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Simulations & Solvers

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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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    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
  • Exporting touchtone files

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    Thank you Ofli for your quick response. That was very helpful!
  • How to get isometric or uniform grid?

    Unsolved grid isometric uniform emfdtd
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  • Current field simulation

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    Dear Liu, Yes, in order to see any losses, you need to set at least a conductivity different to 0. I would advice you to check if you set correct electric properties in the material settings. Best
  • CEM43 license

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  • Frequency sweep using LF model

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  • Loss tangent setting for user defined material

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  • Analysis - Empty Coil - Grid Fail

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    Hello, Do you have any error message appearing in the console? If a grid cannot be created, you have to carefully check the grid settings, and ensure that the number of cells is not the big (if so, you can reduce it by adjusting the padding, for example).
  • Pop-up Alert Stops Stimulation

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    Dear @habib, Just to inform you that has been solved the bug which was causing this pop-up window to appear, and which stopped the script from continuing until the "Ok" button was pressed: [image: 1649688752403-bug.jpg] However, this bug was caused by the code line, which appears in the image: "analysis.RefreshViewers()" With the new S4L v7.0, this line caused this bug for some reason. After removing it, it was possible to avoid that pop-up window. Just to highlight that finding this bug costed 10+ hours, due to the new update. Best, Guillem
  • LF EQS solver diverged/failed

    divergence low-frequency
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  • I'm modeling TEM cell, which is device for generating a electric field

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    @ofli Thank you for texting. Yes. I set up the similar one. I adjusted the size to the edge of the TEMcell tho.
  • Can Acoustic solver works with Flow solver?

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    I am not aware of any coupling implemented for this combination.
  • Programmatically set source settings (neuro)

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  • How to use a script to automatically open an already run simulation

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    @pyf Hi, This is what I found in the tutorial scripts for thermal simulations. Check the RunTutorial function. It may help. Best. def CreateModel(): ... def CreateEmFdtdSimulation(): ... return em_sim def CreateThermalSimulation(em_sim): ... return thermal_sim def AnalyzeEmAndThermalSimulation(em_sim,thermal_sim): # Create extractor for the two simulation output files em_results = em_sim.Results() thermal_results = thermal_sim.Results() # overall field sensors em_overall_field_sensor = em_results[ 'Overall Field' ] em_overall_field_sensor.Normalization.Normalize = True thermal_overall_field_sensor = thermal_results[ 'Overall Field' ] # Create a slice viewer for the SAR slice_field_viewer_sar = analysis.viewers.SliceFieldViewer() slice_field_viewer_sar.Visualization.Smooth = True slice_field_viewer_sar.Inputs[0].Connect( em_overall_field_sensor['SAR(x,y,z,f0)'] ) slice_field_viewer_sar.Update(0) slice_field_viewer_sar.GotoMaxSlice() document.AllAlgorithms.Add( slice_field_viewer_sar ) #THERMAL slice_field_viewer_t = analysis.viewers.SliceFieldViewer() slice_field_viewer_t.Visualization.Smooth = True slice_field_viewer_t.Inputs[0].Connect( thermal_overall_field_sensor['T(x,y,z,t)'] ) slice_field_viewer_t.Update(0) document.AllAlgorithms.Add( slice_field_viewer_t ) def RunTutorial( path document.New() CreateModel() em_sim = CreateEmFdtdSimulation() document.AllSimulations.Add(em_sim) em_sim.UpdateGrid() em_sim.CreateVoxels(path) thermal_sim = CreateThermalSimulation(em_sim) document.AllSimulations.Add(thermal_sim) thermal_sim.UpdateGrid() thermal_sim.CreateVoxels(path) em_sim.RunSimulation(wait=True) thermal_sim.RunSimulation(wait=True) AnalyzeEmAndThermalSimulation(em_sim,thermal_sim) if name == 'main': RunTutorial( project_path )
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    @mingjuan Hi, I recommend updating your driver (https://developer.nvidia.com/opengl-driver).
  • EM LF electro simulation

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  • Subgrid for Acoustic Simulation, to limit grid size?

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    There's no subgridding just a rectilinear / adaptive grid (you can create new grid settings and drag and drop solids or wireframes to these) What you can do (at your own 'risk') is manually set the grid to the resolution you want and not use the automatic grid settings. Typically you want at least 10 points per wavelength (more is better) and the wavelength in air (343 / freq) and water (1500 / freq) are quite different.
  • adding inductive decoupling circuits into the model

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  • Pulse-Echo Ultrasound Acoustic Simulation Time Domain

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    Don't worry about the time step, just make sure it's fine enough, Sim4Life will then interpolate your function into it's own timestep as needed (so, you just need to be careful that your timestep is not too coarse such that Sim4Life won't be able to linearly (I think) interpolate it Essentially, the answer is yes, its sufficient
  • SEFT Tutorial Grid Error

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    Typically 1 MHz is way too large wavelength = speed of sound / frequency resolution = wavelength / 10 so, if you speed of sound in water is 1500 m/s and you want to run a simulation at 100 kHz, then the wavelength is around 15 mm, and the resolution should be at least 1.5mm From the resolution and your domain size you can calculate the grid size Grid Size: max. 20 Mio cells
  • Time domain acoustic simulation- problem with the number of periods

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    @montanaro That would be of great help. Thank you so much Annalisa