Hello everyone, I am very new to openCARP and I'm trying to run my first mini project for bidomain. I have a tetrahedral mesh of a sphere (tag=0) inside a block (tag=1), which is supposed to represent an atrium in a torso respectively. I want to run Courtemanche model starting somewhere within the sphere and propagate everything onto the block. I used another software to generate surface meshes, but later I used meshtool to combine them into tetrahedral and to generate fibres. I confirmed tags with meshtool query tags:
Reading mesh: combined_tet
Myocardium tags:
0
Bath tags:
1
Myocardium tags:
0: 14026441 elems
Bath tags:
1: 346939 elems
Later, I generated the following .par file based on the examples and openCARP Manual - Tissue Simulation: Running in plain mode (not sure if my .par file looks correct, so I would appreciate if someone could also confirm whether it looks legit):
meshname = ./meshes/combined_tet
# ----------------------------------------------------------------
num_phys_regions = 2
phys_region[0].name = "Extracellular"
phys_region[0].ptype = 1
phys_region[0].num_IDs = 2
phys_region[0].ID[0] = 0 # atrium
phys_region[0].ID[1] = 1 # torso
phys_region[1].name = "Intracellular"
phys_region[1].ptype = 0
phys_region[1].num_IDs = 1
phys_region[1].ID[0] = 0
num_imp_regions = 1
imp_region[0].name = "Atrium"
imp_region[0].im = Courtemanche
imp_region[0].im_param = "GCaL-55%,GK1+100%,factorGKur-50%,Gto-65%,GKs+100%,maxIpCa+50%,maxINaCa+60%,GKr*1.6"
imp_region[0].num_IDs = 1
imp_region[0].ID = 0
num_gregions = 2
gregion[0].name = "Atrium"
gregion[0].g_il = 2.9135
gregion[0].g_it = 0.3526
gregion[0].g_in = 0.118
gregion[0].g_el = 1.0283
gregion[0].g_et = 0.4702
gregion[0].g_en = 0.4262
gregion[0].num_IDs = 1
gregion[0].ID = 0
gregion[1].name = "Torso"
gregion[1].g_bath = 0.22
gregion[1].num_IDs = 1
gregion[1].ID = 1
# ----------------------------------------------------------------
num_stim = 1
stimulus[0].stimtype = 0
stimulus[0].strength = 30
stimulus[0].duration = 2.0
stimulus[0].start = 0
stimulus[0].x0 = -15640.7
stimulus[0].xd = 2000.0
stimulus[0].y0 = 6291.57
stimulus[0].yd = 2000.0
stimulus[0].z0 = 21792.4
stimulus[0].zd = 2000.0
# ----------------------------------------------------------------
simID = TESTOUTPUT
tend = 500
spacedt = 1.0
timedt = 1.0
gridout_i = 3
gridout_e = 3
bidomain = 1
dt = 20
Finally, I am running openCARP +F default.par and I am getting the following error (I found a similar question L3 error tag # not found in element list but the answer was not really helpful):
L1 : Warning: Legacy stimuli defined. Please consider switching to stimulus definition "stim[]"!
*** Processing meshes ***
Reading reference mesh: ./meshes/combined_tet.*
Done in 8.020109 sec.
Done in 0.032718 sec.
Processing submeshes
All done in 18.557148 sec.
Writing "Intracellular" surface: combined_tet_i.surf
Writing "Intracellular" mesh: combined_tet_i
Writing "Extracellular" surface: combined_tet_e.surf
Writing "Extracellular" mesh: combined_tet_e
*** Initializing physics ***
Initializing Electrics ..
Setting up ionic models and plugins
-----------------------------------
Assigning IMPS to tagged regions:
Ionic model: Courtemanche to tag region(s) [0].
Ionic model: Courtemanche
GCaL modifier: -55% value: 0.05571
GK1 modifier: +100% value: 0.18
factorGKur modifier: -50% value: 0.5
Gto modifier: -65% value: 0.05782
GKs modifier: +100% value: 0.258
maxIpCa modifier: +50% value: 0.4125
maxINaCa modifier: +60% value: 2560
GKr modifier: *1.6 value: 0.04704
L3 : Region tag 1 in gregion_i[1] not found in element list for Intracellular grid.
L4 : Missing element tags in element file!
Check region ID specs in input files!
application called MPI_Abort(compute, 59) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59
:
system msg for write_line failure : Bad file descriptor
I checked .elem files as well and I can see both tag 1 and tag 0 in there, so I am running out of the ideas. Maybe I did something wrong in .par file?
Thank you I advance!
