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Kncl.cpp
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Kncl.cpp
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/*******************************************************************
Conductance based neocortical network model
Modified version of code by MB (2006)
********************************************************************/
// Libraries
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <time.h>
#include <omp.h>
#include "params.h"
#define NUM_THREADS 40
// Constants
#define PI 3.141592654
#define input_start_time 100000
#define input_end_time 100400
#define Check_time 1000
#define no_clusters 10
#define Mcx_cluster_size 50
#define Min_cluster_size 10
// Network Geometry
#define I_CX 1 // 0 - No layer, 1 - Add Layer
#define I_IN 1 // 0 - No layer, 1 - Add Layer
#define I_GB 0 // 0 - No GABAb from IN to CX, 1 - Yes
#define Mcx (Mcx_cluster_size*no_clusters) // Number of CX cells in X direction
#define Min (Min_cluster_size*no_clusters) // Number of IN cells in X direction
#define Mcx1 1 // Number of CX cells in Y direction
#define Min1 1 // Number of IN cells in Y direction
#define Max Mcx
#define Max1 Mcx1
#define Num_Types 2
#define Num_Cells ((Min*Min1)+(Mcx*Mcx1))
int cell_sizes[2][2] = {{Mcx,Mcx1},
{Min,Min1}};
double Cluster_conn_matrix[no_clusters][no_clusters]; //cluster edge i->o == Cluster_conn_matrix[i][o]
// Boundary conditions
#define BOUND 0 // 0 - flow; 1 - periodic; 9 - no boundary elements
#define BOUNDcx 0 // 0 - flow; 1 - periodic; 9 - no boundary elements
#define SELFINGcx 0 // 0 - CX without self excitation; 1 - with ...
// Connections
#define MS_CX_CX 5
#define MS_CX_CX1 0
#define MS_CX_CX_MAX ((MS_CX_CX > MS_CX_CX1) ? MS_CX_CX : MS_CX_CX1)
#define N_CX_CX 1
#define MS_CX_CX_NMDA 5
#define MS_CX_CX_NMDA1 0
#define MS_CX_CX_NMDA_MAX ((MS_CX_CX_NMDA > MS_CX_CX_NMDA1) ? MS_CX_CX_NMDA : MS_CX_CX_NMDA1)
#define N_CX_CX_NMDA 1
#define MS_CX_IN_NMDA 1
#define MS_CX_IN_NMDA1 0
#define MS_CX_IN_NMDA_MAX ((MS_CX_IN_NMDA > MS_CX_IN_NMDA1) ? MS_CX_IN_NMDA : MS_CX_IN_NMDA1)
#define N_CX_IN_NMDA 1
#define MS_CX_IN 1
#define MS_CX_IN1 0
#define MS_CX_IN_MAX ((MS_CX_IN > MS_CX_IN1) ? MS_CX_IN : MS_CX_IN1)
#define N_CX_IN 1
#define MS_IN_CX 5
#define MS_IN_CX1 0
#define MS_IN_CX_MAX ((MS_IN_CX > MS_IN_CX1) ? MS_IN_CX : MS_IN_CX1)
#define N_IN_CX ((2*MS_IN_CX+1)+4)*Min/Mcx
#define MS_IN_IN 2
#define MS_IN_IN1 0
#define MS_IN_IN_MAX ((MS_IN_IN > MS_IN_IN1) ? MS_IN_IN : MS_IN_IN1)
#define N_IN_IN (2*MS_IN_IN+1)
// Number of ODE for each cell
#define N_RE 7
#define N_TC 12
#define N_GB 2
#define N_DEND 17
#define N_SOMA 9
#define N_CX (N_DEND + N_SOMA)
#define N_IN N_CX
#define N_EQ2 (N_CX*I_CX + N_IN_CX*N_GB*I_CX*I_IN*I_GB)*Mcx*Mcx1
#define N_EQ3 (N_IN*I_IN)*Min*Min1
#define N_EQ (N_EQ2 + N_EQ3) // Total number of ODE
// Reversal potentials
#define EE_Na 50
#define EE_l -61
#define EE_K -95
#define EE_h -50
#define E_LK = -58
int **index_loc_array;
int seizure=0;
double syn_factor=1.5;
// Ratio of the CX-CX, CX-IN connection for between cluster
double Long_range_cxcx_strength=1;
double Long_range_cxin_strength=0.0;
// Declare all the current classes
#include "current_classes.h"
//+++++++++++++++++++ MAIN PROGRAM +++++++++++++++++++++++++++++++++++++++++++
//----------external functuons----------------------------------------------
void index_array(int***);
void rk(unsigned, void (unsigned, double, double*, double*), double, double,
double*, double*, double*, double*);
void calcit(int index,unsigned neq, double x, double *y_ini, double *f_ini);
void calc_syn(int index,unsigned neq, double x, double *y_ini, double *f_ini);
void fun(unsigned, double, double*, double*);
double gaussrand();
//----------external variables ---------------------------------------------
double g_ampa_cx_cx[Mcx][Mcx1], g_nmda_cx_cx, g_nmda_cx_in;
double g_ampa_cx_cx_MINICE, g_ampa_cx_in_MINICE;
double g_ampa_cx_in[Min][Min1], g_gaba_a_in_cx[Mcx][Mcx1];
double g_gaba_b_in_cx, g_gaba_a_in_in;
double g_ext_cx1, g_ext_in1;
FILE *finput, *f_cx, *f_cx_syn, *f_cx_syn_inh, *f_in, *f_py_rates, *g_py_py,*f_in_rates, *g_py_in, *MyFile, *g_in_py, *g_GHVA,*g_GNAP,*g_GKCA, *SynCurrent, *myconnect,*f1000,*f_gaba, *f_par, *log_file, *fsp;
int no_cx[Mcx][Mcx1][N_CX];
int no_in[Min][Min1][N_IN], no_gcx[Mcx][Mcx1][N_IN_CX][N_GB];
int C_CXCX[Mcx][Mcx1][Mcx][Mcx1];
int C_CXIN[Mcx][Mcx1][Min][Min1];
int C_INCX[Min][Min1][Mcx][Mcx1];
int C_ININ[Min][Min1][Min][Min1];
double Cluster_strength_CXCX[Mcx][Mcx1][Mcx][Mcx1];
double Cluster_strength_CXIN[Mcx][Mcx1][Min][Min1];
int k_CXCX[Mcx][Mcx1];
int k_CXIN[Min][Min1];
int k_INCX[Mcx][Mcx1];
int k_ININ[Min][Min1];
int k_CXCXmax=0;
int k_CXINmax=0;
int k_INCXmax=0;
int k_ININmax=0;
int firstflag=0;
double prev[Mcx][Mcx1];
double spikecount[Mcx][Mcx1];
double average_rate_py=0;
double prev_in[Min][Min1];
double spikecount_in[Min][Min1];
double average_rate_in=0;
double E[Mcx][Mcx1];
double GPY = 0;
double GIN = 0;
double GPYPY = 0;
double GPYIN = 0;
int excounter = 0;
int randseed = 0;
//----------external classes (beginning of initialization)------------------
AMPA_D2 a_cx_cx[Mcx][Mcx1];
NMDA_D1 nmda_cx_cx[Mcx][Mcx1];
NMDA_D1 nmda_cx_in[Min][Min1];
AMPA_D2 a_cx_in[Min][Min1];
Gaba_A_D2 ga_in_in[Min][Min1];
Gaba_A_D2 ga_in_cx[Mcx][Mcx1];
GB *gb_in_cx[Mcx][Mcx1];
CX cx_cell[Mcx][Mcx1];
CX in_cell[Min][Min1];
Extern_ampa1 a_ext33[Mcx][Mcx1], a_ext44[Min][Min1];
double my_E_GABA[Mcx][Mcx1];
double my_E_GABA1[Mcx][Mcx1];
double p_gNals, p_gKls, p_gNald, p_gKld, p_gld, p_cldrive, p_cltau, p_extinp;
double networks_ampa[1][no_clusters+2]; //double is needed really for the first column only
//todo merge two funs below
double network_get_node_ampa(int n) { //return multiplicative ampa change if the array contains node n
if (networks_ampa[0][0]==0) return 1;
int i=0; while (networks_ampa[0][++i]!=0) {
if (networks_ampa[0][i]==n) {/*printf("C:%dL:%lf ",n,networks_gkld[0][0]);*/ return networks_ampa[0][0];}
}
return 1;
}
double networks_gkld[1][no_clusters+2]; //double is needed really for the first column only
double network_gkld_get_node_leak(int n, double p_gKld) { //return leak (in [0][0] if the array contains node n
if (networks_gkld[0][0]==0) return p_gKld;
int i=0; while (networks_gkld[0][++i]!=0) {
if (networks_gkld[0][i]==n) {/*printf("C:%dL:%lf ",n,networks_gkld[0][0]);*/ return networks_gkld[0][0];}
}
return p_gKld;
}
// ************************************************************************
int main(int argc,char **argv)
{
//---------allocate place for ALL variables and functions-----------
double y_ini[N_EQ], f_ini[N_EQ];
//---------allocate place for TWO temporal arrays using by RK.C solver
double y1[N_EQ], y2[N_EQ];
//---------general parameters----------------------------------------------
double t = 0, tmax, tmax1, ttime, TAU;
double h = 0.04, g_Extern_ampa1, R;
int i, j, i1, j1, k, ih, ii = 0, i_inp;
double scale;
double g_AMPA_CX_CX, g_NMDA_CX_CX, g_NMDA_CX_IN, g_AMPA_CX_CX_MINICE, g_AMPA_CX_IN_MINICE;
double g_AMPA_CX_IN, g_GABA_A_IN_CX, g_GABA_B_IN_CX;
double g_GABA_A_IN_IN, g_Extern_ampa;
double *tmpa;
int N_deaff = 10;
int myvar = 0;
double myvard=0.0;
ttime=0;
int no_input=0;
index_array(&index_loc_array);
log_file = fopen("logfile", "w");
//----------arrays initialization----------------------------------------------
for(i=N_EQ-1; i>=0; --i){
y_ini[i] = 0, f_ini[i] = 0;
y1[i] = 0, y2[i] = 0; }
//-------parameter initialization (from file)----------------------------------
if (argc <= 1) {
puts("Command parameters");
puts("-----------------------");
puts("Input File"); }
f_par = fopen("par", "r");
no_input=fscanf(f_par, "%lf %lf %lf %lf %lf %lf %lf %lf",
&p_gKld, &p_gNald, &p_gKls, &p_gNals, &p_gld, &p_cldrive, &p_cltau, &p_extinp);
printf("\n %d Var Parameters: p_gKls %lf, p_gNals %lf, p_gKld %lf, p_gNald %lf, p_gld %lf, p_cldrive %lf, p_cltau %lf, p_extinp %lf",
no_input, p_gKls, p_gNals, p_gKld, p_gNald, p_gld, p_cldrive, p_cltau, p_extinp);
fclose(f_par);
if (!(finput=fopen(argv[1],"r"))) {
printf("%s doesn't exist\n",argv[1]);
exit(0); }
no_input=fscanf(finput, "%lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %d",
&tmax, &g_AMPA_CX_CX, &g_NMDA_CX_CX,&g_AMPA_CX_IN, &g_NMDA_CX_IN, &g_GABA_A_IN_CX,
&g_GABA_B_IN_CX, &g_GABA_A_IN_IN,&g_Extern_ampa, &g_Extern_ampa1, &i_inp);
printf("\n %d Parameters: %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %d",
no_input, tmax, g_AMPA_CX_CX, g_NMDA_CX_CX,g_AMPA_CX_IN, g_NMDA_CX_IN, g_GABA_A_IN_CX,
g_GABA_B_IN_CX, g_GABA_A_IN_IN,g_Extern_ampa, g_Extern_ampa1, i_inp);
fclose(finput);
string clusters; //global network connectivity, local (within cluster) will be generated below
string network_gkld_file; //set of global nodes with different gKld value
string network_ampa_file; //set of global nodes with different ampa strength
double cluster_scale=1.0;
double cluster_cutoff=0.01;
add_int_param(randseed);
add_string_param(clusters);
add_double_param(cluster_scale);
add_double_param(p_gKld);
add_string_param(network_gkld_file);
add_string_param(network_ampa_file);
//assert(load_parameters(argv[1]));
assert(cmdline_parameters(argc,argv));
print_parameters();
// double **Cluster_conn_matrix;
// Cluster_conn_matrix = new double *[no_clusters];
// for (int cli=0; cli<no_clusters; cli++)
// Cluster_conn_matrix[cli]=new double[no_clusters];
if (!clusters.empty()) {
FILE *fconn;
fconn = fopen(clusters.c_str(),"r");
double conn; int rlines=0;
for (int i=0; i<no_clusters; i++)
for (int j=0;j<no_clusters; j++){
if (fscanf(fconn, "%lf", &conn)!=1)
printf("Network input error\n"),exit(1);
conn=conn*cluster_scale;
if (conn>cluster_cutoff)
Cluster_conn_matrix[i][j]=conn;
}//for j
} else {
FILE *fconn, *ftmp;
fconn = fopen("conn","r");
ftmp = fopen("rconn","w");
int cx, cy; double conn; int rlines=0;
while(1){
if (fscanf(fconn, "%d %d %lf", &cx, &cy, &conn)!=3)
break;
else{
rlines=rlines+1;
Cluster_conn_matrix[cx-1][cy-1]=conn;
fprintf(ftmp, "Connectivity %lf \n", Cluster_conn_matrix[cx-1][cy-1]);
}
}
printf ("Read %d lines from conn file ", rlines);
if (rlines==0){
printf("ERROR!!!");
exit(0);
}
fclose(ftmp);
} //cluster param empty
// Expected file format: <g_kld value> <number of N rsns nodes> <node 1 index> ... <node N index>
// Node indexing starts from 1 to stay in tune with Matlab scripts
if (!network_gkld_file.empty()) {
FILE *fconn;
fconn = fopen(network_gkld_file.c_str(),"r");
double leak;
int nnodes,node;
if (fscanf(fconn, "%lf %d", &leak, &nnodes)!=2) printf("RSNs leak input error\n"),exit(1);
networks_gkld[0][0]=leak;
for (int i=0;i<nnodes;i++) {
if (fscanf(fconn, "%d", &node)!=1) printf("RSNs leak input error\n"),exit(1);
networks_gkld[0][i+1]=node;
}
printf("\nRSNs leakage: %lf, Nodes: ",networks_gkld[0][0]);
i=1; while (networks_gkld[0][i]!=0) printf("%d ",(int)networks_gkld[0][i++]); printf("\n");
} //network_gkld_file
// Expected file format: <multiplicative ampa value> <number of N rsns nodes> <node 1 index> ... <node N index>
// Node indexing starts from 1 to stay in tune with Matlab scripts
if (!network_ampa_file.empty()) {
FILE *fconn;
fconn = fopen(network_ampa_file.c_str(),"r");
double ampa;
int nnodes,node;
if (fscanf(fconn, "%lf %d", &a, &nnodes)!=2) printf("RSNs ampa input error\n"),exit(1);
networks_ampa[0][0]=ampa;
for (int i=0;i<nnodes;i++) {
if (fscanf(fconn, "%d", &node)!=1) printf("RSNs ampa input error\n"),exit(1);
networks_ampa[0][i+1]=node;
}
printf("\nRSNs ampas: %lf, Nodes: ",networks_ampa[0][0]);
i=1; while (networks_ampa[0][i]!=0) printf("%d ",(int)networks_ampa[0][i++]); printf("\n");
} //network_ampa_file
for (i=0; i<Mcx; i++)
for (j=0; j<Mcx1; j++)
for (k=0; k<N_CX; k++){
no_cx[i][j][k] = k + (j + i*Mcx1) * N_CX;
//printf("\ni:%d j:%d k:%d no_cx:%d",i,j,k,no_cx[i][j][k]);
}
for (i=0; i<Min; i++)
for (j=0; j<Min1; j++)
for (k=0; k<N_IN; k++){
no_in[i][j][k] = Mcx*Mcx1*N_CX*I_CX + k + (j + i*Min1) * N_IN;
//printf("\ni:%d j:%d k:%d no_in:%d",i,j,k,no_in[i][j][k]);
}
//---variable initialization (additional for standart constructor)----------
for(i=Mcx-1; i>=0; --i)
if(I_CX == 1){
for(j=Mcx1-1; j>=0; --j){
spikecount[i][j]=0;
prev[i][j]=-10000;
cx_cell[i][j].init(y_ini+no_cx[i][j][0]);
tmpa=y_ini+no_cx[i][0][0];
a_cx_cx[i][j].iii(1+i*(j));
if(I_IN == 1) {
ga_in_cx[i][j].iii(1+27+i*j);
}
a_ext33[i][j].iii(randseed+i*1000);
}
}
for(j=Min1-1; j>=0; --j)
for(i=Min-1; i>=0; --i)
{
if(I_IN == 1){
spikecount_in[i][j]=0;
prev_in[i][j]=0;
in_cell[i][j].init(y_ini+no_in[i][j][0]);
double tmp=in_cell[i][0].v_SOMA;
double *tmp1=y_ini+no_in[i][0][0];
if(I_CX == 1) {
a_cx_in[i][j].iii(1+17+i*j);
}
a_ext44[i][j].iii(randseed+i*10200);
}
}
if(I_CX == 1){
for(j=Mcx1-1; j >=0; --j)
for(i=Mcx-1; i >=0; --i)
{
g_ampa_cx_cx[i][j] = 0;
g_gaba_a_in_cx[i][j] = 0;
}
g_nmda_cx_cx = 0;
}
if(I_IN == 1){
for(j=Min1-1; j >=0; --j)
for(i=Min-1; i >=0; --i)
g_ampa_cx_in[i][j] = 0;
g_gaba_a_in_in = 0;
}
//----------here we are changing some variables----------------------
srand(3000+randseed);
for(j=Min1-1; j >=0; --j)
for(i=Min-1; i >=0; --i){
in_cell[i][j].rho = 50;
in_cell[i][j].CX_DEND::G_Nap = 0.0;
in_cell[i][j].CX_SOMA::G_Nap = 0.0;
in_cell[i][j].I_Stim1 = 0;
in_cell[i][j].G_h = 0.00;
in_cell[i][j].G_kl = 0.045; // **** K leak dendrite
in_cell[i][j].G_Nal = 0.024; // **** Na leak dendrite
in_cell[i][j].g_kl = 0.045; // **** K leak soma
in_cell[i][j].g_Nal = 0.024; // **** Na leak soma
in_cell[i][j].CX_DEND::Imax = 20;
in_cell[i][j].CX_SOMA::Imax = 20;
in_cell[i][j].CX_DEND::ICl::Cl_inf = 5.0;
in_cell[i][j].CX_DEND::ICl::Cl_inf1 = 5.0;
in_cell[i][j].CX_DEND::ICl::Tau_inf = 0.5;
in_cell[i][j].CX_DEND::ICl::Cl_drive = 50;
in_cell[i][j].CX_DEND::ICl::Cl_Tauinf = 20000;
in_cell[i][j].CX_SOMA::Na_sc = 500;
in_cell[i][j].CX_SOMA::K_sc = 500;
in_cell[i][j].CX_DEND::G_l = 0.010;
in_cell[i][j].CX_SOMA::g_l = 0.0;
in_cell[i][j].CX_SOMA::G_Na = 3200;
in_cell[i][j].CX_SOMA::G_Kv = 200.0;
in_cell[i][j].CX_DEND::G_Na = 1.0;
in_cell[i][j].CX_SOMA::G_KNa = 0.0;
in_cell[i][j].CX_DEND::G_Nap = 0.0;
in_cell[i][j].CX_SOMA::G_Nap = 0.0;
in_cell[i][j].ICa::D = 0.0;
in_cell[i][j].G_h = 0.1;
in_cell[i][j].G_KCa = 0.0;
in_cell[i][j].G_HVA = 0.0;
in_cell[i][j].CX_DEND::G_Km = 0.0;
}
for(j=Mcx1-1; j >=0; --j)
for(i=Mcx-1; i >=0; --i){
double r = (double)rand() / RAND_MAX;
g_AMPA_CX_CX_MINICE = 0;
g_AMPA_CX_IN_MINICE = 0;
int Ni=i/Mcx_cluster_size; // i/50
Ni++; //matlab indexing of ROIs
double p_gKld2 = network_gkld_get_node_leak(Ni, p_gKld); // p_gKld if does not exists
cx_cell[i][j].G_kl = p_gKld2;
cx_cell[i][j].G_Nal = p_gNald;
cx_cell[i][j].g_kl = p_gKls;
cx_cell[i][j].g_Nal = p_gNals;
cx_cell[i][j].CX_DEND::G_l = p_gld;
cx_cell[i][j].CX_SOMA::g_l = 0.0;
cx_cell[i][j].CX_DEND::Imax =20;
cx_cell[i][j].CX_SOMA::Imax = 20;
cx_cell[i][j].G_h = 0.1;
cx_cell[i][j].G_KCa = 2.5;
cx_cell[i][j].G_HVA = 0.013;
cx_cell[i][j].CX_SOMA::G_KNa = 1.5;
cx_cell[i][j].CX_SOMA::G_Kv = 200.0;
cx_cell[i][j].CX_DEND::G_Na = 1.1;
cx_cell[i][j].CX_SOMA::G_Na = 3500;
cx_cell[i][j].CX_DEND::G_Nap = 3.5;
cx_cell[i][j].CX_SOMA::G_Nap = 3.5;
cx_cell[i][j].CX_DEND::G_Km = 0.01;
cx_cell[i][j].ICa::Taur = 300;
cx_cell[i][j].ICa::D = 0.85;
cx_cell[i][j].rho = 165;
cx_cell[i][j].I_Stim1 = 0;
cx_cell[i][j].CX_SOMA::Na_sc = 500;
cx_cell[i][j].CX_SOMA::K_sc = 500;
cx_cell[i][j].CX_DEND::ICl::Cl_inf = 5.0;
cx_cell[i][j].CX_DEND::ICl::Cl_inf1 = 5.0;
cx_cell[i][j].CX_DEND::ICl::Tau_inf = 0.08;
cx_cell[i][j].CX_DEND::ICl::Cl_drive = p_cldrive;
cx_cell[i][j].CX_DEND::ICl::Cl_Tauinf = p_cltau;
}
// --------------------------------
f_cx = fopen("time_cx_new", "w");
f_cx_syn = fopen("time_cx_syn", "w");
f_cx_syn_inh = fopen("time_cx_syn_inh", "w");
f_in = fopen("time_in_new", "w");
f_py_rates = fopen("py_rates", "w");
f_in_rates = fopen("in_rates", "w");
g_py_py = fopen("E_py_py","w");
g_py_in = fopen("py_in","w");
g_in_py = fopen("in_py","w");
myconnect = fopen("connectivity","w");
f1000 = fopen("time_K", "w");
fsp = fopen("spikes", "w");
///----------Connection matrix-------------------------------
printf("\n Begin to set up connection matrix...");
for(j=Mcx1-1; j>=0; --j)
for(i=Mcx-1; i>=0; --i){
k_CXCX[i][j]=0;
for(j1=Mcx1-1; j1>=0; --j1)
for(i1=Mcx-1; i1>=0; --i1){
C_CXCX[i][j][i1][j1]=0;
Cluster_strength_CXCX[i][j][i1][j1]=0;
}
}
for(i=Min-1; i>=0; --i)
for(j=Min1-1; j>=0; --j){
k_ININ[i][j]=0;
for(j1=Min1-1; j1>=0; --j1)
for(i1=Min-1; i1>=0; --i1) C_ININ[i][j][i1][j1]=0;
}
for(i1=Min-1; i1>=0; --i1)
for(j1=Min1-1; j1>=0; --j1){
k_CXIN[i1][j1]=0;
for(j=Mcx1-1; j>=0; --j)
for(i=Mcx-1; i>=0; --i) {
C_CXIN[i][j][i1][j1]=0;
Cluster_strength_CXIN[i][j][i1][j1]=0;
}
}
for(i1=Mcx-1; i1>=0; --i1)
for(j1=Mcx1-1; j1>=0; --j1){
k_INCX[i1][j1]=0;
for(j=Min1-1; j>=0; --j)
for(i=Min-1; i>=0; --i)
C_INCX[i][j][i1][j1]=0;
}
// ****************** Code for cluster ****************
//to ensure correct radius computation we need to calculate with double
double Min_=Min, Min1_=Min1, Mcx_=Mcx, Mcx1_=Mcx1;
// Clusters in 1D
for(int cli=0; cli<no_clusters; cli++) {
printf("Cluster: %d ", cli);
for(i1=cli*Mcx_cluster_size; i1<(cli+1)*Mcx_cluster_size; i1++){
for(j1=0; j1<Mcx1; j1++){
for(i=cli*Mcx_cluster_size; i<(cli+1)*Mcx_cluster_size; i++){
for(j=0; j<Mcx1; j++){
scale = sqrt((double) ((i1-i)*(i1-i) + (j1-j)*(j1-j)));
R = 0;
if(scale <= MS_CX_CX_MAX){
if(R <= 0.2){
C_CXCX[i1][j1][i][j]=1;
k_CXCX[i][j]=k_CXCX[i][j]+1;}
}
if( (scale == 0) && (SELFINGcx == 0) ){
C_CXCX[i1][j1][i][j]=0;
k_CXCX[i][j]=k_CXCX[i][j]-1;}
C_CXCX[i1][j1][i][j] && fprintf(myconnect,"%d %d %d %d %d %d %d \n",1, cli, i1, j1, i, j, C_CXCX[i1][j1][i][j]); //CX->CX 1
}
}
}
}
for(i1=cli*Min_cluster_size; i1<(cli+1)*Min_cluster_size; i1++) //(i1=0; i1<Min; i1++)
for(j1=0; j1<Min1; j1++)
for(i=cli*Min_cluster_size; i<(cli+1)*Min_cluster_size; i++) //(i=0; i<Min; i++)
for(j=0; j<Min1; j++){
scale = sqrt((double) ((i1-i)*(i1-i) + (j1-j)*(j1-j)));
if(scale <= MS_IN_IN_MAX){
C_ININ[i1][j1][i][j]=1;
k_ININ[i][j]=k_ININ[i][j]+1;}
if( scale == 0 ){
C_ININ[i1][j1][i][j]=0;
k_ININ[i][j]=k_ININ[i][j]-1;}
C_ININ[i1][j1][i][j] && fprintf(myconnect,"%d %d %d %d %d %d %d \n",2, cli, i1, j1, i, j, C_ININ[i1][j1][i][j]); //IN->IN 2
}
for(i1=cli*Min_cluster_size; i1<(cli+1)*Min_cluster_size; i1++){ //(i1=0; i1<Min; i1++){
for(j1=0; j1<Min1; j1++){
for(i=cli*Mcx_cluster_size; i<(cli+1)*Mcx_cluster_size; i++){ //for(i=0; i<Mcx; i++){
for(j=0; j<Mcx1; j++){
scale = sqrt((double) ((i1*Mcx_/Min_-i)*(i1*Mcx_/Min_-i)
+ (j1*Mcx1_/Min1_-j)*(j1*Mcx1_/Min1_-j)));
R = 0;
if(scale <= MS_IN_CX_MAX){
if(R <= 0.2){
C_INCX[i1][j1][i][j]=1;
k_INCX[i][j]=k_INCX[i][j]+1;}
C_INCX[i1][j1][i][j] && fprintf(myconnect,"%d %d %d %d %d %d %d \n",3, cli, i1, j1, i, j, C_INCX[i1][j1][i][j]); //IN->CX 3
}
}
}
}
}
for(i1=cli*Mcx_cluster_size; i1<(cli+1)*Mcx_cluster_size; i1++){ //for(i1=0; i1<Mcx; i1++){
for(j1=0; j1<Mcx1; j1++){
for(i=cli*Min_cluster_size; i<(cli+1)*Min_cluster_size; i++) {//for(i=0; i<Min; i++){
for(j=0; j<Min1; j++){
scale = sqrt((double) ((i1*Min_/Mcx_-i)*(i1*Min_/Mcx_-i)
+ (j1*Min1_/Mcx1_-j)*(j1*Min1_/Mcx1_-j)));
R = 0;
if(scale <= MS_CX_IN_MAX){
if(R <= 0.25){
C_CXIN[i1][j1][i][j]=1;
k_CXIN[i][j]=k_CXIN[i][j]+1;}
}
C_CXIN[i1][j1][i][j] && fprintf(myconnect,"%d %d %d %d %d %d %d \n",4, cli, i1, j1, i, j, C_CXIN[i1][j1][i][j]); //CX->IN 4
}
}
}
}
}
k_CXCXmax=k_CXCX[0][0];
k_ININmax=k_ININ[0][0];
k_CXINmax=k_CXIN[0][0];
k_INCXmax=k_INCX[0][0];
for(i=0; i<Mcx; i++)
for(j=0; j<Mcx1; j++){
if(k_CXCX[i][j] > k_CXCXmax) k_CXCXmax=k_CXCX[i][j];
if(k_INCX[i][j] > k_INCXmax) k_INCXmax=k_INCX[i][j];
}
for(i=0; i<Min; i++)
for(j=0; j<Min1; j++) {
if(k_ININ[i][j] > k_ININmax) k_ININmax=k_ININ[i][j];
if(k_CXIN[i][j] > k_CXINmax) k_CXINmax=k_CXIN[i][j];
}
// ************* Cluster *************
// Connect between cluster --- Only in 1D
for(int cli=0; cli<no_clusters; cli++) {
for(i1=cli*Mcx_cluster_size; i1<(cli+1)*Mcx_cluster_size; i1++){
for(j1=0; j1<Mcx1; j1++){
for(int clio=0; clio<no_clusters; clio++) {
if (!(clio==cli)) {
for(i=clio*Mcx_cluster_size; i<(clio+1)*Mcx_cluster_size; i++){
if (Cluster_conn_matrix[cli][clio]>0.0){
for(j=0; j<Mcx1; j++){
scale = sqrt((double) ((i1-(i-(clio-cli)*Mcx_cluster_size))*(i1-(i-(clio-cli)*Mcx_cluster_size)) + (j1-j)*(j1-j)));
R = rand()/(RAND_MAX + 1.0);
if(scale <= Mcx_cluster_size){
if(R <= 0.15){
C_CXCX[i1][j1][i][j]=2; //2 is for long range conns, they don't have NMDA
Cluster_strength_CXCX[i1][j1][i][j]=Cluster_conn_matrix[cli][clio];
k_CXCX[i][j]=k_CXCX[i][j]+1;
C_CXCX[i1][j1][i][j] && fprintf(myconnect,"%d %d %d %d %d %d %lf \n",11, cli, i1, j1, i, j, Cluster_strength_CXCX[i1][j1][i][j]*Long_range_cxcx_strength); //long CX->CX 11
}
}
}
}
}
}
}
}
}
}
// Add connection between CX->IN
for(int cli=0; cli<no_clusters; cli++) {
for(i1=cli*Mcx_cluster_size; i1<(cli+1)*Mcx_cluster_size; i1++){
for(j1=0; j1<Mcx1; j1++){
for(int clio=0; clio<no_clusters; clio++) {
if (!(clio==cli)) {
for(i=clio*Min_cluster_size; i<(clio+1)*Min_cluster_size; i++){
if (Cluster_conn_matrix[cli][clio]>0.0){
for(j=0; j<Min1; j++){
scale = sqrt((double) ((i1*Min_/Mcx_-(i-(clio-cli)*Min_cluster_size))*(i1*Min_/Mcx_-(i-(clio-cli)*Min_cluster_size)) + (j1-j)*(j1-j)));
R = rand()/(RAND_MAX + 1.0);
if(scale <= MS_CX_IN_MAX){
if(R <= 0.25){
C_CXIN[i1][j1][i][j]=2;
Cluster_strength_CXIN[i1][j1][i][j]=Cluster_conn_matrix[cli][clio];
k_CXIN[i][j]=k_CXIN[i][j]+1;
C_CXIN[i1][j1][i][j] && fprintf(myconnect,"%d %d %d %d %d %d %lf \n",12, cli, i1, j1, i, j, Cluster_strength_CXIN[i1][j1][i][j]*Long_range_cxin_strength); //long CX->IN 12
}
}
}
}
}
}
}
}
}
}
fclose(myconnect);
// Figure out maximum connections after connecting clusters
for(i=0; i<Mcx; i++)
for(j=0; j<Mcx1; j++){
if(k_CXCX[i][j] > k_CXCXmax) k_CXCXmax=k_CXCX[i][j];
}
/// print connections
for(j=Mcx1-1; j>=0; --j)
for(i=Mcx-1; i>=0; --i){
// k_CXCX[i][j]=0;
for(j1=Mcx1-1; j1>=0; --j1)
for(i1=Mcx-1; i1>=0; --i1)
0 && printf("%d %d %d \n", i, j, C_CXCX[i][j][i1][j1]);
}
printf("...done");
//----------------CALCULATION----------------------------------------
printf("\nCalculation : t= %lf: tmax= %lf\n", t,tmax);
ih = (int) (1/h);
TAU = h;
double print_time=0.0;
while( t < tmax){
tmax1 = t + TAU;
ii++;
rk(N_EQ, fun, h, t, y_ini, f_ini, y1, y2);
t = tmax1;
if (t>print_time){
printf("Running simulation time: %lf msec \n", t);
print_time=t+1000;
}
//************************************************************************
// Scale conductances
if( (t>50) && (t<(50+1.5*h)) ){
printf("Scale conductance with surface area...\n");
if(I_CX == 1){
for(j = 0; j < Mcx1; ++j)
for(i = 0; i < Mcx; ++i){
g_ampa_cx_cx[i][j] = g_AMPA_CX_CX / cx_cell[0][0].S_CX_DEND;
g_gaba_a_in_cx[i][j] = g_GABA_A_IN_CX / cx_cell[0][0].S_CX_DEND;
// subnetwork AMPA selection
if (networks_ampa[0][0] != 0) {
if (j!=0) { printf("Code not ready for 2D.\n"); return 1; } //not to forget
int cluster = i/Mcx_cluster_size; // i/50
cluster++; //matlab indexing of ROIs
double ampa = network_get_node_ampa(cluster); // rets 1 by default
g_ampa_cx_cx[i][j] *= ampa;
} //subnetwork AMPA
}
g_ampa_cx_cx_MINICE = g_AMPA_CX_CX_MINICE / cx_cell[0][0].S_CX_DEND;
g_nmda_cx_cx = g_NMDA_CX_CX / cx_cell[0][0].S_CX_DEND;
g_ext_cx1 = g_Extern_ampa/cx_cell[0][0].S_CX_DEND;
}
if(I_IN == 1){
for(j = 0; j < Min1; ++j)
for(i = 0; i < Min; ++i){
g_ampa_cx_in[i][j] = g_AMPA_CX_IN / in_cell[0][0].S_CX_DEND;
g_ampa_cx_in_MINICE = g_AMPA_CX_IN_MINICE / in_cell[0][0].S_CX_DEND;
g_nmda_cx_in = g_NMDA_CX_IN / in_cell[0][0].S_CX_DEND;
g_gaba_a_in_in = g_GABA_A_IN_IN / in_cell[0][0].S_CX_DEND;
g_ext_in1 = g_Extern_ampa1/in_cell[0][0].S_CX_DEND;
}
}
printf("...done.");
}
//************************************************************************
// External input
if( (t>5) && (t<(5+1.5*h)) ){
for(i = 0; i < Min; ++i)
for(j = 0; j < Min1; ++j){
a_ext44[i][j].w = 0.12; //0.1;
}
for(i = 0; i < Mcx; ++i)
for(j = 0; j < Mcx1; ++j){
a_ext33[i][j].w = 0.11; //0.1;
}
}
/// Synaptic depression
if(t>1000) {
// SpikeCount
for(j = 0; j < Mcx1; ++j)
for(i = 0; i < Mcx; ++i){
if (cx_cell[i][j].v_SOMA > 10 && (t-prev[i][j])> 2){
fprintf(fsp,"0 %d %d %lf\n",i,j,t);
spikecount[i][j]= spikecount[i][j]+1;
if ( ((spikecount[i][j])/(Check_time/1000)) < 100 )
E[i][j] = 1 - (1 - E[i][j]*(1-0.07)) * exp(-(t-prev[i][j])/700);
prev[i][j] = t;
}
}
for(j = 0; j < Min1; ++j)
for(i = 0; i < Min; ++i){
if (in_cell[i][j].v_SOMA > 10 && (t-prev_in[i][j])> 2){
fprintf(fsp,"1 %d %d %lf\n",i,j,t);
spikecount_in[i][j]= spikecount_in[i][j]+1;
prev_in[i][j] = t;
}
}
}
if(cx_cell[Mcx/2][0].CX_DEND::Ko>6.0) {
t=tmax+10;
printf("\n Seizure !!!");
}
// Compute firing rate and export
if((t>10000) && (ii/(ih*Check_time))*(ih*Check_time) == ii) {
average_rate_py = 0;
average_rate_in = 0;
fprintf(f_in_rates,"%lf \t",t);
fprintf(f_py_rates,"%lf \t",t);
for(j = 0; j < Min1; ++j)
for(i = 0; i < Min; ++i){
fprintf(f_in_rates,"%lf \t",spikecount_in[i][j]);
average_rate_in = average_rate_in + spikecount_in[i][j];
spikecount_in[i][j]=0;
}
average_rate_in = (average_rate_in/Min)/(Check_time/1000);
fprintf(f_in_rates,"%lf \n",average_rate_in);
for(j = 0; j < Mcx1; ++j)
for(i = 0; i < Mcx; ++i){
fprintf(f_py_rates,"%lf \t",spikecount[i][j]);
average_rate_py = average_rate_py + spikecount[i][j];
spikecount[i][j]=0;
}
average_rate_py = (average_rate_py/Mcx)/(Check_time/1000);
fprintf(f_py_rates,"%lf \n",average_rate_py);
fflush(f_py_rates);
fflush(f_in_rates);
}
// Output
if((t > ttime) && ((ii/(2500))*(2500) == ii) ){
fprintf(f_cx,"%lf \t",t);
for(i = 0; i < Mcx; ++i) {
fprintf(f_cx,"%lf \t", cx_cell[i][0].v_SOMA);
fprintf(f_cx_syn,"%lf ", cx_cell[i][0].tot_syn_exc);
cx_cell[i][0].tot_syn_exc=0; //total excitatory synaptic input summed for the whole dt
fprintf(f_cx_syn_inh,"%lf ", cx_cell[i][0].tot_syn_inh);
cx_cell[i][0].tot_syn_inh=0;
}
fprintf(f_cx,"\n");
fprintf(f_cx_syn,"\n");
fprintf(f_cx_syn_inh,"\n");
for(i = 0; i < Mcx; ++i) {
fprintf(f1000,"%lf ", cx_cell[i][0].CX_DEND::Ko);
fprintf(f1000,"%lf ", cx_cell[i][0].CX_DEND::Nai);
fprintf(f1000,"%lf ", cx_cell[i][0].CX_DEND::Cli);
fprintf(f1000,"%lf ", y_ini[no_cx[0][0][1]]); //[Ca]
}
fprintf(f1000,"\n");
for(i = 0; i < Min; ++i){
fprintf(f_in,"%lf ", in_cell[i][0].v_SOMA);
fprintf(f_in,"%lf ", in_cell[i][0].CX_DEND::Ko);
fprintf(f_in,"%lf ", in_cell[i][0].CX_DEND::Nai);
}
fprintf(g_py_py,"\n");
fprintf(f_in,"\n");
fprintf(g_py_in,"\n");
}
}
//--------------------END CALCULATION-------------------------------
//-----------------close ALL files-----------------------------------
printf("\n GPY: %lf", GPY);
printf("\n GIN: %lf", GIN);
printf("\n GPYPY: %lf", GPYPY);
printf("\n GPYIN: %lf", GPYIN);
printf("\n excounter: %d", excounter);
fclose(f_cx);
fclose(f_cx_syn);
fclose(f_cx_syn_inh);
fclose(f_in);
fclose(f1000);
fclose(g_py_in);
fclose(log_file);
printf("\n");
return 0;
}
void index_loc(int index, int *type, int *x, int *y){
int i = 0;
int j = 0;
for(i = 0; i<Num_Types; i++){
index = index - (cell_sizes[i][0]*cell_sizes[i][1]);
if(index < 0){
break;
}
}
index = index + (cell_sizes[i][0]*cell_sizes[i][1]);
for(j = 0; j<cell_sizes[i][0]; j++){
index = index - cell_sizes[i][1];
if(index <0){