onsurface (run.xml)
Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds
Total CPU time 0.02000 seconds; at 10:35:42 Thu 24 Sep 2009
Compartments | Stochastic channels / cpmts | Continuous channels / cpmts | Non Gated channels / cpmts | time/ms | timeStep | CPU Time / s |
3 | 0 / 0 | 0 / 0 | 22387 / 3 | 250.0 | 20 | 0.0100 |
3 | 0 / 0 | 0 / 0 | 22387 / 3 | 250.0 | 50 | 0.0100 |
3 | 0 / 0 | 0 / 0 | 22387 / 3 | 250.0 | 100 | 0.0 |
3 | 0 / 0 | 0 / 0 | 22387 / 3 | 250.0 | 200 | 0.0 |
3 | 0 / 0 | 0 / 0 | 22387 / 3 | 250.0 | 500 | 0.0 |
![]() |
Morphology: ballstick2





Predefined views
whole

end

midrange

start

All files
Model | Preprocessed | Outupt data | Reference data etc |
run.xml ballstick2.xml membrane.xml environment.xml recording.xml leak.xml |
ts-20.ppp ts-50.ppp ts-100.ppp ts-200.ppp ts-500.ppp |
log.txt ts-20.sum ts-50.sum ts-100.sum ts-200.sum ts-500.sum ts-20.dat ts-20.txt ts-50.dat ts-50.txt ts-100.dat ts-100.txt ts-200.dat ts-200.txt ts-500.dat ts-500.txt |
Model
Archive file of the complete model: onsurface.jarrun.xml
<PSICSRun timeStep="0.1ms" runTime="250ms" startPotential="-65mV" method="weighted_crank_nicolson" morphology="ballstick2" environment="environment" properties="membrane" access="recording" squareCaps="true"> <StructureDiscretization baseElementSize="50um"/> <RunSet vary="timeStep" values="[20, 50, 100, 200, 500]us" filepattern="ts-$"/> <info>Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds</info> <ViewConfig> <LineGraph width="500" height="400"> <XAxis min="0" max="250" label="time / ms"/> <YAxis min="-80" max="60" label="potential / mV"/> <LineSet file="ts-500.txt" color="orange" label="500"> </LineSet> <LineSet file="ts-200.txt" color="yellow" label="200"> </LineSet> <LineSet file="ts-100.txt" color="green" label="100"> </LineSet> <LineSet file="ts-50.txt" color="cyan" label="50"> </LineSet> <LineSet file="ts-20.txt" color="blue" label="20"> </LineSet> <View id="whole" xmin="-10." xmax="260." ymin="-100." ymax="100."/> <View id="end" xmin="249" xmax="250.2" ymin="101.93" ymax="101.94"/> <View id="midrange" xmin="80" xmax="90" ymin="25" ymax="30"/> <View id="start" xmin="-0.1" xmax = "2.1" ymin="-70" ymax="-10"/> </LineGraph> </ViewConfig> </PSICSRun>
ballstick2.xml
<CellMorphology id="ballstick2" squareCaps="true"> <Point id="p0" x="0" y="0" z="0" r="8"/> <Point parent="p0" id="p1" x="10" y="0" z = "0" r="8"/> <Point parent="p1" id="p2" x="130" y="0" z = "0" minor="false" r="0.5" onSurface="true"/> <Point parent="p2" id="p2a" x="140" y="30" z = "0" minor="false" r="0.5"/> <Point parent="p0" id="p3" x="0" y="0.0" z = "0" onSurface="true" minor="true" r="1.8"/> <Point parent="p3" id="p4" x="20" y="-20" z = "0" minor="false" r="1.5"/> </CellMorphology>
membrane.xml
<CellProperties id="membrane" membraneCapacitance="1.0uF_per_cm2" cytoplasmResistivity="100.0ohm_cm"> <ChannelPopulation id="population_1" channel="leak" density="25per_um2"/> </CellProperties>
environment.xml
<CellEnvironment id="environment"> <Ion id="K" name="Potassium" reversalPotential="-65mV"/> </CellEnvironment>
recording.xml
<Access id="recording"> <CurrentClamp at="p0" lineColor="red" hold="0.1nA"> </CurrentClamp> <VoltageRecorder at="p1" lineColor="blue"/> </Access>
leak.xml
<KSChannel id="leak" gSingle="0.01pS" permeantIon="K"> <OpenState id="o1"/> </KSChannel>