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from math import pi
import pytest
from testutils import compare_data, tol
@pytest.fixture
def ics_example(neuron_instance):
"""A model to test 3D intracellular rxd is correctly handling NMODL
currents.
"""
h, rxd, data, save_path = neuron_instance
rxd.set_solve_type(dimension=3)
# create cell1 where `x` will be created and leak out
cell1 = h.Section(name="cell1")
cell1.pt3dclear()
cell1.pt3dadd(-1, 0, 0, 1)
cell1.pt3dadd(1, 0, 0, 1)
cell1.nseg = 11
cell1.insert("pump")
# Where?
# the intracellular spaces
cyt = rxd.Region(h.allsec(), name="cyt", nrn_region="i", dx=1.0)
model = (cell1, cyt)
yield (neuron_instance, model)
def test_ics_currents(ics_example):
"""Test ics_example with fixed step methods"""
(h, rxd, data, save_path), (cell1, cyt) = ics_example
x = rxd.Species([cyt], name="x", d=1.0, charge=1, initial=0)
h.finitialize(-65)
h.continuerun(100)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_ics_currents_cvode(ics_example):
"""Test ics_example with variable step methods"""
(h, rxd, data, save_path), (cell1, cyt) = ics_example
x = rxd.Species([cyt], name="x", d=1.0, charge=1, initial=0)
h.CVode().active(True)
h.finitialize(-65)
h.continuerun(100)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
def test_ics_currents_initial(ics_example):
"""Test ics_example with initial values from NEURON"""
(h, rxd, data, save_path), (cell1, cyt) = ics_example
x = rxd.Species([cyt], name="x", d=1.0, charge=1)
h.finitialize(-65)
h.continuerun(100)
if not save_path:
max_err = compare_data(data)
assert max_err < tol
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