openCARP Q&A - Recent questions

Question on units

Thu, 09 Apr 2026 08:45:10 +0000

Hi,

I am working with a heart-in-a-torso setup and the end goal is to compute the ECG at the electrodes on the torso. I have done the openCARP simulation on the heart domain. Next, I need to now compute the Geselowitz integral to compute the ECG, outside of the openCARP setup. So, here is my question on units. Internally, openCARP converts units consistently. But outside, I am converting as follows, but the ECG magnitude seems orders off.

1) Vm in vm.igb is in mV
2) vm_grad (meshtool extract gradient) is in mV/ micron - converted to SI (i.e mV/m)
3) lead field gradient (lf_grad) in 1/micron - converted to SI
4) Volume is converted to m^3 (as openCARP mesh is in microns)
5) Conductivities are already in S/m - so no conversion needed

With these changes, my computed ECG looks like off by a factor of 1000s.. The morphology of the signal seems fine. My question is the following - is my understanding on the units correct?

And a follow-up question on that Does openCARP support Laplace solve where a current is injected at a site as a BC? It was giving 0 output, but it works with voltage source.

Thanks and regards

~anoop

Why are the changes I make in ionic models not applied when creating and loading a dynamic library?

Mon, 09 Mar 2026 15:01:08 +0000

When I modify an ion model, for example by adding a parameter such as Ko to the Severi.model file, create the dynamic library and load the dynamic library file, I receive an error message stating that the added parameter is not recognised for the model.

How to properly use prepacing_lats when you also have scar that changes the intracellular grid in monodomain.

Thu, 05 Mar 2026 19:08:32 +0000

Not sure if this should be a bug report or just a question. I would love to know if there already exists a way around this problem I am having.

I can successfully use the prepacing_lats and associated options to initilize a simulation from a set of prescribed activation times. However, if I do so in a mesh that uses 1) the monodomain and 2) gregions that prescribe some tissue as scar (modeled as extracellular bath and therefore removed from the intracellular grid) I run into indexing issues. Specifically here is my pipeline:

1) Have a generated model
2) Generate a set of prescribed activation times across this model. These activation times are defined across every node of the model.
3) pass the model and activation times to openCARP as well as, on occasion, a retagfile to dynamically change some of the elements to scar tissue. openCARP will then generate an intracellular domain grid (which does not include the scar elements). This present a problem because now the activation times, which were defined on the whole mesh, no longer match up. This leads to an incorrect LAT-based initilization (it still proceeds but with a garbage activation sequence).

The preferred behavior would be for the provided prepacing_lats to be atuomatically clipped by the same process that generates the intracellular grid. I could of course generate the LAT map myself based on what will be the at runtime intracellular grid, but this is clunky especially if I have a combination of pre-defined scar elements and dynamic retagging of scar elements. It seems like openCARP should be able to do this as it already handles re-formatting all of the other node indicies for things like pacing sites, element tags, etc, to match the simulation grid even when they are input and defined in the context of the full mesh.

For context here is an example of what a job call would look like. The $runScript is just a simple carputils tools.carpexample job that parses my inputs and sets up the openCARP call with formatting for things like simulation time and setting up the dynamic retagging. In this case assume the tag 999 corresponds to scar tissue and that the mesh may or may not already have some scar tissue in it.

python3 -u $runScipt \
    --np $SLURM_NTASKS \
    --ParFile $parFile \
    --planFile $planFile\
    --build $build\
    --mesh $mesh \
    --outdir $outdir\
    --ID $outdir\
    --overwrite-behaviour "overwrite" \
    --CARP-opts "-gridout_i 2"\
    --CARP-opts "-prepacing_lats $prepaceFile"\
    --CARP-opts "-prepacing_beats 2"\
    --CARP-opts "-prepacing_bcl 250"\
    --addedTime 1000\
    --numStims 0\
    --RetagFile $retagFile\
    --ReTagVal 999\

3D Ventricular Mesh Shows No Wave Propagation - All Activation Times -1.0 Despite Successful 2D Simulations

Fri, 27 Feb 2026 07:57:48 +0000

Hi, I'm trying to simulate ventricular electrophysiology on a 3D mesh. My 2D tissue simulations work perfectly with realistic wave propagation, but the same setup on 3D ventricular meshes produces no activation (all LATs = -1.0) with clinically-relevant stimulus strengths, or simultaneous activation (no propagation) with extremely high strengths.

My setup is as follows:

Mesh: Extracted left and right ventricles (tags 1 and 2) from the Strocchi et al. four-chamber mesh (Zenodo 3890034), then resampled to ~2mm resolution (114,261 nodes, 588,654 elements)
Model: Ten Tusscher-Panfilov with modified GKs conductance
Solver: Monodomain (bidomain shows same behavior)
Electrode: 82 nodes from clinical RV endocardial pacing site, remapped after resampling using nearest-neighbor matching

Conductivities: g_il=0.174, g_it=0.019, g_in=0.019 S/m (anisotropic, from working 2D example)

What Worked:

2D tissue simulations (10,000 nodes, from openCARP example 02_EP_tissue/08_lats):

Pulse strength: 100 μA/cm²
Result: Realistic propagation with ACTs spreading from 10ms to 21ms
Full parameters in working case available on request

What Didn't Work:

3D ventricular mesh with identical ionic model and conductivity parameters:

Pulse Strength	Result
100 (clinical)	All ACTs = -1.0
500	All ACTs = -1.0
50,000	All ACTs identical within 0.002ms (simultaneous, no propagation)

Specifically, I took these steps to get the 3D meshes that I worked with:

Downloaded Strocchi mesh 01.tar.gz from Zenodo 3890034
Converted from EnSight Gold (.case) to openCARP using: meshtool convert -imsh 01-350um.vtk -ifmt vtk_bin -omsh 01-350um -ofmt carp_txt
Extracted ventricles: meshtool extract mesh -tags 1,2
Resampled to 2mm: meshtool resample mesh -min 1.5 -max 2.5
Remapped electrode using scipy.spatial.cKDTree nearest-neighbor matching

Also, even without extracting ventricles, I subsampled to a smaller box within the original (converted) mesh (i.e. 01-350um) for faster testing, and was getting similar issues, so I don't think the problem was with extracting ventricles or resampling to 2mm. This is how I got the smaller box:

meshtool extract volume \

-msh /workspace/heart_3d/01_convert/01-350um \

-ifmt carp_txt \

-submsh /workspace/heart_3d/01_tiny_full/tiny_block \

-ofmt carp_txt \

-coord 40,2,100,2,360,50

Playing around with the size of the box and the size of the stimulus box (defined by stim[0].elec.p0[0], p0[1], p0[2], p1[0], etc), I noticed that it seems to relate to stimulus strength: the larger the box i choose, the higher the pulse strength needs to be for activation to happen (for example, with a 3x3x9mm box, which comprised 1,448 nodes, pulse strength of 50 was sufficient to produce activations – although, again, they were all nearly identical and did not propagate spatially; whereas with a 10x10x10 box of 24,000 nodes, i needed a pulse strength of 50000 or so to get any activations in the lats file, which were again nearly identical).

So across all the things I've tried with the 3d mesh, even when activation occured, all nodes activate simultaneously (no spatial propagation)

I also performed some diagnostics:

Fiber orientations: 430,555 unique vectors (appropriate variety)
Mesh connectivity: Single connected component confirmed via meshtool
Electrode remapping: Verified nearest-neighbor remapping from original to resampled mesh
Stimulus firing: Stimulus_0.trc file shows current pulse applied correctly
Domain specification: Tried both "intra" and "extra" in .vtx file
Physics: Tested both monodomain and bidomain
Isotropy: Tested isotropic conductivity (g_il=g_it=g_in=0.5) - no improvement

Is there a recommended workflow for going from the Strocchi .case/.geo format to working openCARP simulations? Or alternatively, is there a known issue with this dataset that requires special handling, and is there a better dataset that I should be using for ventricular 3D heart simulations?

Here is an example of code that I used for the runs:

mpiexec -n 24 openCARP \

-meshname ventricles_2mm \

-ellip_use_pt 0 \

-parab_use_pt 0 \

-parab_options_file /usr/local/lib/python3.10/distpackages/carputils/resources/petsc_options/ilu_cg_opts \

-ellip_options_file /usr/local/lib/python3.10/distpackages/carputils/resources/petsc_options/gamg_cg_opts \

-num_phys_regions 2 \

-phys_region[0].ptype 0 \

-phys_region[0].num_IDs 2 \

-phys_region[0].ID[0] 1 \

-phys_region[0].ID[1] 2 \

-phys_region[1].ptype 1 \

-phys_region[1].num_IDs 2 \

-phys_region[1].ID[0] 1 \

-phys_region[1].ID[1] 2 \

-num_gregions 2 \

-gregion[0].num_IDs 1 \

-gregion[0].ID[0] 1 \

-gregion[0].g_il 0.174 \

-gregion[0].g_it 0.019 \

-gregion[0].g_in 0.019 \

-gregion[0].g_el 0.625 \

-gregion[0].g_et 0.236 \

-gregion[0].g_en 0.236 \

-gregion[1].num_IDs 1 \

-gregion[1].ID[0] 2 \

-gregion[1].g_il 0.174 \

-gregion[1].g_it 0.019 \

-gregion[1].g_in 0.019 \

-gregion[1].g_el 0.625 \

-gregion[1].g_et 0.236 \

-gregion[1].g_en 0.236 \

-num_imp_regions 2 \

-imp_region[0].num_IDs 1 \

-imp_region[0].ID[0] 1 \

-imp_region[0].im tenTusscherPanfilov \

-imp_region[0].im_param "GKs*1.0" \

-imp_region[1].num_IDs 1 \

-imp_region[1].ID[0] 2 \

-imp_region[1].im tenTusscherPanfilov \

-imp_region[1].im_param "GKs*1.0" \

-num_stim 1 \

-stim[0].crct.type 0 \

-stim[0].pulse.strength 100.0 \

-stim[0].ptcl.duration 2.0 \

-stim[0].ptcl.npls 1 \

-stim[0].elec.vtx_file electrode_endo_rv \

-num_LATs 2 \

-lats[0].ID ACTs \

-lats[0].all 0 \

-lats[0].mode 0 \

-lats[0].threshold -10 \

-lats[1].ID REPs \

-lats[1].all 0 \

-lats[1].mode 1 \

-lats[1].threshold -70 \

-dt 0.025 \

-tend 400 \

-bidomain 0 \

-simID "3d_heart"

This particular run resulted in all -1.0's in the activation file. The electrode file looked like this:

extra

8370

9953

12497
... (etc)

Let me know if this makes sense and if there is more info I can provide. Maybe there is something obviously wrong with my command – I am new to openCARP. Thank you!

How to add long list of ionic parameters in .par file

Fri, 27 Feb 2026 01:08:24 +0000

Hi , I am trying to use BO ionic model in my simulations with modified parameters from this paper (Weber, F. M., et al. "Adaptation of a minimal four-state cell model for reproducing atrial excitation properties." 2008 Computers in Cardiology. IEEE, 2008.).

Before running simulations I verified the availability of model and nomenclature of parameters using 'bench --imp BO --imp-info'

My issue: I am able to run simulations with the standard set of BO parameters available in CARP but when I try to modify the parameters (23 out of 28 parameters require scaling of the BO model parameters) , I get an error. CARP is not allowing allow me to change or scale beyond 16 parameters. Is there any workaround or syntax to overcome this limit of the max number of ionic channel conductance that can be scaled or prescribed by a value in a .par file ?

Please see the MWE extract from my .par file below for further clarity :

#IONIC SETUP

num_imp_regions = 1

#Myocardium

imp_region[0].im = BO

imp_region[0].im_param = "k_s=1.008,k_so=1.748,k_w_minus=135,tau_fi=0.0678,tau_o1=100,tau_o2=64.87,tau_s1=5.406,tau_s2=52.91,tau_si=6.978,tau_so1=53.54,tau_so2=8.03,tau_v1_minus=65.6,tau_v_pls=0.95,tau_w1_minus=170.8,tau_w2_minus=112.4,tau_w_inf=4.97,tau_w_pls=217,th_o=0.06,th_v_minus=0.172,th_w=0.33,u_s=0.814,u_u=1.02,u_w_minus=0.0744"

Once I run this, I am getting error that openCARP doesn't recognize tau_w_pls which is the 17th ionic parameters in the list. If I delete tau_w_pls , I get error regarding the next (17th) parameter in the list. Seems to be some max limit issue.

I would be thankful for your kind guidance and reply.

re: problem running 1st tutorial after installation

Mon, 23 Feb 2026 15:04:27 +0000

Dear Tobias,

I've now accordingly updated my ./bashrc but still obtain the two errors

cusettings $HOME/.config/carputils/settings.yaml

cusettings: command not found

and 2)

./run.py --EP tenTusscherPanfilov --duration 5000 --bcl 500 --ID exp01 --visualize --vis_var ICaL INa IK1

/home/pkuegler/experiments/tutorials/01_EP_single_cell/01_basic_bench/./run.py:3: SyntaxWarning: invalid escape sequence '\%'

"""

Traceback (most recent call last):

File "/home/pkuegler/experiments/tutorials/01_EP_single_cell/01_basic_bench/./run.py", line 269, in <module>

from carputils import settings

ModuleNotFoundError: No module named 'carputils'

Regarding the installation path I've followed the instructions on

Installing openCARP using the Windows Subsystem for Linux | openCARP

Best, Philipp

problem running 1st tutorial after installation

Wed, 18 Feb 2026 06:32:55 +0000

Dear all,

I've installed all components and in particular have

pkuegler@DESKTOP-PQF7A0H:~$ openCARP -buildinfo

*** GIT tag: v18.1
*** GIT hash: 6eaa147d18b69a6037d05a90b841e23301048a59
*** GIT repo: https://gitlab-ci-token:glcbt-64_W3Tng2n5yJP-sAsajXYz@git.opencarp.org/openCARP/openCARP.git
*** dependency commits:

and

pkuegler@DESKTOP-PQF7A0H:~$ python3 -c "import carputils; print(carputils)"
<module 'carputils' (namespace) from ['/home/pkuegler/carputils']>

Hoever, I now have troubles with the first tutorial Basic single cell EP | openCARP

Calling ./run.py --help

I obtain the error

pkuegler@DESKTOP-PQF7A0H:~/experiments/tutorials/01_EP_single_cell/01_basic_bench$ ./run.py --help
/home/pkuegler/experiments/tutorials/01_EP_single_cell/01_basic_bench/./run.py:3: SyntaxWarning: invalid escape sequence '\%'
"""
Traceback (most recent call last):
File "/home/pkuegler/experiments/tutorials/01_EP_single_cell/01_basic_bench/./run.py", line 269, in <module>
from carputils import settings
ModuleNotFoundError: No module named 'carputils'

==========================

Maybe that error is related to a failure of running

cusettings $HOME/.config/carputils/settings.yaml due to cusettings: command not found

Best, Philipp

Problem with using openMPI for tissue Simulation on HPC cluster

Sat, 14 Feb 2026 22:15:51 +0000

Our HPC uses SLURM as a resource manager and on our old HPC cluster we used the following job script:

#!/usr/bin/bash
#SBATCH --ntasks=8
#SBATCH --account= […]
#SBATCH --partition= […]
#SBATCH --cpus-per-task 1
#SBATCH --time=30:00
export OMP_NUM_THREADS=1

module load OpenMPI

mpirun /home/user/.local/easybuild/software/openCARP/17.0-foss-2023b/bin/openCARP +F MurineMouseCalibratedCV_BlockModel_v17.par

scontrol show job $SLURM_JOB_ID
scontrol write batch_script $SLURM_JOB_ID –

On our new HPC the output looked as there was a problem with using OpenMPI and it seemed that the model ran 8 times in parallel and was very slow in computing.

Installation of opencarp on HPC Cluster

Sat, 14 Feb 2026 22:10:24 +0000

We tried to install opencarp on our HPC using spack according to the openCARP website but got several errors during the compilation process, probably due to incompatibilities with gcc compiler versions. Is there an alternative to using spack?

meshalyzer installation error WSL Windows 11

Wed, 11 Feb 2026 10:23:17 +0000

Dear all,

trying to install openCARP via WSL for Windows11, I ran into the error given below when it comes to the installation of meshalyzer.

Can anyone advise how to overcome this problem ?

Best, Philipp

pkuegler@DESKTOP-PQF7A0H:/mnt/c/WINDOWS/system32/meshalyzer$ cmake --build _build
[ 1%] Generating HDF5DataBrowser.cxx and HDF5DataBrowser.h
[ 1%] Built target create_hdf5_data_browser
[ 2%] Building CXX object src/CMakeFiles/meshalyzer.dir/trimesh.cxx.o
[ 3%] Building CXX object src/CMakeFiles/meshalyzer.dir/TBmeshWin.cc.o
/mnt/c/WINDOWS/system32/meshalyzer/src/TBmeshWin.cc: In member function ‘void TBmeshWin::read_model(Fl_Window*, const char*, bool, bool)’:
/mnt/c/WINDOWS/system32/meshalyzer/src/TBmeshWin.cc:1246:50: error: ‘class Fl_File_Chooser’ has no member named ‘w’
1246 |     auto bt = new Fl_Light_Button(0,0,modchooser.w()-10,25,"Merge pkje file");
      |                                                  ^
/mnt/c/WINDOWS/system32/meshalyzer/src/TBmeshWin.cc:1264:7: error: type ‘<type error>’ argument given to ‘delete’, expected pointer
1264 |       delete bt;
      |       ^~~~~~~~~
gmake[2]: *** [src/CMakeFiles/meshalyzer.dir/build.make:904: src/CMakeFiles/meshalyzer.dir/TBmeshWin.cc.o] Error 1
gmake[1]: *** [CMakeFiles/Makefile2:153: src/CMakeFiles/meshalyzer.dir/all] Error 2
gmake: *** [Makefile:156: all] Error 2

Trying to install carputilsgui and it hangs on Sequoia 15.2

Wed, 04 Feb 2026 21:06:03 +0000

Seems to hang on setting up tutorials...

failed to solve: process "/bin/sh -c mkdir /tutorials && mv /openCARP/external/experiments/tutorials/* /tutorials" did not complete successfully: exit code: 1

Recover ECG from electrodes. Monodomain simulation

Fri, 23 Jan 2026 15:22:19 +0000

I saw in a previous publication that you can obtain the values of electrodes using -phie_rec_ptf from a monodomain simulation. I used as input 10 positions in a .pts file (LA, RA, LL, RL, V1-V6), however in my recovery file phie_recovery.igb, there seems to be 12 columns.

I assume the 12 columns are the 12 leads but I don't know in what order should the electrodes be in or, if preferably, how to obtain the values of the 10 electrodes directly to later get the the 12 leads values.

My .par is this:

simID = /home/bio/jimena.rodriguez/OpenCARP/Simulations/MI_MRI_32/3N_3_ini_ecg

meshname = /home/bio/jimena.rodriguez/OpenCARP/IHD/MI_MRI_32/mesh_wo_scar_apex

num_imp_regions = 1

imp_region[0].im = tenTusscherPanfilov # select ionic model

imp_region[0].name = ENDO_FEC_Healthy_Base

imp_region[0].num_IDs = 2

imp_region[0].ID = 311, 211

imp_region[0].im_param = "flags=ENDO,GKs-40%"

imp_region[0].im_sv_init = "/home/bio/jimena.rodriguez/OpenCARP/Simulations/APs/ENDO/HEALTHY/BASE/ENDO_HEALTHY_BASE.sv"

num_gregions = 1

gregion[0].name = Healthy

gregion[0].num_IDs = 2

gregion[0].ID = 311,211

gregion[0].g_el = 0.3

gregion[0].g_et = 0.12

gregion[0].g_en = 0.12

gregion[0].g_il = 0.22

gregion[0].g_it = 0.05

gregion[0].g_in = 0.05

gregion[0].g_mult = 1.0

num_stim = 2

stim[0].name = "BasicLV"

stim[0].elec.vtx_file = /home/bio/jimena.rodriguez/OpenCARP/IHD/MI_MRI_32/stim_Ext_LVstimulation_mesh_wo_scar.vtx

stim[0].ptcl.start = 0.0

stim[0].pulse.strength = 100.0

stim[0].ptcl.duration = 5.0

stim[1].name = "BasicRV"

stim[1].elec.vtx_file = /home/bio/jimena.rodriguez/OpenCARP/IHD/MI_MRI_32/stim_Ext_RVstimulation_mesh_wo_scar.vtx

stim[1].ptcl.start = 0.0

stim[1].pulse.strength = 100.0

stim[1].ptcl.duration = 5.0

dump_ecg_leads = 1

phie_rec_meth = 1

phie_rec_ptf = /home/bio/jimena.rodriguez/OpenCARP/IHD/MI_MRI_32/elec_file_src

bidomain = 0

spacedt = 1

timedt = 1

parab_solve = 1

dt = 30

tend = 15

Thanks!

How to extract time-varying ion concentrations

Wed, 17 Dec 2025 08:12:32 +0000

Dear developers,

When conducting tissue-level or whole-ventricle simulations, is it possible to extract time-varying ion concentrations?

Any help or ideas would be appreciated, thank you!

Stimulus not selecting any nodes despite correct parameters - Docker version 4f19932

Sat, 06 Dec 2025 19:28:19 +0000

Hi everyone,

I'm new to OpenCARP and having trouble getting stimulus to work in my simulations. I'm using the Docker version (git hash 4f19932) on Mac.

My simulation runs fine - the mesh loads, the Tomek model works, everything completes without errors. But the tissue never gets stimulated. When I check the Stimulus_0.trc file, it shows 0.000 nodes selected every time.

I've tried several approaches:

First attempt - geometric stimulus using x0, xd, y0, yd parameters to define a box on the left side of my tissue. I made sure the coordinates overlap with actual nodes in my mesh, but still 0 nodes selected.

Second attempt - made the stimulus box much bigger to cover the entire left side. Still nothing.

Third attempt - created an explicit vertex file (left_stim.vtx) with 84 specific node numbers and used stimtype 1. The file format looks correct (first line is the count, then one node index per line). Still 0 nodes.

Fourth attempt - tried changing my mesh element regions from 1 to 0 in case there was a mismatch. No difference.

The weird thing is there's no error message - the simulation just runs and ignores the stimulus completely. The electrics.log file doesn't even mention stimulus initialization.

My mesh is a 2D triangular mesh with 1038 nodes and 1804 elements. Here's a typical command I'm using:

openCARP -meshname mesh_name -simID test -tend 100 -dt 0.02 
-parab_solve 1 -num_imp_regions 1 -imp_region[0].im Tomek 
-imp_region[0].num_IDs 1 -imp_region[0].ID[0] 0 
-num_stim 1 -stimulus[0].stimtype 1 
-stimulus[0].vtx_file left_stim.vtx 
-stimulus[0].strength -80.0 -stimulus[0].duration 2.0 
-stimulus[0].start 10.0 -bidomain 0

Is there something obvious I'm missing? Or is there a known issue with stimulus in this Docker version? Any suggestions would be really helpful - I've been stuck on this for a while!

Thanks in advance for any help!

limpetGUI parameter units and use in tissue-level simulations

Wed, 26 Nov 2025 08:39:59 +0000

Dear developers,

I have two questions regarding the use of limpetGUI:
(1) When using limpetGUI, where can I find the units of the parameters shown in the generated plots?
(2) If I want to perform a tissue-level simulation which cannot use bench, can I still use limpetGUI? What would be the appropriate method to do so?

Any help or ideas would be appreciated, thank you!

Installation Error

Mon, 17 Nov 2025 23:19:24 +0000

I am trying to install OpenCarp onto a MacBook Pro with an M1 MAX chip. While following the building from the source guideline, I have been able to successfully use the following commands:

cmake -S. -B_build -DDLOPEN=ON -DBUILD_EXTERNAL=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="/opt/homebrew/" -DCMAKE_C_COMPILER=/usr/bin/clang -DCMAKE_CXX_COMPILER=/usr/bin/clang++ -DOpenMP_omp_LIBRARY="/opt/homebrew/opt/libomp/lib/libomp.dylib" -DCMAKE_CXX_STANDARD_LIBRARIES="/opt/homebrew/opt/libomp/lib/libomp.dylib" -DPETSC_DIR=/opt/homebrew/Cellar/petsc/3.24.1 -DPETSC_ARCH=arch-darwin-c-opt -DPETSC_INCLUDE_DIRS=/opt/homebrew/Cellar/petsc/3.24.1/include -DPETSC_LIBRARIES="/opt/homebrew/Cellar/petsc/3.24.1/lib/libpetsc.dylib

cmake --build _build

However, while I am trying to move towards the next step of installation using this command: make setup, I got these errors:

make update

--- updating openCARP -------------------------------------

Already up to date.

make all

* SIMULATOR: compiling openCARP_p.cc

mpicxx -c -I../param/include -std=c++17 -Wno-deprecated -Wno-unused-result -Wno-deprecated-declarations -Wno-implicit-const-int-float-conversion -Wno-unused-command-line-argument -O2 -g -DWITH_PETSC -DSOLVE_CURRENT -DWITH_BLAS -D_GNU_SOURCE -I. -I../simulator -I../physics/limpet/src -I../fem -I../fem/slimfem -I../fem/slimfem/src -I../physics -I../numerics -I/usr/include/malloc -I../numerics/petsc -I../numerics/ginkgo -I../param/include -I/opt/homebrew/Cellar/petsc/3.24.1/include -I/opt/homebrew/opt/fftw/include -I/opt/homebrew/opt/hdf5-mpi/include -I/opt/homebrew/opt/metis/include -MMD -O0 openCARP_p.cc -o build/openCARP_p.o

make[2]: `libnumerics.opt.a' is up to date.

make[2]: `libfem.opt.a' is up to date.

* creating archive: liblimpet

* Linking binary bench

mpicxx -o bench.opt -std=c++17 -Wno-deprecated -Wno-unused-result -Wno-deprecated-declarations -Wno-implicit-const-int-float-conversion -Wno-unused-command-line-argument -O2 -g -DWITH_PETSC -DSOLVE_CURRENT -DWITH_BLAS -D_GNU_SOURCE -I. -I../../simulator -I../../physics/limpet/src -I../../fem -I../../fem/slimfem -I../../fem/slimfem/src -I../../physics -I../../numerics -I/usr/include/malloc -I../../numerics/petsc -I../../numerics/ginkgo -I../../param/include -I/opt/homebrew/Cellar/petsc/3.24.1/include -I/opt/homebrew/opt/fftw/include -I/opt/homebrew/opt/hdf5-mpi/include -I/opt/homebrew/opt/metis/include -MMD -Wno-shadow -Wno-pedantic -Wno-sign-compare -Wno-switch-default -Wno-format-nonliteral -Wno-narrowing -Wno-newline-eof -Wno-self-assign -Wno-uninitialized -Wno-cast-align -DCPU_GENERATED build/cmdline.o build/bench.o build/bench_utils.o build/clamp.o build/ap_analyzer.o build/restitute.o build/stretch.o build/target.o -Wl,-rpath,/opt/homebrew/Cellar/petsc/3.24.1/lib -L/opt/homebrew/Cellar/petsc/3.24.1/lib -Wl,-rpath,/opt/homebrew/opt/fftw/lib -L/opt/homebrew/opt/fftw/lib -Wl,-rpath,/opt/homebrew/opt/scalapack/lib -L/opt/homebrew/opt/scalapack/lib -Wl,-rpath,/opt/homebrew/opt/hdf5-mpi/lib -L/opt/homebrew/opt/hdf5-mpi/lib -Wl,-rpath,/opt/homebrew/opt/metis/lib -L/opt/homebrew/opt/metis/lib -Wl,-rpath,/opt/homebrew/Cellar/open-mpi/5.0.8/lib -L/opt/homebrew/Cellar/open-mpi/5.0.8/lib -Wl,-rpath,/opt/homebrew/Cellar/gcc/15.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/15 -L/opt/homebrew/Cellar/gcc/15.2.0/lib/gcc/current/gcc/aarch64-apple-darwin23/15 -Wl,-rpath,/opt/homebrew/Cellar/gcc/15.2.0/lib/gcc/current/gcc -L/opt/homebrew/Cellar/gcc/15.2.0/lib/gcc/current/gcc -Wl,-rpath,/opt/homebrew/Cellar/gcc/15.2.0/lib/gcc/current -L/opt/homebrew/Cellar/gcc/15.2.0/lib/gcc/current -lpetsc -lfftw3_mpi -lfftw3 -lscalapack -llapack -lblas -lhdf5_hl_fortran -lhdf5_fortran -lhdf5_hl_f90cstub -lhdf5_f90cstub -lhdf5_hl -lhdf5 -lmetis -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lemutls_w -lheapt_w -lgfortran -lquadmath -lc++ -L. -llimpet.opt -L../../numerics -lnumerics.opt ../../fem/build/sf_interface.o -lz -lm -ldl

ld: warning: ignoring duplicate libraries: '-lc++', '-lgfortran', '-lmpi'

Undefined symbols for architecture arm64:

"SF::init_vector_petsc(SF::abstract_vector<int, double>**)", referenced from:

void SF::init_vector<int, double>(SF::abstract_vector<int, double>**, int, int, int, SF::abstract_vector<int, double>::ltype) in bench.o

void SF::init_vector<int, double>(SF::abstract_vector<int, double>**, SF::abstract_vector<int, double>*) in bench.o

"opencarp::initialize_PETSc(int*, char**, char*, char*)", referenced from:

_main in bench.o

ld: symbol(s) not found for architecture arm64

clang++: error: linker command failed with exit code 1 (use -v to see invocation)

make[2]: *** [bench] Error 1

make[1]: *** [openCARP] Error 2

make: *** [setup] Error 2

Not sure what else I could do to fix this error. Could someone help me with this issue? Thank you so much

Prepace in PSD example

Sat, 01 Nov 2025 23:42:35 +0000

Hi all,

I’m working on the Phase Singularity Distribution experiment from Example 21 (Reentry Induction Protocols). While looking through the induceReentry.py file—specifically the PSD function—I noticed the following parameter settings:

From my understanding, these parameters seem to control the prepacing phase. Could someone clarify what each of these commands actually does? I wasn’t able to find detailed documentation explaining them.

In particular, does this mean that the tissue will be prepaced for 100 beats at the specified basic cycle length before the PSD protocol runs and the rotor is induced? Or is the intended workflow to run the prepacing protocol separately, save the resulting state, and then use that as the starting point for PSD?

I’m trying to better understand the correct approach for prepacing the tissue, so any clarification would be greatly appreciated. Thank you in advance!

vm.igb file has fewer points than the pts file

Mon, 27 Oct 2025 14:30:36 +0000

Hi,

Simulation runs without errors, but when I try to visualize using Meshalyzer, I get a message that vm.igb points number mismatch.

https://docs.google.com/document/d/1K7sOTKKk8BWmpmM7vMhkGAKAGpPXLXhv/edit?usp=drive_link&ouid=115123931559289696344&rtpof=true&sd=true

Any thoughts on how to get opencarp to solve on all nodes.

Thanks.

Suran

The O'Hara model provided in openCARP does not seem to correctly simulate epicardial action potential

Fri, 24 Oct 2025 15:11:26 +0000

Hello,

Running some tests with the O'Hara model provided in openCARP, I noticed that the difference between the endocardial and epicardial version of the model is much smaller than what is described in the original O'Hara paper.

The epicardial action potential (AP) should be shorter than the endocardial AP (Figure 10F in the original paper). However, setting the celltype to 0 (endocardial AP) and 1 (epicardial AP) in the O'Hara model provided in openCARP results in APs that have very similar duration, asillustrated in the attached figure (top right corner).

For comparison, I performed simulations in the Myokit version of the O'Hara model and there the endo-epicardial difference in AP is obvious (top left panel of the figure).

Comparing the endocardial and epicardial simulations in the O'Hara model from openCARP and Myokit (bottom panels), it seems the O'Hara model provided in openCARP does not correctly simulate epicardial AP.

I quickly checked the ion channel conductivities in the openCARP and Myokit versions of the model and they seem to be the same.

Can someone have a look at this?

I ran all the simulations for N=100 beats with BCL = 1000 ms.

how to perform an error exit from openCARP code

Mon, 20 Oct 2025 17:31:15 +0000

What is the preferred way to output an error message and stop openCARP when an error condition makes further execution impossible or useless? I see several approaches being taken in the code, but no convenient function that combines a printf() with an exit() or abort().

Meshtool building error with addons

Mon, 13 Oct 2025 23:29:59 +0000

Hello,

When using meshtool, I encountered the following problem.

I wanted to use the interpolate shelldata utility. To use it, it was necessary to make meshtool using addons, so I modified my_switches.def file in the following way:

#MT_DEBUG = 1 # Compile in debug mode

#MT_STATIC = 1 # Try to link statically

MT_OPENMP = 1 # Use OpenMP

#MT_SANITIZE = 1 # Activate memory sanitizer in compile flags

#MT_ADDONS = 1 # Include addons

MT_SILENT = 1 # Dont show build command

MT_CC_ENV = gnu # choose between intel, gnu, clang

#TUNE_NATIVE = 1 # tune for the native platform (not for deployment)

PAR_MAKE = 16 # choose the number of processes to use for parallel make

#MT_SILENT_PRG = 1 # use silent progress instead of a bar

#MT_GZIP = 1 # whether gzip is available

#WINDOWS_BUILD = 1 # tell build system we are on windows

Unfortunately, during the make process, I received the following error:

make -j16 -s meshtool_deps

make -s meshtool

* building addons ..

/bin/sh: 1: cd: can't cd to meshtool_addons

make[1]: *** [Makefile:165: meshtool] Error 2

make: *** [Makefile:96: parbuild] Error 2

or, in other way:

fatal error: addons_utils.h: No such file or directory

I used the master branch from meshtool git.

Has anyone encountered this problem before or knows what might be causing this error?

Thank you in advance for help!

Stimulus not propagating

Mon, 29 Sep 2025 15:40:39 +0000

Hi,

I am trying to stimulate an external mesh and get activation map. My assumption was that consider the rheobase curve, given a stimulus of strong enough strength and sufficient duration, electrical activity will propagate to neighboring cardiac tissue. I modified the code from 02_EP_tissue/00_simple and 02_EP_tissue/01_basic_usage by changing the stimulus and mesh parameters.

However, I was only able to stimulate the example block mesh. I cannot stimulate an external mesh under same condition, and the activation remains localized like in the picture, not propagating outwards. I varied the stimulus strength, location, duration and geometry, but I am getting strange result combinations. Can anyone help me to suggest how to check the numerics? Or are there physiology parts I should look deeper into?

Thank you!

Dongcheng

Problem with installation during building using CMake

Thu, 25 Sep 2025 19:16:37 +0000

Hi,

I was trying to install OpenCarp on macOS with M3 Max chip, following the building from source instructions, while I am building using CMake, I have complied this command: "cmake -S. -B_build -DDLOPEN=ON -DBUILD_EXTERNAL=ON -DCMAKE_BUILD_TYPE=Release" without an issue, but when I am tring to complie:"cmake --build _build", I got an error:

[ 1%] Built target generate_ION_IF_datatypes_h

[ 10%] Built target param

[ 12%] Built target param-bin

[ 13%] Built target carp

[ 18%] Built target numerics

[ 19%] Built target fem

[ 69%] Built target limpet

[ 71%] Built target physics

[ 73%] Built target simulator

[ 73%] Building CXX object CMakeFiles/opencarp-bin.dir/simulator/main.cc.o

gmake[2]: /usr/local/Cellar/llvm/5.0.1/bin/clang++: No such file or directory

gmake[2]: *** [CMakeFiles/opencarp-bin.dir/build.make:79: CMakeFiles/opencarp-bin.dir/simulator/main.cc.o] Error 127

gmake[1]: *** [CMakeFiles/Makefile2:398: CMakeFiles/opencarp-bin.dir/all] Error 2

gmake: *** [Makefile:156: all] Error 2

I have installed Clang++, which is located at "/opt/homebrew/opt/llvm/bin/clang++". I tried to add this to the PATH, and also tried to replace the location in "CMakeFiles/opencarp-bin.dir/build.make" file, but neither one worked. Could someone help me with this issue?

Thank you so much

Unable to pick vertex on meshalyzer

Mon, 08 Sep 2025 14:43:21 +0000

Hi,

I am trying to follow the meshalyzer examples in Video tutorials | openCARP and running the given ellipsoid example. While the rest of the functions illustrated are fine, I am unable to pick/select specific vertices. I tried on both Windows and my WSL and both did not work. Once I click any vertex, I get the error message in my Linux terminal: "ERROR::SHADER::VERTEX::COMPILATION_FAILED

0:2(12): warning: extension `GL_EXT_clip_cull_distance' unsupported in vertex shader

0:5(7): error: redeclaration cannot change qualification of `gl_ClipDistance'

ERROR::SHADER::PROGRAM::LINKING_FAILED

error: linking with uncompiled/unspecialized shader"

I would like to select specific points to get coordinate. Thank you in advance for your help!

-Dongcheng

How to reliably auto-generate ION_IF_datatypes.h before compiling limpet?

Thu, 24 Jul 2025 12:41:05 +0000

In the limpet physics module of openCARP, the header file ION_IF_datatypes.h (in physics/limpet/src) is automatically generated from imp_list.txt using a Perl script. However, the compilation sometimes failed to generate the file correctly or too late, leading to:

fatal error: ION_IF_datatypes.h: No such file or directory
undefined reference to ION_* (due to missing or stale definitions)

This happened especially when changes in imp_list.txt were made indirectly or in parallel builds.

CMake could not find OpenMP on macOS

Wed, 23 Jul 2025 08:04:21 +0000

On macOS, CMake cannot find OpenMP, although I've installed OpenMP via Homebrew with

brew install libomp

More precisely, when trying to build openCARP, the CMake configuration command

cmake -S. -B_build

gives the following error:

[...]
CMake Error at /opt/homebrew/Cellar/cmake/3.31.2/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:233 (message):
Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
Call Stack (most recent call first):
/opt/homebrew/Cellar/cmake/3.31.2/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:603 (_FPHSA_FAILURE_MESSAGE)
/opt/homebrew/Cellar/cmake/3.31.2/share/cmake/Modules/FindOpenMP.cmake:616 (find_package_handle_standard_args)
CMakeLists.txt:222 (find_package)

How to use f3d files

Mon, 07 Jul 2025 09:03:57 +0000

Hello,

I want to apply the wall thickness over my atria mesh. My meshes are consisted of triangular and line elements.
I have made the "f3d" file with the same name of my mesh (like a data file with the line number equal to my elements number) and I can not see any difference using the f3d files.
Is there any arguments or parameter in the opencarp that should be on that the simulations would be done considering the f3d file?

I customized a fibroblast model to use as a plugin, but an error occurred after I compiled it.

Wed, 02 Jul 2025 09:26:57 +0000

I put it in this path: ~/openCARP_v18/physics/limpet/models
Then return to ~/openCARP_v18 and execute the following command:

cmake -S. -B_build -DUPDATE_IMPLIST=ON

cmake --build _build

Then the following error pops up：

/home/dengdd04/software_installed/opencarp_allversion/openCARP_v18/_build/physics/limpet/imps_src/Fibroblast_Maleckar09.cc: In member function ‘virtual uint32_t limpet::Fibroblast_Maleckar09IonType::moddat() const’:

/home/dengdd04/software_installed/opencarp_allversion/openCARP_v18/_build/physics/limpet/imps_src/Fibroblast_Maleckar09.cc:59:3: error: return-statement with no value, in function returning ‘uint32_t’ {aka ‘unsigned int’} [-fpermissive]

59 | return Fibroblast_Maleckar09_MODDAT;

| ^~~~~~

make[2]: *** [physics/limpet/CMakeFiles/limpet.dir/build.make:1774: physics/limpet/CMakeFiles/limpet.dir/imps_src/Fibroblast_Maleckar09.cc.o] Error 1

make[1]: *** [CMakeFiles/Makefile2:584: physics/limpet/CMakeFiles/limpet.dir/all] Error 2

Has anyone encountered this issue before or knows what might be causing this error?

Thanks in advance for your help!

Forcepss Stimulus Confusion

Fri, 23 May 2025 22:33:49 +0000

Hi all,
I was digging around in the tissue_calibrate tuneCV forcepss stack of code the other day and noticed something confusing I wanted to ask about.
eventually these things call back to tissue_limcyc which sets up the calls to tuneCV. In that setup, tissue_limcyc sets stim params of:
'--stimS', 500,
'--stimV',
Which based on tuneCV I interpret as "do a voltage clamp at 500 strength",
But then I noticed in the actual output logs the voltage clamp is at 0, not 500, because tuneCV calls tuning.CVtuning which, when --stimV is set, hard codes a 0 volt clamp:

if self.stimV:
            # we clamp for 5 ms to be sure to initiate, if possible at all
            stim = ['-stimulus[%d].duration'%(idx),   5.,
                    '-stimulus[%d].stimtype'%(idx),   9,
                    '-stimulus[%d].strength'%(idx),   0. ]

So I was wondering if this should be changed or left alone? I suspect that the voltage clamp at 0 is sufficient to stimulate in most cases, but it does mean that any val passed to --stimS for either tissue_calibrate or tuneCV will have no effect. Or am I misunderstanding something here?

Build on HPC system running very slow.

Wed, 14 May 2025 00:32:12 +0000

We recently acquired a new HPC cluster at our institutions
Each node is configured with:
AMD EPYC 9755 128-Core Processor
~1.1 Tb RAM

I pulled down a fresh clone of openCARP and created a new from source build on one of these nodes. Unfurtunatly, the simulations are taking orders of magnitude longer to finish than they did on our older clusters (ex: a stimulation protocol; that usually takes ~15 min to run on other nodes is now showing estimated comp times of > 1000 DAYS!)

I am working on profiling this build to see where the hangup might be, but wanted to ask:
1) What is the most likely suspect as far as where this slowdown is coming from? Petsc? openMPI ?
2) has anyone had success using profilers like perf, valgrind, or others? If so, how did you go about it.

I suspect that one of the dependancies I have built against is not ideal. I have seen it be the case in the past where openCARP gets fussy about the petsc version or things like that, but I am out of my depth here and would greatly appreciate any advice or help. More details below.

Best,
Jake B

Here are some more details:

Simulation setup:
- S1S2 protocol using a left atrial model of average edge length 350 uM, usualy simulation completion time for a single site is ~10 minutes for the S1 and ~20 to 40 min for the S2 depending on how long after the stimulus we simulate. These numbers are from a 192 core intel based node.

Things I have tried:
- reverting the git repo to match the working build on our intel machines (no change)
- attempting to build petsc from source (either with mpich or using the system openMPI) (both intructed compiler errors that I could not get around)
- yelling at the screen (changed nothing but was somewhat cathartic)

Here is how openCARP is linked for this build:
openCARP/_build/bin$ ldd openCARP
        linux-vdso.so.1 (0x00007ffe778c9000)
        libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x0000726278ae7000)
        libmpi_cxx.so.40 => /lib/x86_64-linux-gnu/libmpi_cxx.so.40 (0x0000726278ace000)
        libpetsc_real.so.3.19 => /usr/lib/petscdir/petsc3.19/x86_64-linux-gnu-real/lib/libpetsc_real.so.3.19 (0x0000726277400000)
        libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x0000726277000000)
        libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x0000726278aa0000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007262789b5000)
        libmpi.so.40 => /lib/x86_64-linux-gnu/libmpi.so.40 (0x00007262772ce000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x0000726276c00000)
        libopen-pal.so.40 => /lib/x86_64-linux-gnu/libopen-pal.so.40 (0x0000726278901000)
        libHYPRE-2.28.0.so => /lib/x86_64-linux-gnu/libHYPRE-2.28.0.so (0x0000726276600000)
        libspqr.so.4 => /lib/x86_64-linux-gnu/libspqr.so.4 (0x0000726276faa000)
        libumfpack.so.6 => /lib/x86_64-linux-gnu/libumfpack.so.6 (0x0000726276ef5000)
        libamd.so.3 => /lib/x86_64-linux-gnu/libamd.so.3 (0x00007262788f2000)
        libcholmod.so.5 => /lib/x86_64-linux-gnu/libcholmod.so.5 (0x0000726276a41000)
        libklu.so.2 => /lib/x86_64-linux-gnu/libklu.so.2 (0x00007262772a3000)
        libdmumps-5.6.so => /lib/x86_64-linux-gnu/libdmumps-5.6.so (0x0000726276200000)
        libscalapack-openmpi.so.2.2 => /lib/x86_64-linux-gnu/libscalapack-openmpi.so.2.2 (0x0000726275c00000)
        libsuperlu.so.6 => /lib/x86_64-linux-gnu/libsuperlu.so.6 (0x0000726276e85000)
        libsuperlu_dist.so.8 => /lib/x86_64-linux-gnu/libsuperlu_dist.so.8 (0x0000726275a29000)
        libtrilinos_ml.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_ml.so.13.2 (0x0000726275600000)
        libfftw3.so.3 => /lib/x86_64-linux-gnu/libfftw3.so.3 (0x0000726275200000)
        libfftw3_mpi.so.3 => /lib/x86_64-linux-gnu/libfftw3_mpi.so.3 (0x00007262788d8000)
        liblapack.so.3 => /lib/x86_64-linux-gnu/liblapack.so.3 (0x0000726274a00000)
        libblas.so.3 => /lib/x86_64-linux-gnu/libblas.so.3 (0x0000726276e18000)
        libptscotch-7.0.so => /lib/x86_64-linux-gnu/libptscotch-7.0.so (0x0000726276525000)
        libhdf5_openmpi.so.103 => /lib/x86_64-linux-gnu/libhdf5_openmpi.so.103 (0x0000726274600000)
        libOpenCL.so.1 => /lib/x86_64-linux-gnu/libOpenCL.so.1 (0x0000726277290000)
        libyaml-0.so.2 => /lib/x86_64-linux-gnu/libyaml-0.so.2 (0x0000726276504000)
        libX11.so.6 => /lib/x86_64-linux-gnu/libX11.so.6 (0x00007262758ec000)
        libmpi_mpifh.so.40 => /lib/x86_64-linux-gnu/libmpi_mpifh.so.40 (0x000072627649f000)
        libgfortran.so.5 => /lib/x86_64-linux-gnu/libgfortran.so.5 (0x0000726274200000)
        /lib64/ld-linux-x86-64.so.2 (0x0000726278e4e000)
        libopen-rte.so.40 => /lib/x86_64-linux-gnu/libopen-rte.so.40 (0x0000726275544000)
        libhwloc.so.15 => /lib/x86_64-linux-gnu/libhwloc.so.15 (0x000072627643e000)
        libevent_core-2.1.so.7 => /lib/x86_64-linux-gnu/libevent_core-2.1.so.7 (0x00007262761cb000)
        libevent_pthreads-2.1.so.7 => /lib/x86_64-linux-gnu/libevent_pthreads-2.1.so.7 (0x0000726277287000)
        libsuitesparseconfig.so.7 => /lib/x86_64-linux-gnu/libsuitesparseconfig.so.7 (0x0000726277282000)
        libcolamd.so.3 => /lib/x86_64-linux-gnu/libcolamd.so.3 (0x0000726276a38000)
        libcamd.so.3 => /lib/x86_64-linux-gnu/libcamd.so.3 (0x0000726276433000)
        libccolamd.so.3 => /lib/x86_64-linux-gnu/libccolamd.so.3 (0x00007262761bf000)
        libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00007262754ee000)
        libbtf.so.2 => /lib/x86_64-linux-gnu/libbtf.so.2 (0x0000726276e12000)
        libmumps_common-5.6.so => /lib/x86_64-linux-gnu/libmumps_common-5.6.so (0x0000726275474000)
        libptscotchparmetisv3-7.0.so => /lib/x86_64-linux-gnu/libptscotchparmetisv3-7.0.so (0x00007262761b8000)
        libmetis.so.5 => /lib/x86_64-linux-gnu/libmetis.so.5 (0x0000726275196000)
        libCombBLAS.so.2.0.0 => /lib/x86_64-linux-gnu/libCombBLAS.so.2.0.0 (0x00007262761a0000)
        libtrilinos_ifpack.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_ifpack.so.13.2 (0x000072627406c000)
        libtrilinos_amesos.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_amesos.so.13.2 (0x0000726275140000)
        libtrilinos_galeri-epetra.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_galeri-epetra.so.13.2 (0x000072627542b000)
        libtrilinos_aztecoo.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_aztecoo.so.13.2 (0x00007262750bb000)
        libtrilinos_zoltan.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_zoltan.so.13.2 (0x0000726274523000)
        libtrilinos_epetraext.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_epetraext.so.13.2 (0x0000726273f00000)
        libscotch-7.0.so => /lib/x86_64-linux-gnu/libscotch-7.0.so (0x0000726273e6b000)
        libtrilinos_epetra.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_epetra.so.13.2 (0x0000726273d08000)
        libtrilinos_teuchosparameterlist.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_teuchosparameterlist.so.13.2 (0x0000726273800000)
        libtrilinos_teuchoscore.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_teuchoscore.so.13.2 (0x00007262749a3000)
        libopenblas.so.0 => /lib/x86_64-linux-gnu/libopenblas.so.0 (0x0000726271420000)
        libptscotcherr-7.0.so => /lib/x86_64-linux-gnu/libptscotcherr-7.0.so (0x000072627619b000)
        libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x0000726276187000)
        liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x0000726275089000)
        libcrypto.so.3 => /lib/x86_64-linux-gnu/libcrypto.so.3 (0x0000726270e00000)
        libcurl.so.4 => /lib/x86_64-linux-gnu/libcurl.so.4 (0x0000726273c47000)
        libsz.so.2 => /lib/x86_64-linux-gnu/libsz.so.2 (0x0000726276182000)
        libxcb.so.1 => /lib/x86_64-linux-gnu/libxcb.so.1 (0x0000726273c1e000)
        libudev.so.1 => /lib/x86_64-linux-gnu/libudev.so.1 (0x0000726273beb000)
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        libtrilinos_teuchosnumerics.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_teuchosnumerics.so.13.2 (0x00007262758c7000)
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        libtrilinos_triutils.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_triutils.so.13.2 (0x0000726273b5e000)
        libscotcherr-7.0.so => /lib/x86_64-linux-gnu/libscotcherr-7.0.so (0x0000726275426000)
        libtrilinos_teuchosparser.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_teuchosparser.so.13.2 (0x0000726270d9e000)
        libtrilinos_kokkoscore.so.13.2 => /lib/x86_64-linux-gnu/libtrilinos_kokkoscore.so.13.2 (0x0000726270d15000)
        libnghttp2.so.14 => /lib/x86_64-linux-gnu/libnghttp2.so.14 (0x0000726271317000)
        libidn2.so.0 => /lib/x86_64-linux-gnu/libidn2.so.0 (0x0000726270cf3000)
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Is it possible to change the stimulus strength and duration in the PSD example?

Fri, 18 Apr 2025 16:23:55 +0000

Hi all,

I’m using carputils to run PSD reentry simulations in 2D tissue with a prepacing phase using the following structure (based on one of the examples):

-prepacing_beats 5  
-prepacing_bcl 1000  
-prepacing_lats sim/LATS.dat

During runtime, I see the message:

L1 : Assuming stimulus strength 60.000000 uA/uF with duration 1.000000 ms for prepacing

I would like to change this default stimulus strength and duration during prepacing, without affecting the main simulation, but there doesn’t seem to be a flag allowing this.

Is this possible? And if so, how can I modify the stimulus settings specifically for the prepacing phase? I’ve looked through many Q&As here and in the documentation, but haven’t found a solution.

Thanks in advance!

Are there predefined cardiac meshes available in OpenCARP for realistic heart geometry simulations?

Fri, 04 Apr 2025 10:11:17 +0000

Hi all,

I'm interested in running simulations on anatomically realistic heart geometries. I was wondering if OpenCARP provides any predefined meshes (ventricular, atrial, whole-heart, etc.) that I could use directly or as a starting point for my simulations.

If such meshes are available, where can I find them? Are they compatible out-of-the-box with the typical monodomain/bidomain setups in OpenCARP?

Thanks a lot in advance!

Best regards,

Is it possible to run simulations on a hollow spherical mesh (no volume)?

Fri, 04 Apr 2025 10:07:18 +0000

Hi everyone,

I'm working on cardiac simulations with OpenCARP and I was wondering if it's possible to run a simulation on a spherical mesh that only has surface elements—essentially a hollow shell with no internal volume. The idea is to have a closed surface that is relatively large, but empty on the inside.

Is this feasible with OpenCARP? Would it be compatible with monodomain or bidomain models? If so, are there any specific considerations I should keep in mind when generating the mesh or setting up the simulation?

Thanks in advance for any guidance!

Best regards,

Order of elements for monolayer triangular meshes

Mon, 17 Mar 2025 14:01:00 +0000

Hi everyone,

I found some strange behavior using openCARP for monolayer meshes (monodomain sim):

When I switch the order of point ids within triangle elements, also the visible conduction velocity changes. (I was inspecting code flipping the normals of all elements by changing the winding order.)

So for a triangle Tr 0 1 2 changing to Tr 2 1 0 this could make sense because of the changed in normal direction (still strange for 2D meshes). However, changing Tr 2 1 0 to Tr 1 0 2 also changes the propagation while not modifying the triangle-based normal direction.

My question would be: Is there some “rule” for triangle elements as for the other types of mesh elements in which order they should be used? And how can I enforce this, or does this effect shrink when going to full geometries?

My guess would be, that this is somewhere in the local coordinate system openCARP builds in SF_fem_utils.h which is only based on the first two triangle indices. But I’m too much of a beginner to understand these inner workings fully.

I attached the results of my experiments. If you need more information let me know.

Fiber direction along x (left to right) sheet direction along y (bottom to top). Courtemanche; just one region, stimulus planar from the bottom. Pts, lon files are the same, apart from the changed index order also the elem file.

Results for a 5x5 cm monolayer triangular mesh

I also did an example with a 3x3 points mesh which also shows a voltage difference between triangles with normals pointing up and down (just exchange the first and last index of each element in the elem file)

Simulation with normals pointing up

Simulation with normals pointing down (First and last index flipped)

Best regards,

Pascal

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How to use .vtx files with meshalyzer?

Sat, 08 Mar 2025 16:06:31 +0000

Hi,

I have created many intermediate .vtx files as part of my workflow. These are different "patches" of the original mesh. Just wanted to check if the extraction was correct and hence wanted to use meshalyzer and superimpose these individual .vtx files onto the original mesh.

Is there a readymade way or I have to use first principles to convert .vtx to .pts and then only use with meshalyzer?

Thanks in advance

~anoop

Remnants of Mac Ports path dependencies?

Mon, 03 Mar 2025 10:36:31 +0000

When playing around with the tutorials (specifically the ECG one) after having installed all dependencies using Homebrew (in opt/homebrew), I noticed that simply copying the commands as per the tutorial into my terminal returned errors saying that the dependencies were not found in the expected directory (opt/local). I think I got the simulation to work after modifying some paths manually. But it didn't work for Meshalyzer. I also noticed that the directories /opt/local appear explicitly in run.py in tutorials/02_EP_tissue/07_extracellular.

Will there be a problem when running my own simulations instead of the tutorials? At some point I want to work with a custom EP model.

Thanks in advance!

units in carputilsGUI

Mon, 03 Mar 2025 06:30:12 +0000

Dear devs,

Using “carputilsGUI”，where can I find the units of the parameters shown in the generated chart?

Any help or ideas would be appreciated, thank you!

Extracting data from bench output bin files

Wed, 26 Feb 2025 14:07:17 +0000

This is probably a naive question. I would like to extract the data for Ca_i from the bin file produced when I use --validate option with bench. But, I can't find any information about the file format and I am not currently using carputils or any of the visualization tools provided with open carp. Is there a straightforward way to translate or extract data from the <problem_name>.Cai.bin file?

If it makes a difference, I am using both the Gaur and OHara models in this study. Gaur includes Cai in the trace file output, OHara does not.

What are the default conductivity values used by openCARP in a monodomain simulation, and how can I modify them?

Wed, 26 Feb 2025 13:37:52 +0000

I am running monodomain simulations in openCARP using the Luo-Rudy 1991 model, but I cannot find clear documentation on the default conductivity values when they are not explicitly defined in the .par file.

I have checked the parameter list in the documentation, but I cannot find references to sigma_i or sigma_e in the monodomain context.

My questions are:

What are the default intracellular and extracellular conductivity values used by openCARP in monodomain simulations?
How can I correctly modify these values in my setup?

Any help or documentation reference would be greatly appreciated.

Thanks in advance!

GRegion axes definition

Thu, 13 Feb 2025 13:13:22 +0000

Hi, I have some questions regarding the parameter description of the different axes (l/n/t) for the extra-/intracellular conductivities.

As far as I understand, the local coordinate system is defined by a fiber direction, sheet direction, and the cross product between these two (sheet normal).

Why is the definition according to the parameter documentation for g_in: "Defines the intracellular conductivity in the local sheet direction" should this be the local sheet normal direction?

Also for the g_it parameter which should be "i.e. perpendicular to the longitudinal fiber 'g_il' and local sheet 'g_it' direction." it looks like a copy-paste error because g_it can't be perpendicular to itself.

As far as I understand it it should be:

fiber direction = g_il

sheet direction = g_it

(sheet) normal = g_in

Or am I missing something?

As a general question: Should the sheet vector in the .lon file point parallel to/along the tissue surface or perpendicular to it?

Best,

Pascal

Example of a simulation on a spherical mesh?

Thu, 06 Feb 2025 18:30:20 +0000

Hi everyone,

I am trying to run a simulation in OpenCARP using a spherical mesh with volume instead of the typical block. So far, I have followed these steps:

I generated a spherical mesh with volume using MATLAB and exported the .elem, .pts, and .lon files.
I loaded the mesh into OpenCARP and attempted to run the simulation.
However, I encountered an error, and the simulation does not run correctly.

Here is the error message from the output:

NaN detected: gregion[0], element 330: 587 572 585 564

Volume: -nan, fib: (1, 0, 0), she: (0, 0, 0), G: (0.136108, 0.0175843, 0.0175843)

Below are the configuration files I am using:

- monodomain.par:
# ionic setup

num_imp_regions = 1

imp_region[0].im = LuoRudy91

# electrical setup

num_stim = 1

stimulus[0].name = "S1"

stimulus[0].stimtype = 0

stimulus[0].strength = 400.0 # Stimulus strength in microamperes

stimulus[0].duration = 2.0

stimulus[0].start = 20.0 # First stimulus starts at 20 ms

bidomain = 0

parab_solve = 1

- run.py:
#!/usr/bin/env python

import os

from datetime import date

from carputils import settings

from carputils import tools

from carputils import mesh

from carputils.carpio import txt

import numpy as np

def parser():

parser = tools.standard_parser()

group = parser.add_argument_group('experiment specific options')

group.add_argument('--duration',

type=float,

default=1000.,

help='Duration of simulation in [ms] (default: 1000.)')

group.add_argument('--S1-strength',

type=float,

default=400., # Stimulus strength in microamperes

help='Stimulus strength in [uA/cm^2] (default: 400.)')

group.add_argument('--S1-dur',

type=float,

default=2., # Stimulus duration in ms

help='Stimulus duration in [ms] (default: 2.)')

return parser

def jobID(args):

"""

Generate name of top-level output directory.

"""

today = date.today()

return '{}_monodomain_{}'.format(today.isoformat(), args.duration)

@tools.carpexample(parser, jobID)

def run(args, job):

# Generate mesh

meshname = 'sphere'

# Query for element labels

_, etags, _ = txt.read(meshname + '.elem')

etags = np.unique(etags)

IntraTags = etags[etags != 0].tolist()

ExtraTags = etags.tolist().copy()

# Calculate number of stimuli

num_stim = int((args.duration - 20) / 500) + 1 # Includes initial stimulus at 20 ms

# Create stimulus settings

stim = ['-num_stim', num_stim]

for i in range(num_stim):

stim += [

f'-stimulus[{i}].name', 'S1',

f'-stimulus[{i}].stimtype', 0,

f'-stimulus[{i}].strength', args.S1_strength,

f'-stimulus[{i}].duration', args.S1_dur,

f'-stimulus[{i}].start', 20 + i * 500 # Stimulus every 500 ms starting at 20 ms

]

# Generate CARP command

cmd = tools.carp_cmd(os.path.join(os.path.dirname(__file__), 'monodomain.par'))

cmd += ['-simID', job.ID,

'-meshname', meshname,

'-dt', 5,

'-tend', args.duration]

cmd += tools.gen_physics_opts(ExtraTags=ExtraTags, IntraTags=IntraTags)

cmd += stim

if args.visualize:

cmd += ['-gridout_i', 3, '-gridout_e', 3, '-spacedt', 0.1]

# Run simulation

job.carp(cmd)

# Visualization (optional)

if args.visualize and not settings.platform.BATCH:

geom = os.path.join(job.ID, os.path.basename(meshname) + '_i')

data = os.path.join(job.ID, 'vm.igb.gz')

view = os.path.join(os.path.dirname(__file__), 'view_vm.mshz')

job.meshalyzer(geom, data, view)

if __name__ == '__main__':

run()

I have checked the OpenCARP documentation and examples, but I haven't found any that use a spherical mesh instead of a block.

Questions:

Has anyone successfully run a simulation on a volumetric spherical mesh?
Is there an example in OpenCARP that uses a sphere instead of a block?

Any advice or references would be greatly appreciated.

Thanks in advance!

Extracting ECG in Bidomain vs Infinite Volume Conductor (IVC)

Wed, 29 Jan 2025 22:40:33 +0000

Hi, I think I started overthinking something, so I need some clarification on how things are implemented in openCARP. I looked at example 07 on ECGs, documentation and some other questions in this forum, however I am still in doubts. Let's say I have the following simulations setups for an atria in a bath:

Bidomain/Pseudo-bidomain:

-num_imp_regions 1

-imp_region[0].name Atrium

-imp_region[0].im Courtemanche

-imp_region[0].num_IDs 1

-imp_region[0].ID[0] 1

-num_gregions 2

-gregion[0].name Bath

-gregion[0].g_bath 0.24725

-gregion[0].num_IDs 1

-gregion[0].ID[0] 0

-gregion[1].name Atria

-gregion[1].g_il 0.3333

-gregion[1].g_it 0.3333

-gregion[1].g_in 0.3333

-gregion[1].g_el 0.6666

-gregion[1].g_et 0.6666

-gregion[1].g_en 0.6666

-gregion[1].num_IDs 1

-gregion[1].ID[0] 1

-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

-phys_region[0].ID[1] 1

-phys_region[1].name Intracellular

-phys_region[1].ptype 0

-phys_region[1].num_IDs 1

-phys_region[1].ID[0] 1

-phie_rec_ptf /home/jg23/ecg

-bidomain 2

Monodomain with IVC/Lead fields:

-num_imp_regions 1

-imp_region[0].name Atrium

-imp_region[0].im Courtemanche

-imp_region[0].num_IDs 1

-imp_region[0].ID[0] 1

-num_gregions 1

-gregion[0].name Atria

-gregion[0].g_il 0.3333

-gregion[0].g_it 0.3333

-gregion[0].g_in 0.3333

-gregion[0].g_el 0.6666

-gregion[0].g_et 0.6666

-gregion[0].g_en 0.6666

-gregion[0].num_IDs 1

-gregion[0].ID[0] 1

-phie_rec_ptf /home/jg23/ecg

-bidomain 0

My questions are:

1. For bidomain/pseudo-bidomain, how can I obtain Phie values to compute ECGs? In a previous question, Toni mentioned loading the phie.igb file and extracting the Phie values at the mesh point indices corresponding to the ECG electrodes locations, which can then be used to calculate ECGs.

2. Following up on question (1), if I include -phie_rec_ptf with ecg.pts in the bidomain/pseudo-bidomain simulation, as show in the example, it generates a phie_recovery.igb file. Can I use this phie_recovery.igb to calculate my bidomain ECGs, or not? The documentation states that phie_rec_ptf is used to recover Phie in monoodomain simulations, but example 07 includes it in bidomain cases, so I'm a bit confused.

3. Does the monodomain with IVC setup look correct or is there something missing? How can I configure the bath conductivity for IVC?

4. Do I need -phys_region for monodomain IVC?

Thanks,

Jakub

"Unrecognized keyword elems" error when running simulation with spherical mesh

Sat, 25 Jan 2025 20:27:53 +0000

Hello!

I'm trying to run a simulation using openCARP with a spherical mesh. However, when I execute the run.py script, I encounter the following error:

*** Unrecognized keyword elems

*** Error reading parameters

Here is the relevant part of my code:

def run(args, job):

# Mesh configuration

meshname = "sphere" # Mesh name

nodes = "sphere.pts" # Nodes file

elems = "sphere.elem" # Elements file

# Read mesh element tags

_, etags, _ = txt.read(elems)

etags = np.unique(etags)

IntraTags = etags[etags != 0].tolist()

ExtraTags = etags.tolist().copy()

# Configure periodic stimuli

num_stim = int((args.duration - 20) / 500) + 1

stim = ['-num_stim', num_stim]

for i in range(num_stim):

stim += [

f'-stimulus[{i}].name', 'S1',

f'-stimulus[{i}].stimtype', 0,

f'-stimulus[{i}].strength', args.S1_strength,

f'-stimulus[{i}].duration', args.S1_dur,

f'-stimulus[{i}].start', 20 + i * 500

]

# Apply stimulus to the spherical surface

stim += [

'-stimulus[0].topo', 'sphere_surface', # Sphere surface

'-stimulus[0].type', 0, # Stimulus type (current)

'-stimulus[0].inside', 1 # Internal or external

]

# Generate the CARP command

cmd = tools.carp_cmd(os.path.join(os.path.dirname(__file__), 'monodomain.par'))

cmd += ['-simID', job.ID,

'-meshname', meshname,

'-nodes', nodes,

'-elems', elems, # This is the parameter causing the error

'-dt', 5,

'-tend', args.duration]

cmd += tools.gen_physics_opts(ExtraTags=ExtraTags, IntraTags=IntraTags)

cmd += stim

# Visualization option

if args.visualize:

cmd += ['-gridout_i', 3, '-gridout_e', 3, '-spacedt', 0.1]

# Run the simulation

job.carp(cmd)

# Visualize results

if args.visualize and not settings.platform.BATCH:

geom = os.path.join(job.ID, os.path.basename(meshname) + '_i')

data = os.path.join(job.ID, 'vm.igb.gz')

view = os.path.join(os.path.dirname(__file__), 'view_vm.mshz')

job.meshalyzer(geom, data, view)

I have verified the following:

The sphere.elem file is present and contains the expected element data in the correct format.
The paths to the sphere.pts and sphere.elem files are correct and accessible.
The monodomain.par file is properly configured with no obvious errors.

Has anyone encountered this issue before or knows what might be causing this error?

Thanks in advance for your help!

How to create a spherical geometry for simulations in OpenCARP?

Tue, 21 Jan 2025 11:34:50 +0000

Hello,

I am working on a simulation in OpenCARP and I want to evaluate the model's behavior in a spherical geometry (i.e., a 2D geometry in a 3D space). I’ve seen that OpenCARP allows working with custom geometries, but I’m unsure how to create and use a spherical geometry within the software.

Are there any predefined surfaces for spherical geometries in OpenCARP, or do I need to create it in another software like MATLAB and then export it? If so, what file format should I use to import the geometry into OpenCARP and ensure it fits the simulation conditions?

Any guidance or examples on how to do this would be greatly appreciated.

Thanks in advance.

Mass Lumping HPC

Sat, 18 Jan 2025 17:18:11 +0000

Hi everyone,

I am running simulations on HPC and I noticed that when I run with mass_lumping=1 everything is fine, but when I run with mass_lumping=0 the simulation diverges on the very first step (L5 : parabolic PDE (PETSc) solver diverged. Reason: indefinite preconditioning.). When I run the same code on my PC, it works with both mass_lumping on and off.

I installed openCARP on HPC by using Spack.

Do you know where I should look for the issue? I guess it could relate to some solver settings, but I don't know where to start investigating this problem.

Best,

Jakub

Bartolucci-Passini-Severi model in tissue

Thu, 16 Jan 2025 10:46:24 +0000

Hello everyone,

I was trying to use the BPS ventricular cell model in a 2D simulation of the “Basic tissue EP” example.

The problem is that the model is particularly stiff, and with bench the simulation converges only for very small time steps (<2 us) or using cvode (max step of 0.3 ms). In either case a simple 2x2 cm tissue takes tens of minutes to solve 20 ms.

I also tried solving the 2 markovian models (for ICaL and IKr) separately with the markov_be method, but I didn’t get a benefit in the maximal step I could use for the integration with bench and so the simulations are still too slow... how can I fix this?

Here is the cellML of the model:

https://models.cellml.org/workspace/5fd/file/36c7253c0426d8fcd7326ec104e162b44b656174/BPS2020.cellml

(with a mistake in Cao: the control value is 1.8 not 0.9), I'm also attaching how I imported it in EasyML:

https://opencarp.org/q2a/?qa=blob&qa_blobid=11054773068091813872

Thank you for the support,

Eugenio

Fenton-Karma CellML to EasyML

Fri, 06 Dec 2024 16:42:40 +0000

Hello, could someone assist me with converting Fenton-Karma model from CellML to EasyML.

CellML repo: https://models.cellml.org/e/5bc/fenton_karma_1998_BR.cellml/view

I tried to run with command:
/usr/local/lib/opencarp/share/openCARP/physics/limpet/src/python/cellml_converter.py --Vm=u --Istim=J_stim fenton_karma_1998_BR.cellml > fenton_karma_1998_BR.model

Fenton-Karma has u as transmembrane voltage, but later it also has this scaling of u to Vm (Vm=V_0+u(V_fi−V_0)) so I get lost with units and other variables later when translating to C. I would appreciate some support with that.

Thank you,

Jakub

Electrocardiography simulation implement in Abaqus

Wed, 27 Nov 2024 12:35:56 +0000

Hello,

this is my first time using this program electrocardiography. I have a question about the implementation of the data from opencarp. The points from the heart model, how can I proceed to put the data on abaqus? Do I need c++ or other programs?

I would kindly ask to ask a precise procedure how I can implement it. I was not able to find any way to do it.

Poor Internode Scaling With MPI/Petsc

Tue, 19 Nov 2024 02:09:46 +0000

Hello,

We have been using openCARP to perform S1-S2 threshold activation studies. We are noticing some weird behaviour on our clusters and wondering if you could point us in the right direction.

When we run our simulations on a single node, we see very good scaling up to 80 cores on our large memory node. However, when we try to use two or three 32 core nodes together performance is significantly worse. For example a simulation for just S1 takes 8 minutes with 80 cores, when we use 3 nodes (96 cores) it takes 30 minutes. Do you have any ideas on what can be going wrong here?

We have compiled openCARP with the instructions given in the documentation. For Petsc the only change we have made is that we use openMPI as that is what is installed on our clusters. The specific commit of the code we are using is: 675501a5e0e0fac521aa3e1ef2950c2f9012457b. We have also tried to use different meshes for our simulations and observe the same behaviour.

Please let me know if you require any additional information.

Thanks!

Locating Default Neumann Boundary Conditions in OpenCARP Source Code

Fri, 08 Nov 2024 15:46:08 +0000

Hi everyone,

I'm new to OpenCARP and have a question about boundary conditions. In the OpenCARP manual, it states that homogeneous Neumann boundary conditions are applied by default (pages 22, 24, and 143). I also saw confirmation of this in a response on the forum (https://opencarp.org/q2a/560/what-are-the-default-boundary-conditions-used-in-opencarp). However, I haven't been able to locate where exactly these default boundary conditions are implemented in the source code.

If anyone could point me to the relevant part of the code or offer any additional guidance on this, I’d greatly appreciate it.

Thank you all!

Best regards,
Estela