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add i_membrane to compute and report with coreneuron (WIP) #31

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add i_membrane to compute and report with coreneuron (WIP) #31

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11 changes: 10 additions & 1 deletion commonutils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,6 @@ def timeit(message, rank):
print ('%gs %s' % ((x - _timeit), message))
_timeit = x


# function to register section-segment mapping with bbcore write
def setup_nrnbbcore_register_mapping(rings):

Expand Down Expand Up @@ -144,6 +143,11 @@ def setup_nrnbbcore_register_mapping(rings):
v.record(seg._ref_v)
v.label("soma %d %d" % (isec, seg.node_index()))
recordlist.append(v)

i_membrane = h.Vector()
i_membrane.record(seg._ref_i_membrane_)
i_membrane.label("soma i_membrane %d %d" % (isec, seg.node_index()))
recordlist.append(i_membrane)
isec += 1

#for sections in dendrite
Expand All @@ -157,6 +161,11 @@ def setup_nrnbbcore_register_mapping(rings):
v.record(seg._ref_v)
v.label("dend %d %d" % (isec, seg.node_index()))
recordlist.append(v)

i_membrane = h.Vector()
i_membrane.record(seg._ref_i_membrane_)
i_membrane.label("dend i_membrane %d %d" % (isec, seg.node_index()))
recordlist.append(i_membrane)
isec += 1

#register soma section list
Expand Down
5 changes: 4 additions & 1 deletion ringtest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -157,6 +157,7 @@ def create_rings():
## CoreNEURON setting ##

h.cvode.cache_efficient(1)
h.cvode.use_fast_imem(1)

if use_coreneuron:
from neuron import coreneuron
Expand All @@ -174,8 +175,10 @@ def create_rings():
report_conf_file = "report.conf"
sim_conf_file = "sim.conf"
if settings.rank == 0:
write_report_config(report_conf_file, "soma.h5", "Mosaic", "compartment", "v",
write_report_config(report_conf_file, "soma_v.h5", "Mosaic", "compartment", "v",
"mV", "SONATA", 2, 1, 0, tstop, list(range(ncell)))
write_report_config(report_conf_file, "soma_i_membrane.h5", "Mosaic", "compartment", "v",
"nA", "SONATA", 2, 1, 0, tstop, list(range(ncell)))
write_spike_config(report_conf_file, "spikes.h5", ["default"], [0])
write_sim_config(sim_conf_file, "corenrn_data", report_conf_file, tstop)
coreneuron.sim_config=sim_conf_file
Expand Down