Genesis 2 Backwards Compatibility Bridge

Index of group ./specifications/heccer/pool-nernst

concentration dependent nernst potential calculation

1. Concentration dependent nernst potential calculation.

Startup command : src/ns-sli ..//tests/scripts/heccer/pool1-nernst.g

1.1. Is the concentration dependent nernst potential calculated correctly ?

1. Expected output

Initiated
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.0389187
00004 :: CONCEPTGATE 1 1 (nil)							 0.0826021
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 0
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (0) (nil) (nil) (nil)							 4e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.068)
-------
Iteration 0
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (1e-06)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.0389187
00004 :: CONCEPTGATE 1 1 (nil)							 0.0826021
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 1.21291e-12
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (1.21291e-12) (nil) (nil) (nil)							 4.00915e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.068)
-------
Iteration 100
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0.000101)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.0389143
00004 :: CONCEPTGATE 1 1 (nil)							 0.0826031
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 1.2128e-12
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (1.2128e-12) (nil) (nil) (nil)							 4.58443e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.0680033)
-------
Iteration 200
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0.000201)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.0389101
00004 :: CONCEPTGATE 1 1 (nil)							 0.0826041
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 1.21271e-12
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (1.21271e-12) (nil) (nil) (nil)							 4.79601e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.0680067)
-------
Iteration 300
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0.000301)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.038906
00004 :: CONCEPTGATE 1 1 (nil)							 0.0826051
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 1.21261e-12
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (1.21261e-12) (nil) (nil) (nil)							 4.8738e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.06801)
-------
Iteration 400
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0.000401)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.0389019
00004 :: CONCEPTGATE 1 1 (nil)							 0.0826061
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 1.21252e-12
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (1.21252e-12) (nil) (nil) (nil)							 4.90237e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.0680133)
-------
Iteration 500
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0.000501)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.0388979
00004 :: CONCEPTGATE 1 1 (nil)							 0.0826071
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 1.21242e-12
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (1.21242e-12) (nil) (nil) (nil)							 4.91284e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.0680165)
-------
Iteration 600
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0.000601)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.0388939
00004 :: CONCEPTGATE 1 1 (nil)							 0.0826081
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 1.21233e-12
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (1.21233e-12) (nil) (nil) (nil)							 4.91664e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.0680198)
-------
Iteration 700
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0.000701)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.0388901
00004 :: CONCEPTGATE 1 1 (nil)							 0.082609
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 1.21225e-12
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (1.21225e-12) (nil) (nil) (nil)							 4.918e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.0680231)
-------
Iteration 800
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0.000801)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.0388863
00004 :: CONCEPTGATE 1 1 (nil)							 0.08261
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 1.21216e-12
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (1.21216e-12) (nil) (nil) (nil)							 4.91846e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.0680264)
-------
Iteration 900
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0.000901)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.0388826
00004 :: CONCEPTGATE 1 1 (nil)							 0.082611
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 1.21208e-12
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (1.21208e-12) (nil) (nil) (nil)							 4.91859e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.0680297)
-------
Final Iteration
Heccer (pcName) : (/hardcoded_neutral)
Heccer (iStatus) : (20)
Heccer (iErrorCount) : (0)
Heccer Options (iOptions) : (0)
Heccer Options (dIntervalStart) : (-0.1)
Heccer Options (dIntervalEnd) : (0.05)
Heccer Options (dConcentrationGateStart) : (4e-05)
Heccer Options (dConcentrationGateEnd) : (0.3)
Heccer Options (iIntervalEntries) : (3000)
Heccer Options (iSmallTableSize) : (149)
Heccer (dTime) : (0.001)
Heccer (dStep) : (1e-06)
Compartment (mc.iType) : (1)
Tables (iTabulatedGateCount) : (2)
Compartment operations
-----
00000 :: FINISH
00001 :: FINISH
Mechanism operations
-----
00000 :: COMPARTMENT							 -9.35826e-12 0 86876 1.00001
00001 :: INITIALIZECHANNEL 0.147021 1.75467e-09
00002 :: LOADVOLTAGETABLE
00003 :: CONCEPTGATE 0 1 (nil)							 0.038879
00004 :: CONCEPTGATE 1 1 (nil)							 0.0826119
00005 :: UPDATECOMPARTMENTCURRENT
00006 :: REGISTERCHANNELCURRENT
00007 :: FLUXPOOL							 1.212e-12
00008 :: EXPONENTIALDECAY 75790.3 4e-05 1.005
			 (1.212e-12) (nil) (nil) (nil)							 4.9186e-05
00009 :: FINISH
VM Diagonals (pdDiagonals[0]) : (1.00001)
VM Axial Resistances (pdResults[0]) : (0)
VM Axial Resistances (pdResults[1]) : (0)
VM Membrane Potentials (pdVms[0]) : (-0.0680329)

2. Comment

The expected output has the INTERNALNERNST opcode removed, which is different from the heccer stand-alone expected output.  Heccer does not detect the nernst element because it is not attached to a channel.