Adapt NEURON's standard exp2syn for use and validation

* Add a tweaked version of exp2syn.mod that is modparser compatible.
* Add option to simple_synapse.py to choose which syn type to use.
* Compatibility tweak for runinng nrn scripts with nrniv -python

mechanisms/CMakeLists.txt

-set(mechanisms pas hh expsyn)
+set(mechanisms pas hh expsyn exp2syn)
 
 set(modcc "${CMAKE_BINARY_DIR}/external/bin/modcc")
 

mechanisms/mod/exp2syn.mod

+NEURON {
+	POINT_PROCESS Exp2Syn
+	RANGE tau1, tau2, e
+	NONSPECIFIC_CURRENT i
+}
+
+UNITS {
+	(nA) = (nanoamp)
+	(mV) = (millivolt)
+	(uS) = (microsiemens)
+}
+
+PARAMETER {
+	tau1=.1 (ms) : <1e-9,1e9>
+	tau2 = 10 (ms) : <1e-9,1e9>
+	e=0	(mV)
+}
+
+ASSIGNED {
+	factor
+}
+
+STATE {
+	A : (uS)
+	B : (uS)
+}
+
+INITIAL {
+	LOCAL tp
+	A = 0
+	B = 0
+	tp = (tau1*tau2)/(tau2 - tau1) * log(tau2/tau1)
+	factor = -exp(-tp/tau1) + exp(-tp/tau2)
+	factor = 1/factor
+}
+
+BREAKPOINT {
+	SOLVE state METHOD cnexp
+	i = (B - A)*(v - e)
+}
+
+DERIVATIVE state {
+	A' = -A/tau1
+	B' = -B/tau2
+}
+
+NET_RECEIVE(weight) {
+	A = A + weight*factor
+	B = B + weight*factor
+}

nrn/simple_synapse.py

@@ -8,7 +8,20 @@ from neuron import gui, h
 
 parser = argparse.ArgumentParser(description='generate spike train ball and stick model with hh channels at soma and pas channels in dendrite')
 parser.add_argument('--plot', action='store_true', dest='plot')
-args = parser.parse_args()
+parser.add_argument('--synapse', metavar='SYN', dest='synapse',
+                    choices=['exp', 'exp2'],
+                    default='exp',
+                    help='use synapse type SYN (exp or exp2)')
+
+# hack to make things work with nrniv ... -python:
+# throw away args before -python foo.py if -python present.
+
+if '-python' in sys.argv:
+    argv = sys.argv[sys.argv.index('-python')+2:]
+else:
+    argv = sys.argv
+
+args = parser.parse_args(argv)
 
 soma = h.Section(name='soma')
 dend = h.Section(name='dend')
@@ -62,8 +75,16 @@ for nseg in [5, 11, 51, 101] :
     dend.nseg=nseg
 
     # add a synapse
-    syn_ = h.ExpSyn(dend(0.5))
-    syn_.tau = 2
+    if args.synapse == 'exp':
+        syn_ = h.ExpSyn(dend(0.5))
+        syn_.tau = 2
+    elif args.synapse == 'exp2':
+        syn_ = h.Exp2Syn(dend(0.5))
+        syn_.tau1 = 0.5 # artificially slow onset
+        syn_.tau2 = 2
+    else:
+        raise RuntimeError('unrecognized synapse type')
+
     ncstim = h.NetCon(stim, syn_)
     ncstim.delay = 1 # 1 ms delay (arrives at 10ms)
     ncstim.weight[0] = 0.04 # NetCon weight is a vector
@@ -127,7 +148,7 @@ end = timer()
 print "took ", end-start, " seconds"
 
 # save the spike info as in json format
-fp = open('simple_synapse.json', 'w')
+fp = open('simple_'+args.synapse+'_synapse.json', 'w')
 json.dump(results, fp, indent=2)
 
 if args.plot :