./bemi --help
This is the BEMI code for solving the EMI model with the boundary element method (BEM)
Different geometries (cells arrangements) are hardcoded in the executable. Look into src/emi_model/MultiDomain.cpp.
Run the code from the ./build folder as ./bemi OPTIONS, where OPTIONS is a combination of the below.
Results are stored in the ./results folder.
The following options are available:
--- General options:
-ofile : name of output file. Default: sol.
-refsol : name of the reference solution (if available). Default: ""
If available, errors are computed at the end of the simulation.
-ofreq : Output frequency. Default: -1
- If 0 writes solution only at the end of simulation.
In general, used to generate a reference solution.
- If >0 writes solution every ofreq time steps,
- If -1 never writes the solution.
In general, used to generate a solution and just compare it against a reference solution.
-bin : Writes solution in binary format. Default: false.
-vtk : Writes solution in vtk format. Default: false.
--- Time integration options:
-tend : Final time. Default: 1.
-dt : Time step size. Default: 1e-2.
When running with an adaptive step size, this is the initial step size.
-rfreq : Frequency at which the spectral radii are re-estimated. Default: 10
-verb : Enables or disables verbosity. Default: true.
-dtadap : Enables/disables time step adaptivity. Default: false.
-atol : sets the absolute tolerance for error control. Default: 1e-2.
-rtol : sets the relative tolerance. Default: rtol=atol.
-oec : sets the error controller. Values are 1,2,3 for
I=Integral, PI=Proportional I, PPI= Predictive PI controllers
respectively. Default: 3.
-convtest : If true, performs a time convergence test instead, i.e. runs several simulations and checks errors. Default: false
If not provided, a reference solution is computed on the fly.
-maxpow : Minimal step size used for the convergence test is dt=tend/2^maxpow. Default: 6
-minpow : Maximal step size used for the convergence test is dt=tend/2^minpow. Default: 3
--- EMI model options:
-ndom : choose the geometry. A number from 0 to 7. Default: 6.
- 0: Two non touching inner domains, smoothed half circles. Outer domain is a circle.
- 1: Two non touching inner domains, half circles. Outer domain is a circle.
- 2: Two touching inner domains, half circles. Outer domain is a circle.
- 3: One inner domain, a circle. Outer domain is a circle.
- 4: A spiral of cells. Outer domain is a square.
- 5: A cluster of ten cells. Outer domain is an ellipse.
- 6: A rectangular cluster of cells. Number of cells, size, shape, etc are specified via command line. See below.
- 7: The microcard logo
-dG : Target mesh size. Default: 1e-3.
-Rl : Gap junctions resistivity. Default: 0.00145.
-si : Inner cells electric conductivity. Default: 3.
-se : Outer domain electric conductivity. Default: 20.
-Imax : Stimulus intensity (applied for 1ms). Default: 120.
--- Additional options only valid for ndom=6:
-cl : cells length. Default: 1e-2.
-cw : cells width. Default: 0.2e-2.
-Rl : Longitudinal gap junctions resistivity. Default: 0.00145.
-Rt : Transversal gap junctions resistivity. Default: 0.00145.
-nx : Number of cells in horizontal direction. Default: 10
-ny : Number of cells in vertical direction. Default: 2
-va : Amplitude of vertical gap junctions waves. Default: 5e-5.
-vf : Frequency of vertical gap junctions waves. Default: 0 (a segment).
-vs : Smoothness of vertical gap junctions: waves or squared waves. Default: true (wave).
-ha : Amplitude of horizontal permeble curves (PC). Default: 0.
-hl : Length of horizontal PC. Default: 20e-4.
-hs : Smoothness of horizontal PC: waves or squared waves. Default: true (wave).
-op : Enables/disables the only perpendicular PC permeability. Default: false.
-hp : Relative position of horizontal PC. Default: 0.5 (centered).
-halt : Alternation of horizontal PC. Default: -1.
- -1: No alternation, no PC. The whole horizontal gap junction is a fully permeable segment.
- 0: No alternation. The PCs are placed one above the other.
- 1: Alternation. The PCs are placed at relative positions hp and 1-hp.
- 2: Random. The PCs are randomly placed on the horizontal gap junction.
-hprob : Probability at which the horizontal PC becomes impermeable. Default: 0
-nic : When ny=2, stimulates 1 or 2 of the leftmost cells. Default: 1