Genesis 2 Backwards Compatibility Bridge

Index of group ./specifications/heccer/channel2-nernst1

Channel and Nernst equation integration

1. Solved nernst potential application for two channel reversal potentials

Startup command : src/ns-sli ..//tests/scripts/heccer/channel2-nernst1.g

1.1. Is the solved nernst potential applied for two channel reversal potentials ?

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 :: INTERNALNERNST 0.013363 2.4 (4e-05)							 0.147021
00010 :: 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 :: INTERNALNERNST 0.013363 2.4 (4.00915e-05)							 0.146991
00010 :: 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 :: INTERNALNERNST 0.013363 2.4 (4.58443e-05)							 0.145199
00010 :: 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 :: INTERNALNERNST 0.013363 2.4 (4.79601e-05)							 0.144596
00010 :: 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 :: INTERNALNERNST 0.013363 2.4 (4.8738e-05)							 0.144381
00010 :: 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 :: INTERNALNERNST 0.013363 2.4 (4.90237e-05)							 0.144303
00010 :: 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 :: INTERNALNERNST 0.013363 2.4 (4.91284e-05)							 0.144274
00010 :: 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 :: INTERNALNERNST 0.013363 2.4 (4.91664e-05)							 0.144264
00010 :: 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 :: INTERNALNERNST 0.013363 2.4 (4.918e-05)							 0.14426
00010 :: 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 :: INTERNALNERNST 0.013363 2.4 (4.91846e-05)							 0.144259
00010 :: 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 :: INTERNALNERNST 0.013363 2.4 (4.91859e-05)							 0.144259
00010 :: 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 :: INTERNALNERNST 0.013363 2.4 (4.9186e-05)							 0.144259
00010 :: 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

It doesn't look like this test will have output that will line up with the heccer output without some hacky work. The script detects the two nernst instances, one in each compartment and produces output from it's function. This output is not present int he heccer expected output, so filtering of output must be done on the seen output rather than the expected. Even so, some of the numerical values are a bit off, most likely due to the presence of the nernst function calculations on the reversal potential.

3. This test is currently not executed

(disabled is 'It doesn't look like this test will have output that will line up with the heccer output without some hacky work. The script detects the two nernst instances, one in each compartment and produces output from it's function. This output is not present int he heccer expected output, so filtering of output must be done on the seen output rather than the expected. Even so, some of the numerical values are a bit off, most likely due to the presence of the nernst function calculations on the reversal potential.')