propensity, stoch, i-1))
vox.add_reaction(ss.Reaction(k, propensity, stoch))
# Pass the voxels with the reaction(s) to the simulator object
s = ss.Simulator(domain)
# Run the simulation. Arguments: path to output file, time step, number of steps
s.run("rdme_example_2.dat", 0.01, 200)
# Read the file containing the data
data = np.loadtxt("rdme_example_2.dat")
time = data[:, 0]
num_A = data[:, 1:]
x = np.arange(0.5, 10.5)
# We generate a canvas for the figure
fig, ax = plt.subplots()
ax.bar(x, num_A[0], label="t = {:.2}".format(time[0]))
ax.bar(x, num_A[50], label="t = {:.2}".format(time[50]), alpha=0.5)
ax.bar(x, num_A[100], label="t = {:.2}".format(time[100]), alpha=0.5)
