def test_plot_per_reaction_contribution():
rd = _get_decay_rd(1)
tout = np.linspace(0, 3.0, 7)
y0 = [3.0, 1.0]
integr = run(rd, y0, tout)
axes = plot_per_reaction_contribution(integr, [0, 1])
for ax in axes:
assert isinstance(ax, matplotlib.axes.Axes)
def integrate_rd(tend=10.0, N=1, nt=500, jac_spy=False,
linear_solver='default', logy=False, logt=False,
plot=False, savefig='None', verbose=False, graph=False,
**kwargs):
"""
Integrates the reaction system defined by
:download:`four_species.json <examples/four_species.json>`
"""
rd = load(os.path.join(os.path.dirname(
__file__), 'four_species.json'), N=N, x=N, logy=logy, logt=logt)
y0 = np.array([1.3, 1e-4, 0.7, 1e-4])
y0 = np.concatenate([y0/(i+1)*(0.25*i**2+1) for i in range(N)])
t0 = 1e-10
if linear_solver == 'default':
if rd.N == 1:
linear_solver = 'dense'
elif rd.N > 1:
linear_solver = 'banded'
if linear_solver not in ('dense', 'banded'):
raise NotImplementedError("dense or banded linear_solver")
import matplotlib.pyplot as plt
if jac_spy:
fout = np.empty(rd.n*rd.N)
rd.f(t0, y0, fout)
print(fout)
if linear_solver == 'dense':
jout = np.zeros((rd.n*rd.N, rd.n*rd.N), order='F')
rd.dense_jac_cmaj(t0, y0, jout)
coloured_spy(np.log(np.abs(jout)))
elif linear_solver == 'banded':
# note rd.n*3 needed in call from scipy.integrate.ode
jout = np.zeros((rd.n*2+1, rd.n*rd.N), order='F')
rd.banded_packed_jac_cmaj(t0, y0, jout)
coloured_spy(np.log(np.abs(jout)))
print(jout)
plt.show()
else:
tout = np.linspace(t0, tend, nt)
integr = run(rd, y0, tout, **kwargs)
if verbose:
print(integr.info)
if plot:
plt.figure(figsize=(6, 4))
for i, l in enumerate('ABCD'):
plt.plot(integr.tout, integr.Cout[:, 0, i], label=l)
plt.title("Time evolution of concentrations")
plt.legend()
save_and_or_show_plot(savefig=savefig)
plt.figure(figsize=(6, 10))
plot_jacobian(
rd,
np.log(integr.tout) if rd.logt else integr.tout,
np.log(integr.Cout) if rd.logy else integr.Cout,
'ABCD',
lintreshy=1e-10
)
plt.tight_layout()
if savefig != 'None':
base, ext = os.path.splitext(savefig)
savefig = base + '_jacobian' + ext
save_and_or_show_plot(savefig=savefig)
plt.figure(figsize=(6, 10))
plot_per_reaction_contribution(
integr,
'ABCD'
)
plt.tight_layout()
if savefig != 'None':
savefig = base + '_per_reaction' + ext
save_and_or_show_plot(savefig=savefig)
if graph:
print(rsys2graph(ReactionSystem.from_ReactionDiffusion(rd, 'ABCD'),
'four_species_graph.png', save='.'))
return integr
