Parallel network simulations with NEURON (Migliore et al 2006)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:64229
The NEURON simulation environment has been extended to support parallel network simulations. The performance of three published network models with very different spike patterns exhibits superlinear speedup on Beowulf clusters.
Reference:
1 . Migliore M, Cannia C, Lytton WW, Markram H, Hines ML (2006) Parallel Network Simulations with NEURON. J Comp Neurosci 21:110-119 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Methods;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu];
/
netmod
parscalebush
AMPA.mod *
arhRT03.mod *
cadecay.mod
cadRT03.mod
cah.mod
calRT03.mod
catRT03.mod *
GABAa.mod *
GABAb.mod *
intf.mod
k2RT03.mod *
kahpRT03.mod
kaRT03.mod *
kca.mod *
kcRT03.mod
kdr.mod
kdrp.mod
kdrRT03.mod *
kmRT03.mod *
misc.mod
myfit.mod
na.mod
nafRT03.mod *
nap.mod
napRT03.mod *
NMDA.mod *
nstim.mod
stats.mod
vecst.mod
batch.hoc
bg
bg_cvode.inc
boltz_cvode.inc
geneval_cvode.inc
geom.hoc
init.hoc
netcon.inc
network.hoc
nqsnet.hoc
nspike.dat
params.hoc
parnetwork.hoc
parnqsnet.hoc
perfrun.hoc
prebatch_.hoc
run.hoc
spkplt.hoc *
x_vs_nspike.hoc
                            
: $Id: intf.mod,v 1.3 2006/02/14 13:11:29 hines Exp $

:* main COMMENT
COMMENT
artificial cell incorporating 4 input weights with different time constants and signs
typically a fast AMPA, slow NMDA, fast GABAA, slow GABAB
features:
  1. Mg dependence for NMDA activation
  2. "G-protein" cooperativity for GABAB activation
  3. depolarization blockade
  4. AHP affects both Vm and refractory period  (adaptation)
  5. decrementing excitatory and/or inhibitory activity post spk (another adaptation)
since artificial cells only do calculations when they receive events, a set of vec
  pointers are maintained to allow state var information storage when event arrives
  (see initrec() and record())
ENDCOMMENT

:* main VERBATIM block
VERBATIM
extern void* vector_arg();
extern FILE* hoc_obj_file_arg(int narg);
extern int list_vector_px(Object *ob, int i, double** px);
extern int list_vector_px2 (Object *ob, int i, double** px, void** vv);
extern Object** hoc_objgetarg();
extern int ivoc_list_count(Object*);
extern Object* ivoc_list_item(Object*, int);
static void hxe() { hoc_execerror("",0); }
static void initmodel();

extern double hoc_epsilon;
#define PI 3.141592653589793115997963468544
#define UINT_MAX	4294967295U  /* from /usr/include/limits.h */
#define nil 0
#define SOP (((id0*) _p_sop)->vp)
#define IDP (*((id0**) &(_p_sop)))
#define NSW 20  /* just store voltages */
#define WSW 0  /* unused; left over from old wrecord() for states */
#define WSZ 1000000 /* use internal vectors statt external */
#define NSV 7  /* 6 state variables (+ 1 for time) */

typedef struct VPT {
 unsigned int  id;
 unsigned int  size;
 unsigned int  p;
 double* vvo[NSV];
 void*    vv[NSV];
} vpt;

typedef struct ID0 {
 vpt*     vp;
 unsigned int  id;
 unsigned int rvb;
 unsigned int rvi;
 int rve;
 short     type;
 short     col;
 short     record;
 short     wrec;
 short     jitter;
 short     input;
 short     vinflg;
 short     invl0;
} id0;

/* globals -- range vars must be malloc'ed in the CONSTRUCTOR */
static vpt* vp; /* vp and ip are used as temporary pointers */
static id0* ip;
static char *name;
static int  errflag;      /* turn on after generating an error message */
static double *vsp, *wsp, *jsp, *invlp; /* accessed by all INTF */
static unsigned int jtpt,jitmax;
static double vii[NSV];   /* temp storage */
static unsigned int wwpt,wwsz,wwaz; /* pointer, size for shared ww
vectors */
FILE *wf1, *wf2;
void*    ww[NSW];
double* wwo[NSW];
float  wwt[WSZ]; float www[WSZ]; unsigned int wwi[WSZ]; char wws[WSZ];
ENDVERBATIM

:* NEURON, PARAMETER, ASSIGNED blocks
NEURON {
  ARTIFICIAL_CELL INTF
  RANGE VAM, VNM, VGA, VGB, AHP            :::: cell state variables
  RANGE tauAM, tauNM, tauGA, tauGB, tauahp, ahpwt :::: time constants and AHP weight
  RANGE VGBdel,tGB,VGBa,rebound,offsetGB   :::: GABAB and rebound
  RANGE RMP,VTH,Vm,Vblock,refractory       :::: Vblock for depol blockade
  RANGE taum,invl,oinvl,WINV,invlt         :::: interval bursting params
  RANGE t0,tg,twg,tGB,refrac               :::: t0,tg,tGB save times for analytic calc
  RANGE nbur,tbur,cbur                     :::: burst size, interval and statevar
  POINTER sop                              :::: Structure pointer for other range vars
  GLOBAL AMdec,NMdec,GAdec,GBdec           :::: decrement exc bzw inh activations after a spike
  GLOBAL vdt,next,WEX,mg,RES,ESIN,Bb,Psk   :::: table look up values for exp,sin,NMDA-Mg dep
  GLOBAL tauGBGP,wGBGP,GPkd,Gn             :::: GABAB G-protein dependence (cooperativity)
  GLOBAL EAM, ENM, EGA, EGB, spkht         :::: "reverse potential" distance from rest
  GLOBAL prnum,wwwid,wwht,nsw              :::: for debugging moves; width/ht for pop spikes
}

PARAMETER {
  tauAM = 10 (ms)
  tauNM = 300 (ms)
  tauGA = 10 (ms)
  tauGB = 300 (ms)
  tauGBGP = 50 (ms) : drop off for burst effect on GABAB (G-protein)
  taum =  10 (ms)
  invl =  100 (ms)
  WINV =  0
  wGBGP = 1 (ms) : augmentation of G-protein with a spike
  GPkd  = 100    : maintain between 50 and 500 since table only up to 10 spikes (with wGBGP=1)
  ahpwt = 0
  tauahp= 10 (ms)
  refrac = 5 (ms)
  wwwid = 10
  wwht = 10
  VTH = -45      : fixed spike threshold
  Vblock = -20   : level of depolarization blockade
  vdt = 0.1      : time step for saving state var
  mg = 1         : for NMDA Mg dep.
  sop=0
  AMdec=1       : default is no fall-off
  NMdec=1
  GAdec=1
  GBdec=1
  nbur=1
  tbur=2
  VGBdel=30
  rebound=0.01 : cannot be set to 0
  offsetGB=0
  RMP=-65
  EAM = 65
  ENM = 90
  EGA = -15
  EGB = -30
  spkht = 50
  prnum = -1
  nsw=0
}

ASSIGNED {
  VAM
  VNM
  VGA
  VGB
  VGBa
  AHP
  t0(ms)
  tGB(ms)
  tg(ms)
  twg(ms)
  refractory
  next
  WEX
  RES
  ESIN
  Gn
  Bb
  Psk
  cbur
  Vm
  invlt
  oinvl
}

:* CONSTRUCTOR, DESTRUCTOR, INITIAL
: create a structure to save the identity of this unit and short integer flags
CONSTRUCTOR {
  VERBATIM 
  { int lid,lty,lco;
    if (ifarg(2)) { lid=(int) *getarg(2); } else { lid= UINT_MAX; }
    if (ifarg(3)) { lty=(int) *getarg(3); } else { lty= -1; }
    if (ifarg(4)) { lco=(int) *getarg(4); } else { lco= -1; }
    _p_sop = (void*)ecalloc(1, sizeof(id0));
    ip = IDP;
    ip->id=lid; ip->type=lty; ip->col=lco; 
    ip->invl0 = ip->record = ip->jitter = ip->input = 0; /* all flags
off */
    ip->rve=-1;
  }
  ENDVERBATIM
}

DESTRUCTOR {
  VERBATIM { 
  free(IDP);
  }
  ENDVERBATIM
}

INITIAL {
  VAM = 0
  VNM = 0
  VGA = 0
  VGB = 0
  VGBa = 0
  t0 = t
  tGB = t
  tg = 0
  twg = 0
  offsetGB=0
  AHP=0
  invlt = -1
  VERBATIM
  jtpt=0;    /* ok to initialize since not altered during init */
  errflag=0;
  ENDVERBATIM
  refractory = 0 : 1 means cell is absolute refractory
  : init with vinset(0) if will turn on via a NetCon with w5=1
  if (vinflag()) { randspk() net_send(next,2) }
  if (recflag()) { recini() } : recini() resets for recording, cf recinit()
}

:* NET_RECEIVE
NET_RECEIVE (wAM,wNM,wGA,wGB,wflg) { LOCAL tmp,rflg,wrec,id,jflg,iflg,invlflg,ty
  INITIAL { wNM=wNM wGA=wGA wGB=wGB wflg=0}
  : intra-burst, generate next spike as needed
  VERBATIM
  ip = IDP;  /* grab all the flags */
  _lrflg=(double)ip->record; _ljflg=(double)ip->jitter; _liflg=(double)ip->input; 
  _linvlflg=(double)ip->invl0; _lwrec=(double)ip->wrec; _lid=(double)ip->id; 
  _lty=(double)ip->type; 
  ENDVERBATIM
  if (flag==4) { : mid-burst
    cbur=cbur-1  : count down the spikes
    if (cbur>0) { net_send(tbur,4) 
    } else { net_send(refrac-AHP/10, 3) }
    if (jflg) { tmp= t+jitter()/10 } else { tmp=t }
    net_event(tmp)
    if (rflg) { recspk(tmp) }
    if (wrec) { wrecord(t) }
    : if (wrec) { wrecordOLD(tmp,-1,0) }
  : start reading random spike times (or burst times) from vsp vector pointer
  : this is signaled externally from a netstim with wflg=1, will turn off on next stim 
  : (NB wflg used in completely different context for GABAB) 
  } else if (flag==0 && wGB==0 && wflg==1) {
    VERBATIM
    ip->input=1;
    ENDVERBATIM
    iflg=1 : two versions of the same flag
    wflg=2 : set flag to turn off next time an external event comes from here
    randspk() 
    net_send(next,2)
  } else if (flag==0 && wGB==0 && wflg==2) { : flag to stop random spikes
    VERBATIM
    ip->input=0;
    ENDVERBATIM
    iflg=0 : two versions of the same flag
    wflg=1  : flag to turn on next time
  } else {  : external input
    if (rflg) { record() }
    if (wrec) { wrecord(1e9) }
    : update all statevars
    if (VAM>hoc_epsilon)  { VAM = VAM*EXP(-(t - t0)/tauAM) } else { VAM=0 } :AMPA
    if (VNM>hoc_epsilon)  { VNM = VNM*EXP(-(t - t0)/tauNM) } else { VNM=0 } :NMDA
    if (VGA< -hoc_epsilon){ VGA = VGA*EXP(-(t - t0)/tauGA) } else { VGA=0 } :GABAA    
    VGB = esinr(t-tGB) : VGB has to update each t but calc based on triggering tGB and val VGBa
    if (AHP< -hoc_epsilon){ AHP = AHP*EXP(-(t-t0)/tauahp) } else { AHP=0 } : adaptation
    : for debugging if (VGA<EGA) { pid() printf("CC: %g %g %g %g %g\n",t,VGA,wGA,EGA,Vm) }
    Vm = VAM+VNM+VGA+VGB+AHP : membrane deviation from rest
    if (Vm>100||Vm<-60){ pid() 
      printf("WARN:t=%g Vm=%g (%g,%g,%g,%g,%g)\n",t,Vm,VAM,VNM,VGA,VGB,AHP) }
    if (flag==0) { : only add weights if an external excitation
      : AMPA Erev=0 (0-RMP==65 mV above rest)
      if (wAM>0 && VAM<EAM) { 
        tmp = wAM*(1-Vm/EAM)
        VAM = VAM + tmp
        : if (wrec) { wrecordOLD(t,0,tmp) }
      }
      : NMDA; Mg effect based on total activation in rates()
      if (wNM>0 && VNM<ENM) { rates(RMP+Vm)
        tmp = wNM*Bb*(1-Vm/ENM) 
        VNM = VNM + tmp
        : if (wrec) { wrecordOLD(t,1,tmp) }
      } 
      if (VNM>1.2*ENM) { pid() : signal if some nasty number creeps in here
        : allow it to creep over by a little which can happend with coincident spikes
        printf("**** ERR: t=%g VNM=%g wNM=%g ENM=%g Vm=%g\n",t,VNM,wNM,ENM,Vm) 
      }
      : GABAA and GABAB: note that all wts are positive
      if (wGA>0 && VGA>EGA) { 
        tmp = wGA*(1-Vm/EGA) 
        VGA = VGA - tmp
        : if (wrec) { wrecordOLD(t,2,tmp) }
      }
      if (wGB>0) { net_send(VGBdel,5) } : delayed effect
      if (invlflg) { : repetitive activity weight
        Vm = RMP+VAM+VNM+VGA+VGB+AHP
        if (invlt==-1) { : activate for first time
          if (Vm>RMP) {
            oinvl=invl
            invlt=t
            net_send(invl,1) 
          }
        } else {
          tmp=shift(Vm)
          if (tmp!=0)  {
            net_move(tmp) 
            if (id()<prnum) {
               pid() printf("**** MOVE t=%g to %g Vm=%g %g,%g\n",t,tmp,Vm,invlt,oinvl) }
          }
        }      
      }
    } else if (flag==5) { : flag==5 to set GABAB weight after a delay
      offsetGB = VGB : current position
      : wflg overloaded; 50 is tauGBGP for GB cooperativity
      : wflg will augment each time there is spike coming in through this line
      wflg=wflg*EXP(-(t-tGB)/tauGBGP)+wGBGP 
      coop(wflg)               : cooperativity -- need mult presyn spikes to activate
      : calculate separately based on VGBa and tGB
      if (VGB>EGB) { 
        tmp = wGB*(1-Vm/EGB)*Gn 
        VGB = VGB - tmp
        : if (wrec) { wrecordOLD(t,3,tmp) }
      }
      VGBa= VGB
      tGB=t : restart for VGB
    : flag==2 -- read off external vec (vsp) for next random spike time
    } else if (flag==2) { 
      if (iflg==0) { flag=-1 : turned off in meantime so don't spike below
      } else { 
        randspk() 
        net_send(next,2) 
        if (WEX<0) { 
          net_event(t)   : bypass activation calculation
          if (rflg) { recspk(t) }
          if (wrec) { wrecord(t) }
          : if (wrec) { wrecordOLD(t,-1,0) }
        } else {
          tmp = WEX*(1-Vm/EAM)
          VAM = VAM + tmp
          : if (wrec) { wrecordOLD(t,0,tmp) }
        }
      }
    } else if (flag==1) { 
      : Vm=RMP+VAM+VNM+VGA+VGB+AHP
      if (WINV<0) { 
        net_event(t)   : bypass activation calculation
        if (rflg) { recspk(t) }
        if (wrec) { wrecord(t) }
        : if (wrec) { wrecordOLD(t,-1,0) }
      } else {
        tmp = WINV*(1-Vm/EAM)
        VAM = VAM + tmp :: activate interval depolarization
        : if (wrec) { wrecordOLD(t,0,tmp) }
      }
      oinvl=invl
      invlt=t
      net_send(invl,1) 
    } else if (flag==3) { 
      refractory = 0 :end of refractory period
    }
    : 3 causes of spiking: between VTH and Vblock, random from vsp (flag 2), within burst (v.s.)
    Vm = VAM+VNM+VGA+VGB+RMP+AHP
    if (refractory==0 && (Vm>VTH && Vm<Vblock)) {
      AHP = AHP - ahpwt
      if (jflg) { tmp=t+jitter() } else { tmp=t }
      net_event(tmp)
      if (rflg) { recspk(tmp) }
      if (wrec) { wrecord(tmp) }
      : if (wrec) { wrecordOLD(tmp,-2,0) }
      VAM=VAM*AMdec VNM=VNM*NMdec
      VGA=VGA*GAdec VGB=VGB*GBdec
      if (nbur>1) { cbur=nbur-1 net_send(tbur,4) 
      } else { net_send(refrac-AHP/10, 3) } : AHP doubles as a refrac period extender
      refractory = 1
    }
    t0 = t
  }
}

:* ancillary functions
:** randspk() sets next to next val in vector, this vector is handled globally
PROCEDURE randspk () {
  VERBATIM 
  ip=IDP;  
  if (ip->rvi > ip->rve) { ip->input=0;
  } else { 
    WEX=wsp[ip->rvi];
    next=vsp[ip->rvi++]-t; /* vector contains absolute times; adjust to make
interval */
  }
  ENDVERBATIM
  : net_send(next,2) : must be called from appropriate blocks
}

:** val(t,tstart) fills global vii[] to pass values back to record() (called from record())
VERBATIM
double val (double xx, double ta) { 
  vii[1]=VAM*EXP(-(xx - ta)/tauAM);
  vii[2]=VNM*EXP(-(xx - ta)/tauNM);
  vii[3]=VGA*EXP(-(xx - ta)/tauGA);
  vii[4]=esinr(xx-tGB);
  vii[5]=AHP*EXP(-(xx - ta)/tauahp);
  vii[6]=vii[1]+vii[2]+vii[3]+vii[4]+vii[5];
}
ENDVERBATIM

:** valps(t,tstart) like val but builds voltages for pop spike
VERBATIM
double valps (double xx, double ta) { 
  vii[1]=VAM*EXP(-(xx - ta)/tauAM);
  vii[2]=VNM*EXP(-(xx - ta)/tauNM);
  vii[3]=VGA*EXP(-(xx - ta)/tauGA);
  vii[4]=esinr(xx-tGB);
  /* vii[5]=AHP*EXP(-(xx - ta)/tauahp); */
  vii[6]=vii[1]+vii[2]+vii[3]+vii[4];
}
ENDVERBATIM

:** record() stores values since last tg into appropriate vecs
PROCEDURE record () {
  VERBATIM {
  int k; double ti;
  vp = SOP;
  if (tg>=t) return;
  if (vp->p >= vp->size) { if (errflag) return; 
    printf("**** WARNING out of recording room for INTF type%d id%d at %g****\n",IDP->type,IDP->id,t);
    printf("**************** WARNING: No further WARNINGS ****************\n");
    errflag=1; return; }
  for (ti=tg;ti<=t && vp->p < vp->size;ti+=vdt,vp->p++) { 
    val(ti,tg);  
    vp->vvo[0][vp->p]=ti;
    for (k=1;k<NSV;k++) if (vp->vvo[k]!=0) { /* not nil pointer */
      vp->vvo[k][vp->p]=vii[k]+RMP;
    }
  }
  tg=t;
  }
  ENDVERBATIM
}

:** recspk() records a spike by writing a 10 into the main VM vector
PROCEDURE recspk (x) {
  VERBATIM { int k;
  vp = SOP;
  record();
  if (vp->p >= vp->size || vp->vvo[6]==0) return; 
  vp->vvo[0][vp->p-1]=_lx;
  vp->vvo[6][vp->p-1]=spkht; /* the spike */
  tg=_lx;
  }
  ENDVERBATIM
}

:** recclr() clear the vectors pointers
PROCEDURE recclr () {
  VERBATIM 
  {int k;
  if (IDP->record) {
    if (SOP!=nil) {
      vp = SOP;
      vp->size=0; vp->p=0;
      for (k=0;k<NSV;k++) { vp->vv[k]=nil; vp->vvo[k]=nil; }
    } else printf("INTF recclr ERR: nil pointer\n");
  }
  IDP->record=0;
  }
  ENDVERBATIM 
}

:** recfree() free the vpt pointer memory
PROCEDURE recfree () {
  VERBATIM
  if (SOP!=nil) {
    free(SOP);
    SOP=nil;
  } else printf("INTF recfree ERR: nil pointer\n");
  IDP->record=0;
  ENDVERBATIM
}

:** initvspks() sets up vector from which to read random spike times 
: this is a range procedure
: all cells share one vector but read from different locations
: (CHANGED from intervals and global proc in v224)
PROCEDURE initvspks () {
  VERBATIM 
  {int max, i, err=0; 
    double *iv, last;
    if (! ifarg(1)) {printf("Return initvspks(ivspks,vspks,wvspks)\n"); return 0.;}
    ip=IDP;
    i = vector_arg_px(1, &iv);
    max=vector_arg_px(2, &vsp);
    if (max!=i) {err=1; printf("initvspks ERR: vecs of different size\n");}
    if (max==0) {err=1; printf("initvspks ERR: vec not initialized\n");}
    max=vector_arg_px(3, &wsp);
    if (max!=i) {err=1; printf("initvspks ERR: 3rd vec is of different size\n");}
    ip->vinflg=1;
    for (i=0; i<max && (int)iv[i] != ip->id ; i++); /* move forward to
first */
    if (i==max) { 
      printf("initvspks WARN: %d not found in ivspks\n",ip->id); 
      ip->vinflg=0; ip->rve=-1;
      return(0.); 
    }
    ip->rvb=ip->rvi=i;
    last=vsp[i++];
    for (; i<max && (int)iv[i] == ip->id ; i++) { /* move forward to
last */
      if (vsp[i]<=last) { err=1; 
        printf("initvspks ERR: nonmonotonic for cell#%d: %g %g\n",ip->id,last,vsp[i]); }
      last=vsp[i];
    }
    ip->rve=i-1;
    if (err) { ip->rve=0; hoc_execerror("",0); }
  }
  ENDVERBATIM
}

:** initjitter() sets up vector from which to read jitter
: this is a global not a range procedure -- just call once
PROCEDURE initjitter () {
  VERBATIM 
  {int max, i, err=0;
    jtpt=0;
    if (! ifarg(1)) {printf("Return initjitter(vec)\n"); return(0.);}
    max=vector_arg_px(1, &jsp);
    if (max==0) {err=1; printf("initjitter ERR: vec not initialized\n");}
    for (i=0; i<max; i++) if (jsp[i]<=0) {err=1;
      printf("initjitter ERR: vec should be >0: %g\n",jsp[i]);}
    if (err) { jsp=nil; jitmax=0.; return(0.); }/* hoc_execerror("",0); */
    if (max != jitmax) {
      printf("WARNING: resetting jitmax_INTF to %d\n",max); jitmax=max; }
  }
  ENDVERBATIM
}

:* initinvl() sets up vector from which to read intervals
: this is a global not a range procedure -- just call once
PROCEDURE initinvl () {
  VERBATIM 
  printf("initinvl() NOT BEING USED\n"); return(0.);
  ENDVERBATIM
}

: invlflag() used internally; can't set from here; use initinvl() and range invlset()
FUNCTION invlflag () {
  VERBATIM
  ip=IDP;
  if (ip->invl0==1 && invlp==nil) { /* err */
    printf("INTF invlflag ERR: pointer not initialized\n"); hoc_execerror("",0); 
  }
  _linvlflag= (double)ip->invl0;
  ENDVERBATIM
}

:** shift() returns the appropriate shift
FUNCTION shift (vl) { 
  VERBATIM   
  double expand, tmp, min, max;
/*if (invlp==nil) {printf("INTF invlflag ERRa: pointer not initialized\n"); hoc_execerror("",0);
 */
  if ((t<(invlt-invl)+invl/2) && invlt != -1) { /* don't shift if less than halfway
through */
    _lshift=0.;  /* flag for no shift */
  } else {
    expand = -(_lvl-(-65))/20; /* expand positive if hyperpolarized */
    if (expand>1.) expand=1.; if (expand<-1.) expand=-1.;
    if (expand>0.) { /* expand interval */
      max=1.5*invl;
      tmp=oinvl+0.8*expand*(max-oinvl); /* the amount we can add to the
invl */
    } else {
      min=0.5*invl; 
      tmp=oinvl+0.8*expand*(oinvl-min); /* the amount we can reduce current
invl */
    }
    if (invlt+tmp<t+2) { /* getting too near spike time */
      _lshift=0.;
    } else {
      oinvl=tmp; /* new interval */
      _lshift=invlt+oinvl;
    }
  }
  ENDVERBATIM
}

:* recini() called from INITIAL block to set vp->p to zero and open up vectors
PROCEDURE recini () {
  VERBATIM 
  { int k;
  if (SOP==nil) { 
    printf("INTF record ERR: but pointer not initialized\n"); hoc_execerror("",0); 
  } else {
    vp = SOP;
    vp->p=0;
    /* open up the vector maximally before writing into it; will correct size in
fini */
    for (k=0;k<NSV;k++) if (vp->vvo[k]!=0) vector_resize(vp->vv[k], vp->size);
  }}
  ENDVERBATIM
}

:** fini() to finish up recording -- should be called from FinishMisc()
PROCEDURE fini () {
  VERBATIM 
  {int k;
  /* initialization for next round, this will not be set if job terminates
prematurely */
  IDP->rvi=IDP->rvb;  /* -- see vinset() */
  if (IDP->wrec) { wrecord(1e9); }
  if (IDP->record) {
    record(); /* finish up */
    for (k=0;k<NSV;k++) if (vp->vvo[k]!=0) { /* not nil pointer */
      vector_resize(vp->vv[k], vp->p);
    }
  }}
  ENDVERBATIM
}

:** chk([flag]) with flag=1 prints out info on the record structure
:                    flag=2 prints out info on the global vectors
PROCEDURE chk () {
  VERBATIM 
  {int i,lfg;
  ip=IDP;
  printf("ID:%d; typ: %d; rec:%d wrec:%d inp:%d jit:%d invl:%d\n",ip->id,ip->type,ip->record,ip->wrec,ip->input,ip->jitter,ip->invl0);
  if (ifarg(1)) lfg=(int) *getarg(1); else lfg=0;
  if (lfg==1) {
    if (SOP!=nil) {
      vp = SOP;
      printf("p %d size %d tg %g\n",vp->p,vp->size,tg);
      for (i=0;i<NSV;i++) printf("%d %x %x;",i,vp->vv[i],vp->vvo[i]);
    } else printf("Recording pointers not initialized");
  }
  if (lfg==2) { 
    printf("Global vectors for input and jitter: \n");
    if (vsp!=nil) printf("VSP: %x (%d/%d-%d)\n",vsp,ip->rvi,ip->rvb,ip->rve); else printf("no VSP\n");
    if (jsp!=nil) printf("JSP: %x (%d/%d)\n",jsp,jtpt,jitmax); else printf("no JSP\n");
  }
  if (lfg==3) { 
    if (vsp!=nil) { printf("VSP: (%d/%d-%d)\n",ip->rvi,ip->rvb,ip->rve); 
      for (i=ip->rvb;i<=ip->rve;i++) printf("%d:%g  ",i,vsp[i]);
      printf("\n");
    } else printf("no VSP\n");
  }
  if (lfg==4) {  /* was used to give invlp[],invlmax */
  }
  if (lfg==5) { 
    printf("wwpt %d wwsz %d\n WW vecs: ",wwpt,wwsz);
    printf("wwwid %g wwht %d nsw %g\n WW vecs: ",wwwid,(int)wwht,nsw);
    for (i=0;i<NSW;i++) printf("%d %x %x;",i,ww[i],wwo[i]);
  }}
  ENDVERBATIM
}

:** id() and pid() identify the cell -- printf and function return
FUNCTION pid () {
  VERBATIM 
  printf("INTF%d(%d/%d) ",IDP->id,IDP->type,IDP->col);
  _lpid = (double)IDP->id;
  ENDVERBATIM
}

FUNCTION id () {
  VERBATIM 
  _lid = (double)IDP->id;
  ENDVERBATIM
}

FUNCTION type () {
  VERBATIM 
  _ltype = (double)IDP->type;
  ENDVERBATIM
}

FUNCTION col () {
  VERBATIM 
  ip = IDP; 
  if (ifarg(1)) ip->col = (short) *getarg(1);
  _lcol = (double)ip->col;
  ENDVERBATIM
}

:** initrec(name,vec) sets up recording of name (see varnum for list) into a vector
PROCEDURE initrec () {
  VERBATIM 
  {int i; void *vv;
  name = gargstr(1);
  if (SOP==nil) { 
    IDP->record=1;
    SOP = (vpt*)ecalloc(1, sizeof(vpt));
    SOP->size=0;
  }
  if (IDP->record==0) {
    recini();
    IDP->record=1;
  }
  vp = SOP;
  i=(int)varnum();
  if (i==-1) {printf("INTF record ERR %s not recognized\n",name); hoc_execerror("",0); }
  vp->vv[i]=vector_arg(2);
  vector_arg_px(2, &(vp->vvo[i]));
  if (vp->size==0) { vp->size=(unsigned int)vector_buffer_size(vp->vv[i]);
  } else if (vp->size != (unsigned int)vector_buffer_size(vp->vv[i])) {
    printf("INTF initrec ERR vectors not all same size: %d vs %d",vp->size,vector_buffer_size(vp->vv[i]));
    hoc_execerror("", 0); 
  }} 
  ENDVERBATIM
}

:** varnum(statevar_name) returns index number associated with particular variable name
: called by initrec() using global name
FUNCTION varnum () { LOCAL i
  i=-1
  VERBATIM
  if (strcmp(name,"time")==0)      { _li=0.;
  } else if (strcmp(name,"VAM")==0) { _li=1.;
  } else if (strcmp(name,"VNM")==0) { _li=2.;
  } else if (strcmp(name,"VGA")==0) { _li=3.;
  } else if (strcmp(name,"VGB")==0) { _li=4.;
  } else if (strcmp(name,"AHP")==0) { _li=5.;
  } else if (strcmp(name,"V")==0) { _li=6.;
  } else if (strcmp(name,"VM")==0) { _li=6.; /* 2 names for V */
  }
  ENDVERBATIM
  varnum=i
}

:** vecname(INDEX) prints name when given an index
PROCEDURE vecname () {
  VERBATIM
  int i; 
  i = (int)*getarg(1);
  if (i==0)      printf("time\n");
  else if (i==1) printf("VAM\n");
  else if (i==2) printf("VNM\n");
  else if (i==3) printf("VGA\n");
  else if (i==4) printf("VGB\n");
  else if (i==5) printf("AHP\n");
  else if (i==6) printf("V\n");
  ENDVERBATIM
}

:* rebuild() -- build the vvo vectors from stored wwo information
PROCEDURE rebuild () { LOCAL s0,w0,wwaz,ii,wflg,tmp
  VERBATIM
  int ii,jj; double i0,tstop;
  ip = IDP; vp=SOP; /* grab all the flags */
  ip->record=1; ip->input=0; i0=wwo[1][0];
  initmodel(); _lwwaz=wwaz; _lii=0.;
  tstop=(ifarg(1))?(*getarg(1)):0.;
  ENDVERBATIM
  WHILE (ii<wwaz) { : no 'for' loop in NMODL
    VERBATIM
    int ii=(int)_lii;
    if (wwo[1][ii]!=i0) {
      printf("ERROR wrong id at %d %g not %g\n",ii,wwo[1][ii],i0); hoc_execerror("", 0);}
    t=wwo[0][ii]; _ls0=wwo[2][ii]; _lw0=wwo[3][ii];
    ENDVERBATIM
    record()
    : update all statevars
    if (VAM>hoc_epsilon)  { VAM = VAM*EXP(-(t - t0)/tauAM) } else { VAM=0 } :AMPA
    if (VNM>hoc_epsilon)  { VNM = VNM*EXP(-(t - t0)/tauNM) } else { VNM=0 } :NMDA
    if (VGA< -hoc_epsilon){ VGA = VGA*EXP(-(t - t0)/tauGA) } else { VGA=0 } :GABAA    
    VGB = esinr(t-tGB) : VGB has to update each t but calc based on triggering tGB and val VGBa
    if (AHP< -hoc_epsilon){ AHP = AHP*EXP(-(t-t0)/tauahp) } else { AHP=0 } : adaptation
    if (s0==0) { VAM = VAM + w0 }
    if (s0==1) { VNM = VNM + w0 }
    if (s0==2) { VGA = VGA - w0 }
    if (s0==3) { 
      offsetGB = VGB : current position
      VGB = VGB - w0
      VGBa= VGB
      tGB=t
    }
    if (s0==-2) { 
      recspk(t) 
      AHP = AHP - ahpwt
      VAM=VAM*AMdec VNM=VNM*NMdec
      VGA=VGA*GAdec VGB=VGB*GBdec
    }
    if (s0==-1) { recspk(t) }
    t0 = t
    ii = ii+1
  }
  if (tstop>0) {
    VERBATIM
    t=tstop;  /* not allowed to set t in a mod file */
    ENDVERBATIM
    record()
  }
}

:* wrec block
:** initwrecOLD(vec1,vec2,vec3,vec4) sets up recording of external events
PROCEDURE initwrecOLD () {
  VERBATIM 
  {int k;
  if (! ifarg(4)) { /* assign 2 files */
    wwsz=WSZ;
    wf1 = hoc_obj_file_arg(1);
    wf2 = hoc_obj_file_arg(2);
  } else if (! ifarg(8)) { /* assign 4 vectors */
    if (WSW!=4) { 
      printf("INTF initwrec ERR w-vecs compiled for 4 args\n");
      hoc_execerror("",0); }
    IDP->wrec=1;
    for (k=0;k<WSW;k++) {
      ww[k]=vector_arg(k+1);
      wwaz=vector_arg_px(k+1, &(wwo[k]));
    }
    if (wwsz==0) wwsz=(unsigned int)vector_buffer_size(ww[0]); 
    for (k=0;k<WSW;k++) if (wwsz!=(unsigned int)vector_buffer_size(ww[k])) {
      printf("INTF initwrec ERR w-vecs size err: %d,%d,%d",k,wwsz,vector_buffer_size(ww[k]));
    }
  } else { /* assign 8 vectors */
    if (WSW!=8) { 
      printf("INTF initwrec ERR w-vecs compiled for 8 args\n");
      hoc_execerror("",0); }
    IDP->wrec=1;
    for (k=0;k<WSW;k++) {
      ww[k]=vector_arg(k+1);
      wwaz=vector_arg_px(k+1, &(wwo[k]));
    }
    if (wwsz==0) wwsz=(unsigned int)vector_buffer_size(ww[0]); 
    for (k=0;k<WSW;k++) if (wwsz!=(unsigned int)vector_buffer_size(ww[k])) {
      printf("INTF initwrec ERR w-vecs size err: %d,%d,%d",k,wwsz,vector_buffer_size(ww[k]));
    }
  }}
  ENDVERBATIM
}

:** initwrec(name,vec) sets up recording of name (see varnum for list) into a vector
PROCEDURE initwrec () {
  VERBATIM 
  {int i, k, num, cap;  Object* ob;
    ob =   *hoc_objgetarg(1); /* list of vectors */
    num = ivoc_list_count(ob);
    if (num>NSW) { printf("INTF initwrec() WARN: can only store %d ww vecs\n",NSW); hxe();}
    nsw=(double)num;
    for (k=0;k<num;k++) {
      cap = list_vector_px2(ob, k, &wwo[k], &ww[k]);
      if (k==0) wwsz=cap; else if (wwsz!=cap) {
        printf("INTF initwrec ERR w-vecs size err: %d,%d,%d",k,wwsz,cap); hxe(); }
    }
  }
  ENDVERBATIM
}

:** wrecord()
PROCEDURE wrecordOLD (t,s0,w0) {
  VERBATIM {
  int k; double id = (double)IDP->id;
  if (wwpt >= wwsz) { 
    wwpt=0;
    fprintf(wf1,"//b8 %d INTF %g %d\n",WSZ,_lt,ftell(wf2));
    fwrite(&wwt,sizeof(float),WSZ,wf2);  /* write out the size */
    fwrite(&wwi,sizeof(int),WSZ,wf2);  /* write out the size */
    fwrite(&wws,sizeof(char),WSZ,wf2);  /* write out the size */
    fwrite(&www,sizeof(float),WSZ,wf2);  /* write out the size */
  } 
  /* wwo[0][wwpt]=_lt; wwo[1][wwpt]=id; wwo[2][wwpt]=_ls0; wwo[3][wwpt]=_lw0; wwpt++
 */
  wwt[wwpt]=(float)_lt; 
  wwi[wwpt]=(unsigned int)IDP->id; 
  wws[wwpt]=(char)_ls0; 
  www[wwpt]=(float)_lw0; 
  wwpt++;
  }
  ENDVERBATIM
}

: popspk() is paste on gaussian for a pop spk: with vdt=0.1 -20 to 20 is 4 ms
: needs to be above location where is actively accessed
PROCEDURE popspk (x) {
  TABLE Psk DEPEND wwwid,wwht FROM -40 TO 40 WITH 81
  Psk = -wwht*exp(-2.*x*x/wwwid/wwwid)
}

PROCEDURE pskshowtable () {
  VERBATIM 
  int j;
  printf("_tmin_popspk:%g -_tmin_popspk:%g\n",_tmin_popspk,-_tmin_popspk);
  for (j=0;j<=-2*(int)_tmin_popspk+1;j++) printf("%g ",_t_Psk[j]);
  printf("\n");
  ENDVERBATIM 
}

:** wrecord() records voltages onto single global vector
PROCEDURE wrecord (te) {
  VERBATIM 
  {int j,k,max,wrp; double ti;
  wrp=(int)IDP->wrec-1;
  if (_lte<1.e9) { /* a spike recording */
    max=-(int)_tmin_popspk; /* max of table max=-min */
    k=(int)floor(_lte/vdt+0.5);
    for (j= -max;j<=max && k+j>0 && k+j<wwsz;j++) {
      wwo[wrp][k+j] += _t_Psk[j+max]; /* direct copy from the Psk table */
    }
  } else if (twg>=t) { return;
  } else {
    for (ti=twg,k=(int)floor(twg/vdt+0.5);ti<=t && k<wwsz;ti+=vdt,k++) { 
      valps(ti,twg);  /* valps() for pop spike calculation */
      wwo[wrp][k]+=vii[6];
    }
    twg=ti;
  }
  }
  ENDVERBATIM
}

FUNCTION wrec () {
  VERBATIM
  ip=IDP;
  if (ifarg(1)) ip->wrec = (short) *getarg(1);
  _lwrec=(double)ip->wrec;
  ENDVERBATIM
}

FUNCTION wwszset () {
  VERBATIM
  if (ifarg(1)) wwsz = (short) *getarg(1);
  _lwwszset=(double)wwsz;
  ENDVERBATIM
}

:** wwfree()
FUNCTION wwfree () {
  VERBATIM
  int k;
  IDP->wrec=0;
  wwsz=0; wwpt=0; nsw=0.;
  for (k=0;k<NSW;k++) { ww[k]=nil; wwo[k]=nil; }
  ENDVERBATIM
}

:* jitter
:** jitter() reads out of a noise vector (call from NET_RECEIVE block)
FUNCTION jitter () {
  if (jitmax>0 && jtpt>=jitmax) {  jtpt=0
    printf("Warning, cycling through jitter vector at t=%g\n",t) }
  if (jitmax>0) {
    VERBATIM 
    _ljitter = jsp[jtpt++];
    ENDVERBATIM
  } else { jitter=0 }
}

:** initialize globals shared by all INTFs
PROCEDURE global_init () {
  popspk(0) : recreate table if any change in wid or ht
  VERBATIM
{  int j,k;
  if (nsw>0. && wwo[0]!=0) { /* do just once */
    printf("Initializing ww to record for %g (%g)\n",vdt*wwsz,vdt);
    wwpt=0;
    for (k=0;k<(int)nsw;k++) {
      vector_resize(ww[k], wwsz);
      for (j=0;j<wwsz;j++) wwo[k][j]=0.;
    }
  } else printf("global_init WARNING: wrec not initialized\n");
}
  ENDVERBATIM
}

PROCEDURE global_fini () {
  VERBATIM
  int k;
  for (k=0;k<(int)nsw;k++) vector_resize(ww[k], (int)floor(t/vdt+0.5));
  ENDVERBATIM
}

PROCEDURE global_finiOLD () {
  VERBATIM
  {int k;
  if (IDP->wrec) {
    if (wwo[0]!=0) { 
      for (k=0;k<WSW;k++) vector_resize(ww[k], wwpt);
    } else {
      fprintf(wf1,"//b8 %d INTF %g %d\n",wwpt,t,ftell(wf2));
      fwrite(&wwt,sizeof(float),wwpt,wf2);  /* write out the size */
      fwrite(&wwi,sizeof(int),wwpt,wf2);  /* write out the size */
      fwrite(&wws,sizeof(char),wwpt,wf2);  /* write out the size */
      fwrite(&www,sizeof(float),wwpt,wf2);  /* write out the size */
      printf("Closing file with wwpt=%d at location %d\n",wwpt,ftell(wf2));
      fclose(wf1); fclose(wf2);
    }
  } else {
  printf("WARNING: global_fini() called from %d:%d with no wrec pointers\n",IDP->type,IDP->id);
  }}
  ENDVERBATIM
}

:** setting and getting flags: fflag, record,input,jitter
FUNCTION fflag () { fflag=1 }
FUNCTION thresh () { thresh=VTH-RMP }

: reflag() used internally; can't set from here; use recinit()
FUNCTION recflag () { 
  VERBATIM
  _lrecflag= (double)IDP->record;
  ENDVERBATIM
}

: vinflag() used internally; can't set from here; use global initvspks() and range vinset()
FUNCTION vinflag () {
  VERBATIM
  ip=IDP;
  if (ip->vinflg==0 && vsp==nil) { /* do nothing */
  } else if (ip->vinflg==1 && ip->rve==-1) {
    printf("INTF vinflag ERR: pointer not initialized\n"); hoc_execerror("",0); 
  } else if (ip->rve >= 0) { 
    if (vsp==nil) {
      printf("INTF vinflag ERR1: pointer not initialized\n"); hoc_execerror("",0); 
    }
    ip->rvi=ip->rvb;
    ip->input=1;
  }
  _lvinflag= (double)ip->vinflg;
  ENDVERBATIM
}

: jitset([val]) set or get the jitter flag
FUNCTION jitset () {
  VERBATIM
  ip=IDP;
  if (ifarg(1)) ip->jitter = (short) *getarg(1);
  _ljitset=(double)ip->jitter;
  ENDVERBATIM
}

: invlset([val]) set or get the invl flag
FUNCTION invlset () {
  VERBATIM
  ip=IDP;
  if (ifarg(1)) ip->invl0 = (short) *getarg(1);
  _linvlset=(double)ip->invl0;
  ENDVERBATIM
}

: vinset([val]) set or get the input flag (for using shared input from a vector)
FUNCTION vinset () {
  VERBATIM
  ip=IDP;
  if (ifarg(1)) ip->vinflg = (short) *getarg(1);
  if (ip->vinflg==1) {
    ip->input=1;
    ip->rvi = ip->rvb;
  }
  _lvinset=(double)ip->vinflg;
  ENDVERBATIM
}

:* TABLES
PROCEDURE EXPo (x) {
  TABLE RES FROM -20 TO 0 WITH 5000
  RES = exp(x)
}

FUNCTION EXP (x) {
  EXPo(x)
  EXP = RES
}

FUNCTION esinr (x) {
  ESINo(PI*x/tauGB)
  if        (x<tauGB)   {    esinr= (VGBa-offsetGB)*ESIN +offsetGB
  } else if (x>2*tauGB) {    esinr= 0
  } else {                   esinr= rebound*VGBa*ESIN }
}

PROCEDURE ESINo (x) {
  TABLE ESIN FROM 0 TO 2*PI WITH 3000 : one cycle
  ESIN = sin(x)
}

PROCEDURE rates(vv) {
  TABLE Bb DEPEND mg FROM -100 TO 50 WITH 300
  : from Stevens & Jahr 1990a,b
  Bb = 1 / (1 + exp(0.062 (/mV) * -vv) * (mg / 3.57 (mM)))
}

PROCEDURE coop (x) {
  TABLE Gn DEPEND GPkd FROM 0 TO 10 WITH 100
  : from Destexhe and Sejnowski, PNAS 92:9515 1995
  Gn = (x^4)/(x^4+GPkd) : n=4; kd=100
}

Loading data, please wait...