I've now got a minimal complete (if nonsensical) example that shows my problem more clearly. There's also a possible solution, which I got to by examining the NEURON source code, in particular by doing some printf debugging in setup_tree_matrix() in treeset.c. It seems that the rhs argument feeds into the solver directly, but any species-specific currents (e.g. ica) are not incorporated as components of the total current before the solver is called. So setting the relevant element of the current pointer neuron.rxd.rxd._curr_ptrs

and the element of rhs corresponding to the same segment is necessary to see current injected by the callback routine manifest in the current, voltage and concentration. However, I'm not sure if this is the intended mode of operation

I should add that I'm using python2.7 and the version of NEURON from the default mercurial branch.

Code: Select all

```
from neuron import *
from neuron import rxd
import neuron.rxd.rxd as nrr
import random
import matplotlib.pyplot as plt
def _kn_currents(rhs):
nrr._currents(rhs)
cur = -random.random()/10
## This line alters ica, but on its own does not seem to affect
## the voltage
nrr._curr_ptrs[0][0] += cur
## This line is necessary to change the voltage
rhs[1] += -cur
nrr._callbacks[2] = _kn_currents
sh = h.Section()
sh.insert("pas")
r = rxd.Region([sh], nrn_region='i')
ca = rxd.Species(r, name='ca', charge=2, initial=0.0)
rec_t = h.Vector()
rec_t.record(h._ref_t)
rec_v = h.Vector()
rec_v.record(sh(0.5)._ref_v)
rec_ica = h.Vector()
rec_ica.record(sh(0.5)._ref_ica)
rec_cai = h.Vector()
rec_cai.record(sh(0.5)._ref_cai)
init()
run(15)
fig, ax = plt.subplots(nrows=3, ncols=1, figsize=(2.25*2, 2.5*2))
plt.subplots_adjust(left=0.2, top=0.95, bottom=0.1)
ax[0].plot(rec_t, rec_v)
ax[0].set_xlabel("")
ax[0].set_ylabel("V (mV)")
ax[0].axis(ymin=-80, ymax=50)
ax[1].plot(rec_t, rec_ica)
ax[1].set_xlabel("")
ax[1].set_ylabel("ICa (mA/cm2)")
ax[1].axis(ymin=-0.1, ymax=0.1)
ax[2].plot(rec_t, rec_cai)
ax[2].set_xlabel("")
ax[2].set_ylabel("[Ca] (mM)")
ax[2].axis(ymin=0, ymax=0.001)
fig.show()
```