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This is because a parallel beam uses the surface area of the source shape as a fluence normalization factor. E.g. in egs_parallel_beam, the getFluence function is:

    EGS_Float getFluence() const {
        return count/shape->area();
    };

And for a cylinder shape:

    EGS_Float area() const {
        return 2*M_PI*R*(R+h);
    };

This value of fluence is used to normalize the energy/dose deposited. However, the fluence is not what is used as the "number of primary particles" for the scored phase-space. Therefore the source normalization is lost when you go to use the phase-space. I'll have to give some thought to whether we should make a change. For now, you can recover the original …

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