mosinit_RUNonly.hoc

////////////////////////////////////////////////////////////////////////////////
// COMMENTS  
// 
// in set parameters we changed bicarb -- change it back? different citation?
// 
// Not opening file correctly. Need to create directory for data?
// 

//////////////////// set the random number generator //////////////////////////
use_mcell_ran4(0)                                                                   

//////////////////// model and interface scripts //////////////////////////////
xopen("setParameters.hoc")
xopen("makeCell.hoc")
xopen("makeWindows.hoc")
xopen("writeGeometry.hoc")


strdef filename, fprefix
fprefix = "no_data"
objref runfile

// create vectors to store header information 
objref main_head, list_head, sec_head
objref soma_count, prox_count, midd_count, dist_count

soma_count = new Vector()
prox_count = new Vector()
midd_count = new Vector()
dist_count = new Vector()

//create lists to store lists of sections
objref soma_ecl, soma_KCC2_membp, soma_calc, soma_act_kin, soma_act_phos
objref prox_ecl, prox_KCC2_membp, prox_calc, prox_act_kin, prox_act_phos
objref midd_ecl, midd_KCC2_membp, midd_calc, midd_act_kin, midd_act_phos
objref dist_ecl, dist_KCC2_membp, dist_calc, dist_act_kin, dist_act_phos

//create vectors to store data for writing
objref Ecl_info, KCC2_MP_info, Ca_info, kin_info, phos_info

//create vector for storing spike timingg interval values
objref timesteps
timesteps = new Vector()

proc add_timestep(){
	timesteps.append(5) //,-15,-10,-5,-4,-3,-2,-1,0,1,2,3,4,5,10,15,25,50)
}
add_timestep()


// finalize vectors to store data values
Ecl_info 	 = new Vector()
KCC2_MP_info = new Vector()
Ca_info 	 = new Vector()
kin_info 	 = new Vector()
phos_info 	 = new Vector()


// the sampling frequency for recording (in Hz)
rsamp = 2000                // sampling frequency 
rstep = 1/(rsamp/1000)      // don't change this, it is the time per sample in milliseconds
nstep = tstop*(rsamp/1000)  // don't change this, it is the number of samples per run, used to set aside space in memory for each vector
ind_start = 0.1*nstep 		// beginning of plasticity induction interval, based on start time of 10000 ms in a 100000 ms run
ind_end = (0.4*nstep)-1		// end of plasticity induction interval, based on induction for 30s in a 100000 ms run



//-----------------------------------------------------------------------------
// init()
//-----------------------------------------------------------------------------
// the finalization procedure for the numerical integrator                        /
proc init() {                                                                       // sets everything to starting values
	finitialize(v_init)                                                               // ffinalize takes as an argument voltage of all sections you want it to finalize 

	if (cvode.active()) {  
		cvode.re_init()
	} else {
		fcurrent()
	}
	frecord_init()
	//reseed()
}


proc run_sim() {local i, j, step, num_steps
	for step = 0, timesteps.size()-1 {
		clamp_start = start_paired + timesteps.x[step]
		xopen("makeClamp.hoc")
		//data_init()
		run()
	}
}

print "          ... cell created successfully."