def setup_reaction_simulator(self,
simulation_type,
abundances,
temperature,
t_span,
dt=0.01,
system_volume=1e-15):
"""Build a simulator instance for reaction simulations.
Parameters
----------
simulation_type : str
Type of simulation. "deterministic" or "stochastic"
abundances : array_like
Abundances of all species
temperature : float
Simulation temperature
t_span : 2-tuple
Time span of the reactions users want to simulate, from `t_span[0]`
to ``t_span[1]``.
dt : float
Size of time steps users want to simulate. Relevant
only for deterministic simulations.
system_volume : float
Volume of reaction system. Relevant only for stochastic
simulations.
Returns
-------
simulator : `ReactionSimulator`
`ReactionSimulator` instance. Either child class
`DeterministicSimulator` or `StochasticSimulator`.
Examples
--------
>>> reader = XMLReader("tests/rxns.xml")
>>> reaction_system = reader.get_reaction_systems()[0]
>>> concs = np.array([1., 2., 1., 3., 1.])*1e-05
>>> det_sim = reaction_system.setup_reaction_simulator(
... 'deterministic', concs, 800, [0, 0.1], dt=0.1)
>>> det_sim.simulate()
([0, 0.1], [array([ 1.00000000e-05, 2.00000000e-05, 1.00000000e-05,
3.00000000e-05, 1.00000000e-05]), array([ 1.31232803e-05, 1.68767197e-05, 1.33004078e-05,
2.67881559e-05, 9.91143627e-06])])
"""
choices = ['stochastic', 'deterministic']
if simulation_type not in choices:
raise ValueError
if simulation_type == 'deterministic':
determine_sim = simulator.DeterministicSimulator(
self, abundances, temperature, t_span, dt)
return determine_sim
else:
stochastic_sim = simulator.StochasticSimulator(
self, abundances, temperature, t_span, system_volume)
return stochastic_sim
def test_neg_temp():
concs = [1., 2., 1., 3., 1.]
reader = chemkin.XMLReader("tests/rxns.xml")
reaction_system = reader.get_reaction_systems()[0]
try:
simulator.DeterministicSimulator(reaction_system,
concs,
-800, [0, 2],
dt=1)
except ValueError as err:
assert (type(err) == ValueError)
def test_solver_not_implemented():
concs = np.array([1., 2., 1., 3., 1.]) * 1e-05
reader = chemkin.XMLReader("tests/rxns.xml")
reaction_system = reader.get_reaction_systems()[0]
det_sim = simulator.DeterministicSimulator(reaction_system,
concs,
800, [0, 0.01],
dt=0.01)
try:
det_sim.simulate('forward_euler')
except ValueError as err:
assert (type(err) == ValueError)
def test_sim_rk45_neg_concentration():
concs = np.array([1., 2., 1., 3., 1.]) * 1e-05
reader = chemkin.XMLReader("tests/rxns.xml")
reaction_system = reader.get_reaction_systems()[0]
det_sim = simulator.DeterministicSimulator(reaction_system,
concs,
800, [0, 0.01],
dt=0.01)
try:
det_sim.simulate('rk45')
except ValueError as err:
assert (type(err) == ValueError)
def test_sim_backward_euler():
concs = np.array([1., 2., 1., 3., 1.]) * 1e-05
reader = chemkin.XMLReader("tests/rxns.xml")
reaction_system = reader.get_reaction_systems()[0]
det_sim = simulator.DeterministicSimulator(reaction_system,
concs,
800, [0, 0.01],
dt=0.01)
t, y = det_sim.simulate('backward_euler')
y0 = y[0]
y1 = y[1]
assert np.allclose(t, [0, 0.01])
assert np.allclose(
y0,
np.array([
1.00000000e-05, 2.00000000e-05, 1.00000000e-05, 3.00000000e-05,
1.00000000e-05
]))
assert np.allclose(
y1,
np.array([
1.03940908e-05, 1.96059092e-05, 1.04083239e-05, 2.95987926e-05,
9.99288345e-06
]))