openCARP Q&A - Recent questions and answers

Answered: Question on units

Mon, 13 Apr 2026 07:40:55 +0000

Hey Anoop,

I am not sure if it is just a typo on your end because you say it correctly. But, if you want everything in SI units, you have to convert vm_grad to V/m not mV/m. That alone would explain the 1000x magnitude error in your ECGs. Otherwise, it looks correct to me.

The Laplace solver currently does not support current injection. Only dirichlet boundary conditions in the form of an extracellular potential stimulus.

Best,

Tobias

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

Mon, 16 Mar 2026 13:07:39 +0000

Hey Jake,

I think there is currently no way around the indexing issue you experience when you essentially remove parts of the mesh from the intracellular grid at runtime.

The retagging and setup of the mesh is separate from the electrics setup where the LAT prepacing is processed. The electrics setup does not know about the retagging at all and gets initialized from the "new" mesh. That also makes it a bit more difficult to implement such behavior.

The simplest way to achieve what you want to do is to not move the scar tissue into the extracellular bath, but to keep it intracellular with a very small (but non-zero) isotropic conductivity. For monodomain, this might even be the preferred solution, since the scar tissue can still act as a sink for electrical charges. If you move the tissue to extracellular bath, you implicitly get the zero flux Neumann boundary condition on all scar borders.

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

Mon, 09 Mar 2026 15:06:49 +0000

I debugged the process of loading the model and found that bench.cc switches to my local _build folder at some point and uses the model file located there. I opened a ticket [#155] for this issue so that at least a warning is issued or, better yet, the correct file is loaded from the outset.

However, a current workaround is to rename the modified model. When I named the model Severi2.model, created the dynamic library and then loaded it, adding the Ko parameter was effective.

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

Fri, 27 Feb 2026 09:20:43 +0000

Hey Konstantine,

Thank you for the detailed question.

In general, these meshes are fine for simulations with openCARP with a few caveats.

The one thing that will mess up your entire setup is that those meshes are all in mm. For openCARP you want µm! I suggest taking the 01-350um.vtk. Just convert it to µm first. You can use the -scale option when using meshtool convert to convert the vtk to openCARP format. (Additional info: The case file uses tag instead of elemTag. That might also cause some issues along the line, as meshtool potentially only recognizes elemTag. Not 100% certain about that though)

The other thing is that you say you want to resample to 2mm. That will not give you any meaningful results. Especially with the conductivities you chose. When solving the monodomain/bidomain equations, it is recommended to have a mesh resolution of at least 500µm (300µm better, 100µm ideal). Otherwise, you run into all kinds of numerical issues. https://www.nature.com/articles/s44161-025-00641-1 is worth a read if you want to know more about potential consequences of low mesh resolutions in cardiac modeling.

Otherwise, I don't see anything wrong with your command on first glance. Try it after converting to µm and using an appropriate mesh resolution and report back if there are still some problems!

Best, Tobias

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

Fri, 27 Feb 2026 06:18:01 +0000

Hi Ovais,

It seems that there is a spelling mistake in the variable that you are modifying (tau_w_plus not tau_w_pls). The exact names can be obtained using the following command line in the terminal (see below).

Let me know if this helps or if you are still getting an error.

Cheers,

Jorge

bench.opt --imp Bueno --imp-info

Ionic model:

------------

Metadata:

Authors: Alfonso Bueno-Orovio, Elizabeth M. Cherry, Flavio H. Fenton

Year: 2008

Title: Minimal model for human ventricular action potentials in tissue

Journal: Journal of Theoretical Biology, 253.3

DOI: 10.1016/j.jtbi.2008.03.029

Comment: Script includes the option to switch via flag between the original model (normalized Vm and Iion scale, 0-1) and a transformed version of the model with physiological Vm and Iion scales based on a resting membrane potential of V_0=-84mV. The transformed model is used by default.

Name: Bueno

Parameters:

V_0 -84

V_mu 85.7

k_s 2.0994

k_so 2

k_w_minus 200

modelformulation 0

tau_fi 0.1

tau_o1 470

tau_o2 6

tau_s1 2.7342

tau_s2 2

tau_si 2.9013

tau_so1 40

tau_so2 1.2

tau_v1_minus 75

tau_v2_minus 10

tau_v_plus 1.4506

tau_w1_minus 6

tau_w2_minus 140

tau_w_inf 0.0273

tau_w_plus 280

theta_o 0.006

theta_v 0.3

theta_v_minus 0.2

theta_w 0.13

u_o 0

u_s 0.9087

u_so 0.65

u_u 1.56

u_w_minus 0.016

w_inf_star 0.78

flags TRANSFORM|ORIGINAL

State variables:

Answered: re: problem running 1st tutorial after installation

Mon, 23 Feb 2026 15:58:17 +0000

Hello, if your carputils repository is located at /home/pkuegler/carputils , I think the easiest way to go for installing carputils is to run "pip install /home/pkuegler/carputils", then you should be able to run the tutorial.

Probably it's also better to run "python3 run.py", to ensure that the right version of Python is used.

Answered: problem running 1st tutorial after installation

Wed, 18 Feb 2026 07:39:31 +0000

Hey Philipp,

which installation path for carputils did you choose? Via pip or the developer route?

If you chose the developer route, you have to add the following to your .bashrc:

export PATH=$PATH:$HOME/openCARP/external/carputils/bin export PYTHONPATH=$PYTHONPATH:$HOME/openCARP/external/carputils

cusettings should than be found, since it is located in carputils/bin. That is mainly important to tell carputils scripts which openCARP executable to use and other useful things for the installation.

The PYTHONPATH is what's needed for python to import carputils as a module.

If your problem should persist, pleases give more information about which installation path you followed and your python version.

Best,

Tobias

Answered: Problem with using openMPI for tissue Simulation on HPC cluster

Sat, 14 Feb 2026 22:18:06 +0000

We could solve the problem by modifying the script as follows:

Instead of

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

use

module use /home/user/.local/easybuild/modules/all
module load openCARP/17.0-foss-2023b
mpirun /home/user/.local/easybuild/software/openCARP/17.0-foss-2023b/bin/openCARP +F MurineMouseCalibratedCV_BlockModel_v17.par

resulting in a final script:

#!/usr/bin/bash
#SBATCH --ntasks=8
#SBATCH --account=[…]
#SBATCH --partition=[…]
#SBATCH --cpus-per-task 1
#SBATCH --time=0:30:00
export OMP_NUM_THREADS=1

module use /home/user/.local/easybuild/modules/all
module load openCARP/17.0-foss-2023b

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 -

Answered: Installation of opencarp on HPC Cluster

Sat, 14 Feb 2026 22:11:40 +0000

We finally managed to install openCARP using easybuild running the following commands:

module load EasyBuild
eb --robot openCARP-17.0-foss-2023b.eb

Answered: meshalyzer installation error WSL Windows 11

Fri, 13 Feb 2026 08:47:35 +0000

It seems that some recent changes made to meshalyzer recently broke the compatibility with FLTK v1.3, and that version 1.4 is needed.

We will work on fixing this and updating the documentation, but in the meantime you can install FLTK v1.4 manually:

wget https://github.com/fltk/fltk/releases/download/release-1.4.4/fltk-1.4.4-source.tar.gz

tar xvf fltk-1.4.4-source.tar.gz

cd fltk-1.4.4/

cmake -S. -B_build

cmake --build _build --parallel 4

cd _build/

sudo make install

Then you can try to recompile meshalyzer. I advise you to delete the _build folder before recompiling, so that the right version of FLTK is found.

Answered: Trying to install carputilsgui and it hangs on Sequoia 15.2

Thu, 05 Feb 2026 11:12:43 +0000

Hello,

I pushed some fixes to the git repository, you should now be able to install carputilsGUI using the "developer installation" from the latest version of the master branch .

I would advise to remove all existing Docker volumes/containers/images related to carputilsGUI before rerunning "docker compose up".

Let me know if you have any further issue

Answered: Recover ECG from electrodes. Monodomain simulation

Tue, 27 Jan 2026 15:05:08 +0000

Hi Jimena,

Thanks for bringing this up! At the moment the phie_recovery module does not implement the phie_rec_meth and dump_ecg_leads arguments. Although the parser accepts those parameters without raising an error, they are essentially placeholders and have no functionality.

Can you share your phie_rec_ptf (in your case "elec_file_src") and the phie_recovery.igb? Alternatively a reproducible experiment could also help me pin down the issue.

Cheers, Julian

Answered: How to extract time-varying ion concentrations

Wed, 17 Dec 2025 09:14:24 +0000

Hey,

the following example shows how to use the gvec[] interface to export any state variable in tissue simulations.

If you have any further questions, please let us know!

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

Mon, 08 Dec 2025 09:21:52 +0000

Hey,

without having all the details of what you tried, I can try to address some common pitfalls I've came across myself with setting stimuli:

I've noticed you use the old stimulus parameter. This is a legacy parameter and only supported for backward compatibility. Please use the up to date stim convention.

When I check the Stimulus_0.trc file, it shows 0.000 nodes selected every time.

The trace file Stimulus_0.trc does not show you the selected nodes. It contains the waveform function of the chosen stimulus, i.e. its combinations of time and normalized amplitude. This function is later multiplied by stim.strength at corresponding time-steps. If you want to see the selected nodes, use the parameter stim[0].elec.dump_vtx_file 1, which will create a .vtx file containing the node IDs of the stimulus.

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.

For geometric definitions, it is important to get all the associated parameters correct for the shape you are using, e.g. for a block you need to make sure to have p0 defined as the lower left corner and p1 as the upper right corner. If you mix this up, you might end up with a block definition that doesn't catch the desired points.

Why your stimulus is not working:

You are defining an extracellular current stimulus (type = 1) in a monodomain simulation. This is not possible, since there is no extracellular domain defined in monodomain setups. Use a transmembrane current (type = 0) instead.

Answered: limpetGUI parameter units and use in tissue-level simulations

Thu, 27 Nov 2025 10:44:25 +0000

Hey,

1) The units of the output generated by bench should follow the documentation in the openCARP manual, section 3.1.4. This should be the same in limpetGUI plots.

2) As far as I know, limpetGUI can only be used for trace output from bench. If you want to perform tissue simulations with openCARP, there are multiple ways of visualizing the results.

There are some examples on the webpage in the section visualization. The most simple way would probably be to use meshalyzer. openCARP's output is in the igb format, which means you can also use IGB Utils to process the simulation results further.

Answered: Installation Error

Tue, 18 Nov 2025 07:09:48 +0000

In which directory are you running the build commands.

I have a feeling that you are mixing the CMake and make based workflows. It should be

either CMake: https://opencarp.org/download/installation#building-using-cmake
or make: https://opencarp.org/download/installation#building-using-the-makefi

Answered: Prepace in PSD example

Mon, 03 Nov 2025 08:51:13 +0000

Hey, you can find the documentation of these (and all other parameters) in the manual or on openCARP parameters. If you have read these already, would you mind sharing what was unclear to you and leave some hints on how we can improve the documentation of these parameters to make it more clear? We would appreciate it!

Otherwise, its pretty much what the descriptions says:

prepacing_lats is the file that contains the activation times used to start the prepacing from on the tissue level.

prepacing_beats defines how many beats are used to prepace the ionic models for a single cell. This state is then saved and applied to the tissue.

prepacing_bcl sets the basic cycle length for the single cell prepacing.

So it's pretty much the same as running single cell experiments in bench using the same number of beats/bcl and then start openCARP tissue simulations using the saved state from bench to initialize the ionic models. Except, that we also use activation times to introduce the phase singularity.

Hope that helps!

Answered: vm.igb file has fewer points than the pts file

Wed, 29 Oct 2025 08:52:07 +0000

Hey,

vm is normally computed on all nodes belonging to the intracellular region of your mesh. It is difficult to help you without any information about your setup. Please share your parameter file from the simulation and maybe some info about the mesh you are using.

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

Mon, 27 Oct 2025 09:32:50 +0000

Hey, I have checked the endo and epi variants for 100 beats at 1000ms BCL and can't confirm your findings. I have a suspicion, but I need the commands you are using to simulate your results to confirm. Could you please paste the commands that you used here?

Answered: how to perform an error exit from openCARP code

Tue, 21 Oct 2025 09:28:36 +0000

Hey Mark,

I think the common approach in the code would be to use the combination of

log_msg(out, level, flag, fmt)
exit(EXIT_FAILURE)

log_msg() safely prints an error/warning message either to a file or command line depending on the parameters used. Theoretically, the documentation states that using level as MAX_LOG_LEVEL (=5) means catastrophic failure. At the moment, the call to exit() is not included in the function. Maybe this could be done to simplify the process.

Answered: Meshtool building error with addons

Tue, 14 Oct 2025 13:46:30 +0000

Hi!

The "meshtool_addons" is an additional codebase that allows us to distinguish between code we want to share with the public, and code that we do not want to publish.

As you dont have access to the meshtool_addons, you cannot build meshtool with this flag turned on.

Best wishes, Aurel

Answered: Stimulus not propagating

Tue, 30 Sep 2025 07:17:09 +0000

Your mesh is very coarse. Average edge length: 1.1mm. (meshtool query edges -msh ellipsoid)

You should aim for at max 400µm (see this openCARP example for background).

Answered: Problem with installation during building using CMake

Fri, 26 Sep 2025 08:19:05 +0000

Hey,

it seems like your cmake tries to access clang with an old (non-existing) path. To my understanding, (on newer Macs at least) homebrew does not install packages in /usr/local/Cellar/ anymore but rather in /opt/homebrew/Cellar.

Try the following to let cmake make use of the llvm installed by homebrew:

# Set standard C compilers
export CC=clang
export CXX=clang++
# Set LLVM ENVs
export LDFLAGS="-L/opt/homebrew/opt/llvm/lib"
export CPPFLAGS="-I/opt/homebrew/opt/llvm/include"
# Update PATH env
PATH=/opt/homebrew/bin:$PATH
PATH=/opt/homebrew/opt/llvm/bin:$PATH
export PATH

Hope this helps!

Answered: Unable to pick vertex on meshalyzer

Tue, 09 Sep 2025 08:19:26 +0000

Hey,

normally it is sufficient to load the mesh, click on the "Pick Vertex" button once (or simply "P" on the keyboard) and then select the desired vertex on the mesh. Clicking the "?" button will open a window with the coordinates of that point and all sorts of other information.

If you already know the ID of the vertex, you can also type the ID in the data field next to "Vertex" and click the "?" button.

Sometimes I end up with a similar situation as in your pictures, where the background gets black and all nodes are shown if I try to pick a point. However, I am not sure how that happens exactly and I can't reproduce that consistently. I am not aware of a windows specific bug in that case and I can't test it on windows either right now. But if the above instructions don't help, let me know and I will try to reproduce it on a windows machine.

Best,

Tobias

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

Thu, 24 Jul 2025 12:46:07 +0000

We fixed this in MR !330 by:

Creating a dedicated generate_ION_IF_datatypes target.
Explicitly declaring its dependency in the limpet build target
Adding ${CMAKE_CURRENT_BINARY_DIR} to the include paths

Here’s the working implementation:

# Path to Perl scripts
set(LIMPET_PERL "${CMAKE_CURRENT_SOURCE_DIR}/src/perl")
set(GENERATED_ION_IF_H "${CMAKE_CURRENT_BINARY_DIR}/ION_IF_datatypes.h")

# Header generation from imp_list.txt
add_custom_command(
  OUTPUT "${GENERATED_ION_IF_H}"
  COMMAND perl -w -I${LIMPET_PERL} ${LIMPET_PERL}/ION_IF.h.pl
  DEPENDS
    ${CMAKE_CURRENT_SOURCE_DIR}/models/imp_list.txt
    ${LIMPET_PERL}/ION_IF.h.pl
    ${LIMPET_PERL}/common.pl
  COMMENT "Generating ION_IF_datatypes.h from imp_list.txt"
  VERBATIM
)

# Always run this target
add_custom_target(generate_ION_IF_datatypes ALL
  DEPENDS "${GENERATED_ION_IF_H}"
)

# Add dependency and include path to limpet
if (TARGET limpet)
  add_dependencies(limpet generate_ION_IF_datatypes)
  target_include_directories(limpet PRIVATE "${CMAKE_CURRENT_BINARY_DIR}")
endif()

that:

Ensures the header is always generated before limpet builds
Prevents parallel build issues or missing include errors
Clean separation of logic; easy to update if the generator script changes in the future

Reference
Implemented and validated in MR !330

Answered: CMake could not find OpenMP on macOS

Wed, 23 Jul 2025 08:05:23 +0000

If libomp has been installed via homebrew, this can be solved by exporting the following environment variable:

export OpenMP_ROOT=$(brew --prefix)/opt/libomp

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

Mon, 07 Jul 2025 19:25:44 +0000

It's hard to provide guidance when the .cc/.h/.model files are not attached.

Answered: How to use f3d files

Mon, 07 Jul 2025 12:33:38 +0000

Hey,

f3d files are not supported in openCARP. The required format for mesh files is specified in the User Manual (https://opencarp.org/documentation/user-manual) in sections 4.1.2 to 4.1.4.

If your current mesh already contains the surfaces and you want to create a volumetric mesh, you first have to find a suitable tool to generate a volume mesh from the surface mesh and then convert it to the openCARP format. meshtool is capable of this for common file types. Gmsh is another alternative (but requires conversion to openCARP format after meshing).

Answered: Forcepss Stimulus Confusion

Fri, 13 Jun 2025 09:13:41 +0000

Hi Jake,
yes, you're right, the stimulus strength '--stimS' is ignored if the voltage-clamp flag
‘--stimV’ is set in tuneCV. As you commented, a voltage clamp at 0mV is sufficient
to trigger stimulation for most of the ionic models. But there are models, as I
learned the hard way, where 0mV is not a good choice because somewhere in
the code of the ionic model a scaling operation is performed with the inverse
strength and you end up with a division by zero and NaNs in the output. I
temporarily fixed the issue by changing the strength in the tuneCV code to
0.1mV (or -0.1mV).

To make a long story short: Yes, the value of the “--stimS” argument should also
be used for voltage clamps in tuneCV and the stimulus strength should also be
provided to the user in the ForCEPSSs framework.

It's on my TODO list, but not at the top.

BW - Matthias.

Answered: Build on HPC system running very slow.

Tue, 20 May 2025 02:06:23 +0000

I finally got it working as expected. The key was some combination of petsc mpi blas lapack.
I built all of these from source to get the newest versions. With the following, I was able to get it running fast again:
gcc 14
petsc 3.23.2 (compiled against blas 3.10 lapack 3.12)
using the mpich that comes with petsc

Answered: Is it possible to change the stimulus strength and duration in the PSD example?

Mon, 21 Apr 2025 11:23:16 +0000

Hey,

currently this is not possible. But I opened an issue and a merge request which exposes these parameters to be changed at runtime. If you want to use this feature before the MR is reviewed and accepted, you have to checkout the branch prepacing_stimulus and build openCARP from source.

Then you can set the options

-prepacing_stimdur (in ms)
-prepacing_stimstr (in uA/uF)

to change the values to your desire.

Best, Tobias

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

Fri, 04 Apr 2025 16:21:54 +0000

Yes, openCARP monodomain and bidomain simulations are compatible with surface meshes.

The mesh should be in micrometers and the mesh resolution should be no larger than 500 micrometers to obtain good solutions (ideally 100-200 micrometers if possible). It should be available in the openCARP format (please refer to the manual for details) and it should contain element tags to assign properties such as conductivity and a fiber direction. If your mesh is in a format like vtk, you can use meshtool convert to convert it to openCARP format.

For the setup of the simulation you can follow the examples provided on the website.

Best, Tobias

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

Fri, 04 Apr 2025 16:09:10 +0000

Hey,

There are currently no realistic heart geometries delivered with openCARP. If you are interested, there are some realistic heart geometries available from publications that should be compatible with openCARP monodomain/bidomain simulations. However, there might be some preprocessing necessary.

e.g. https://zenodo.org/records/3890034 for whole heart meshes or https://zenodo.org/records/5571925 for atrial meshes based on a statistical shape model.

Alternatively, you can check out the community experiments on the openCARP website https://opencarp.org/community/community-experiments. These should be ready to use in openCARP!

Best, Tobias

Answered: Order of elements for monolayer triangular meshes

Thu, 20 Mar 2025 14:36:20 +0000

Hi!

I had a further look at this. I can confirm your observations on the meshes you provided. There is a certain spatial coherrence to the numerical error (even on regular refinements of your mesh), that I have not seen before. Really weird. The funny thing is that any regular & irregular triangulations of the same domain that I produced do not have the same kind of problems (keeping everything else the same).

It is not clear to me if there is an issue to fix or we are just observing a special property of the specific triangulation you produced. The solutions of uniform refinements of this mesh still converge towards the real solution, and it is clear that solutions of unconverged discretizations have numerical errors, but the spatial error patterns that manifest along the way are definitiely unexpected.

I will discuss this at times with collegues, but I dont see a direct way forward at this point.

Best, Aurel

Answered: How to use .vtx files with meshalyzer?

Mon, 10 Mar 2025 08:21:37 +0000

I don't think meshalyzer can read in vtx files directly.

The easiest option seems to be using what's described in this question (not the answer): https://opencarp.org/q2a/125/display-point-that-varies-time-with-auxiliary-grid-meshalyzer

Answered: units in carputilsGUI

Mon, 03 Mar 2025 11:45:19 +0000

Hello,

Depending on the case, it can be:

- in the parameter description, shown by clicking on the question mark in the parameter box.

- in the documentation of the given example: https://opencarp.org/documentation/examples

- for generic openCARP options, units are available in the user manual: https://opencarp.org/documentation/user-manual

I hope this helps.

Answered: Remnants of Mac Ports path dependencies?

Mon, 03 Mar 2025 11:31:23 +0000

Hello James,

Could you tell exactly where you find this reference to /opt/local in the file run.py?
I couldn't find it by searching the file.

Answered: Extracting data from bench output bin files

Thu, 27 Feb 2025 13:32:42 +0000

I think this script can be helpful: https://git.opencarp.org/openCARP/carputils/-/blob/master/bin/bin2h5.py?ref_type=heads

Indeed, the format is not documented in the manual currently. I've opened an issue and of course we welcome contributions: https://git.opencarp.org/openCARP/openCARP/-/issues/371

What is included in the trace depends on which quantities are labeled with .trace() in the .model file. See here for the Gaur example: https://git.opencarp.org/openCARP/openCARP/-/blob/master/physics/limpet/models/Gaur.model?ref_type=heads#L454

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

Wed, 26 Feb 2025 14:00:00 +0000

Conductivities are assigned to gRegions.

The default values can be queried from the help and found in chapter 15.2 of the manual:

https://opencarp.org/documentation/user-manual

If you don't define a region explicitly, the default values will be assigned to the whole mesh.

This example can be a good starting point: https://opencarp.org/documentation/examples/02_ep_tissue/05b_conductive_heterogeneity

Answered: GRegion axes definition

Tue, 18 Feb 2025 12:34:57 +0000

Hi!

You understood correct, the help text was not great. I changed it.

Best, Aurel

Answered: Example of a simulation on a spherical mesh?

Fri, 07 Feb 2025 12:08:00 +0000

Hey,

The error you are getting suggests that your mesh contains bad elements. In this case it points out that element 330 has no volume. You need to fix the mesh before anything else.

Regarding your questions, there is currently no example on the homepage that simulates on a sphere, since the built in meshing tool can only create spherical tag regions but no spherical mesh. But in general, it should not make a difference in terms of running a simulation on a block or a sphere as long as you provide a correct mesh and boundary conditions. With regards to the boundary conditions, I refer you to my answer to your previous thread, since you do not appear to have made those changes yet.

Best,

Tobias

Answered: Extracting ECG in Bidomain vs Infinite Volume Conductor (IVC)

Thu, 30 Jan 2025 08:20:16 +0000

Hi!

Specifying -phie_rec_ptf always activates the phie-recovery mechanism, which is independet from your Bi- or Monodomain reaction-diffusion modes. As such, you should get the same phie_recovery.igb, in peudo-bidomain and in monodomain mode (only bidomain might be slightly different due to a possible changed activation sequence due to bath loading effects etc.).

To calculate bidomain ECGs, you need to interpolate the volumetric data in phie.igb onto your ecg points. You can du this any way you like, two low-effort possibilities would be:

1) extract the mesh vertex indices closest to your ECG points with "meshtool query idxlist" and then extract traces at those indices with "igbextract".

2) define a geometry holding your ECG points, and use "meshtool interpolate nodedata" to interpolate the phie.igb onto that geometry.

Best, Aurel

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

Sat, 25 Jan 2025 21:21:39 +0000

Hey,

you get this error, since there is no such parameter as -elems in openCARP. The same goes for the parameter -nodes.

In openCARP it is sufficient to supply the parameter -meshname with the base name of your mesh files. In your case -meshname sphere. Then, the files sphere.pts, sphere.elem and sphere.lon should be present in the path of you simulation. I don't spot any other obvious errors right now, so the simulation should start if you make those adaptations to your script.

Best,

Tobias

Answered: How to create a spherical geometry for simulations in OpenCARP?

Tue, 21 Jan 2025 13:03:11 +0000

Hey!

There are 2 options.

1) You create the geometry with third-party software. In Gmsh for example you could export your geometry as a .vtk file and use meshtool to convert it to openCARP format. In the openCARP parameter file you set this geometry using the parameter meshname. Make sure the mesh dimensions are in micrometers.

2) For some simple geometries you can use mesher which is supplied with carputils. I suggest looking at the tissue examples on the openCARP webpage to familiarize yourself with this tool. I only found the mesh.SphereRegion method in carputils, but I think it is only used for tagging a mesh and not creating one.

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

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that:

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

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Mass Lumping HPC

Bartolucci-Passini-Severi model in tissue

Fenton-Karma CellML to EasyML

Electrocardiography simulation implement in Abaqus

Poor Internode Scaling With MPI/Petsc

Locating Default Neumann Boundary Conditions in OpenCARP Source Code

Reference
Implemented and validated in MR !330