From 9dd7045464774957160b4c455b9b512bfcee48f8 Mon Sep 17 00:00:00 2001 From: JCGoran Date: Thu, 24 Oct 2024 13:02:16 +0200 Subject: [PATCH] Remove ELECTRODIFFUSION dir (#37) --- nmodl/ELECTRODIFFUSION/elnadif.mod | 41 ----- nmodl/ELECTRODIFFUSION/ramp.ses | 239 ----------------------------- 2 files changed, 280 deletions(-) delete mode 100755 nmodl/ELECTRODIFFUSION/elnadif.mod delete mode 100755 nmodl/ELECTRODIFFUSION/ramp.ses diff --git a/nmodl/ELECTRODIFFUSION/elnadif.mod b/nmodl/ELECTRODIFFUSION/elnadif.mod deleted file mode 100755 index 7b248e6..0000000 --- a/nmodl/ELECTRODIFFUSION/elnadif.mod +++ /dev/null @@ -1,41 +0,0 @@ -COMMENT -Longitudinal diffusion of sodium (no buffering) -(equivalent modified euler with standard method and -equivalent to diagonalized linear solver with CVODE ) -ENDCOMMENT - -NEURON { - SUFFIX nadifl - USEION na READ ina WRITE nai - RANGE D -} - -UNITS { - (mM) = (milli/liter) - (um) = (micron) - FARADAY = (faraday) (coulomb) - PI = (pi) (1) -} - -PARAMETER { - D = .6 (um2/ms) -} - -ASSIGNED { - ina (milliamp/cm2) - diam (um) -} - -STATE { - nai (mM) -} - -BREAKPOINT { - SOLVE conc METHOD sparse -} - -KINETIC conc { - COMPARTMENT PI*diam*diam/4 {nai} - ELECTRODIFFUSION D*PI*diam*diam/4 {nai 1} - ~ nai << (-ina/(FARADAY)*PI*diam*(1e4)) -} diff --git a/nmodl/ELECTRODIFFUSION/ramp.ses b/nmodl/ELECTRODIFFUSION/ramp.ses deleted file mode 100755 index b0aed42..0000000 --- a/nmodl/ELECTRODIFFUSION/ramp.ses +++ /dev/null @@ -1,239 +0,0 @@ -{load_file("nrngui.hoc")} -objectvar save_window_, rvp_ -objectvar scene_vector_[8] -objectvar ocbox_, ocbox_list_, scene_, scene_list_ -{ocbox_list_ = new List() scene_list_ = new List()} -{pwman_place(0,0,0)} - -//Begin CellBuild[0] -{ -load_file("celbild.hoc", "CellBuild") -} -{ocbox_ = new CellBuild(1)} -{object_push(ocbox_)} -{ -version(5.1) -continuous = 1 -} -{object_push(topol)} -{ -first = 0 -slist.remove_all() -sname = "dend" -objref tobj -} -{ -tobj = new CellBuildSection("dend",0, 0, tobj, 0) slist.append(tobj) - tobj.position(0,0,120,0) tobj.lx=59.1217 tobj.ly=-8.58139 tobj.i3d=0 -all_init() -} -for i=0, slist.count-1 {slist.object(i).rdses()} -{object_pop()} -{ -} -{object_push(subsets)} -{first = 0} -{consist()} -{object_pop()} -{ -} -{object_push(geom)} -{ -first = 0 -tobj = new GeoSpec(0) -tobj.value = 50 -bild.topol.slist.object(0).geo.append(tobj) -tobj = new GeoSpec(1) -tobj.value = 1 -bild.topol.slist.object(0).geo.append(tobj) -tobj = new GeoSpec(4) -tobj.value = 50 -bild.topol.slist.object(0).geo.append(tobj) -set_default() -} -{object_pop()} -{ -} -{object_push(memb)} -{first=0} -{ -tobj = new MechanismStandard("nadifl") -tobj.set("D_nadifl", 0.6, 0) -tobj = new MStanWrap(tobj, 1) -bild.subsets.snlist.object(0).ml.append(tobj) -} -{object_pop()} -{ -} -{object_push(manage)} -{ -first = 0 -classname = "Cell" -etop=1 esub=1 egeom=1 emem=1 -itop=1 isub=0 igeom=0 imem=0 -bild.topol.names_off = 0 -bild.topol.circles_off = 0 -output_index = 0 output_x = 1 -} -{object_pop()} -{ -cexport() -} -{object_pop()} -{ -save_window_=ocbox_.gtopol -save_window_.size(-200,200,-150,150) -scene_vector_[2] = save_window_ -ocbox_.gtopol = save_window_ -save_window_.save_name("ocbox_.gtopol") -} -{ -ocbox_.map("CellBuild[0]", 365, 181, 822.72, 374.4) -} -objref ocbox_ -//End CellBuild[0] - - -//Begin PointProcessGroupManager -{ -load_file("pointgrp.hoc") -} -{ -ocbox_ = new PointProcessGroupManager(0) -} -{object_push(ocbox_)} -{ -ms = new MechanismStandard("SEClamp") -ms.set("rs", 0.01, 0) -ms.set("dur1", 1, 0) -ms.set("amp1", 0, 0) -ms.set("dur2", 1999, 0) -ms.set("amp2", 100, 0) -ms.set("dur3", 1e+09, 0) -ms.set("amp3", 0, 0) -mnews("SEClamp", ms) -select(0) -execute("dend ocbox_.move(0)") -ms = new MechanismStandard("SEClamp") -ms.set("rs", 0.01, 0) -ms.set("dur1", 1, 0) -ms.set("amp1", 0, 0) -ms.set("dur2", 1999, 0) -ms.set("amp2", 0, 0) -ms.set("dur3", 1e+09, 0) -ms.set("amp3", 0, 0) -mnews("SEClamp", ms) -select(1) -execute("dend ocbox_.move(1)") -} -{object_pop() doNotify()} -{ -ocbox_ = ocbox_.v1 -ocbox_.map("PointProcessGroupManager", 398, 367, 618.24, 348.48) -} -objref ocbox_ -//End PointProcessGroupManager - -{ -save_window_ = new Graph(0) -save_window_.size(0,4000,-80,40) -scene_vector_[4] = save_window_ -{save_window_.view(0, -80, 4000, 120, 540, 24, 300.48, 200.32)} -graphList[0].append(save_window_) -save_window_.save_name("graphList[0].") -save_window_.addexpr("v(.5)", 1, 1, 0.8, 0.9, 2) -} -{ -xpanel("RunControl", 0) -v_init = 0 -xvalue("Init","v_init", 1,"stdinit()", 1, 1 ) -xbutton("Init & Run","run()") -xbutton("Stop","stoprun=1") -runStopAt = 5 -xvalue("Continue til","runStopAt", 1,"{continuerun(runStopAt) stoprun=1}", 1, 1 ) -runStopIn = 100 -xvalue("Continue for","runStopIn", 1,"{continuerun(t + runStopIn) stoprun=1}", 1, 1 ) -xbutton("Single Step","steprun()") -t = 4000 -xvalue("t","t", 2 ) -tstop = 4000 -xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 ) -dt = 137.301 -xvalue("dt","dt", 1,"setdt()", 0, 1 ) -steps_per_ms = 40 -xvalue("Points plotted/ms","steps_per_ms", 1,"setdt()", 0, 1 ) -xcheckbox("Quiet",&stdrun_quiet,"") -realtime = 9 -xvalue("Real Time","realtime", 0,"", 0, 1 ) -xpanel(29,144) -} - -//Begin VariableTimeStep -{ -ocbox_ = NumericalMethodPanel[0] -} -{object_push(ocbox_)} -{ -atol_ = 0.001 CVode[0].atol(atol_) -restore(301, 1) -} -{object_pop()} -{ -ocbox_.map("VariableTimeStep", 25, 539, 272.64, 113.28) -} -objref ocbox_ -//End VariableTimeStep - -{ -xpanel("na_ion (Globals)", 0) -nai0_na_ion = 10 -xvalue("nai0_na_ion","nai0_na_ion", 1,"", 0, 0 ) -nao0_na_ion = 140 -xvalue("nao0_na_ion","nao0_na_ion", 1,"", 0, 0 ) -xpanel(347,675) -} -{ -save_window_ = new Graph(0) -save_window_.size(0,50,0,100) -scene_vector_[5] = save_window_ -{save_window_.view(0, 0, 50, 100, 886, 26, 300.48, 200.32)} -flush_list.append(save_window_) -save_window_.save_name("flush_list.") -objectvar rvp_ -rvp_ = new RangeVarPlot("v") -dend rvp_.begin(0) -dend rvp_.end(1) -rvp_.origin(0) -save_window_.addobject(rvp_, 2, 1, 0.8, 0.9) -} -{ -save_window_ = new Graph(0) -save_window_.size(0,50,0,41) -scene_vector_[6] = save_window_ -{save_window_.view(0, 0, 50, 41, 888, 294, 300.48, 200.32)} -flush_list.append(save_window_) -save_window_.save_name("flush_list.") -objectvar rvp_ -rvp_ = new RangeVarPlot("nai") -dend rvp_.begin(0) -dend rvp_.end(1) -rvp_.origin(0) -save_window_.addobject(rvp_, 2, 1, 0.8, 0.9) -} -{ -save_window_ = new Graph(0) -save_window_.size(0,4000,0,38) -scene_vector_[7] = save_window_ -{save_window_.view(0, 0, 4000, 38, 539, 289, 300.48, 200.32)} -graphList[0].append(save_window_) -save_window_.save_name("graphList[0].") -save_window_.addvar("dend.nai(0.01)", 2, 1, 0.8, 0.9, 2) -save_window_.addvar("dend.nai(0.17)", 3, 1, 0.8, 0.9, 2) -save_window_.addvar("dend.nai(0.33)", 4, 1, 0.8, 0.9, 2) -save_window_.addvar("dend.nai(0.49)", 5, 1, 0.8, 0.9, 2) -save_window_.addvar("dend.nai(0.67)", 6, 1, 0.8, 0.9, 2) -save_window_.addvar("dend.nai(0.85)", 7, 1, 0.8, 0.9, 2) -save_window_.addvar("dend.nai(0.97)", 8, 1, 0.8, 0.9, 2) -} -objectvar scene_vector_[1] -{doNotify()}