I am having some trouble switching ionic models to the MitchellSchaeffer model. When I run bench --list-imps I see the MitchellSchaeffer model listed (see ouput below). However, when I try to run a simulation where the MitchellSchaeffer is set as the ionic model (see .par file below), I get an error that the MitchellSchaeffer is illegal. See command output below.
Bench output:
openCARP/_build/bin/bench --list-imps
Ionic models:
AlievPanfilov
AslanidiSleiman
Augustin
Bondarenko
Campos
Courtemanche
DiFrancescoNoble
DrouhardRoberge
Fox
Grandi
GrandiPanditVoigt
HodgkinHuxley
Inada
IribeKohl
Kurata
Loewe
LuoRudy91
LuoRudy94
MacCannell
MahajanShiferaw
Maleckar
MitchellSchaeffer
Nygren
OHara
Pathmanathan
Plonsey
Ramirez
Shannon
Skibsbye
Steward
Tomek
WangSobie
tenTusscherPanfilov
Plug-ins:
Defib_AshiharaTrayanova
Electroporation_DeBruinKrassowska98
Electroporation_DeBruinKrassowska99
Fibroblast_MacCannell
Fibroblast_Morgan
IACh_Cheng
IChR2_WilliamsXu
IKATP_Ferrero
INa_Bondarenko
ISAC_Hu
Stress_Land12
Stress_Land17
Stress_Lumens
Stress_Niederer
Stress_Rice
.par file:
##############################################################
output_level = 10
##############################################################
dt = 20 #us
timedt = 10 #ms
spacedt = 4
experiment = 0
parab_solve = 1
mass_lumping = 0
##############################################################
num_imp_regions = 3
##############################################################
imp_region[0].im = MitchellSchaeffer
imp_region[0].num_IDs = 1
imp_region[0].ID[0] = 0
#imp_region[0].im_param = "V_max=40.,V_min=-86.2,tau_open=80.0,tau_out=5.4"
#
##fibrosis
imp_region[1].im = MitchellSchaeffer
imp_region[1].num_IDs = 1
imp_region[1].ID[0] = 1
#imp_region[1].im_param = "V_max=20.,V_min=-86.2,tau_open=80.0,tau_out=5.4,tau_close=200"
#
##scar
imp_region[2].im = MitchellSchaeffer
imp_region[2].num_IDs = 1
imp_region[2].ID[0] = 2
#imp_region[1].im_param = "V_max=20.,V_min=-86.2,tau_open=80.0,tau_out=5.4"
#
##############################################################
num_gregions = 3
##############################################################
## https://doi.org/10.1038/s41597-023-02416-4
gregion[0].g_il = 0.34
gregion[0].g_it = 0.06
gregion[0].g_in = 0.06
gregion[0].num_IDs = 1
gregion[0].ID[0] = 1
#
gregion[1].g_il = 0.03
gregion[1].g_it = 0.03
gregion[1].g_in = 0.03
gregion[1].num_IDs = 1
gregion[1].ID[0] = 2
#
gregion[2].g_il = 0
gregion[2].g_it = 0
gregion[2].g_in = 0
gregion[2].num_IDs = 1
gregion[2].ID[0] = 3
#
command line output:
#-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# Launching openCARP Simulation /uufs/chpc.utah.edu/common/home/ranjan-data//ActiveProjects/GeneralSystemTesting/VentricleTest//s1s2Test/S1
#-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/uufs/chpc.utah.edu/common/home/ranjan-data/ActiveProjects/CommonCode/carpBuilds/notchpeak_cpu/openCARP/_build/bin/openCARP \
+F /uufs/chpc.utah.edu/common/home/ranjan-data//ActiveProjects/GeneralSystemTesting/VentricleTest//ventricularParams.par \
-ellip_use_pt 0 \
-parab_use_pt 0 \
-parab_options_file /uufs/chpc.utah.edu/common/home/u6010393/ranjan-data/ActiveProjects/CommonCode/codeRepos/carputils/carputils/resources/petsc_options/ilu_cg_opts \
-ellip_options_file /uufs/chpc.utah.edu/common/home/u6010393/ranjan-data/ActiveProjects/CommonCode/codeRepos/carputils/carputils/resources/petsc_options/gamg_cg_opts \
-simID /uufs/chpc.utah.edu/common/home/ranjan-data//ActiveProjects/GeneralSystemTesting/VentricleTest//s1s2Test/S1 \
-meshname /uufs/chpc.utah.edu/common/home/ranjan-data//ProcessedData/MED3/model/med03_ventricles \
-tend 3600.0 \
-num_tsav 2 \
-write_statef stimulation_save_state \
-num_stim 1 \
-stim[0].name s1s2stim \
-stim[0].elec.vtx_file /uufs/chpc.utah.edu/common/home/ranjan-data//ActiveProjects/GeneralSystemTesting/VentricleTest//stim_01.vtx \
-stim[0].ptcl.npls 8 \
-stim[0].ptcl.bcl 500 \
-stim[0].ptcl.duration 1.0 \
-stim[0].pulse.strength 500.0 \
-stim[0].crct.type 0 \
-stim[0].ptcl.start 0.0 \
-num_adjustments 1 \
-adjustment[0].variable "MitchellSchaeffer.tau_close" \
-adjustment[0].file /uufs/chpc.utah.edu/common/home/ranjan-data//ProcessedData/MED3/model/apd_tauClose.adj \
-tsav[0] 1800 \
-tsav[1] 3600
*** GIT tag: latest-79-g82fecd3d
*** GIT hash: 82fecd3d70c50db25d96441762f188d29bb2ae61
*** GIT repo: https://git.opencarp.org/openCARP/openCARP.git
*** dependency commits:
L2 : Output directory exists: /uufs/chpc.utah.edu/common/home/ranjan-data//ActiveProjects/GeneralSystemTesting/VentricleTest//s1s2Test/S1
L4 : Warning: No physics region defined! Please set phys_region parameters to correctly define physics.
L4 : IntraElec and ExtraElec domains will be derived from fibers.
*** Processing meshes ***
Reading reference mesh: /uufs/chpc.utah.edu/common/home/ranjan-data//ProcessedData/MED3/model/med03_ventricles.*
Done in 2.072022 sec.
Renormalised 1203539 longitudinal and 0 sheet-transverse fibre vectors.
Done in 0.007316 sec.
Processing submeshes
Submesh name: Autogenerated intracellular Electrics
Extraction done in 0.283267 sec.
Submesh name: Autogenerated intracellular Electrics
Using KDtree partitioner ..
Partitioning done in 0.000478 sec.
Redistributing done in 0.278690 sec.
Canonical numbering done in 0.287829 sec.
PETSc numbering done in 0.107967 sec.
===== Parallel mesh statistics =====
#pid #nodes #elems #interf #alg
0 259343 1210340 0 259343
Multiplicities :
L5 : Illegal IM specified: MitchellSchaeffer
L5 : Run bench --list-imps for a list of all available models.
All done in 3.084048 sec.
*** Initializing physics ***
Initializing Electrics ..
Setting up ionic models and plugins
-----------------------------------
Assigning IMPS to tagged regions:
