# S.E. Mazzaglia Nov 14, 2009

# Example macro file to show how to change geometric properties and voxelization of the phantom/detector

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


##########################
# Set of the physic models
#
#/Physics/addPhysics standard_opt3                       # Electromagnetic model
#/Physics/addPhysics elastic                             # Hadronic elastic model
#/Physics/addPhysics binary                              # Hadronic inelastic model
#/Physics/addPhysics local_ion_ion_inelastic             # Hadronic inelastic model for ions (local physic list)
#/Physics/addPhysics radioactive_decay

#
# Or alternatively:
#
/Physics/addPhysics QGSP_BIC_EMY
/Physics/addPhysics radioactive_decay

# Initialize geometry and physic 
/run/initialize

#############################
# Initialize graphic system #     
#############################
# 
/vis/scene/create
/vis/open OGL
/vis/viewer/flush
/vis/viewer/set/viewpointThetaPhi 30 140 deg
/vis/scene/add/trajectories
/vis/scene/endOfEventAction accumulate -1 # this accumulate infinite tracks 
# zoom to phantom...
/vis/viewer/panTo 1.5 0.5
/vis/viewer/zoomTo 3

##########################
# Set here the cut and the step max for the tracking. 
# Suggested values of cut and step:
#
/Physics/setCuts 0.01 mm
/Step/waterPhantomStepMax 0.01 mm 

#########################

#########################
# Set the primary particle type,
# energy and position along the X direction
#
/gun/particle proton
/beam/energy/meanEnergy 62 MeV
/beam/energy/sigmaEnergy 400 keV
/beam/position/Xposition -2700 mm




# Copy & Paste in a new macro the previous and ONE of the following groups of commands
# in order to change the Phantom & Detector geometry!




############################
# Change Phantom geometry  #              
############################
# Move Phantom 10 cm forward the default position (20, 0 , 0 cm)
# Position refers to the center of the phantom box respect to the center of the World
/changePhantom/position 30. 0. 0. cm
/changePhantom/update

# Enlarge Phantom to (42, 40, 40 cm) respect to the default sizes (40, 40, 40 cm)
# Null or negative parameters mean "leave it unchanged"
/changePhantom/size 42. 0. 0. cm
/changePhantom/update
#
/run/beamOn 300
#
############################
# Change Detector geometry #
############################
# Change detector size along X dimension
# "0" parameter means "leave it unchanged"
/changeDetector/size 41. 0. 0. cm

# The following line moves the detector 1 cm forward (along the beam direction),
# respect to the default position inside the phantom (0, 18, 18 cm).
# Displacement parameters refer to the lower left corner of the detector respect to that of the phantom
# by the point of view of the beam.
# Negative parameters means "leave it unchanged"
/changeDetector/displacement 1. -1. -1. cm
#
/run/beamOn 300
#
###########################
# Change Detector Voxels  #
###########################
#
# Use the following line if you need more slabs along the X direction, leaving unchanged the other sizes
# Null or negative parameters mean "leave it unchanged"
/changeDetector/voxelSize 100. 0. 0. um
/changePhantom/update
# StepMax SHOULD not be bigger than 5% of the dose slice thickness!
/Step/waterPhantomStepMax 0.005 mm 
#################################################################################################


####################################
# Change Phantom/Detector geometry #
####################################
##########################################################################################
# Cut & paste the following commands in order to create, starting from the default sizes, 
# an unique, 10 microns depth, slab in the detector,
# enlarging it to fit to the phantom Y and Z sizes 

# Set voxel size along X to 10 microns
/changeDetector/voxelSize 10 0 0 um
# Put detector in the lower left corner of the phantom
/changeDetector/displacement 0 0 0
# Resize the detector to fit voxel X size and phantom Y and Z sizes
/changeDetector/size 0.01 400 400 mm
# Enlarge voxel Y and Z sizes to fit to that of the phantom (in order to have a simple slab)
/changeDetector/voxelSize 0 400 400 mm

# Optionally, fit completely the phantom to the detector
/changePhantom/size 0.01 0 0 mm
/changePhantom/update
#########################################################################################

##########################################################################################
# Cut & paste the following commands in order to create, starting from the default sizes, 
# a full voxellized (200 by 200 by 200) detector

/changeDetector/voxelSize 0 200 200 um
/changeDetector/displacement 0 0 0
/changePhantom/size 4 4 4 cm
/changePhantom/update
##########################################################################################