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generate_config_state.cpp
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generate_config_state.cpp
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/* configure the network */
/* neuron groups */
int EC_LI_II_Multipolar_Pyramidal=sim.createGroup("EC_LI_II_Multipolar_Pyramidal",
p.EC_LI_II_Multipolar_Pyramidal_Count, EXCITATORY_NEURON, ANY, GPU_CORES);
int MEC_LII_Stellate=sim.createGroup("MEC_LII_Stellate",
p.MEC_LII_Stellate_Count, EXCITATORY_NEURON, ANY, GPU_CORES);
int EC_LII_Axo_Axonic=sim.createGroup("EC_LII_Axo_Axonic",
p.EC_LII_Axo_Axonic_Count, INHIBITORY_NEURON, ANY, GPU_CORES);
int MEC_LII_Basket=sim.createGroup("MEC_LII_Basket",
p.MEC_LII_Basket_Count, INHIBITORY_NEURON, ANY, GPU_CORES);
int EC_LII_Basket_Multipolar=sim.createGroup("EC_LII_Basket_Multipolar",
p.EC_LII_Basket_Multipolar_Count, INHIBITORY_NEURON, ANY, GPU_CORES);
int CA1_Pyramidal=sim.createGroup("CA1_Pyramidal",
p.CA1_Pyramidal_Count, EXCITATORY_NEURON, ANY, GPU_CORES);
int MEC_LII_Basket_Speed=sim.createGroup("MEC_LII_Basket_Speed",
p.MEC_LII_Basket_Speed_Count, INHIBITORY_NEURON, ANY, GPU_CORES);
int MEC_LII_Stellate_Speed=sim.createGroup("MEC_LII_Stellate_Speed",
p.MEC_LII_Stellate_Speed_Count, EXCITATORY_NEURON, ANY, GPU_CORES);
// assign group numbers for later access
p.EC_LI_II_Multipolar_Pyramidal_Group = EC_LI_II_Multipolar_Pyramidal; // 0
p.MEC_LII_Stellate_Group = MEC_LII_Stellate; // 1
p.EC_LII_Axo_Axonic_Group = EC_LII_Axo_Axonic; // 2
p.MEC_LII_Basket_Group = MEC_LII_Basket; // 3
p.EC_LII_Basket_Multipolar_Group = EC_LII_Basket_Multipolar; // 4
p.CA1_Pyramidal_Group = CA1_Pyramidal; // 5
p.MEC_LII_Basket_Speed_Group = MEC_LII_Basket_Speed; // 6
p.MEC_LII_Stellate_Speed_Group = MEC_LII_Stellate_Speed; // 7
/* neuron type parameters */
sim.setNeuronParameters(EC_LI_II_Multipolar_Pyramidal, 375.0f, 0.0f, 0.37f, 0.0f, -70.53f, 0.0f, -39.99f,
0.0f, 0.001f, 0.0f, 0.01f, 0.0f, 3.96f, 0.0f, -54.95f, 0.0f,
7.0f, 0.0f, 0); // C,k,vr,vt,a,b,vpeak,c,d
// Ensemble file: k,a,b,d,C,vr,vt,c,vpeak.
// 1->2, 2->5, 3->6, 4->9, 5->1, 6->3, 7->4, 8->8, 9->7
sim.setNeuronParameters(MEC_LII_Stellate, 118.000000f, 0.0f, 0.62f, 0.0f, -58.53f, 0.0f,
-43.52f, 0.0f, 0.005f, 0.0f, 11.69f, 0.0f, 11.48f, 0.0f,
-49.52f, 0.0f, 0.0f, 0.0f, 0);
sim.setNeuronParameters(EC_LII_Axo_Axonic, 20.0f, 0.0f, 1.0f, 0.0f, -55.0f, 0.0f,
-40.0f, 0.0f, 0.15f, 0.0f, 8.0f, 0.0f, 25.0f, 0.0f,
-55.0f, 0.0f, 200.0f, 0.0f, 0);
sim.setNeuronParameters(MEC_LII_Basket, 20.0f, 0.0f, 1.0f, 0.0f, -55.0f, 0.0f,
-40.0f, 0.0f, 0.15f, 0.0f, 8.0f, 0.0f, 25.0f, 0.0f,
-55.0f, 0.0f, 200.0f, 0.0f, 0);
sim.setNeuronParameters(EC_LII_Basket_Multipolar, 20.0f, 0.0f, 1.0f, 0.0f, -55.0f, 0.0f,
-40.0f, 0.0f, 0.15f, 0.0f, 8.0f, 0.0f, 25.0f, 0.0f,
-55.0f, 0.0f, 200.0f, 0.0f, 0);
sim.setNeuronParameters(MEC_LII_Basket_Speed, 20.0f, 0.0f, 1.0f, 0.0f, -55.0f, 0.0f,
-40.0f, 0.0f, 0.15f, 0.0f, 8.0f, 0.0f, 25.0f, 0.0f,
-55.0f, 0.0f, 200.0f, 0.0f, 0);
sim.setNeuronParameters(MEC_LII_Stellate_Speed, 118.000000f, 0.0f, 0.62f, 0.0f, -58.53f, 0.0f, -43.52f,
0.0f, 0.005f, 0.0f, 11.690000f, 0.0f, 11.48f, 0.0f, -49.52f, 0.0f,
50.0f, 0.0f, 0);
// C,k,vr,vt,a,b,vpeak,c,d
sim.setNeuronParameters(CA1_Pyramidal, 530.0f, 0.0f, 1.7382527828120673f, 0.0f, -69.97816841048154f, 0.0f, -57.42740032f,
0.0f, 0.0028211397234640546f, 0.0f, -0.7818603847193373f, 0.0f, 24.44743634f, 0.0f, -60.35222718f,
0.0f, 25.0f, 0.0f, 0);
/* neuron connection parameters */
setInExcConns(&sim, &p);
double gc2inwt = p.grc_to_in_wt;
MexHatConnection* MexHatConn;
SomeToSomeConnection* SomeToSomeConn;
sim.connect(EC_LI_II_Multipolar_Pyramidal, MEC_LII_Stellate, "one-to-one", 1.0f, 1.0f,
RangeDelay(1), RadiusRF(-1), SYN_FIXED, p.dir_to_grc_g_fast, p.dir_to_grc_g_slow); // 0 DIR
p.conn_offset = 0;
if (p.spin2in_active) {
p.grc_to_in_wt = p.spdin2inwt;
SomeToSomeConn = new SomeToSomeConnection(&p);
sim.connect(MEC_LII_Basket_Speed, EC_LII_Axo_Axonic, SomeToSomeConn, p.grc_to_in_g_fast, p.grc_to_in_g_slow, SYN_FIXED);
}
if (p.spex2in_active) {
p.grc_to_in_wt = p.spdex2inwt;
SomeToSomeConn = new SomeToSomeConnection(&p);
sim.connect(MEC_LII_Stellate_Speed, EC_LII_Axo_Axonic, SomeToSomeConn, p.grc_to_in_g_fast, p.grc_to_in_g_slow, SYN_FIXED);
}
p.grc_to_in_wt = gc2inwt;
SomeToSomeConn = new SomeToSomeConnection(&p);
sim.connect(MEC_LII_Stellate, EC_LII_Axo_Axonic, SomeToSomeConn, p.grc_to_in_g_fast, p.grc_to_in_g_slow, SYN_FIXED);
MexHatConn = new MexHatConnection(&p);
sim.connect(EC_LII_Axo_Axonic, MEC_LII_Stellate, MexHatConn, p.in_to_grc_g_fast, p.in_to_grc_g_slow, SYN_FIXED); // 2 IN->GC one-to-many
////
p.conn_offset = 1;
if (p.spin2in_active) {
p.grc_to_in_wt = p.spdin2inwt;
SomeToSomeConn = new SomeToSomeConnection(&p);
sim.connect(MEC_LII_Basket_Speed, MEC_LII_Basket, SomeToSomeConn, p.grc_to_in_g_fast, p.grc_to_in_g_slow, SYN_FIXED);
}
if (p.spex2in_active) {
p.grc_to_in_wt = p.spdex2inwt;
SomeToSomeConn = new SomeToSomeConnection(&p);
sim.connect(MEC_LII_Stellate_Speed, MEC_LII_Basket, SomeToSomeConn, p.grc_to_in_g_fast, p.grc_to_in_g_slow, SYN_FIXED);
}
p.grc_to_in_wt = gc2inwt;
SomeToSomeConn = new SomeToSomeConnection(&p);
sim.connect(MEC_LII_Stellate, MEC_LII_Basket, SomeToSomeConn, p.grc_to_in_g_fast, p.grc_to_in_g_slow, SYN_FIXED);
MexHatConn = new MexHatConnection(&p);
sim.connect(MEC_LII_Basket, MEC_LII_Stellate, MexHatConn, p.in_to_grc_g_fast, p.in_to_grc_g_slow, SYN_FIXED); // 2 IN->GC one-to-many
////
p.conn_offset = 2;
if (p.spin2in_active) {
p.grc_to_in_wt = p.spdin2inwt;
SomeToSomeConn = new SomeToSomeConnection(&p);
sim.connect(MEC_LII_Basket_Speed, EC_LII_Basket_Multipolar, SomeToSomeConn, p.grc_to_in_g_fast, p.grc_to_in_g_slow, SYN_FIXED);
}
if (p.spex2in_active) {
p.grc_to_in_wt = p.spdex2inwt;
SomeToSomeConn = new SomeToSomeConnection(&p);
sim.connect(MEC_LII_Stellate_Speed, EC_LII_Basket_Multipolar, SomeToSomeConn, p.grc_to_in_g_fast, p.grc_to_in_g_slow, SYN_FIXED);
}
p.grc_to_in_wt = gc2inwt;
SomeToSomeConn = new SomeToSomeConnection(&p);
sim.connect(MEC_LII_Stellate, EC_LII_Basket_Multipolar, SomeToSomeConn, p.grc_to_in_g_fast, p.grc_to_in_g_slow, SYN_FIXED);
MexHatConn = new MexHatConnection(&p);
sim.connect(EC_LII_Basket_Multipolar, MEC_LII_Stellate, MexHatConn, p.in_to_grc_g_fast, p.in_to_grc_g_slow, SYN_FIXED); // 2 IN->GC one-to-many
// added connections for less total AA connections //
/////////////////////////////////////////////////////
sim.connect(CA1_Pyramidal, MEC_LII_Stellate, "one-to-one", 1.0f, 1.0f,
RangeDelay(1), RadiusRF(-1), SYN_FIXED, p.pc_to_grc_g_fast, p.pc_to_grc_g_slow); // 3 PCs
/* STP parameters */
// Keivan data conversion: g = conductance; t_d = STPtdAMPA or STPtdGABAa; t_r = tauX; t_f = tauU; u = U;
sim.setSTP(EC_LI_II_Multipolar_Pyramidal, MEC_LII_Stellate, true, STPu(0.1802, 0.0f),
STPtauU(49.9201, 0.0f),
STPtauX(152.8565, 0.0f),
STPtdAMPA(3.3800, 0.0f),
STPtdNMDA(150.0, 0.0f),
STPtdGABAa(6.0, 0.0f),
STPtdGABAb(150.0, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
sim.setSTP(CA1_Pyramidal, MEC_LII_Stellate, true, STPu(0.1231, 0.0f),
STPtauU(49.71, 0.0f),
STPtauX(153.4, 0.0f),
STPtdAMPA(3.3800, 0.0f),
STPtdNMDA(150.0, 0.0f),
STPtdGABAa(6.0, 0.0f),
STPtdGABAb(150.0, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
sim.setSTP(MEC_LII_Stellate, EC_LII_Axo_Axonic, true, STPu(0.1672, 0.0f),
STPtauU(49.9201, 0.0f),
STPtauX(167.6863, 0.0f),
STPtdAMPA(3.0845, 0.0f),
STPtdNMDA(150.0, 0.0f),
STPtdGABAa(6.0, 0.0f),
STPtdGABAb(150.0, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
sim.setSTP(MEC_LII_Stellate, MEC_LII_Basket, true, STPu(0.1672, 0.0f),
STPtauU(49.9201, 0.0f),
STPtauX(152.8565, 0.0f),
STPtdAMPA(2.8868, 0.0f),
STPtdNMDA(150.0, 0.0f),
STPtdGABAa(6.0, 0.0f),
STPtdGABAb(150.0, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
sim.setSTP(MEC_LII_Stellate, EC_LII_Basket_Multipolar, true, STPu(0.1973, 0.0f),
STPtauU(49.9201, 0.0f),
STPtauX(136.5698, 0.0f),
STPtdAMPA(2.6407, 0.0f),
STPtdNMDA(150.0, 0.0f),
STPtdGABAa(6.0, 0.0f),
STPtdGABAb(150.0, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
sim.setSTP(EC_LII_Axo_Axonic, MEC_LII_Stellate, true, STPu(0.1453, 0.0f),
STPtauU(27.3057, 0.0f),
STPtauX(420.8379, 0.0f),
STPtdAMPA(5.0f, 0.0f),
STPtdNMDA(150.0f, 0.0f),
STPtdGABAa(4.5605f, 0.0f),
STPtdGABAb(150.0f, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
sim.setSTP(MEC_LII_Basket, MEC_LII_Stellate, true, STPu(0.1513, 0.0f),
STPtauU(27.8100, 0.0f),
STPtauX(443.4992, 0.0f),
STPtdAMPA(5.0f, 0.0f),
STPtdNMDA(150.0f, 0.0f),
STPtdGABAa(4.4880f, 0.0f),
STPtdGABAb(150.0f, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
sim.setSTP(EC_LII_Basket_Multipolar, MEC_LII_Stellate, true, STPu(0.1617, 0.0f),
STPtauU(30.5434, 0.0f),
STPtauX(382.4847, 0.0f),
STPtdAMPA(5.0f, 0.0f),
STPtdNMDA(150.0f, 0.0f),
STPtdGABAa(4.9477f, 0.0f),
STPtdGABAb(150.0f, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
if (p.spin2in_active == 1) {
sim.setSTP(MEC_LII_Basket_Speed, EC_LII_Axo_Axonic, true, STPu(0.1638, 0.0f),
STPtauU(57.57, 0.0f),
STPtauX(119, 0.0f),
STPtdAMPA(6.205, 0.0f),
STPtdNMDA(150.0, 0.0f),
STPtdGABAa(6.0, 0.0f),
STPtdGABAb(150.0, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
sim.setSTP(MEC_LII_Basket_Speed, MEC_LII_Basket, true, STPu(0.1638, 0.0f),
STPtauU(57.57, 0.0f),
STPtauX(119, 0.0f),
STPtdAMPA(6.205, 0.0f),
STPtdNMDA(150.0, 0.0f),
STPtdGABAa(6.0, 0.0f),
STPtdGABAb(150.0, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
sim.setSTP(MEC_LII_Basket_Speed, EC_LII_Basket_Multipolar, true, STPu(0.1638, 0.0f),
STPtauU(57.57, 0.0f),
STPtauX(119, 0.0f),
STPtdAMPA(6.205, 0.0f),
STPtdNMDA(150.0, 0.0f),
STPtdGABAa(6.0, 0.0f),
STPtdGABAb(150.0, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
}
if (p.spex2in_active == 1) {
sim.setSTP(MEC_LII_Stellate_Speed, EC_LII_Axo_Axonic, true, STPu(0.1672, 0.0f),
STPtauU(49.9201, 0.0f),
STPtauX(167.6863, 0.0f),
STPtdAMPA(3.0845, 0.0f),
STPtdNMDA(150.0, 0.0f),
STPtdGABAa(6.0, 0.0f),
STPtdGABAb(150.0, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
sim.setSTP(MEC_LII_Stellate_Speed, MEC_LII_Basket, true, STPu(0.1672, 0.0f),
STPtauU(49.9201, 0.0f),
STPtauX(152.8565, 0.0f),
STPtdAMPA(2.8868, 0.0f),
STPtdNMDA(150.0, 0.0f),
STPtdGABAa(6.0, 0.0f),
STPtdGABAb(150.0, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
sim.setSTP(MEC_LII_Stellate_Speed, EC_LII_Basket_Multipolar, true, STPu(0.1973, 0.0f),
STPtauU(49.9201, 0.0f),
STPtauX(136.5698, 0.0f),
STPtdAMPA(2.6407, 0.0f),
STPtdNMDA(150.0, 0.0f),
STPtdGABAa(6.0, 0.0f),
STPtdGABAb(150.0, 0.0f),
STPtrNMDA(0.0f, 0.0f),
STPtrGABAb(0.0f, 0.0f));
}
/* neuron monitors */
#if monitor_voltage
sim.setNeuronMonitor(MEC_LII_Stellate,"DEFAULT");
sim.setNeuronMonitor(MEC_LII_Basket,"DEFAULT");
sim.setNeuronMonitor(CA1_Pyramidal,"DEFAULT");
#endif
#if monitor_voltage2
sim.setNeuronMonitor(EC_LII_Axo_Axonic,"DEFAULT");
sim.setNeuronMonitor(EC_LII_Basket_Multipolar,"DEFAULT");
sim.setNeuronMonitor(EC_LI_II_Multipolar_Pyramidal,"DEFAULT");
#endif