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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
  • Convergence Level in S4L

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    A simulation can end in a couple different cases: If the specified level of convergence is reached, or if the specified number of periods are simulated. In the case of that tutorial, the simulation is set to run for 15 periods, and so it ended before a -50 dB convergence was reached. Convergence is a spectrum, and the level of convergence required for a given application is up to the user's discretion.
  • Orientation of antennas affect simulation results

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    Thanks Ofi. How can I fix this or is this something I need to account for?
  • tutorial not running

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  • FDFD solver tutorials

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  • Thermal external input file

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  • Modeling Ferrite in an FDTD Simulation

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    ofliO
    Hi @arc Please check "Console" window (open it via menu VIEW | Console if it is not open) to see what kind of error you are getting. The reason for failed simulation might be related to something else. You can easily test with an existing tutorial example. For example, open Dipole Antenna Tutorial, model a rectangular brick next to the dipole, clone one of the existing simulation settings and drag&drop this new brick into the simulation set its material such that rel/ Permeability o 1e4 generate grid, voxel and run to see if it also fails I hope it helps.
  • Python API for Debye dispersive model

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    Yes, You need to import XMaterials and specify the material model to be linear dispersive, as in the following example (which should be easy to extend), where parameters for one Debye pole are assigned. import XMaterials as xm # Adding a new MaterialSettings material_settings = emfdtd.MaterialSettings() material_settings.ElectricProps.MaterialModel = material_settings.ElectricProps.MaterialModel.enum.LinearDispersive # Specify settings for dispersive poles material_settings.raw.ElectricDispersiveSettings.StartFrequency = 10.e6 material_settings.raw.ElectricDispersiveSettings.EndFrequency = 100000.e6 material_settings.raw.ElectricDispersiveSettings.Conductivity = 0. material_settings.raw.ElectricDispersiveSettings.Permittivity = 11.098 debye_pole_01 = xm.LinearDispersionPole() debye_pole_01.Active = True debye_pole_01.Type = xm.LinearDispersionPole.ePoleType.kDebye debye_pole_01[xm.LinearDispersionPole.ePoleProperty.kDebyeAmplitude] = 1.0 debye_pole_01[xm.LinearDispersionPole.ePoleProperty.kDebyeStaticPermittivity] = 22.67 debye_pole_01[xm.LinearDispersionPole.ePoleProperty.kDebyeInfinityPermittivity] = 11.098 debye_pole_01[xm.LinearDispersionPole.ePoleProperty.kDebyeDamping] = 3.234e-11 # Add dispersive poles to the Linear Electric Dispersion Viewer material_settings.raw.ElectricDispersiveSettings.Poles = [debye_pole_01]
  • Ohmic QS simulation with anisotropic material fails

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    I suspect that this is because the grid from your LF simulation does not match the grid that you use in your isotropic and anisotropic simulations. The isotropic simulation runs fine because it does not use your cache file. The anisotropic simulation has stored those conductivity values expecting a specific grid. Try right clicking on the grid settings folder in the simulation from which you are creating your anisotropy tensor, select "Copy Grid Configuration", then "Paste Grid Configuration" on the anisotropic simulation. If you want to include features in your anisotropic simulation that you don't don't want to have simulated in your initial LF simulation, you can still include include objects in your initial simulation so that they are considered for the gridding without assigning them material properties, using them as a boundary condition or voxeling them. Just drag the object directly into the grid settings folder. That way your grid can always match.
  • FDTD simulation failure in sensor post-processing stage

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    ofliO
    Hi @yiyang did it happen with one particular simulation project or does it always happen? Please (if you can) share the project with Sim4Life Application team via sending an email to s4-support@zmt.swiss to check. Thanks
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  • Acoustic simulation

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    We use standard units in the acoustic solver, which means we're solving the wave equation in pressure which has units of Pa. Note though that the acoustic equation is Linear (careful, this doesn't apply to the nonlinear solver), which means that you can arbitrarily scale the input signal by a scalar and the output (in pressure) will be exactly the same and scaled by that same constant. (You need to be careful when you consider energy related quantitites which are something something pressure squared) Essentially, find the scaling factor between pressure and voltage (assuming linearity), then run your simulation with an arbitritrary amplitude and then scale the pressure output.
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  • Import Voxels - How to Assign Materials?

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    @dbsim4 Answering my own question: In the Modelling tab (not simulation), each imported label/voxel type can be assigned a material in the Controller window. Auto Assign seems to work decently well if the materials in the file are well named. Probably should be done before dragging the model into the Simulation.
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    @montanaro Thank you! The acoustic reflection simulation is now behaving and giving results which map to what you'd expect. Thank you so much for helping! Jean
  • PdhAddCounter for processor total failed

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  • Sensors placement

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  • Running the simulation causes the software to hang

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  • Unable to see 1g and 10g SAR Values

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    ofliO
    Dear Shreya, I assume you meant simulated 1g and 10g SAR values. If you are referring to dipole antenna tutorial, it is not possible to extract SAR values since the simulation project does not contain any lossy object - it is just a dipole antenna in free-space. Please check "SAR in a Flat Phantom" tutorial and section 3.1.4 of Sim4Life tutorial document for details related to SAR simulation and extractions.
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