As you know the ref concentration indicates the minimum value for the diffusion type doping. I think a concentration of 1e6 cm-3 is negligible, so as long as the value is small enough the chosen number in our examples is arbitrary.
In your case I recommend visualizing the doping once you set up the simulation; for this mesh the structure and visualize grid>N. Does the profile match your intended doping? Using a constant doping as you described is a good way to fix the minimum doping value across the entire simulation.
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