# G.A.P.Cirrone
# cirrone@lns.infn.it
#
# Macro file recommended for the use with proton beams and built-in physic list.
# This macro uses the physics list already contained in the Geant4 distribution
# 
#    The 'Reference Physics Lists' can be activated setting a specific enviroment variable to the name
#    of the physics. For example if the QGSP_BIC Reference Physics Lists must be activated the User 
#    must set export PHYSLIST=QGSP_BIC (or setenv PHYSLIST QGSP_BIC).
#    A 'Reference Physics Lists' contains all the physics process necessary to a particle transport
#    If the User set the PHYSLIST variable Hadrontherapy will start with the defaultMacroWithReferencePhysicsList.mac
#    macro. See this macro file for more details

#########################
# Set of the verboses 
#
/control/verbose 1
/tracking/verbose 0
/run/verbose 1
/event/verbose 0

##########################
# Set of the physic models
#
/Physics/addPhysics QGSP_BIC_EMY



##########################
# Initialisation procedure
#
/run/initialize

#########################
# Set the primary particle type,
# energy and position along the X direction
#
#---------------------------gps-----------------
/gps/pos/shape Circle
/gps/pos/centre -310. 0. 0. cm
/gps/pos/radius 0. mm
/gps/pos/sigma_r 2. mm
/gps/particle proton
/gps/pos/type Beam


# the incident surface is in the y-z plane

/gps/pos/rot1 0 1 0
/gps/pos/rot2 0 0 1

# the beam is travelling along the x-axis without any angular dispersion (angular despersion set to 0.0)
#

/gps/ang/rot1 0 0 1
/gps/ang/rot2 0 1 0 
/gps/ang/type beam1d 
/gps/ang/sigma_r 0. deg


# the beam energy is in gaussian profile
#
/gps/ene/type Gauss
/gps/ene/mono 62 MeV
/gps/ene/sigma 0.3 MeV

#/beamLine/RangeShifter/RSMat G4_PLEXIGLASS
#/beamLine/RangeShifter/thickness 13 mm
/beamLine/FinalCollimator/halfInnerRad 12.5 mm

##########################
# Set here the cut and the step max for the tracking. 
# Suggested values of cut and step:
# Set cuts OUTSIDE the detector
# 
/run/setCut 1 mm

# Set cuts ONLY inside the detector
#
/run/setCutForRegion DetectorLog 0.05 mm

/Step/waterPhantomStepMax 1 mm 

#########################
############################################################################################################################## 
# 							 DETECTOR DESCRIPTION
###################################################
# USE THE FOLLOWING FOUR LINES FOR DEFINITION OF PHANTOM
###################################################
#
#/changePhantom/position 20. 0. 0. cm
#/changePhantom/update

/changePhantom/size 40 40 40  cm
/changePhantom/position 20 0 0 cm

###################################################
# USE THE FOLLOWING FOR A VOXELLIZED DETECTOR
###################################################
#


/changeDetector/size 4 4 4 cm
/changeDetector/voxelSize .1 40 40 mm

# Put the detector in the lower left corner of the phantom
#
/changeDetector/displacement 0 18 18 cm
/changePhantom/update


# Visualisation 
#
/vis/scene/create
/vis/open OGL
/vis/viewer/flush
/vis/viewer/set/viewpointThetaPhi 30 140 deg
/vis/viewer/zoomTo 1
#/vis/viewer/panTo 100  20 cm
/vis/viewer/panTo -10  0 cm
/vis/scene/add/trajectories
/tracking/storeTrajectory 1
/vis/scene/endOfEventAction accumulate -1
/vis/viewer/update

#########################
# Display the event number
# during the run
# 
/event/printEventNumber 1


# Default material is liquid water (G4_WATER)
#/changePhantom/material G4_Pb

# For dose/fleunce computation of primary and secondary particles
#/analysis/secondary true

# For dose average LET computations of primary and secondary particles
#/analysis/computeLet

/run/beamOn 10
#########################
# Move the generated .root & .out
# files into the
# "SimulationOutputs" folder
# if this folder has been created

/control/shell mv DoseDistribution.root experimentalData/proton/BraggPeak/protonBraggPeak.root		
/control/shell mv Dose.out experimentalData/proton/BraggPeak/Dose.out