Add mousify mod files

common/mod/VecStim.mod

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+COMMENT
+/**
+ * @file VecStim.mod
+ * @brief
+ * @author king
+ * @date 2011-03-16
+ * @remark Copyright © BBP/EPFL 2005-2011; All rights reserved. Do not distribute without further notice.
+ */
+ENDCOMMENT
+
+
+: Vector stream of events
+NEURON {
+    THREADSAFE
+    ARTIFICIAL_CELL VecStim
+    RANGE ping, index, etime
+}
+
+PARAMETER {
+    ping = 1 (ms)
+}
+
+ASSIGNED {
+    index  : The index(+1) of the last retrieved element. See element()
+    etime (ms)
+    space
+}
+
+
+VERBATIM
+#if defined(NRN_VERSION_GTEQ)
+#if NRN_VERSION_GTEQ(9,0,0)
+#define NRN_VERSION_GTEQ_9_0_0
+#endif
+#endif
+#ifdef STIM_DEBUG
+# define debug_printf(...) printf(__VA_ARGS__)
+#else
+# define debug_printf(...)
+#endif
+ENDVERBATIM
+
+
+INITIAL {
+VERBATIM
+ #ifndef CORENEURON_BUILD
+ // This Mechanism is not useful for CoreNeuron, since it has its own implementation
+ // Therefore we should avoid even compiling it together, but for backwards compat keep guards
+ENDVERBATIM
+    index = 0
+    if(element()) {
+        net_send(etime - t, 1)
+    }
+    if (ping > 0) {
+        net_send(ping, 2)
+    }
+VERBATIM
+ #endif
+ENDVERBATIM
+}
+
+
+NET_RECEIVE (w) {
+    if (flag == 1) {  : deliver event
+    VERBATIM
+        debug_printf("[VecStim] net_event(): index=%d, etime=%g, t=%g\n", (int)index - 1, etime, t);
+    ENDVERBATIM
+        net_event(t)
+
+        : schedule next event
+        if (element() > 0) {
+            if (etime < t) {
+                printf("[VecStim] WARNING: spike time (%g ms) before current time (%g ms)\n",etime,t)
+            } else {
+                net_send(etime - t, 1)
+            }
+        }
+    } else if (flag == 2) { : ping - reset index to 0
+        :printf("flag=2, etime=%g, t=%g, ping=%g, index=%g\n",etime,t,ping,index)
+        if (index == -2) { : play() has been called
+            printf("[VecStim] Detected new time vector.\n")
+            restartEvent()
+        }
+        net_send(ping, 2)
+    }
+}
+
+
+COMMENT
+/**
+ * Resume the event delivery loop for NEURON restore.
+ */
+ENDCOMMENT
+PROCEDURE restartEvent() {
+    index = 0
+VERBATIM
+#ifndef CORENEURON_BUILD
+    while (element(_threadargs_) && etime < t) {}  // Ignore past events
+    if (index > 0) {
+        // Invoke low-level artcell_net_send, since generic NMODL net_send is only
+        // available in INITIAL and NET_RECEIVE blocks. It takes an ABSOLUTE time instead
+        debug_printf("[VecStim] restartEvent(delay=%g): index=%d, etime=%g, t=%g\n", delay, (int)index - 1, etime, t);
+        #if defined(NRN_VERSION_GTEQ_9_0_0)
+        artcell_net_send(_tqitem, (double*)0, _ppvar[1].get<Point_process*>(), etime, 1.0);
+        #else
+        artcell_net_send(_tqitem, (double*)0, (Point_process*)_ppvar[1]._pvoid, etime, 1.0);
+        #endif
+    }
+#endif
+ENDVERBATIM
+}
+
+
+VERBATIM
+#ifndef NRN_VERSION_GTEQ_8_2_0
+extern double* vector_vec();
+extern int vector_capacity();
+extern void* vector_arg();
+#endif
+ENDVERBATIM
+
+
+COMMENT
+/**
+ * \brief Retrieves an element (spike time) from the source vector, store in etime.
+ *
+ * \return The index+1 of the element (=~ true). Otherwise 0 (not initialized or end)
+ *
+ * NOTE: For back-compat index is incremented *after* the element is retrieved, making
+ *   it like a base-1 indexing scheme, or representing the next elements index.
+ */
+ENDCOMMENT
+FUNCTION element() {
+VERBATIM
+    const int i = (int)index;
+    IvocVect* const vv = *((IvocVect**)(&space));
+
+    int size; double* px;
+    if (i < 0 || vv == NULL)
+        return 0;
+
+    size = vector_capacity(vv);
+    px = vector_vec(vv);
+    if (i < size) {
+        etime = px[i];
+        index += 1.;
+        debug_printf("[VecStim] element(): index=%d, etime=%g, t=%g\n", (int)index - 1, etime, t);
+        return index;
+    }
+    index = -1;
+    return 0;
+ENDVERBATIM
+}
+
+
+PROCEDURE play() {
+VERBATIM
+    #ifndef CORENEURON_BUILD
+    void** vv;
+    vv = (void**)(&space);
+    *vv = NULL;
+    if (ifarg(1)) {
+        *vv = vector_arg(1);
+    }
+    index = -2;
+    #endif
+ENDVERBATIM
+}
+

mousify/README.md

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+Simulation Models :: mousify
+----------------------------
+
+These hoc and mod files implement the mousify specific cell mechanism.
+
+
+Versions
+--------
+
+2019.1 - First import after splitting of neurodamus and models
+2021.11 - Start using aggregate neurodamus-models repo, drop common submodule
+
+
+Common models
+-------------
+
+TLDR: Run `./fetch_common.bash` to init and update common.
+
+Most Blue Brain models depend on a set of common mods, among themProbAMPANMDA and ProbGABAAB.
+Previously the current repo would include them as a submodule. However, besides overly
+complicating the deployment process, it could lead to situations of outdated versions of these files.
+
+Since 2021.11 all BBP maintained models therefore drop submodules and implement a fetch_common.bash
+script which will ensure that you have locally the latest common files.
+
+Therefore, every time you wish to init or fetch updates for common, simply:
+
+ > `./fetch_common.bash`
+

mousify/hoc/AMPANMDAHelper.hoc

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+../../common/hoc/AMPANMDAHelper.hoc

mousify/hoc/DetAMPANMDAHelper.hoc

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+../../common/hoc/DetAMPANMDAHelper.hoc

mousify/hoc/DetGABAABHelper.hoc

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+../../common/hoc/DetGABAABHelper.hoc

mousify/hoc/GABAABHelper.hoc

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+../../common/hoc/GABAABHelper.hoc

mousify/hoc/GluSynapseHelper.hoc

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+../../common/hoc/GluSynapseHelper.hoc

mousify/mod/CaDynamics.mod

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+: Dynamics that track inside calcium concentration
+: modified from Destexhe et al. 1994
+
+NEURON	{
+	SUFFIX CaDynamics
+	USEION ca READ ica WRITE cai
+	RANGE decay, gamma, minCai, depth
+}
+
+UNITS	{
+	(mV) = (millivolt)
+	(mA) = (milliamp)
+	FARADAY = (faraday) (coulombs)
+	(molar) = (1/liter)
+	(mM) = (millimolar)
+	(um)	= (micron)
+}
+
+PARAMETER	{
+	gamma = 0.05 : percent of free calcium (not buffered)
+	decay = 80 (ms) : rate of removal of calcium
+	depth = 0.1 (um) : depth of shell
+	minCai = 1e-4 (mM)
+}
+
+ASSIGNED	{ica (mA/cm2)}
+
+INITIAL {
+	cai = minCai
+}
+
+STATE	{
+	cai (mM)
+}
+
+BREAKPOINT	{ SOLVE states METHOD cnexp }
+
+DERIVATIVE states	{
+	cai' = -(10000)*(ica*gamma/(2*FARADAY*depth)) - (cai - minCai)/decay
+}

mousify/mod/Ca_HVA.mod

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+: Reference:		Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993
+
+NEURON	{
+	SUFFIX Ca_HVA
+	USEION ca READ eca WRITE ica
+	RANGE gbar, g, ica 
+}
+
+UNITS	{
+	(S) = (siemens)
+	(mV) = (millivolt)
+	(mA) = (milliamp)
+}
+
+PARAMETER	{
+	gbar = 0.00001 (S/cm2) 
+}
+
+ASSIGNED	{
+	v	(mV)
+	eca	(mV)
+	ica	(mA/cm2)
+	g	(S/cm2)
+	mInf
+	mTau
+	mAlpha
+	mBeta
+	hInf
+	hTau
+	hAlpha
+	hBeta
+}
+
+STATE	{ 
+	m
+	h
+}
+
+BREAKPOINT	{
+	SOLVE states METHOD cnexp
+	g = gbar*m*m*h
+	ica = g*(v-eca)
+}
+
+DERIVATIVE states	{
+	rates()
+	m' = (mInf-m)/mTau
+	h' = (hInf-h)/hTau
+}
+
+INITIAL{
+	rates()
+	m = mInf
+	h = hInf
+}
+
+PROCEDURE rates(){
+	UNITSOFF
+    :   if((v == -27) ){        
+    :       v = v+0.0001
+    :   }
+		:mAlpha =  (0.055*(-27-v))/(exp((-27-v)/3.8) - 1)
+		mAlpha = 0.055 * vtrap(-27 - v, 3.8)        
+		mBeta  =  (0.94*exp((-75-v)/17))
+		mInf = mAlpha/(mAlpha + mBeta)
+		mTau = 1/(mAlpha + mBeta)
+		hAlpha =  (0.000457*exp((-13-v)/50))
+		hBeta  =  (0.0065/(exp((-v-15)/28)+1))
+		hInf = hAlpha/(hAlpha + hBeta)
+		hTau = 1/(hAlpha + hBeta)
+	UNITSON
+}
+
+FUNCTION vtrap(x, y) { : Traps for 0 in denominator of rate equations
+	UNITSOFF
+	if (fabs(x / y) < 1e-6) {
+		vtrap = y * (1 - x / y / 2)
+	} else {
+		vtrap = x / (exp(x / y) - 1)
+	}
+	UNITSON
+}