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There is some difference when I used the GPS and ParticleGun to sumulate neutron capture ,I found that the quantity of capture atom is quiet different , the quantity of using ParticleGun is twice as GPS.Of course the particle source conditions are same.
ParticleGun and GPS have some commands in common, and if you use only those commands the results should be the same. But the ParticleGun does not have any commands for “isotropic mono neutron” so I am not surprised the results are different.
Mmm. Perhaps you should let us see your code. For example, an isotropic distribution is uniform in cos(theta), not theta. To be safe, use G4RandomDirection.