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# i_membrane + electrode current sums to 0 when electrode parameters are time dependent.
# This test revealed a fast_imem bug that needed fixing #2733
from neuron import h, gui
from neuron import coreneuron
import math
pc = h.ParallelContext()
def chkvec(v, str, tol=1e-10):
x = v.c().abs().max()
# print(str, " ", x)
assert math.isclose(x, 0.0, abs_tol=tol)
def seclamp(s):
stim = h.SEClamp(s(0.5))
stim.amp1 = -65
stim.dur1 = 1
stim.amp2 = -10
stim.dur2 = 100
stim.rs = 10
return stim
def iclamp(s):
stim = h.IClamp(s(0.5))
stim.delay = 1.0
stim.dur = 0.1
stim.amp = 0.3
return stim
def triangle_stim(stimref, step, min, max):
tstim = h.Vector(20).indgen(step)
istim = tstim.c().fill(min)
for i in range(1, len(istim), 2):
istim[i] = max
istim.play(stimref, tstim, 1)
return tstim, istim
def tst(xtrcell, secondorder, cvactive, corenrn, seclmp):
# print(xtrcell, secondorder, cvactive, corenrn, seclmp)
cv = h.cvode
cv.use_fast_imem(1)
h.secondorder = secondorder
cv.active(cvactive)
s = h.Section("s")
s.L = 10
s.diam = 10
s.nseg = 1
s.insert("hh")
imvec = None
if xtrcell:
s.insert("extracellular")
imvec = h.Vector().record(s(0.5)._ref_i_membrane)
vstim = None
rstim = None
if seclmp:
stim = seclamp(s)
stim.dur1 = 100
vstim = triangle_stim(stim._ref_amp1, 0.5, -65, -10)
rstim = triangle_stim(stim._ref_rs, 1, 1000, 100)
else:
stim = iclamp(s)
stim.dur = 100
vstim = triangle_stim(stim._ref_amp, 0.5, 0, 0.001)
tvec = h.Vector().record(h._ref_t)
vvec = h.Vector().record(s(0.5)._ref_v)
istimvec = h.Vector().record(stim._ref_i)
imemvec = h.Vector().record(s(0.5)._ref_i_membrane_)
if hasattr(stim, "vc"):
vstimvec = h.Vector().record(stim._ref_vc)
rsstimvec = h.Vector().record(stim._ref_rs)
glist = []
def fstim():
if h.cvode.active():
return istimvec.c()
# current balance and imembrane calculation takes place at t + .5*dt
# SEClamp conductance is evaluated (Vector.play) at t + .5*dt
# But recording is at time t + dt.
# So use rsstimvec to evaluate clamp resistance at midpoint
# of each step. That is the resistance for the entire step.
rs = rsstimvec.c().add(rsstimvec.c().rotate(1)).mul(0.5)
rs[0] = rsstimvec[0]
vc = vstimvec.c()
v = vvec.c()
if h.secondorder:
v = vvec.c().add(vvec.c().rotate(1)).mul(0.5)
v[0] = vvec[0]
s = vc.sub(v).div(rs)
return s
def plt(vec, vecstr):
return # comment out if want to see plots
g = h.Graph()
glist.append(g)
vec.label(vecstr)
vec.line(g, tvec)
g.exec_menu("View = plot")
g.exec_menu("10% Zoom out")
return g
# run
# h.steps_per_ms = 400
h.tstop = 10
pc.set_maxstep(10)
h.finitialize(-65)
if corenrn:
coreneuron.enable = True
coreneuron.verbose = 0
pc.psolve(h.tstop)
coreneuron.enable = False
coreneuron.verbose = 2
else:
h.run()
plt(vvec, "v")
plt(imemvec, "i_membrane_")
plt(istimvec, "stim.i")
tmp = (imemvec.c().sub(istimvec), "i_membrane_ - stim_i")
plt(*tmp)
if cv.active() or not seclmp:
chkvec(*tmp)
if xtrcell:
pass
plt(imvec, "i_membrane")
plt(imvec.c().mul(s(0.5).area() / 100).sub(istimvec), "i_membrane - stim_i")
tmp = (
imvec.c().mul(s(0.5).area() / 100).sub(imemvec),
"i_membrane - i_membrane_",
)
plt(*tmp)
chkvec(*tmp)
if hasattr(stim, "vc"):
pass
g = plt(rsstimvec, "stim.rs")
if g:
rstim[1].line(g, rstim[0], 2, 1)
plt(vstimvec, "stim.vc")
tmp = (imemvec.c().sub(fstim()), "i_membrane_ - fstim()")
plt(*tmp)
chkvec(*tmp)
cv.use_fast_imem(0)
h.secondorder = 0
return glist
def test_imem():
# tst(xtrcell, secondorder, cvactive, corenrn, seclmp)
cnlist = [0]
if "NRN_ENABLE_CORENEURON" in h.nrnversion(6):
# coreneuron submodule doesn't have update from #2733
# and this test should be skipped in 8.2
pass
# cnlist.append(1)
for seclmp in [0, 1]:
tst(1, 0, 0, 0, seclmp)
tst(0, 0, 1, 0, seclmp)
for secondorder in [0, 2]:
for corenrn in cnlist:
tst(0, secondorder, 0, corenrn, seclmp)
if __name__ == "__main__":
test_imem()
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