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> How can I plot physical quantities such as flux or energy distribution ?
There is no plotting facility in Geant4 but you may make histograms or ntuples and write them out at the end of run for plotting by a plotter such as OpenScientist (http://openscientist.lal.in2p3.fr/) or ROOT (http://root.cern.ch/). geant4/examples/basic/B4 shows how to do this.
> 2) Is MOMO only graphical GUI for geant4 is there another one?
There is Xm and Qt, but I think you mean an interface for designing geometry. Only MOMO can do this.
> 3) Do you familiar with SimpleGeo that represent excellent graphical interface for making FLUKA geometry. is it have plugin to export geometry for geant4?
I'm not familiar with this.
> 4) how should I compile geant4 files with QT under windows?
I am not a Windows user but I believe it is straightforward using the instructions in the Installation Guide using CMake.