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by (180 points)

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:

1 Answer

0 votes
by (180 points)
After working with it for a while, the problem seems to be line endings in the .par file. It had windows line endings but was being ran with a linux opencarp build. The simulationmakes it past the setup stage now. Instead, I am getting stuck with the petsc solver diverging which I suspect is a different issue.
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