{load_file("nrngui.hoc") } //I assume these libraries will load from the first /nrn path {load_file("stdrun.hoc")} {load_file("stdlib.hoc")} {load_file("netparmpi.hoc")} {load_file("./externals.hoc")} {load_file("./templates/syn.tem")} {load_file("./templates/gap.tem")} {load_file("./templates/iapp.tem")} {load_file("./templates/pyrkop.tem")} {load_file("./templates/bwb.tem")} {load_file("./templates/ok.tem")} {load_file("./parameters/synapses.tem")} {load_file("./parameters/manycells.tem")} {load_file("./templates/TGbignet2.tem")} if(doextra){ //print "doing EXTRACELLULAR stuff..........." {load_file("./interpxyz.hoc")} // only interpolates sections that have extracellular {load_file("./setpointers.hoc")} // has the function grindaway() in interpxyz.hoc to set up pointers {load_file("./field.hoc")} //functions to calculate the extracellular voltage {load_file("./calcrxc_a.hoc")} //function to create the transfer resistance from each section } strdef cmd numiters=1 objref pr, pc, nil, pyrspiketau_vec, baskspiketau_vec, baskconnvector, ipspg_vec, fih_progress, hines hinest1=startsw() hinest2=startsw() gapstyle=96 //split baskets right, many tests gapstyle=97 gapstyle=0 //this is to signify running it with the newer version, with the noisesyn mods added //29 ungapped baskets, 2 rows of 10 inline gaps between pyr cells (.01 - high) 1-10 and 41-50 antennaDC=1.3 //constant current added to antenna cells //1.3 default realrunFlag=1 shortspikeFlag=1 //celsius = 34 //for some reason this line gives an error for being out of range iteration=0 {cvode.active(0)} num_trials=1 //set number of different trials for each combination of pyrspike_tau, baskspike_tau, baskconnvector, and ipspgmax. There will be a different global seed for each simulation gind_start=0 //global index at which to start, in the parameter sweep {pyrspiketau_vec = new Vector()} {baskspiketau_vec = new Vector()} {baskconnvector = new Vector()} {ipspg_vec = new Vector()} // {pyrspiketau_vec.append(0.1)} //mean time between arrival of noise events to pyramidal cells (so smaller number implies more intense noise) // {baskspiketau_vec.append(6)} //mean time between arrival of noise events to basket cells (so smaller number implies more intense noise) {baskconnvector.append(100)} //controls what percentage of possible connections from basket cells to pyramidal cells are realized {ipspg_vec.append(5.5)} //gmax for bask->pyr synapses, which goes into _f# in the filename default 5.5 objref s pc = new ParallelContext() pc.subworlds(1) func getTstop() { return Tstop } proc prinit() { //had to change name because non-pr functions couldn't address pr print "prinit funct running" {pr.setScatteredVoltages(-85, -60)} {pr.connectNetwork($1,$2)} // took this out of init() in TGbignet2.tem {pr.setSeed($3)} //set global index for Random123 // { pr.activeSynapsesZero()} //CF: This inactivates all connections. I have no idea why you would want to do this. finitialize() finitialize() } proc TG(){ //print "TG func running" pr = new TGbignet2() ////main program to build the network and generate stimuli and noise print "==============>>>>>>" print pr } func onerun() {local id, num, ipspg, pyrthr, basketthr, pyr_spike_tau, bask_spike_tau, bask_perc, temp_time, temp_tau,ii localobj pc, fo, fo1, forast,forast2 print "onerun func running" id= hoc_ac_ pc = new ParallelContext() s=new Shape() s.show(0) if(doextra) { print "Doing EXTRACELLULAR stuff..... ....." setpointers() setelec(-50,$6, $7) } print "id_world number ", pc.id_world, " id_bbs ", pc.id_bbs, " id ", id, " pc.id ", pc.id {pr.recordVoltages()} {pr.pnm.set_maxstep(0.01)} {pr.pnm.want_all_spikes()} runningTime = startsw() stdinit() bask_perc=$3 //percentage of inhibitory connections that are allowed to exist ipspg=$4 print "ipspg=",ipspg g_ind=$5 prinit(bask_perc,ipspg,g_ind) //added this extra function to allow for non-pr functions. The input is passed to connectNetwork as the connthr normmean=0 //can set this to $5 if useful in the future pyr_spike_tau=$1 pyr_nospike_tau=1 bask_spike_tau=$2 bask_nospike_tau=6 { pr.activatePyrSynapses(pyr_spike_tau,pyr_nospike_tau) } { pr.activateAntSynapses(pyr_spike_tau,pyr_nospike_tau) } { pr.activateBaskSynapses(bask_spike_tau,bask_nospike_tau) } { pr.addAntennaDC(antennaDC) } pc.post(id, pyrthr, ipspg, basketthr) forast = new File() forast2 = new File() sprint(cmd, "data/spikes_b%4.2f_p%4.2f_g%4.2f_f%d.dat", bask_spike_tau, pyr_spike_tau, ipspg,bask_perc) { forast.wopen(cmd) } sprint(cmd, "data/spikes_b%4.2f_p%4.2f_g%4.2f_f%d_SUM.dat", bask_spike_tau, pyr_spike_tau, ipspg,bask_perc) { forast2.aopen(cmd) } //advance through simulation in increments of t_seg (defined in externals.hoc); after every t_seg, write voltage data to files, and delete vectors containing this data, //so that program does not run out of memory t_curr = 0 while (t_curr < Tstop-dt){ //include the '-dt' to account for rounding error; otherwise, may get error in writeVoltages print "Time = ",t_curr if(t_curr + t_seg < Tstop) { { pr.pnm.pcontinue(t_curr+t_seg)} } else { {pr.pnm.pcontinue(Tstop)} } for i=0, pr.pnm.spikevec.size-1 { forast.printf("%-10.6lf, %d\n", pr.pnm.spikevec.x[i], pr.pnm.idvec.x[i]) forast2.printf("%-10.6lf, %d\n", pr.pnm.spikevec.x[i], pr.pnm.idvec.x[i]) //{ pr.sado() } } pr.pnm.spikevec.resize(0) pr.pnm.idvec.resize(0) pr.writeVoltages(bask_spike_tau, pyr_spike_tau, ipspg, bask_perc,t_curr) t_curr = t_curr + t_seg } {forast.close()} {forast2.close()} runningTime = startsw() - runningTime iteration=iteration+1 print "Running Time: ", runningTime, "iteration: ",iteration if (realrunFlag){ {fo=new File()} {sprint(cmd, "spikes_b%4.2f_p%5.3f_g%4.2f_f%d.dat", bask_spike_tau, pyr_spike_tau,ipspg,bask_perc)} {fo.aopen("data/spikelog.dat")} {fo.printf("%s\n",cmd)} {fo.close()} {fo=new File()} {sprint(cmd, "sum_b%4.2f_p%5.3f_g%4.2f_f%d.dat", bask_spike_tau, pyr_spike_tau,ipspg,bask_perc)} {fo.aopen("data/sumlog.dat")} {fo.printf("%s\n",cmd)} {fo.close()} pr.writeParameters(bask_spike_tau, pyr_spike_tau, gapstyle, ipspg, bask_nospike_tau, pyr_nospike_tau, antennaDC, Tstop, t_seg) //write parameters to file } {pc.gid_clear()} {pr.pnm.pc.gid_clear()} pr=nil return id } proc progress() { print t cvode.event(t+100, "progress()" ) } proc hines1() { printf("pc.id_world= %d pc.id_bbs= %d t= %g dt= %g dreal=%g treal=%g\n", pc.id_world, pc.id_bbs, t, dt, startsw()-hinest2, startsw()-hinest1) hinest2 = startsw() cvode.event(t + 10, "hines1()") } {pc.runworker()} proc series() {local i, j, k, delay, tstop, id, spkcnt, tmax, gid, num,ycor,zcor ycor=$1 zcor=$2 for i = 0, pyrspiketau_vec.size()-1 { for j = 0, baskspiketau_vec.size()-1 { for k = 0, baskconnvector.size()-1 { for l = 0, ipspg_vec.size()-1 { for m = 0, num_trials-1 { //generate a different global index for each simulation g_index = gind_start+i*baskspiketau_vec.size()*baskconnvector.size()*ipspg_vec.size()*num_trials + j*baskconnvector.size()*ipspg_vec.size()*num_trials + k*ipspg_vec.size()*num_trials + l*num_trials + m print "g_index=", g_index {pc.submit("onerun", pyrspiketau_vec.x[i], baskspiketau_vec.x[j], baskconnvector.x[k], ipspg_vec.x[l],g_index,ycor,zcor)} } } } } } while ((id= pc.working())!=0) { pc.take(id, &num) printf("num= %d", num) } } // For loops to simulate large electrodes and micro electrode arrays for(ycor=-50;ycor<55;ycor=ycor+5){ for(zcor=-50;zcor<55;zcor=zcor+5){ TG() series(ycor,zcor) //this line actually runs the simulation print "YCOR=",ycor,"ZCOR=",zcor } } /* //series(0,0) { TG() series(0,0) //this line actually runs the simulation }*/ {pc.done()} //deneme() //quit()
