voltage sensitive gj crash betse
Thanks for the wonderful simulation.
I tried to run betse with slight parameter modification and it crashed.
here how to replicate the issue:
betse config ./test.yaml
edit the following parameters in test.yaml
gap junction surface area: 5.0e-7
voltage sensitive gj: true
run betse sim test.yaml
the simulation run fine without any errors.
change 2. voltage sensitive gj: true
to voltage sensitive gj: false
run betse sim test.yaml
the simulation crash with the following log (attached)
Thanks for the help
[betse] Creating computational matrices for cell-cell transfers...
[betse] Creating gap junctions...
[betse] Creating core computational matrices...
[betse] Cell cluster creation complete!
[betse] This world contains 225 cells.
[betse] Each cell has an average of 5.51 nearest-neighbours.
[betse] The "basic" ion profile enables the "sodium", "potassium", "proteins", and "anion" ions.
[betse] If you have selected features using other ions, they will be ignored.
[betse] Extracellular spaces enabled: True
[betse] Cells per environmental grid square: 0.72
[betse] Electroosmotic fluid flow: False
[betse] Force-induced cell deformation: False
[betse] Osmotic pressure: False
[betse] Auxiliary molecules and properties are enabled from the
[betse] "General Networks" section of the main configuration file.
[betse] Seed completed in 7.48 seconds.
[betse] Now using seed to run initialization.
[betse] Cell cluster loaded.
[betse] Creating core computational matrices...
[betse] This world contains 225 cells.
[betse] Each cell has an average of 5.51 nearest-neighbours.
[betse] The "basic" ion profile enables the "sodium", "potassium", "proteins", and "anion" ions.
[betse] If you have selected features using other ions, they will be ignored.
[betse] Extracellular spaces enabled: True
[betse] Cells per environmental grid square: 0.72
[betse] Electroosmotic fluid flow: False
[betse] Force-induced cell deformation: False
[betse] Osmotic pressure: False
[betse] Auxiliary molecules and properties are enabled from the
[betse] "General Networks" section of the main configuration file.
[betse] Initializing tissue and boundary profiles...
[betse] Initializing general network...
[betse] Reading additional substance data...
[betse] Initializing substances/reaction network...
[betse] Writing substance growth/decay equations...
[betse] Writing passive electrodiffusion equations...
[betse] Writing reaction network matrix for cell zone...
[betse] Writing reaction network matrix for env zone...
[betse] Reading channel input data...
[betse] You are using the vgNa channel: Nav1p3
[betse] You are using the vgK channel: Kv1p5
[betse] You are using a K+ Leak channel
[betse] Your initialization is running from 0 to 5.00 s of in-world time in 500 time steps (4 sampled).
[betse] Solver: Full BETSE simulator in use.
[betse] This run should take approximately 2.890000s to compute...
[betse] /home/hananel/git_repo/betse/betse/science/sim_toolbox.py:110: RuntimeWarning: overflow encountered in exp
Keq = np.exp(-(deltaGATP_o / (p.R * T) - ((p.F * Vm) / (p.R * T))))
[betse] /home/hananel/git_repo/betse/betse/science/sim_toolbox.py:60: RuntimeWarning: overflow encountered in exp
exp_alpha = np.exp(-alpha)
[betse] /home/hananel/git_repo/betse/betse/science/sim_toolbox.py:62: RuntimeWarning: overflow encountered in expm1
deno = -np.expm1(-alpha) # calculate the denominator for the electrodiffusion equation,..
[betse] /home/hananel/git_repo/betse/betse/science/sim_toolbox.py:65: RuntimeWarning: invalid value encountered in true_divide
flux = -((Dc*alpha)/d)*((cB -cA*exp_alpha)/deno)*rho
[betse] Simulation halted prematurely due to computational instability.
[betse] Initialization saved to:
/home/hananel/git_repo/Tests/betse/b-issue/INITS
Exiting prematurely due to fatal error:
list index out of range