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--- examples:sim_background [2014/01/20 11:21] – [How to run the code] zenke
+++ examples:sim_background [2014/01/20 11:31] – [The important bits] zenke
@@ Line 18: / Line 18: @@
 ===== The important bits =====
+Similar to other network simulations such as [[sim_isp_orig]] we start by defining two [[manual:NeuronGroup|neuron groups]]. The ''sim_background'' simulation supports a selection of different neuron models via command line parameters which is why this section looks a little more sophisticated than examples you might have encountered before. The simulation file further allows to specify the conductance ratio between AMPA and NMDA conductance via the function calls ''set_ampa_nmda_ratio(ratio)''
+<code c++>
+    NeuronGroup * neurons_e;
+    if ( adapt ) {
+        neurons_e = new AIFGroup(ne);
+        ((AIFGroup*)neurons_e)->set_ampa_nmda_ratio(ampa_nmda_ratio);
+        ((AIFGroup*)neurons_e)->dg_adapt1=1.0;
+    } else {
+        if ( loadbalance )
+            neurons_e = new IFGroup(ne,1.2,(1.2*ne+ni));
+        else
+            neurons_e = new IFGroup(ne);
+        ((IFGroup*)neurons_e)->set_ampa_nmda_ratio(ampa_nmda_ratio);
+    }
+    IFGroup * neurons_i = new IFGroup(ni);
+    // initialize membranes
+    neurons_i->set_tau_mem(10e-3);
+    neurons_e->random_mem(-60e-3,10e-3);
+    neurons_i->random_mem(-60e-3,10e-3);
+    ((IFGroup*)neurons_i)->set_ampa_nmda_ratio(ampa_nmda_ratio);
+</code>
+The non-plastic connections between the different neuron groups are set up in this section
+<code c++>
+msg = "Setting up I connections ...";
+    logger->msg(msg,PROGRESS,true);
+    SparseConnection * con_ie = new SparseConnection(neurons_i,neurons_e,
+            w_ie,sparseness,GABA);
+    SparseConnection * con_ii = new SparseConnection(neurons_i,neurons_i,
+            w_ii,sparseness,GABA);
+    msg =  "Setting up E connections ...";
+    logger->msg(msg,PROGRESS,true);
+    SparseConnection * con_ei;
+    if ( !ei_plastic ) {
+        con_ei = new SparseConnection(neurons_e,neurons_i,
+                w_ei, sparseness,GLUT);
+    } else {
+        if (infilename.empty()) {
+            con_ei = new TripletConnection(neurons_e,neurons_i,
+                w_ei, sparseness,
+                tau_hom, eta, kappa, wmax, GLUT);
+        } else {
+            string str;
+            str = infilename;
+            str += ".ei.wmat";
+            stringstream oss;
+            oss << "Loading weight matrix from " << str;
+            logger->msg(oss.str(),PROGRESS,true);
+            con_ei = new TripletConnection(neurons_e,neurons_i,
+                str.c_str(),
+                tau_hom, eta, kappa, wmax, GLUT);
+        }
+    }
+</code>
+Finally triplet STDP is setup here. The code again looks a bit more complicated since the simulation supports the use of different flavours of [[TripletSTDPConnection]], the optional addition of Gaussian noise on the initial weights the loading of a predefined connectivity matrix via [[wmat]] file.
+<code c++>
+TripletConnection * con_ee;
+    if (infilename.empty()) {
+        if (decay)
+            con_ee = new TripletDecayConnection(neurons_e,neurons_e,
+                w_ee, sparseness,
+                tau_hom, eta, tau_decay,
+                kappa, wdecay, wmax, GLUT);
+        else
+            con_ee = new TripletConnection(neurons_e,neurons_e,
+                w_ee, sparseness,
+                tau_hom, eta, kappa, wmax, GLUT);
+        // con_ee->set_min_weight(wmin);
+        if ( noisyweights )
+            con_ee->random_data(w_ee,w_ee/4);
+        for ( int i = 0 ; i < n_strengthen ; ++i ) {
+            con_ee->set_data(i,i*(wmax/n_strengthen));
+        }
+    }
+    else {
+        string str;
+        str = infilename;
+        str += ".wmat";
+        stringstream oss;
+        oss << "Loading weight matrix from " << str;
+        logger->msg(oss.str(),PROGRESS,true);
+        if (decay)
+            con_ee = new TripletDecayConnection(neurons_e,neurons_e,
+                str.c_str(),tau_hom,eta,tau_decay,kappa,wdecay,wmax,GLUT);
+        else
+            con_ee = new TripletConnection(neurons_e,neurons_e,
+                str.c_str(),tau_hom,eta,kappa,wmax,GLUT);
+        sprintf(strbuf, "%s.e.nstate", infilename.c_str());
+        neurons_e->load_from_file(strbuf);
+        sprintf(strbuf, "%s.i.nstate", infilename.c_str());
+        neurons_i->load_from_file(strbuf);
+        // primetime = 0;
+    }
+</code>