// $Id: setup.hoc,v 1.2 2008/10/06 16:35:44 samn Exp $
//================================================================
// INSERTED /usr/site/nrniv/local/hoc/setup.hoc
// =Id= setup.hoc,v 1.24 2006/11/08 00:51:51 billl Exp
// variables normally controlled by SIMCTRL
// load_file("setup.hoc")
load_file("stdgui.hoc")
show_panel=0
strdef simname, filename, output_file, datestr, uname, comment, section, osname
objref tmpfile,nil,graphItem,sfunc
sfunc = hoc_sf_ // from stdlib.hoc
proc chop () { sfunc.left($s1,sfunc.len($s1)-1) }
tmpfile = new File()
simname = "sim" // helpful if running multiple simulations simultaneously
runnum = 1 // updated at end of run
system("uname -m",uname) // keep track of type of machine for byte compatibility
chop(uname)
system("date +%y%b%d",datestr)
chop(datestr) // may prefer to downcase later
sprint(output_file,"data/%s.%02d",datestr,runnum) // assumes a subdir called data
if (unix_mac_pc()==1) osname = "Linux" else if (unix_mac_pc()==2) {
osname = "Mac" } else if (unix_mac_pc()==3) osname = "PC"
printStep = 0.25 // time interval for saving to vector
graph_flag=0
batch_flag=1
xwindows = 0 // can still save but not look without xwindows
// load_file("nrnoc.hoc")
// END /usr/site/nrniv/local/hoc/setup.hoc
//================================================================
//================================================================
// INSERTED /usr/site/nrniv/simctrl/hoc/nrnoc.hoc
// =Id= nrnoc.hoc,v 1.74 2007/11/20 07:51:52 billl Exp
proc nrnoc () {}
// Users should not edit nrnoc.hoc or default.hoc. Any local
// changes to these files should be made in local.hoc.
// key '*&*' is picked up by to indicate command for emacs
proc elisp () { printf("*&* %s\n",$s1) }
// if (not exists(simname)) { strdef simname, output_file, datestr, comment }
// Simctrl.hoc will automatically load stdgraph.hoc which automatically
// loads stdrun.hoc
strdef temp_string_, user_string_ // needed for simctrl
/* Global variable default values. NOTE that stdrun.hoc, stdgraph.hoc
and simctrl.hoc all contain variable definitions and thus default.hoc
should be loaded after these files */
//================================================================
// INSERTED /usr/site/nrniv/simctrl/hoc/default.hoc
// =Id= default.hoc,v 1.5 2003/07/08 16:16:52 billl Exp
/* This file contains various global defaults for hoc
** Users should not edit nrnoc.hoc or default.hoc. Any local
changes to these files should be made in local.hoc.
----------------------------------------------------------------*/
/*------------------------------------------------------------
Object defaults
------------------------------------------------------------*/
/*** Define a "nil" object ***/
objectvar nil
/*------------------------------------------------------------
String defaults
------------------------------------------------------------*/
/*** "Section" is used if errors are found in the initializiations ***/
strdef section
/*** Misc defines used by graphic routines ***/
temp_string_ = "t"
tempvar = 0
/*------------------------------------------------------------
Simulation defaults
------------------------------------------------------------*/
/* To be consistent w/the nmodl values */
FARADAY = 96520. /* Hoc default = 96484.56 */
PI = 3.14159 /* Hoc default = 3.1415927 */
/* 0=off, 1=on */
print_flag = 0 /* Write to output file */
graph_flag = 1 /* Plot output */
iv_flag = 1 /* Using Interviews plotting */
batch_flag = 0 /* Using batch_run() */
compress_flag = 0 /* Compress output file when saved */
stoprun = 0 /* 0=running, 1=stopped */
iv_loaded = 0 /* Load initial iv stuff on once */
init_seed = 830529
run_seed = 680612
t = 0 /* msec */
dt = .01 /* msec */
tstop = 100 /* msec */
printStep = 0.1 /* msec */
plotStep = 0.1 /* msec */
flushStep = 0.1 /* msec */
eventStep = 50 /* Number of nstep's before a doEvent */
secondorder = 0
celsius = 6.3 /* degC */
v_init = -70 /* (mV) */
global_ra = 200 /* (ohm-cm) specific axial resisitivity */
/*** Ion parameters ***/
ca_init = 50e-6 /* mM */
na_init = 10 /* mM */
k_init = 54.4 /* mM */
// END /usr/site/nrniv/simctrl/hoc/default.hoc
//================================================================
/* Allows arrays of strings */
objref hoc_obj_[2]
//================================================================
// INSERTED /usr/site/nrniv/simctrl/hoc/simctrl.hoc
// =Id= simctrl.hoc,v 1.14 2000/11/27 21:59:33 billl Exp
// Graphic routines for neuremacs simulation control
proc sim_panel () {
xpanel(simname)
xvarlabel(output_file)
xbutton("Init", "stdinit()")
xbutton("Init & Run", "run()")
xbutton("Stop", "stoprun=1")
xbutton("Continue till Tstop", "continueRun(tstop)")
xvalue("Continue till", "runStopAt", 1, "{continueRun(runStopAt) stoprun=1}", 1, 1)
xvalue("Continue for", "runStopIn", 1, "{continueRun(t + runStopIn) stoprun=1}", 1,1)
xbutton("Single Step", "steprun()")
xvalue("Tstop", "tstop", 1, "tstop_changed()", 0, 1)
graphmenu()
sim_menu_bar()
misc_menu_bar()
xpanel()
}
proc misc_menu_bar() {
xmenu("Miscellaneous")
xbutton("Label Graphs", "labelgrs()")
xbutton("Label With String", "labelwith()")
xbutton("Label Panel", "labelpanel()")
xbutton("Parameterized Function", "load_template(\"FunctionFitter\") makefitter()")
xmenu()
}
proc sim_menu_bar() {
xmenu("Simulation Control")
xbutton("File Vers", "elisp(\"sim-current-files\")")
xbutton("File Status...", "elisp(\"sim-rcs-status\")")
xbutton("Sim Status", "elisp(\"sim-portrait\")")
xbutton("Load Current Files", "elisp(\"sim-load-sim\")")
xbutton("Load Templates", "elisp(\"sim-load-templates\")")
xbutton("Load File...", "elisp(\"sim-load-file\")")
xbutton("Save Sim...", "elisp(\"sim-save-sim\")")
xbutton("Set File Vers...", "elisp(\"sim-set-file-ver\")")
xbutton("Read Current Vers From Index", "elisp(\"sim-read-index-file\")")
xbutton("Read Last Saved Vers", "elisp(\"sim-read-recent-versions\")")
xbutton("Output to sim buffer", "elisp(\"sim-direct-output\")")
xmenu()
}
proc labelpanel() {
xpanel(simname,1)
xvarlabel(output_file)
xpanel()
}
proc labels () {
labelwith($s1)
labelgrs()
}
proc labelgrs () { local i, j, cnt
for j=0,n_graph_lists-1 {
cnt = graphList[j].count() - 1
for i=0,cnt labelgr(graphList[j].object(i))
}
}
proc labelwith () { local i, j, cnt
temp_string_ = user_string_ // save the old one
if (numarg() == 1) { /* interactive mode */
user_string_ = $s1
} else {
string_dialog("write what?", user_string_)
}
for j=0,n_graph_lists-1 {
cnt = graphList[j].count() - 1
for i=0,cnt {
graphList[j].object(i).color(0)
graphList[j].object(i).label(0.5,0.9,temp_string_)
graphList[j].object(i).color(1)
graphList[j].object(i).label(0.5,0.9,user_string_)
}
}
}
proc labelgr () { local i
$o1.color(0) // white overwrite
for (i=0;i<10;i=i+1) { // erase every possible runnum for this date
sprint(temp_string_,"%s %d%d",datestr,i,i)
$o1.label(0.1,0.7,temp_string_) }
$o1.color(1) // back to basic black
sprint(temp_string_,"%s %02d",datestr,runnum)
$o1.label(0.1,0.7,temp_string_)
}
// END /usr/site/nrniv/simctrl/hoc/simctrl.hoc
//================================================================
proc run () {
running_ = 1
stdinit()
continueRun(tstop)
finish()
}
proc continueRun () { local rt, rtstart, ts
if (numarg()==1) ts=$1 else ts=t+1e3
realtime = 0 rt = screen_update_invl rtstart = startsw()
eventcount=0
eventslow=1
stoprun = 0
if (using_cvode_) {
if (cvode.use_local_dt || (cvode.current_method()%10) == 0) {
cvode.solve(ts)
flushPlot()
realtime = startsw() - rtstart
return
}
} else {
ts -= dt/2
}
while (t<ts && stoprun==0) {
step()
realtime = startsw() - rtstart
if (realtime >= rt) {
// if (!stdrun_quiet) fastflushPlot()
screen_update()
//really compute for at least screen_update_invl
realtime = startsw() - rtstart
rt = realtime + screen_update_invl
}
}
if (using_cvode_ && stoprun == 0) { // handle the "tstop" event
step() // so all recordings take place at tstop
}
flushPlot()
realtime = startsw() - rtstart
}
proc stdinit() {
cvode_simgraph()
realtime = 0
setdt()
init()
initPlot()
}
proc init () {
cvode_simgraph()
initMech()
initMisc1()
// Initialize state vars then calculate currents
// If user hand-set v in initMisc1() then v_init should be > 1000,
// else all compartments will be set to v_init
if (v_init < 1000) {
finitialize(v_init)
} else {
finitialize()
}
// Set ca pump and leak channel for steady state
setMemb()
initMisc2()
if (cvode_active()) cvode.re_init() else fcurrent()
frecord_init()
}
// Initialization of mechanism variables
// NOTE: if any changes are made to the NEURON block of any local mod
// file, the user must add the necessary inits to initMisc1()
proc initMech () {
forall {
if ((!ismembrane("pas")) && (!ismembrane("Passive"))) {
// Allow for either pas or Passive mod file usage
// errorMsg("passive not inserted")
}
if (ismembrane("na_ion")) {
nai = na_init
nai0_na_ion = na_init
}
if (ismembrane("k_ion")) {
ki = k_init
ki0_k_ion = k_init
}
if (ismembrane("ca_ion")) {
cai = ca_init
cai0_ca_ion = ca_init
}
}
}
//* setMemb complex -- multiple names for passive mech
//** declarations
iterator scase() { local i
for i = 1, numarg() { temp_string_ = $si iterator_statement }}
objref paslist,pasvars[3],XO
double pasvals[2],x[1]
paslist = new List()
for ii=0,2 pasvars[ii]= new String()
for scase("fastpas","pas","Pass","Passive") paslist.append(new String(temp_string_))
//** getval(),setval() -- return/set the hoc value of a string
func retval () { return getval($s1) }
func getval () {
sprint(temp_string2_,"x=%s",$s1)
execute(temp_string2_)
return x
}
proc setval () {
sprint(temp_string2_,"%s=%g",$s1,$2)
execute(temp_string2_)
}
//** findpas()
// assumes that we are starting in a live section since looks for pass mech there
qx_=0
proc findpas () {
for ii=0,paslist.count-1 {
XO=paslist.object(ii)
if (ismembrane(XO.s)) {
// print XO.s,"found"
pasvars[2].s=XO.s
sprint(pasvars[0].s,"g_%s(qx_)",XO.s)
for scase("e","erev","XXXX") { // look for the proper prefix
sprint(temp_string_,"%s_%s",temp_string_,XO.s)
if (name_declared(temp_string_)==1) break
}
if (name_declared(temp_string_)==0) { // not found
printf("SetMemb() in nrnoc.hoc: Can't find proper 'erev' prefix for %s\n",XO.s)
} else {
sprint(pasvars[1].s,"%s(qx_)",temp_string_)
}
}
}
}
proc setMemb () {
if (!secp()) return
findpas() // assume that passive name is the same in all sections
forall for (qx_,0) { // will eventually want 'for (x)' to handle all the segments
if (ismembrane(pasvars[2].s)) {
for ii=0,1 pasvals[ii]=getval(pasvars[ii].s)
setmemb2()
for ii=0,1 setval(pasvars[ii].s,pasvals[ii])
}
}
}
// secp() determine whether any sections exist
func secp () { local n
n=0
forall n+=1
if (n>0) return 1 else return 0
}
func setother () {return 0} // callback stub
proc setmemb2 () { local iSum, ii, epas, gpas
if (!secp()) return
gpas=pasvals[0] epas=pasvals[1]
// Setup steady state voltage using leak channel
iSum = 0.0
if (ismembrane("na_ion")) { iSum += ina(qx_) }
if (ismembrane("k_ion")) { iSum += ik(qx_) }
if (ismembrane("ca_ion")) { iSum += ica(qx_) }
iSum += setother()
if (iSum == 0) { // Passive cmp so set e_pas = v
epas = v
} else {
if (gpas > 0) { // Assume g set by user, calc e
epas = v + iSum/gpas
} else { // Assume e set by user, calc g
if (epas != v) {
gpas = iSum/(epas - v)
} else { gpas=0 }
}
if (gpas < 0) errorMsg("bad g", gpas)
if (epas < -100 || epas > 0) {
printf(".")
// printf("%s erev: %g %g %g\n",secname(),e_pas,ina,ik)
}
}
pasvals[0]=gpas pasvals[1]=epas
}
proc finish () {
/* Called following completion of continueRun() */
finishMisc()
if (graph_flag == 1) {
if (iv_flag == 1) {
flushPlot()
doEvents()
} else {
graphmode(-1)
plt(-1)
}
}
if (print_flag == 1) {
wopen("")
}
}
/*------------------------------------------------------------
User definable GRAPHICS and PRINTING routines
------------------------------------------------------------*/
proc outputData() {
// Default procedure - if outputData() doesn't exist in the run file
if (graph_flag == 1) {
if (iv_flag == 1) {
Plot()
rt = stopsw()
if (rt > realtime) {
realtime = rt
fastflushPlot()
doNotify()
if (realtime == 2 && eventcount > 50) {
eventslow = int(eventcount/50) + 1
}
eventcount = 0
}else{
eventcount = eventcount + 1
if ((eventcount%eventslow) == 0) {
doEvents()
}
}
} else {
graph(t)
}
}
if (print_flag == 1) {
if (t%printStep <= printStep) { printOut() }
}
}
proc printOut() {
/* Default procedure - if printOut() doesn't exist in the run file */
}
proc initGraph() {
/* Default procedure - if initGraph() doesn't exist in the run file */
graph()
}
proc initPrint() {
/* Default procedure - if initPrint() doesn't exist in the run file */
wopen(output_file)
}
/*------------------------------------------------------------
User definable BATCH RUN routines
------------------------------------------------------------*/
proc nextrun() {
// Called from finishmisc() following completion of batch in an autorun
wopen("")
runnum = runnum + 1
sprint(output_file,"data/b%s.%02d", datestr, runnum)
}
// commands for emacs
proc update_runnum() {
runnum = $1
sprint(output_file,"data/%s.%02d", datestr, runnum)
print "^&^ (progn (sim-index-revert)(setq sim-runnum ",runnum,"))" }
proc nrn_write_index() { printf("&INDEX& %s\n",$s1) }
proc nrn_update () { elisp("nrn-update") }
proc nrn_message () { printf("!&! %s\n",$s1) }
/*------------------------------------------------------------
User definable INITIALIZATION and FINISH routines
------------------------------------------------------------*/
// Default procedure - if initMisc1() doesn't exist in the run file
// Initializations performed prior to finitialize()
// This should contain point process inits and inits for any changes
// made to the NEURON block of any local mod file
proc initMisc1() { }
// Default procedure - if initMisc2() doesn't exist in the run file
// Initializations performed after finitialize()
proc initMisc2() { }
// Default procedure - if finishMisc() doesn't exist in the run file
proc finishMisc() { }
/*------------------------------------------------------------
Miscellaneous routines
------------------------------------------------------------*/
proc errorMsg() {
/* Print warning, assumes arg1 is string and arg2 if present is a
variable value */
sectionname(section)
if (numarg() == 0) {
printf("ERROR in errorMsg(): Needs at least 1 argument.\n")
} else if (numarg() == 1) {
printf("ERROR: %s in section %s.\n", $s1, section)
} else {
printf("ERROR: %s in section %s (var=%g).\n", $s1, section, $2)
}
}
proc clear() {
/* Clear non-interviews plot window */
plt(-3)
}
func mod() { local x, y
/* Mod function for non-integers */
x=$1
y=$2
return (x/y - int(x/y))
}
proc whatSection() { print secname() }
proc print_pp_location() { local x //arg1 must be a point process
x = $o1.get_loc()
sectionname(temp_string_)
printf("%s located at %s(%g)\n", $o1, temp_string_, x)
pop_section()
}
//* set method with method()
proc method () { local prc
if (numarg()==0) {
if (cvode_active() && cvode_local()) { printf("\tlocal atol=%g\n",cvode.atol)
} else if (cvode_active()) { printf("\tglobal atol=%g\n",cvode.atol)
} else if (secondorder==2) { printf("\tCrank-Nicholson dt=%g\n",dt)
} else if (secondorder==0) { printf("\timplicit dt=%g\n",dt)
} else { printf("\tMethod unrecognized\n") }
return
}
if (numarg()==2) prc = $2 else prc=0
finitialize()
if (strcmp($s1,"global")==0) {
cvode_active(1)
cvode.condition_order(2)
if (prc) cvode.atol(prc)
} else if (strcmp($s1,"local")==0) {
cvode_local(1)
cvode.condition_order(2)
if (prc) cvode.atol(prc)
} else if (strcmp($s1,"implicit")==0) {
secondorder=0
cvode_active(1)
cvode_active(0)
if (prc) dt=prc
} else if (strcmp($s1,"CN")==0) {
secondorder=2
cvode_active(1) // this turns off local
cvode_active(0)
if (prc) dt=prc
} else {
printf("Integration method %s not recognized\n",$s1)
}
}
//* Load local modifications to nrnoc.hoc and default.hoc
//================================================================
// INSERTED /usr/site/nrniv/simctrl/hoc/local.hoc
// $Header: /u/samn/mysql_neuron_test/RCS/setup.hoc,v 1.2 2008/10/06 16:35:44 samn Exp $
//
// This file contains local modifications to nrnoc.hoc and default.hoc
//
// Users should not edit nrnoc.hoc or default.hoc. Any local
// changes to these files should be made in this file.
// ------------------------------------------------------------
//* MODIFICATIONS TO NRNOC.HOC
// The procedures declared here will overwrite any duplicate
// procedures in nrnoc.hoc.
// ------------------------------------------------------------
//*MODIFICATIONS TO DEFAULT.HOC
//
// Vars added here may not be handled properly within nrnoc.hoc
//------------------------------------------------------------
//** String defaults
//** Simulation defaults
long_dt = .001 // msec
objref sfunc,tmpfile
sfunc = hoc_sf_ // needed to use is_name()
tmpfile = new File() // check for existence before opening a user's local.hoc file
proc write_comment () {
tmpfile.aopen("index")
tmpfile.printf("%s\n",$s1)
tmpfile.close()
}
func asin () { return atan($1/sqrt(1-$1*$1)) }
func acos () { return atan(sqrt(1-$1*$1)/$1) }
objref mt[2]
mt = new MechanismType(0)
proc uninsert_all () { local ii
forall for ii=0,mt.count()-1 {
mt.select(ii)
mt.selected(temp_string_)
if (strcmp(temp_string_,"morphology")==0) continue
if (strcmp(temp_string_,"capacitance")==0) continue
if (strcmp(temp_string_,"extracellular")==0) continue
if (sfunc.substr(temp_string_,"_ion")!=-1) continue
mt.remove()
// print ii,temp_string_
}
}
condor_run = 0 // define for compatability
// END /usr/site/nrniv/simctrl/hoc/local.hoc
//================================================================
if (xwindows && graph_flag) { nrnmainmenu() } // pwman_place(50,50)
print "Init complete.\n"
// END /usr/site/nrniv/simctrl/hoc/nrnoc.hoc