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Simulations & Solvers

FDTD, Low-Frequency, Neuron, Mode-Matching, Flow, Acoustics, etc...

258 Topics 775 Posts

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  • FDTD, Low-Frequency, Neuron, Mode-Matching, Flow, Acoustics, etc...

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    G
    Dear Geremia, Here is the procedure I use for S4L: Prerequisites: The Yale Neuron compiler 8.2.6 for Windows https://github.com/neuronsimulator/nrn/releases/tag/8.2.6 You can use newer versions, but this one works best with S4L. Create a directory for a particular neuron structure, at root level: hoc files, asc, etc. a subdirectory called 'mechanisms': all your mod files. From a console, run the Yale Compiler on your 'mechanisms' directory: > nrnivmodl if it succeeds, it will create a nrnmech.dll file. move the nrnmech.dll file to root level (where your hoc files are) and clean the 'mechanisms' directory - all the .c and .o files. Compress into a zip file the main directory (that contains the hoc files, nrnmech.dll and 'mechanisms' dir). Change the extension to .hocz Now, in S4L use the import button to import your new neuron model, your newly created hocz file. Regards, Guillermo
  • H

    Simulations fail when multiple simulations are submitted

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    By default, Sim4Life tries to use all available resources to start as many simulations as you submit or have cores or GPUs available. The first simulation usually starts fine, and the rest fail due to insufficient licenses. You have the option to limit the number of simultaneous simulations in the ARES tool. Please change the Resource Management Option from Concurrent Jobs to One Job at a time as in the attached screenshot. [image: 1569997460703-ares3.jpg]
  • S

    what's the difference between red lines and white lines in gridding?

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    S
    Thank you for the great explanation.
  • S

    Temporal interface- SAM head- Low frequency solver

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  • K

    Question about setting up sources in acoustic simulations

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    H
    Hi @Kihyun, To create an acoustic simulation, click on “Sources”, then change the excitation signal from “Sinusoidal” to “User Defined.” This will provide an “Expression” field that you can edit as needed. I also recommend checking the Acoustic Tutorial in Section 3.7 of the Sim4Life Manual, which you can access from the top ribbon under “Help.” [image: 1761036820889-sim4life_jvkul06rui.png] [image: 1761036826795-sim4life_q3dc6omg4u.png]
  • R

    How to sense values on head.

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    R
    Solved it - Model the electrode as PEC and use the voltage reader
  • A

    This topic is deleted!

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  • S

    Using Server for Parameter Sweep

    remote solver isolve parameter sweep default setting
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    Hi everyone, I'm using Sim4Life and currently working with the Optimizer tool. I would like to run the optimization algorithm on a network server using ARES instead of executing it on my local machine. However, I can't seem to find an option in the simulation settings that allows me to select the server as the execution target — the optimizer always defaults to running locally. Is it now possible to run parameter sweeps and optimization tasks on a remote machine in the network (without using a remote desktop session)? If so, how can I configure this in Sim4Life? Thanks in advance!
  • G

    How to simulate frequency-dependent conductivity of biological tissue using EM LF Electro Ohmic Quasi-Static solver?

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    G
    Dear, @AntoninoMC Thank you very much for your detailed clarification. I now understand the fundamental difference between the Ohmic solver and the QS solver, and I have also tried some test runs with the QS solver, which helped me to grasp the impact of frequency dependence more clearly. In my current application, I am applying a voltage to the human body and measuring the potential difference between two points on the head. I am particularly interested in how the measured potential difference changes with the frequency of the applied current. The frequency range I am considering is typically from about 10 kHz up to 100 kHz, but I am also exploring much lower frequencies, down to around 100 Hz. If you could kindly point me to relevant references or scientific literature that discuss similar applications or provide guidance on which dielectric properties are most suitable in this frequency range, it would be extremely helpful. Thank you again for your support.
  • C

    Is there any way to retrieve and use results for an EMLF simulation that has not completed running?

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  • M

    Jobs suddenly remain queued indefinitely ... another story

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    B
    If simulations are queued indefinitely, this could be an indication of a license issue. To run a simulation, the solver needs to 'check out' a license feature from the license server. When it completes, it marks that license feature as available again. Sometimes, if the application were to crash for some reason, the license feature is not correctly marked as available, preventing other simulations from proceeding because they think the feature isn't currently available to checkout. To resolve this, one thing to try would be to stop and restart license software, or to reinstall the license to ensure that all license features are reset.
  • M

    Procedure for writing input files without actually queueing and running them...

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    B
    After creating the voxels for a simulation, the input file can be created without submitting the simulation by right-clicking on 'Solver' in the simulation configuration and selecting 'Write Input File'.
  • R

    Question about "Thickness Factor" in Single Element Focused Ultrasound Simulation

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    The Thickness Factor defines the thickness of the Piezo element and the Reflector as a fraction of the acoustic wavelength (determined from frequency and Speed of Sound). By default, n=10, so the fraction is 1/10. This is a parameter which should help to nicely design the SEFT such that it gets correctly voxeled later on (so not too thin) but also doesn't cover too much space (not too thick). Theoretically, the reflector and the active element can be as thin as a single cell layer, but you don't know the computational cell size when drawing the model. Since the voxeler is set to have a max step size of lambda/10, due to stability considerations, the Piezo and reflector will always be nicely and continuously voxeled when using the default Thickness Factor of 1/10. You can find more information about the Acoustic Solver, including relevant equations, in a thesis titled "Multi-Physics Computational Modeling of Focused Ultrasound Therapies", upon which the Acoustic Solver in Sim4Life is based.
  • A

    Question Regarding Temporal Interference Tutorial in Sim4Life

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    Hello, I have the same issue. Currently using Sim4Life 8.2.0.16876. I wonder if there is any new update on this. Many thanks, Ines
  • S

    EM-LF Solver- Tutorials Not Running

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    S
    OK, I will share it. Thanks
  • V

    XCore.CLog error

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    brynB
    it seems to happen (in Sim4Life 9.0.0) when you switch to the analysis tag after sending a solver job on the cloud. I guess it can be ignored and will be fixed in an upcoming update-fix release
  • V

    Solver Error in EM-LF Simulation on Yoon-son Model

    em-lf
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    Hi, Did you run your simulation using our SMALL server (16 CPU cores, 32 GB RAM) or the LARGE server (48 CPU cores, 96 GB RAM)? Also, could you let us know the total number of cells in your simulation? As a general suggestion for optimizing memory usage, you can start by running a simulation with a coarse grid to identify regions where the fields are negligible. Based on this, you can adjust the grid padding settings to exclude those body regions from the simulation domain, effectively "cropping" unnecessary areas and reducing the computational load.
  • A

    What is your experience with asking AI technical questions about sim4life?

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    I used it to get information for high level workflows. It can also come with suggestions for code, obviously, but it often invents functions that don't exist and implementations for me has not been very AI-powered. But the theoretical discussions are quite good.
  • V

    Stimulation source & impedance settings in EM-LF Ohmic Quasi-Static Solver

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    Here is the Web Manual section containing this information: 2.11.3.9 Neuro-stimulation with Imperfect Electrode-Skin Contact. Additionally, Yoon-Sun Arm Stimulation tutorial also includes this new feature. For more information or examples you can contact us at s4l-support@zmt.swiss. Thanks!
  • C

    Applying Non-Uniform Conductivity in LF Electro Quasi-Static model for skin

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    C
    Hi In Sim4Life the tissue properties are provided as a single values. However, the IT’IS website provides supplemental information on the tissue properties. In addition to the average value, you can find the standard deviation, minima and maxima. Low Frequency (Conductivity) » IT'IS Foundation](https://itis.swiss/virtual-population/tissue-properties/database/low-frequency-conductivity/)
  • P

    Jobs suddenly remain queued indefinitely

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    P
    After a call with S4L support, here is the solution for future reference: My machine had two GPUs connected, one of them old and deactivated. However, the script ExtractCudaInfo.py detected both of these in the line 'num_gpus = int(xml_root.find("attached_gpus").text)' and then got stuck trying to find information on the deactivated GPU. A quick fix for the issue is therefore to manually set the correct number, in my case 'num_gpus=1', in the script.