/usr/share/nrn/lib/hoc/stdrun.hoc is in neuron 7.5-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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cvode = new CVode()
{load_file("stdlib.hoc", "String")}
begintemplate NEURONMainMenu // avoid some namespace pollution
public filemenu, miscellaneous_add, misclist
objref rwl_, rwf_, sf_, tobj
objref ldfile, misclist
strdef tstr, rwdname
proc init() {
sf_ = new StringFunctions()
if (unix_mac_pc() == 1 || unix_mac_pc() == 4) {
rwdname = "$(HOME)/.NRNWorkingDirs"
}else{
rwdname = "$(NEURONHOME)/RecentWorkingDirs"
}
misclist = new List()
if (ropen("RCS/nrnversion,v")) {
ropen()
miscellaneous_add("Archive and Hardcopy", "prjnrn()")
}
}
proc miscellaneous_add() {
misclist.append(new String($s1))
misclist.append(new String($s2))
}
proc filemenu() {
xmenu("File")
xbutton("load session", "load(\"*.ses\", 1)")
xbutton("load hoc", "load(\"*.hoc\", 0)")
if (unix_mac_pc() != 1) {
xbutton("load dll", "load(\"*.dll\", 2)")
}
xbutton("save session", "save_ses_nrnmainmenu()")
xbutton("working dir", "change_working_dir()")
if (unix_mac_pc() != 0) {
xmenu("recent dir", "recent_working_dirs()")
}
xbutton("Print", "print_session(0)")
xbutton("Quit", "quit()")
xmenu()
}
proc load() {
if (object_id(ldfile) == 0) {
ldfile = new File()
}
ldfile.chooser("r", "Load", $s1, "Load", "Cancel", getcwd())
if (ldfile.chooser()) {
if ($2 == 2) {
nrn_load_dll(ldfile.getname)
}else{
load_file($2, ldfile.getname)
}
}
}
proc change_working_dir() {
if (object_id(ldfile) == 0) {
ldfile = new File()
}
ldfile.chooser("d", "Directory", "", "Move To", "Cancel", getcwd())
if (ldfile.chooser()) {
read_recent_working_dirs()
change_working_dir1(ldfile.dir)
}
}
func change_working_dir1() {
if(chdir($s1) != 0) {
sprint(tstr, "No such directory: %s", $s1)
continue_dialog(tstr)
return 0
}
print "Changed working directory to ", $s1
ldfile = new File()
write_recent_working_dirs()
if (!default_dll_loaded_) {
if (unix_mac_pc() == 2) {
if(nrn_load_dll("nrnmac.dll") != 0){
default_dll_loaded_ = 1
}
}
if (unix_mac_pc() == 3) {
if (nrn_load_dll("nrnmech.dll") != 0) {
default_dll_loaded_ = 1
}
}
}
return 1
}
proc change_working_dir2() {
tobj = rwl_.object($1)
rwl_.remove($1)
if (change_working_dir1(tobj.s) == 0) {
while (string_dialog("Working Directory", tobj.s)) {
if (change_working_dir1(tobj.s) == 1) {
break
}
}
}
}
proc read_recent_working_dirs() {local i
rwf_ = new File()
rwl_ = new List()
if (rwf_.ropen(rwdname)) {
while (!rwf_.eof()) {
rwf_.gets(tstr)
sf_.left(tstr, sf_.len(tstr) - 1)
tobj = new String(tstr)
rwl_.append(tobj)
}
rwf_.close()
}
}
proc write_recent_working_dirs() {local i
rwf_ = new File()
tstr = getcwd()
if (rwf_.wopen(rwdname)) {
rwf_.printf("%s\n", tstr)
for i=0, rwl_.count-1 {
if (strcmp(rwl_.object(i).s, tstr) != 0) {
rwf_.printf("%s\n", rwl_.object(i).s)
}
if (i > 10) break
}
rwf_.close()
}
}
proc recent_working_dirs() {local i
read_recent_working_dirs()
for i=0, rwl_.count-1 {
sprint(tstr, "change_working_dir2(%d)", i)
xbutton(rwl_.object(i).s, tstr)
}
}
proc save_ses_nrnmainmenu() {
if (object_id(ldfile) == 0) {
ldfile = new File()
}
ldfile.chooser("w", "Save Session", "*.ses", "Save", "Cancel", ldfile.dir)
if (ldfile.chooser()) {
ldfile.close()
sprint(tstr, "save_session(\"%s\",\"{load_file(\\\"nrngui.hoc\\\")}\")", ldfile.getname)
execute(tstr)
}
}
endtemplate NEURONMainMenu
using_cvode_ = 0 // now controlled in NumericalMethodPanel
{load_file("atoltool.hoc")}
{load_file("varmeth1.hoc")}
{load_file("movierun.hoc")}
objref tobj, tobj1, nrnmainmenu_, numericalmethodpanel, pyobj
stdrun_quiet = 0
realtime=0
{units(&realtime, "s")}
screen_update_invl = .05
{variable_domain(&screen_update_invl, .01, 1e9) units(&screen_update_invl, "s")}
tstop = 5
{variable_domain(&tstop, 0, 1e9) units(&tstop, "ms")}
stoprun = 0
steps_per_ms = 1/.025
{variable_domain(&steps_per_ms, 1e-6, 1e6)}
nstep_steprun=1
runStopAt = tstop
{variable_domain(&runStopAt, 0, 1e9) units(&runStopAt, "ms")}
runStopIn = 1
{variable_domain(&runStopIn, 0, 1e6) units(&runStopIn, "ms")}
global_ra = 35.4
{variable_domain(&global_ra, 1e-3, 1e6) units(&global_ra, "ohm-cm")}
strdef temp_string_, temp_string2_
temp_string_ = "t"
proc prjnrn() { // Project management.
save_session("start.ses")
print_session(1, "prjnrnpr")
}
/* stylized control processes for nrncontrolmenu() */
{load_file("pointbsr.hoc", "PointBrowser")}
strdef tstr
{load_file("wingroup.hoc", "WindowMenu")}
if (name_declared("mapped_nrnmainmenu_") == 0) {
mapped_nrnmainmenu_ = 0
}
proc nrnmainmenu() {
if (mapped_nrnmainmenu_ == 1) {
return
}
nrnmainmenu_ = new NEURONMainMenu()
mapped_nrnmainmenu_ = 1
xpanel("NEURON Main Menu")
nrnmainmenu_.filemenu()
buildmenu()
toolmenu()
graphmenu()
vectormenu()
windowmenu()
helpmenu()
xpanel(0,25)
if (object_id(WindowMenu[0].pwm) == 0) {
// some sessions need a PWManager which used not to
// exist until the Window menu was used
WindowMenu[0].pwm = new PWManager()
}
// also many idioms assume there is no PWManager window at this point
//so close it.
if (PWManager[0].manager < PWManager[0].count) {
PWManager[0].close(PWManager[0].manager)
}
}
proc helpmenu() {
if (nrnpython("import webbrowser")) {
xmenu("Help", 1)
xbutton("Programmer's Reference", "nrnpython(\"webbrowser.open('https://neuron.yale.edu/neuron/static/new_doc/index.html')\")")
xbutton("Tutorials", "nrnpython(\"webbrowser.open('http://neuron.yale.edu/neuron/docs')\")")
xbutton("NEURON Forum", "nrnpython(\"webbrowser.open('https://neuron.yale.edu/phpBB/')\")")
xbutton("NEURON Models on ModelDB", "nrnpython(\"webbrowser.open('http://senselab.med.yale.edu/ModelDB/ModelList.cshtml?id=1882')\")")
xmenu()
}
}
proc buildmenu() {local has_rxd
has_rxd = 0
if (nrnpython("import neuron")) {
pyobj = new PythonObject()
has_rxd = pyobj.neuron._has_scipy()
}
xmenu("Build", 1)
xbutton("single compartment", "load_file(\"single.hoc\") makesinglecompartment()")
xbutton("Cell Builder", "load_file(\"celbild.hoc\") makecellbuilder()")
xmenu("NetWork Cell")
xbutton("From Cell Builder", "load_file(\"netbild.hoc\") makenetreadycell()")
xbutton("Artificial Cell", "load_file(\"netbild.hoc\") makeartcelltype()")
xmenu()
xbutton("NetWork Builder", "load_file(\"netbild.hoc\") makenetbuilder()")
xbutton("Linear Circuit", "load_file(\"lincir.hoc\") makeCircuit()")
// xbutton("Channels", "channel_builder()")
xmenu("Channel Builder")
xbutton("Density", "load_file(\"chanbild.hoc\", \"ChannelBuild\") chanbild(1)")
xbutton("Point", "load_file(\"chanbild.hoc\", \"ChannelBuild\") chanbild(0)")
xmenu("import KSChan", "cbimportmenu()")
xmenu()
if (has_rxd) {
xbutton("RxD Builder", "nrnpython(\"import neuron.rxd.gui\") nrnpython(\"neuron.rxd.gui.RxDBuilder()\")")
}
xmenu()
}
proc cbimportmenu() {local i, j
load_file("chanbild.hoc")
tobj = new List("KSChan")
tobj1 = new List("ChannelBuild")
for i=0, tobj1.count-1 {
j = tobj.index(tobj1.object(i).ks)
if (j != -1) {
tobj.remove(j)
}
}
for i=0, tobj.count - 1 {
sprint(tstr, "chanbild(%s)", tobj.object(i))
xbutton(tobj.object(i).name, tstr)
}
if (tobj.count == 0) {
xbutton("No uncontrolled KSChan", "")
}
objref tobj, tobj1
}
running_ = 0
proc toolmenu() {
xmenu("Tools", 1)
xbutton("RunControl", "nrncontrolmenu()")
// xbutton("RunButton", "xpanel(\"Run\") xbutton(\"Init & Run\", \"run()\") xpanel()")
xbutton("RunButton", "xpanel(\"Run\") xcheckbox(\"Init & Run\", &running_,\"runbutton()\") xpanel()")
xbutton("VariableStepControl", "numericalmethodpanel.map()")
xbutton("Parallel Computing", "load_file(\"parcom.hoc\", \"ParallelComputeTool\") execute(\"ParallelComputeTool[0].map()\")")
pointprocessesmenu()
distmechmenu()
fittingmenu()
impedancemenu()
xbutton("Model View", "load_file(\"mview.hoc\", \"ModelView\") execute(\"mview()\")")
xbutton("Movie Run", "load_file(\"movierun.hoc\") movierunpanel()")
xmenu("Miscellaneous", "miscellaneousmenu()", 1)
xmenu()
}
proc vectormenu() {
xmenu("Vector", 1)
xbutton("Save to File", "load_file(\"stdlib.hoc\",\"clipboard_save\") clipboard_save()")
xbutton("Retrieve from File", "load_file(\"stdlib.hoc\",\"clipboard_retrieve\") clipboard_retrieve()")
xbutton("Gather Values", "load_file(\"gatherv.hoc\") makeGatherVec()")
xbutton("Play", "load_file(\"vplay.hoc\") makeVectorPlay()")
xbutton("Display", "load_file(\"vecwrap.hoc\") makeVecWrap()")
xbutton("Draw", "load_file(\"mkcurve.hoc\") makeMakeCurve()")
xmenu()
}
proc windowmenu() {
tobj = new WindowMenu()
sprint(tstr, "%s.make()", tobj)
xmenu("Window", tstr, 1)
objref tobj
}
proc graphmenu() {
xmenu("Graph", 1)
xbutton("Voltage axis", "newPlotV()")
xbutton("Current axis", "newPlotI()")
xbutton("State axis", "newPlotS()")
xbutton("Shape plot", "newshapeplot()")
xbutton("Vector movie", "newvectorplot()")
xbutton("Phase Plane", "newphaseplane()")
xbutton("Grapher", "load_file(\"grapher.hoc\") makegrapher(1)")
xmenu()
}
proc pointprocessesmenu() {
xmenu("Point Processes")
xmenu("Managers")
xbutton("Point Manager", "load_file(\"pointman.hoc\") makeppm()")
xbutton("Point Group", "load_file(\"pointgrp.hoc\") makeppgm()")
xbutton("Electrode", "load_file(\"electrod.hoc\") makeelectrode()")
xmenu()
xmenu("Viewers", "pointmenu()")
xmenu()
}
proc distmechmenu() {
xmenu("Distributed Mechanisms")
xmenu("Managers")
xbutton("Inserter", "load_file(\"inserter.hoc\", \"Inserter\") makeinserter()")
xbutton("Homogeneous Spec", "load_file(\"showmech.hoc\") makeshowmechanism()")
xmenu()
xmenu("Viewers", "distmechviewers()")
xbutton("celsius", "celsius_panel()")
xbutton("globalRa", "globalra_panel()")
xmenu()
}
proc distmechviewers() {
xbutton("Shape Name", "load_file(\"shapebox.hoc\", \"MenuExplore\") makeMenuExplore()")
xbutton("Name Values", "nrnallsectionmenu()")
nrnglobalmechmenu()
}
proc celsius_panel() {
xpanel("Temperature")
xpvalue("celsius", &celsius, 1)
xpanel()
}
proc globalra_panel() {
xpanel("forall Ra=global_ra")
xvalue("global Ra", "global_ra", 1, "set_ra()", 1, 1)
xpanel()
}
proc fittingmenu() {
xmenu("Fitting")
xbutton("Parameterized Function", "load_file(\"funfit.hoc\") makefitter()")
xbutton("Run Fitter", "load_file(\"runfit.hoc\") makerunfitter()")
xbutton("Multiple Run Fitter", "load_file(\"mulfit.hoc\") makemulrunfitter()")
xmenu()
}
proc impedancemenu() {
xmenu("Impedance")
xbutton("Frequency", "load_file(\"impratio.hoc\") makeImpRatio()")
xbutton("Path", "load_file(\"impedanx.hoc\") makeImpx()")
xbutton("log(A) vs x", "load_file(\"logax.hoc\") makelogax()")
xbutton("Shape", "load_file(\"attshape.hoc\") makeImpShape()")
xmenu()
}
proc miscellaneousmenu() {local i
xbutton("Import 3D", "load_file(\"import3d.hoc\") makeimport3dtool()")
xmenu("Family")
xbutton("Family", "load_file(\"family.hoc\",\"Family\") makeFamily()")
xbutton("Command", "load_file(\"stdlib.hoc\",\"ExecCommand\") newcommand()")
xmenu()
xmenu("Builders")
xbutton("Kinetic Scheme Builder", "load_file(\"kinbuild.hoc\") makekineticbuilder()")
xmenu()
for (i=0; i < nrnmainmenu_.misclist.count; i += 2) {
xbutton(nrnmainmenu_.misclist.object(i).s, nrnmainmenu_.misclist.object(i+1).s)
}
}
v_init = -65
{units(&v_init, "mV")}
numericalmethodpanel = new NumericalMethodPanel()
func cvode_active() {
if (numarg() == 1) {
numericalmethodpanel.varstep($1)
}
return cvode.active()
}
func cvode_local() {
if (numarg() == 1) {
numericalmethodpanel.localstep($1)
}
return cvode.use_local_dt()
}
proc nrncontrolmenu() {
xpanel("RunControl")
xpvalue("Init", &v_init, 1, "stdinit()", 1)
xbutton("Init & Run", "run()")
xbutton("Stop", "stoprun=1")
xvalue("Continue til", "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("t", "t", 2)
xvalue("Tstop", "tstop", 1, "tstop_changed()", 0, 1)
xpvalue("dt", &dt, 1, "setdt()")
xvalue("Points plotted/ms", "steps_per_ms", 1, "setdt()", 0, 1)
xpvalue("Scrn update invl", &screen_update_invl, 1)
// xcheckbox("Quiet", &stdrun_quiet)
xpvalue("Real Time", &realtime)
xpanel()
}
func set_v_init() {local old
old = v_init
if (numarg(1)) {
v_init = $1
}
return old
}
proc stdinit() {
cvode_simgraph()
realtime = 0
setdt()
init()
initPlot()
}
proc init() {
finitialize(v_init)
// fcurrent() // no longer necessary. finitialize now
// initializes all conductances and currents as well as states.
// Extra initialization should normally go here.
// If you change any states or parameters after an finitialize
// then you should complete the initialization with
/*
if (cvode.active()) {
cvode.re_init()
}else{
fcurrent()
}
frecord_init()
*/
}
n_graph_lists = 4
objectvar graphList[n_graph_lists], graphItem, flush_list, fast_flush_list
for i=0,n_graph_lists-1 graphList[i] = new List(1)
flush_list = new List(1)
fast_flush_list = new List(1)
proc set_ra() {/* this alleviates the backward compatibility problems */
if (numarg() == 1) {
global_ra = $1
}
forall Ra = global_ra
}
proc runbutton() {
if (running_ == 0) {
stoprun = 1
return
}
execute1("run()")
running_ = 0
stoprun = 0
}
proc run() {
running_ = 1
stdinit()
continuerun(tstop)
}
func stoppedrun() { return stoprun }
proc setdt() {local Dt, dtnew
if (using_cvode_) return
Dt = 1/steps_per_ms
nstep_steprun = int(Dt/dt)
if (nstep_steprun == 0) {
nstep_steprun = 1
}
dtnew = Dt/nstep_steprun
if (abs(dt*nstep_steprun*steps_per_ms - 1) > 1e-6) {
print "Changed dt"
dt = dtnew
}
}
eventslow=1
eventcount=0
proc continuerun() {local rt, rtstart, ts
realtime = 0 rt = screen_update_invl rtstart = startsw()
eventcount=0
eventslow=1
stoprun = 0
if (using_cvode_) {
cvode.event($1)
ts = $1
if (cvode.use_local_dt) {
cvode.solve(ts)
flushPlot()
realtime = startsw() - rtstart
return
}
}else{
ts = $1 - 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 steprun() {
step()
flushPlot()
}
proc step() {local i
if (using_cvode_) {
advance()
}else for i=1,nstep_steprun {
advance()
}
Plot()
}
proc advance() {
fadvance()
}
proc cvode_simgraph() {local i, j
cvode.simgraph_remove()
if (cvode.active && cvode.use_local_dt) {
for j=0,n_graph_lists-1 {
for i=0,graphList[j].count-1 graphList[j].object(i).simgraph()
}
}
}
proc initPlot(){local i, j, cnt
if (cvode.active && cvode.use_local_dt) {
flushPlot()
return
}
for j=0,n_graph_lists-1 {
cnt = graphList[j].count() - 1
for (i=cnt; i >= 0; i=i-1) if (graphList[j].object(i).view_count() == 0){
graphList[j].remove(i)
cnt = cnt - 1
}
for i=0,cnt graphList[j].object(i).begin()
}
cnt = flush_list.count() -1
for (i=cnt; i >= 0; i=i-1) if (flush_list.object(i).view_count() == 0){
flush_list.remove(i)
}
cnt = fast_flush_list.count() -1
for (i=cnt; i >= 0; i=i-1) if (fast_flush_list.object(i).view_count() == 0){
fast_flush_list.remove(i)
}
Plot()
flushPlot()
}
proc tstop_changed() {local i, j, cnt
for j=0,2 {
cnt = graphList[j].count() - 1
for i=0,cnt {
graphItem = graphList[j].object(i)
graphItem.size(0, tstop, graphItem.size(3), \
graphItem.size(4))
}
}
}
proc Plot() {local i, j, cnt, dt2
if (using_cvode_) {
dt2=0
}else{
dt2 = dt/2
}
cnt = graphList[0].count() - 1
for i=0,cnt graphList[0].object(i).plot(t)
cnt = graphList[1].count() - 1
for i=0,cnt graphList[1].object(i).plot(t - dt2)
cnt = graphList[2].count() - 1
for i=0,cnt graphList[2].object(i).plot(t + dt2)
cnt = graphList[3].count() - 1
for i=0,cnt graphList[3].object(i).plot(t)
}
proc screen_update() {local i
if (!stdrun_quiet) {
cnt = flush_list.count() - 1
for i=0,cnt flush_list.object(i).begin()
for i=0,cnt flush_list.object(i).flush()
cnt = fast_flush_list.count() - 1
for i=0,cnt fast_flush_list.object(i).fastflush()
fastflushPlot()
doNotify()
}
}
proc flushPlot() {local i, j, cnt
screen_update()
for j=0,n_graph_lists-1 {
cnt = graphList[j].count() - 1
for i=0,cnt graphList[j].object(i).flush()
}
cnt = flush_list.count() - 1
if (cnt >= 0) {
for i=0,cnt flush_list.object(i).flush()
}
cnt = fast_flush_list.count() - 1
if (cnt >= 0) {
for i=0,cnt fast_flush_list.object(i).flush()
}
if (!stdrun_quiet) {
doEvents()
}
}
proc fastflushPlot() {local i, j, cnt
for j=0,n_graph_lists-1 {
cnt = graphList[j].count() - 1
for i=0,cnt graphList[j].object(i).fastflush()
}
// doEvents()
}
proc newPlotV() {
newPlot(0,tstop,-80,40)
graphItem.save_name("graphList[0].")
graphList[0].append(graphItem)
graphItem.addexpr("v(.5)")
}
proc newPlotI() {
newPlot(0,tstop,-1,1)
graphItem.save_name("graphList[1].")
graphList[1].append(graphItem)
}
proc newPlotS() {
newPlot(0,tstop,0,1)
graphItem.save_name("graphList[2].")
graphList[2].append(graphItem)
}
proc newPlot() {local w, h
graphItem = new Graph()
graphItem.size($1,$2,$3,$4)
graphItem.xaxis() // view axis for x and y
/*
w = $2 - $1
h = $4 - $3
graphItem.size($1- w/10, $2+w/10, $3-h/10, $4+h/10)
*/
}
proc addplot() {
$o1.size(0,tstop,-1,1)
graphList[$2].append($o1)
}
proc newshapeplot() {
if(!execute1("v", 0)) {
continue_dialog("No accessed section: Can't start a PlotShape")
return
}
graphItem = new PlotShape()
fast_flush_list.append(graphItem)
graphItem.save_name("fast_flush_list.")
}
proc newvectorplot() {
graphItem = new Graph()
flush_list.append(graphItem)
graphItem.save_name("flush_list.")
}
proc newphaseplane() {
graphItem = new Graph()
string_dialog("x axis expression", temp_string_)
graphItem.xexpr(temp_string_)
sprint(temp_string_, "x-axis: %s", temp_string_)
graphItem.label(.5, .9, temp_string_)
graphItem.save_name("graphList[3].")
graphList[3].append(graphItem)
temp_string_ = "t"
}
proc channel_builder() {
if (name_declared("nrnccmb_Channels") == 0) {
print "Loading Robert Cannon's Catacomb channel builder. This may take a minute."
}
if (load_java("nrnccmb.Channels")) {
tobj = new List("nrnccmb_Channels")
if (tobj.count == 0) {
execute("tobj = new nrnccmb_Channels()")
}else{
tobj = tobj.object(0)
}
tobj.map()
objref tobj
}else{
continue_dialog("The Catacomb simulator (ccmb.jar) is not in the CLASSPATH.")
}
}
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