I am not sure the best way to send it as I can't attach anything to comments, but I will try and paste the text here. Please let me know if anything is unclear.
This is my Gmsh file, bidomain_005cm3.geo , including instructions for how to run everything at the top :
// -----------------------------------------------------------------------------
//
// This Gmsh script attempts to produce a simple cuboidal mesh that can be used in openCARP.
//
// To create the corresponding .msh file, run
// gmsh -3 bidomain_005cm3.geo
//
// Converting to CARP directly using meshtool doesn't seem to work, but it can be
// converted to VTK first from the Gmsh GUI :
// gmsh bidomain_005cm3.msh
// Select 'File -> Export', then choose the file extension 'VTK' and save the mesh as 'bidomain_005cm3.vtk'.
//
// Then, it can be converted to CARP format using
// meshtool convert -imsh bidomain_005cm3.vtk -ifmt vtk -omsh bidomain_005cm3 -ofmt carp_txt
//
// The resulting .elem, .lon, and .pts files is then run with the s1.par file, with
// openCARP +F s1.par
//
// which gives the error : "L5 : error: Empty stimulus[0] electrode def! Aborting!"
// -----------------------------------------------------------------------------
//Dimensions all in micrometres
lc = 100; //dx = 100um
Lx = 1444;
Ly = 2604;
Lz = 1590;
Point(1) = {0, 0, 0, lc};
Point(2) = {0, 0, Lz, lc};
Point(3) = {Lx, 0, Lz, lc};
Point(4) = {Lx, 0, 0, lc};
Point(5) = {0, Ly, 0, lc};
Point(6) = {0, Ly, Lz, lc};
Point(7) = {Lx, Ly, Lz, lc};
Point(8) = {Lx, Ly, 0, lc};
Line(1) = {1, 2};
Line(2) = {2, 3};
Line(3) = {3, 4};
Line(4) = {4, 1};
Curve Loop(1) = {1, 2, 3, 4};
Plane Surface(1) = {1};
Extrude {0,Ly,0} {Surface{1};}
-------------------------------------------------------------------
and here is the parameters file, s1.par:
# ----------------------------------------
# Output Folder Name
# ----------------------------------------
simID = Test_Output/Bidomain-005cm3-Gmsh
# ----------------------------------------
# Meshname
# ----------------------------------------
meshname = bidomain_005cm3
# ----------------------------------------
# Definition of physics region
# ----------------------------------------
num_phys_regions = 2
phys_region[0].name = "Intracellular domain"
phys_region[0].ptype = 0
phys_region[0].num_IDs = 1
phys_region[0].ID[0] = 1
phys_region[1].name = "Extracellular domain"
phys_region[1].ptype = 1
phys_region[1].num_IDs = 1
phys_region[1].ID[0] = 1
# ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ---------------
# Definition of ionic model and plugins (IMP) for each unique tagged
# region in the mesh
# ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ------ ----- ----
num_imp_regions = 1
imp_region[0].im = Shannon
num_gregions = 1
# --------------------
# Definition of stimuli
# --------------------
num_stim = 1
#stimulus[0].name = "S1"
#stimulus[0].stimtype = 0
#stimulus[0].strength = 0.0
#stimulus[0].duration = 2.0
#stimulus[0].start = 0.
#stimulus[0].npls = 1
#stimulus[0].x0 = 0.0
#stimulus[0].xd = 222.0
#stimulus[0].y0 = 0.0
#stimulus[0].yd = 222.0
#stimulus[0].z0 = 0.0
#stimulus[0].zd = 222.0
stim[0].name = "S1"
stim[0].elec.geom_type = 2
stim[0].elec.p1 = 222.0
stim[0].elec.p0 = 0.0
stim[0].ptcl.duration = 2.0
stim[0].pulse.strength = 300
# -------------------------------
# Definition of general parameters
# -------------------------------
tend = 15.0 # t_end - end of simulation
spacedt = 0.1 # Interval to output data to files
timedt = 0.1 # Interval to print progress to sceen
vofile = "vm.igb" # Output filename: Prevents invalid read when defined
# --------------------------------------------------
# Definition of solving problem and numerical methods
# --------------------------------------------------
bidomain = 1
parab_solve = 1
