WCSim.mac

# Sample setup macro with no visualization

/run/verbose 1
/tracking/verbose 0
/hits/verbose 0
/grdm/verbose 0


###############
# GEOMETRY
###############

## select the geometry
# Default config if you do nothing is currently SuperK
# If you do use a geometry other than SuperK, then you *must*
#  uncomment the line /WCSim/Construct after the chosen geometry
#  and all other geometry related commands
#  or you'll get a seg fault or wrong results

#some geometries can be tuned by config file options
# it is important to do things in the correct order
#/WCSim/WCGeom GEOM to set the defaults
#/WCSim/commands to modify the defaults
#/WCSim/Construct

#Use the standard SK geometry
# no extra commands required


#Use the nuPRISM geometry w/ mPMTs DEPRECATED (use IWCD_mPMT_WithOD below)
#/WCSim/WCgeom nuPRISMShort_mPMT
#then set options
#/WCSim/Construct
## OR for single mPMT mode or updating mPMT parameters:
#/control/execute macros/mPMT_nuPrism1.mac
#/control/execute macros/mPMT_nuPrism2.mac

#Note that whilst you can change the number of PMTs
# in the HK FD ID using these photocoverage parameters,
# it is up to you to verify that you have produced
# a valid geometry.
#Suggestions of things to check
# - Has an extra tower of PMTs been built?
#   (Check this via the std error stream)
#   This can cause tracks to get stuck & be killed
# - Is the layout of the ID PMTs (20" + OD) sensible?
#   (Plot the position of each PMT. See $WCSIM_SOURCE_DIR/sample-root-scripts/plot_pmts.C)
#   When there is e.g. a low number of mPMTs
#   unrealistic stripes of mPMTs are produced
#   that may cause odd output
# - Is the number of hits consistent with expectation?
#   For example, compare the number of hits per PMT
#   using the default geometry with your geometry
#   using e.g. a particle gun with sufficient statistics

#Use the HK FD ID-only geometry DEPRECATED (use HyperK_HybridmPMT_NoOD_Realistic)
#/WCSim/SetPMTPercentCoverage  20.2150576375662
#/WCSim/SetPMTPercentCoverage2 10.1075288187831
#/WCSim/WCgeom HyperK_HybridmPMT
#/WCSim/Construct


#Use the HK FD ID + OD geometry DEPRECATED (use HyperK_HybridmPMT_WithOD_Realistic below)
#/WCSim/SetPMTPercentCoverage  20.2150576375662
#/WCSim/SetPMTPercentCoverage2 10.1075288187831
#/WCSim/WCgeom HyperK_HybridmPMT_WithOD
#/control/execute macros/geom_hk_mpmt_options.mac
#/control/execute macros/geom_hk_od_options.mac
#/WCSim/Construct


#Use the HK FD Realistic ID + OD geometry
#/WCSim/WCgeom HyperK_HybridmPMT_WithOD_Realistic
#/WCSim/Construct


#Use the HK FD Realistic IDonly geometry
# Note that the difference between this & the realisitc ID + OD geometry above is
# that the OD PMTs are not placed in the geometry.
# All other aspects of the OD geometry are there (ID/OD deadspace, tyvek, etc.)
# This means that you get a speed win in terms of hit stuff (e.g. PMT & electronics simulation, triggering)
# which is thought to be a small fraction of running time compared with the Geant4 particle propagation
#/WCSim/WCgeom HyperK_HybridmPMT_IDonly_Realistic
#/WCSim/Construct


# Some other SuperK options (different to the default 20" 40% case)
#/WCSim/WCgeom SuperK_20inchPMT_20perCent # Note: the actual coverage is 20.27%
#/WCSim/WCgeom SuperK_20inchBandL_20perCent # Note: the actual coverage is 20.27%
#/WCSim/WCgeom SuperK_12inchBandL_15perCent # Note: the actual coverage is 14.59%
#/WCSim/WCgeom SuperK_20inchBandL_14perCent # Note: the actual coverage is 13.51%
#/WCSim/Construct

# This is the updated IWCD geometry as of 20250128
#/WCSim/WCgeom IWCD_mPMT
#/WCSim/Construct

# This is the updated IWCD geometry as of 20250128, plus OD
#/WCSim/WCgeom IWCD_mPMT_WithOD
#/WCSim/Construct

# Use the WCTE geometry (16c4r from CAD)
#/WCSim/WCgeom nuPRISMBeamTest_16cShort_mPMT
# Rotate barrel by half a tower (needed for correct WCTE geometry)
#/WCSim/Geometry/RotateBarrelHalfTower true
#/WCSim/Construct

# true --> default (old) replica method to place PMTs. 
# false --> new placement method, does not use replica in construction, place PMT one by one
#/WCSim/PMT/ReplicaPlacement true
############################################################################################
##These comments are only useful when using 
#/WCSim/PMT/ReplicaPlacement false
# Apply random fluctuation to PMT placement. Argument specifies the Gaussian 1 sigma value in 1D
# The fluctuation is applied at the last step of position calculation
#/WCSim/PMT/PositionVariation 0 mm
# Change the ID radius at top, middle and bottom for PMT placement
# The PMT positions and directions are calculated such that the PMTs are always touching
# and perpendicular to the ID wall in the same (z,theta) coordinates 
#/WCSim/PMT/TankRadiusChange 0 0 0 mm
# Read PMT positions from input file. This overrides the auto positioning algorithm
# The (z,theta) coordinates are calculated from the input, and r is auto-tuned as above
# This table corresponds to the nuPRISMBeamTest_16cShort geometry
#/WCSim/PMT/PositionFile data/mPMT_Position_WCTE.txt
############################################################################################
#/WCSim/Construct

# Set Gadolinium doping (concentration is in percent)
# Default is no Gd doping
#WARNING This is in the wrong place. If you want to turn it on in your detector
#it must go between /WCSim/WCgeom & /WCSim/Construct
#/WCSim/DopingConcentration 0.1
#/WCSim/DopedWater false

##################
# MISCELLANEOUS
##################

#Added for the PMT QE option 08/17/10 (XQ)
# 1. Stacking only mean when the photon is generated
# the QE is applied to reduce the total number of photons
# 2. Stacking and sensitivity detector
# In the stacking part, the maximum QE is applied to reduce
# the total number of photons
# On the detector side, the rest of QE are applied according to QE/QE_max
# distribution. This option is in particular important for the WLS
# 3. The third option means all the QE are applied at the detector
# Good for the low energy running.
# 4. Switch off the QE, ie. set it at 100%
#
# Studies in ~2022 suggest that SensitiveDetector_Only is the most correct

#/WCSim/PMTQEMethod     Stacking_Only
#/WCSim/PMTQEMethod     Stacking_And_SensitiveDetector
/WCSim/PMTQEMethod     SensitiveDetector_Only
#/WCSim/PMTQEMethod     DoNotApplyQE

#turn on or off the collection efficiency
/WCSim/PMTCollEff on

# command to choose save or not save the pi0 info 07/03/10 (XQ)
/WCSim/SavePi0 false

##################
# AmBe CALIBRATION SOURCE
##################
# - BGO Placement: Default in source code is false. If set to true, you'll place the BGO inside
# the detector geometry at (0,0,0) position. This is only supported if you use ambeevt generator
# so you can see the tag scintillation light for the AmBe source.
#/WCSim/BGOPlacement
# Note that /WCSim/BGOPlacement *must* be set before /WCSim/Construct
#
# - BGO Position: Place the source in a different position using X, Y and Z coordinates
#/WCSim/BGOPosition 1 1 1 m


# - /WCSim/SaveCapture & /process/inactivate nKiller: Default not set.
# Also specially needed for AmBe calibration. The first command makes sure the Capture processes
# are being saved. The second one ensures Geant4 is not killing neutrons too early in the run,
# so we can have neutronCapture at any time in the run.
# Note that the nKiller process is not defined in the FTFP_BERT_HP
#  (can be turned on via /WCSim/physics/list FTFP_BERT_HP in jobOptions.mac)
# and so will cause a fatal crash.
# When using FTFP_BERT_HP, neutrons are not killed an so you just have
# to set /WCSim/SaveCapture true
#/WCSim/SaveCapture true
#/process/inactivate nKiller

##################
# DIGITISER & TRIGGER
##################

#choose the Trigger & Digitizer type
/DAQ/Digitizer SKI
/DAQ/Trigger NDigits
#/DAQ/Trigger NoTrigger

#grab the other DAQ options (thresholds, timing windows, etc.)
/control/execute macros/daq.mac

##################
# DARK NOISE
##################

#There is an independent messenger class instance for each PMT type
# tank is the default one & is present in all geometries
# tankPMT2 is for the second ID PMT type (i.e. mPMTs in HK FD)
# OD is for the OD
#In typical use, it is important that all PMT types are setup with the same dark noise time windows

# default dark noise frequency (and conversion factor) is a PMT property, set in the code.
#  The default is ON
# Below gives possibility to overwrite nominal values, eg. to switch OFF the Dark Noise.
/DarkRate/SetDetectorElement tank
#/DarkRate/SetDarkRate 0 kHz   #Turn dark noise off
#/DarkRate/SetDarkRate 4.2 kHz #This is the value for SKI set in SKDETSIM. This is the default value for HK FD 20" Box and Line PMTs that has been used in WCSim since 2020
#/DarkRate/SetDarkRate 8.4 kHz #For 20 inch HPDs and Box and Line PMTs, based on High QE 20 inch R3600 dark rate from EGADS nov 2014
#/DarkRate/SetDarkRate 3.0 kHz #For 12 inch HPDs and Box and Line PMTs, based on High QE 20 inch R3600 dark rate from EGADS nov 2014

#It is more user friendly if the dark rate above is the requested digitised hit dark rate
#Since dark hits are created in "true" space, more true hits are required to be simulated,
# as hits are reduced by PMT/digitiser thresholds & integration
#The dark rate conversion factor is the multiplicative factor in order to do this
# This is now a PMT property and can be overridden here
#WARNING the default values need checking for all but the following types:
#  BoxandLine20inchHQE, PMT3inchR14374, PMT8inch
#/DarkRate/SetConvert 1.367  #For Normal PMT
#/DarkRate/SetConvert 1.119 #For HPDs
#/DarkRate/SetConvert 1.110 #For Box and Line PMTs

# Select which time window(s) to add dark noise to
#/DarkRate/SetDarkMode 0 to add dark noise to a time window starting at
#/DarkRate/SetDarkLow to /DarkRate/SetDarkHigh [time in ns]
#/DarkRate/SetDarkMode 1 adds dark noise hits to a window of
#width /DarkRate/SetDarkWindow [time in ns] around each hit
#i.e. hit time +- (/DarkRate/SetDarkWindow) / 2
# WARNING: this DarkMode 1 "around physics hit window" is performed separately for each PMT type.
# Therefore, if you have no physics hits on a PMT type in an event,
# you will have no dark noise on that PMT type in that event
# (only when running with DarkMode 1)
/DarkRate/SetDetectorElement tank
/DarkRate/SetDarkMode 1
/DarkRate/SetDarkWindow 4000

/DarkRate/SetDetectorElement OD
#/DarkRate/SetDarkRate 0 kHz
#/DarkRate/SetDarkRate 1 kHz
#/DarkRate/SetConvert 1.367 #for 8" PMTs in HK OD
/DarkRate/SetDarkMode 1
/DarkRate/SetDarkWindow 4000

/DarkRate/SetDetectorElement tankPMT2
#/DarkRate/SetDarkRate 0 kHz
#/DarkRate/SetDarkRate 1 kHz
#/DarkRate/SetConvert 1.110 #for PMT3inchR14374 PMTs in HK mPMT
#/DarkRate/SetConvert 1.126 #for PMT3inchR12199_02 PMTs in HK mPMT. WARNING value needs checking!
/DarkRate/SetDarkMode 1
/DarkRate/SetDarkWindow 4000

##################
# VISUALISATION
##################
#Uncomment one of the lines below if you want to use the OGLSX or RayTracer visualizer
#/control/execute macros/visOGLSX.mac
#/control/execute macros/visRayTracer.mac
#/control/execute macros/visOGLQt.mac

##################
# OPTICAL PHYSICS
##################
## The WCSimOpticalPhysics class uses the same Messenger commands as G4OpticalPhysics (need to set macros/jobOptions.mac)
## New photocathode models can be used for PMT photon detection. See macros/tuning_parameters.mac


##################
# PHYSICS
##################
## It should be noted that only one /mygen/generator can be run
## at once.

## select the input nuance-formatted vector file
## This can be from a generator (e.g. NEUT, sntools)
## or your own (see $WCSIM_SOURCE_DIR/sample-root-scripts/MakeKin.py for a script to make such files)
#/mygen/generator muline
#/mygen/vecfile inputvectorfile
#/mygen/vecfile h2o.2km.001-009x3_G4.kin
#/mygen/vecfile mu+.out
# define units used for time in kin file
#/mygen/time_unit ns

## Or you can use the G4 Particle Gun
## for a full list of /gun/ commands see:
## https://geant4-userdoc.web.cern.ch/UsersGuides/ForApplicationDeveloper/html/Control/AllResources/Control/UIcommands/_gun_.html
/mygen/generator gun
/gun/particle e-
#/gun/particle pi0
/gun/energy 5 MeV
/gun/direction 1 0 0
/gun/position 0 0 0  

## Or you can use the G4 General Particle Source
## you can do a lot more with this than a monoenergetic, monodirectional, single-particle gun
## for a full list of /gps/ commands see:
## https://geant4-userdoc.web.cern.ch/UsersGuides/ForApplicationDeveloper/html/GettingStarted/generalParticleSource.html
## https://geant4-userdoc.web.cern.ch/UsersGuides/ForApplicationDeveloper/html/Control/AllResources/Control/UIcommands/_gps_.html
#/mygen/generator gps
#/gps/particle e-
#/gps/energy 500 MeV
#/gps/direction 1 0 0
#/gps/position 0 0 0

## Or you can use the datatable option
## This is similar to the nuance format option, though this uses datatable formatted files.
## Datatables are formatted as follows:
## | Index of particle in event | PDG code | Energy | X | Y | Z | Px | Py | Pz | Time |
## Note that the column separators "|" are for clarity in describing the format, and should not be included in the file
## Note also that comments are allowed in the data table file by starting lines with a "#"
#/mygen/generator datatable
#/mygen/vecfile inputDataTableFile

## Or you can use the laser option
## This is equivalent to the gps command, except that the gps particle energies are saved ignoring their mass
## for a full list of /gps/ commands see the links above
## It is used for laser calibration simulation
#/mygen/generator laser
#/gps/particle opticalphoton
#/gps/energy 2.505 eV
#/gps/direction 1 0 0
#/gps/position 0 0 0
#/gps/number 1000
#/gps/ang/type iso
#/gps/ang/mintheta 0 deg
#/gps/ang/maxtheta 30 deg
#/gps/ang/minphi 0 deg
#/gps/ang/maxphi 360 deg

## Or you can use a cosmics generator
## Based on the SuperK flux extrapolated at HyperK site in Mozumi
## Muons are generated according to this flux and their position is extrapolated outside the tank
## Useful to study muons tracks in both OD and ID
#/mygen/generator cosmics
#/mygen/cosmicsfile data/MuonFlux-HyperK-ThetaPhi.dat

## Or you can use an IBD generator
## This requires a spectrum file to generate events weighted by fluxes across an energy spectrum
#/mygen/generator ibd
#/mygen/ibd_database DatabasePath
#/mygen/ibd_model ModelName (see ./data/DSNBFluxes.json for models)

## Or you can use the hepmc3 generator to read nuhepmc3 files
## The option hepmc3positionGenMode will either generate random, isotropic positions in the ID (true) or will read positions from the file (false)
#/mygen/generator hepmc3
#/mygen/hepmc3file HepMC3Filepath
#/mygen/hepmc3positionGenMode true/false


## Radioactive option
## Generate radioactive decay in the water or on the PMTs
#/mygen/generator radioactive
## This window should match the one in biasprofile.dat (see below)
#/mygen/radioactive_time_window 1.e-4
## The following list the different isotope to take into account, where they decay,
## and what are their activities in the full ID detector (for Water) or in the PMT (for PMT)
#/mygen/isotope Tl208 PMT 2.8
#/mygen/isotope Bi214 PMT 27.
#/mygen/isotope K40 PMT 94.
#/mygen/isotope Bi214 water 264. ### HK
##Clear the source and tell GPS to make multiple vertices
#/gps/source/clear

## Radon option
## Generate Bi214 decay in the water following a Model extracted from SK-IV solar data
#/mygen/generator radon
## This window should match the one in biasprofile.dat if time bias is used (see below)
#/mygen/radioactive_time_window 1.e-4
## Needed if time bias is not used, in order to keep timing below one sec.
#/DAQ/RelativeHitTime true
## The following set which scenario is used to scale SK model to HK
#/mygen/radon_scaling A # 	Relative scaling with respect to full ID volume (Pessimistic, should be default for now)
#/mygen/radon_scaling B #	Absolute scaling with respect to ID border (Optimistic)
#/mygen/radon_scaling 0 #	Uniform distribution
#/mygen/radon_symmetry 1 #	Divide the detector in x slices using the theta symmetry
##Clear the source and tell GPS to make multiple vertices
#/gps/source/clear

## Needed to prevent other decay than Bi-214
/grdm/nucleusLimits 214 214 83 83 
## if you need to use time bias
#/grdm/decayBiasProfile data/biasprofile.dat
#/grdm/analogueMC 0
#/grdm/BRbias 0

## Gamma-conversion option
## Use GPS commands to specify the the gamma energy, direction, etc.
## The GPS vertex position corresponds to the point of gamma-conversion
#/mygen/generator gamma-conversion
#/gps/particle gamma
#/gps/energy 10 MeV
#/gps/direction 1 0 0
#/gps/position 0 0 0

# Or you can use the AmBe Calibration Source Generator.
# This launches two primary particles in a random direction from the (0,0,0): one neutron and one gamma.
# The energy of the gamma can be:
# - 4.4 MeV 65% of the time.
# - 7.7 MeV 8%  of the time.
# - 0.0 MeV 26% of the time.
# Neutron Energy is taken from a simulated realistic AmBe Spectrum depending on the Gamma Energy.
# In order to run this correctly, the AmBe source must be in the geometry & neutron capture must be activated - for details see the "AmBe CALIBRATION SOURCE" section above
#/mygen/generator ambeevt

# Or inject photon from mPMT LED
# (Note that these are LEDs positioned in the standard mPMT modules.
#  They are not LEDs in the LED-mPMT modules)
#/mygen/generator mPMT-LED
# Use PMTid (from 1 to totalNum_mPMTs) to specify source mPMT
# Use LEDid (from 0 to 11) to specify LED position, theta and phi directional change from nominal direction
#/mPMTLED/PMTid 1
#/mPMTLED/LEDid 0 0 0
# Use GPS commands to define photon energy, number and angular distribution
#/gps/energy 2.505 eV
#/gps/number 100000
# Specify a cos(theta) Gaussian profile with 15 deg FWHM
#/gps/ang/type user
#/gps/ang/user_coor true
#/gps/ang/surfnorm false
#/gps/hist/type theta
#/control/execute data/theta_cos15deg_FWHM.txt

##################
# TRACKING
##################
## Commands to control which true particle tracks are tracked and saved to the output file:
## By default, save all tracks in the chain from primaries to those that produce Cherenkov photons that produce hits
## To disable this behaviour and only save tracks of particular creation processes and particle types, set to false
#/Tracking/saveHitProducingTracks false
## By default, all electrons, muons, pions, kaons, protons and neutrons are saved, and particles created by Decay, conv,
## nCapture or OpWLS processes
## Add additional PDG codes of particle types or additional Geant4 process names of creation processes of tracks to save
## Note that optical photons have PDG code 0 in Geant4
#/Tracking/trackParticle 0
#/Tracking/trackProcess Cerenkov
## Due to the typically very large number of optical photons, a fraction can be tracked by setting the percentage to randomly draw
## Note that the value is a percentage from 0.0 to 100.0, not fraction 0.0 to 1.0
/Tracking/fractionOpticalPhotonsToDraw 0.0


##################
# OUTPUT
##################
## Boolean to select whether to save the NEUT RooTracker vertices in the output file, provided you used
## a NEUT vector file as input
/WCSimIO/SaveRooTracker 0

## change the name of the output root file, default = wcsim.root
/WCSimIO/RootFile wcsim_output.root

## save in a flat tree format, with multiple trees for different elements (vertices, tracks, true hits, digits, etc.)
## Currently the trees are created, but unfilled, if you turn this option on
## (The code needs finessing by someone, if there is a desire to bring this format back)
#/WCSimIO/WriteFlatRootFile true

## set a timer running on WCSimRunAction
#/WCSimIO/Timer false

##################
# NUMBER OF EVENTS TO RUN
##################
# It is possible to perform multiple runs of WCSim in a single process
# The benefit of this is to reduce the time spent on WCSim initialisation
# in a use case e.g. simulating events at multiple source positions
# In order to do this, you can repeat the /run/beamOn command e.g.
# /gun/direction -1 0 0
# /run/beamOn 2
# /gun/direction 1 0 0
# /run/beamOn 3
# However, be warned that you cannot change all options between runs
# - All parameters in tuning_parameters.mac and jobOptions.mac changed will have no effect
# - Some parameters in WCSim.mac may not have an effect (e.g. geometry)
# - It is up to you to perform the bookkeeping of which events were run with which options, but to help with this:
# -- The options tree will be filled with one entry for each run
# -- The EventHeader has a run number that specifies the run (and corresponding options tree entry) for a given event
# It is therefore your responsibility to confirm that the options you are changing work as expected in multi-run mode

# There is a memory leak when doing TTree::GetEntry() when reading files. It is also presumed that filling is leaky. It is strongly recommended not to generate or analyse O(1000) events in a single job

/run/beamOn 10
#exit