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1. The collimated source is a bit tricky to explain, the distance parameter is really more of a normalization tool. Yes, it will affect the normalization of the kerma results since they are normalized "per fluence". For most sources the fluence is just the number of source particles, but for the collimated source this is not the case. See this presentation for a detailed explanation: https://slides.com/ftessier/egsnrc-collimated-source/fullscreen
2. The calculation geometry overrides the simulation geometry. The simulation geometry is not used at all in this case (except it is the default for egs_view when you visualize).

For the rest I'm going to check with Ernesto, he will have more insight..

Thanks! This is the problem, the source needs to be moved /u/RaGa1131. The distance input doesn't do what you think. See the explanation in that link above.

See here for more on the source normalization:

https://slides.com/ftessier/egsnrc-collimated-source/fullscreen

If you want to use the collimated source, I highly recommend working through this set of slides by Fred:

https://slides.com/ftessier/egsnrc-collimated-source/fullscreen

There is also a worked example in the getting-started manual that helps illustrate the normalization of the collimated source.

Keep in mind that this source employs a possible approximation, if you are using it to speed up simulation of an isotropic source. By not simulating particles emitted "backwards", you miss out on any contributions from those that would have scattered back into your region of interest.