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from .testutils import compare_data, tol
def test_pure_diffusion(neuron_instance):
"""Test 1D diffusion in a single section"""
h, rxd, data, save_path = neuron_instance
dend = h.Section()
dend.diam = 2
dend.nseg = 101
dend.L = 100
diff_constant = 1
r = rxd.Region([dend])
ca = rxd.Species(
r, d=diff_constant, initial=lambda node: 1 if 0.4 < node.x < 0.6 else 0
)
h.finitialize(-65)
for t in [25, 50, 75, 100, 125]:
h.continuerun(t)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_pure_diffusion_cvode(neuron_instance):
"""Test 1D diffusion in a single section with the variable step method."""
h, rxd, data, save_path = neuron_instance
dend = h.Section()
dend.diam = 2
dend.nseg = 101
dend.L = 100
diff_constant = 1
r = rxd.Region(h.allsec())
ca = rxd.Species(
r, d=diff_constant, initial=lambda node: 1 if 0.4 < node.x < 0.6 else 0
)
# enable CVode and set atol
h.CVode().active(1)
h.CVode().atol(1e-6)
h.finitialize(-65)
for t in [25, 50, 75, 100, 125]:
h.continuerun(t)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
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