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Simulations & Solvers

269 Topics 801 Posts

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

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

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    16 Topics
    39 Posts
    G
    Hi, I'm trying to simulate a synapse between two identical neuron models, imported from the same .hoc file. I set the simulation as follow (see screenshot): -both neuron have the same HOC Model Settings -The first neuron "L23_PC_cADpyr229_1", pre-synaptic, has an IClamp on its soma -The second neuron "L23_PC-cADpyr229_2", post-synaptic, has a Exp2Syn point process on dendrite 9 -The network connection was created drag & dropping the first neuron's model and the Exp2Syn point process of the second neuron in the network connection settings [image: 1778756649765-f7472fbe-2fe9-4244-9297-34d7a1f29c16-image.png] If I try to run the simulation I get the error messages: Simulation : [Error] Failed to create neuron group ids. Error : Failed to write the input file Error : Unable to start simulation: failed to write input files. How can I solve this error? I already tried using different neurons from different .hoc files. Thank you in advance
  • R

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

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    B
    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.
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    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
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    EM-LF Solver- Tutorials Not Running

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    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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    C
    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.
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    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

    em-lf neurostim
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    C
    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!
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    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/)
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    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.
  • V

    High Field Values at Extremities

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    Hi @bryn, I think you’re right. The issue appears to be related to the boundary conditions on the outer bounding box. I changed the boundary to a flux(0) condition, and that resolved the problem with the localized high field values at the extremities. Thank you!
  • A

    "wire radius"

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    brynB
    Please give more context. E.g., "in the modeler when I use tool X", or in a "Y simulation" there is an option. or in this other thread (link) I asked about Z Then it will be easier to answer your question.
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    Modulated source in thermal simulation

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    @Sylvain Hi, thank you for your reply. I changed modulated field to El. Loss Density and everything works.
  • R

    Thermal, unable to write input files.

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    R
    Thank you. Uploaded.
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    MQS solver errors

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    H
    sending you an email via support
  • C

    LF Electro Ohmic Quasi-Stat. gives unexpected current density

    lf quasi-static ohmic quasistat current density low frequency
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    This topic is deleted!

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  • C

    How to get inhomogeneous B0 maps

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  • A

    Simulation outputs

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    A
    Great! Goit it, thank you so much. One last question regarding where the simulation outputs are located and saved. The coordinates of the voxelized entities where can be found? Thank you so much for your time
  • P

    White matter anisotropy

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    G
    @bryn Thanks, I found it!
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    Unable to start simulation: failed to write input files.

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    ofliO
    Hi @tayjiekai sim4life.lite is the student version of our online simulation platform sim4life.science and comes with certain limitations. As indicated by the error message, it does not support a number of neurons exceeding 10. If the limitations of sim4life.lite are too restrictive for your work, I suggest transitioning to the full Sim4Life web version at sim4life.science.