# G. Danielsen, A. Heikkinen, P. Kaitaniemi
#
# Macro file for IAEA geometry for a carbon beams in water.

/control/getEnv G4SYSTEM
 
#########################
# Set of the verboses 
#
/control/verbose 1
/tracking/verbose 0
/run/verbose 1
/event/verbose 0

/analysis/setAnalysisFile IAEA.root

##########################
# Set of the physic models
#
/physic/addPhysics emstandard_opt3                     # Electromagnetic model
/physic/addPhysics elastic                             # Hadronic elastic model
/physic/addPhysics binary                              # Hadronic inelastic model
/physic/addPhysics local_incl_ion_ion_inelastic        # Hadronic inelastic model for ions (local physics list)
/physic/addPhysics radioactive_decay                   # Radioactive decay

##########################
#       Geometry         #
##########################
/geometrySetup/selectGeometry IAEA  # Select the IAEA geometry
/iaea/waterPhantomThickness 27.9 cm #default is 27.9, zero will remove phantom

#############################
#    Beam energy detection  #
#############################
# define scoring mesh for energy deposits
# If attenuation measures are not needed this is redundant
# and time-consuming. Even pretty small runs give good attenuation graphs.

#/score/create/boxMesh boxMesh_1

#Box size is the radius of the box ie 20x20x20 gives 40x40x40 outer dimensions
#/score/mesh/boxSize 13.95 16. 16. cm        # The box size and translation may require adjustement

#this translates the middle of the mesh-box.
#/score/mesh/translate/xyz 69 0.0 0.0 cm
#/score/mesh/nBin 400 1 1      # 400 bins in x-direction, 1 in y and z directions, changes require change in code

#
# define scorers and filters
# is not able to filter ions.

#/score/quantity/energyDeposit eDep
#/score/quantity/population eDep
#/score/quantity/nOfStep nOfStepGamma
#/score/filter/particle gammaFilter gamma
#/score/quantity/nOfStep nOfStepEMinus
#/score/filter/particle eMinusFilter e-
#/score/quantity/nOfStep nOfStepEPlus
#/score/filter/particle ePlusFilter e+
#/score/close

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

##########################
#     Visualisation      #
##########################

####### DAWNFILE ###### 
#/vis/scene/create
#/vis/open DAWNFILE
#/vis/viewer/flush
#/vis/viewer/set/viewpointThetaPhi 45 45	 deg
#/vis/viewer/zoom 0
#/vis/viewer/pan 0 0 cm
#/vis/scene/add/trajectories
#/vis/scene/endOfEventAction accumulate
#/tracking/storeTrajectory 1

#/vis/viewer/update
#/vis/scene/add/trajectories
#/vis/modeling/trajectories/create/drawByCharge
#/vis/modeling/trajectories/drawByCharge-0/default/setDrawStepPts true
#/vis/modeling/trajectories/drawByCharge-0/default/setStepPtsSize 2
#/vis/scene/endOfEventAction accumulate

####### OGLIX #######
#/vis/scene/create
##/vis/open OGLSX
#/vis/open OGLIX
##/vis/open OGLIX 600x600-100+0
##/vis/drawVolume
##/vis/viewer/set/viewpointThetaPhi 0 0 deg
#/vis/viewer/set/viewpointThetaPhi 45 45 deg
##/vis/viewer/zoom 1.0
#/vis/scene/add/trajectories
#/vis/modeling/trajectories/create/drawByCharge
#/vis/modeling/trajectories/drawByCharge-0/default/setDrawStepPts true
#/vis/modeling/trajectories/drawByCharge-0/default/setStepPtsSize 2


# Draw only certain particles
#/vis/filtering/trajectories/create/particleFilter
#    Now select filtered particles
#/vis/filtering/trajectories/particleFilter-0/add gamma
#/vis/filtering/trajectories/particleFilter-0/add electron
#/vis/filtering/trajectories/particleFilter-0/add neutron
#/vis/filtering/trajectories/particleFilter-0/add proton
#/vis/filtering/trajectories/particleFilter-0/invert true # charged particles only
#/tracking/storeTrajectory 1
#/vis/scene/endOfEventAction accumulate

##########################
# Set here the cut and the step max for the tracking. 
# Fixme, recommenadtions needed
#
/physic/setCuts 0.8 cm
#/physic/setCuts 0.4 cm
/Step/waterPhantomStepMax 0.5 cm
#/Step/waterPhantomStepMax 0.01 mm 

#########################
# Set the primary particle type,
# energy and position along the X direction
#
/gun/particle ion
/gun/ion 6 12 6     # Carbon-12

/beam/energy/meanEnergy 4800 MeV # 400MeV/u * C12 = 4800
/beam/energy/sigmaEnergy 24 MeV # dE/E = 5e-3
/beam/position/Yposition/sigmaY 1.7 mm # 4mm * 2.35 ~ 1.7
/beam/position/Zposition/sigmaZ 1.7 mm
/beam/momentum/sigmaY 0.001
/beam/momentum/sigmaZ 0.001

#########################
# Start of the run
#

/beam/position/Xposition 0 cm
/beam/position/Yposition 0 cm
/beam/position/Zposition 0 cm

#/run/beamOn 100    # For test/visualization
/run/beamOn 200000   # Default value in release
#/run/beamOn 10000  # Good for basic physics run (takes few min)
#/run/beamOn 400000 # Accurate results with good statistics 


#/score/dumpQuantityToFile boxMesh_1 eDep eDep.txt

# Example of running in loop 
/control/alias initialValue 0
/control/alias   finalValue 3
/control/alias     stepSize 1
#/control/loop macro/iaea.loop counterName {initialValue} {finalValue} {stepSize}
#/control/unalias initialValue