[Run issue]:Question About Adding DoseScorer – Is This Error Normal?

[v587aaaaa3]

Contact Details

[email protected]

What was the issue?

Hello,

I am trying to add DoseScorer to my code, but I encountered the following message:

G4WT2 > This hit's energy deposit would have been: 8.22e-06 MeV
G4WT2 >
Topas experienced an error in scoring.
G4WT2 > A scorer in the Component: "Nucleus"
G4WT2 > has been called for a hit in the non-parameterized volume named: "Nucleus/FiberCylinder2727"
G4WT2 > But this deos not make sense, as this scorer should only get called for hits
G4WT2 > in a parameterized volume (volume name would include the string "_Division").
G4WT2 > We think this may sometimes happen because Geant4 navigation gets into a corrupted state.
G4WT2 > This hit will be omitted from scoring.
G4WT2 > A note at end of session will show total number of unscored steps and the total unscored energy.
G4WT2 > In some cases the unscored energy is small enough that you can ignore this issue.

I would like to know if this error is normal and, if not, what settings or configurations I should adjust to resolve this issue.

Thank you for your assistance!

Best Regards,

Wei Kaijie

TOPAS-nBio category

Scoring

Version

3.0

What Operative System (OS) are you running on?

Linux (Debian/Ubuntu)

Relevant log output

i:Ts/NumberOfThreads 			= 0
# -- Geometry
# World
d:Ge/World/HLX                          = 7.0 um
d:Ge/World/HLY                          = 7.0 um
d:Ge/World/HLZ                          = 7.0 um
b:Ge/World/Invisible                    = "true"
s:Ge/World/Material                     = "G4_WATER"

# Nucleus
s:Ge/Nucleus/Type                       = "TsNucleus"
s:Ge/Nucleus/Parent                     = "World"
s:Ge/Nucleus/Material                   = "G4_WATER"
s:Ge/Nucleus/Color                      = "White"
s:Ge/Nucleus/DNAModel					= "Sphere"
d:Ge/Nucleus/NucleusRadius              = 4.65 um
i:Ge/Nucleus/HilbertCurveLayer          = 4
i:Ge/Nucleus/HilbertCurve3DRepeat       = 30
s:Ge/Nucleus/HilbertCurveFileName       = "supportFiles/HilbertPoints_iteration1.dat"
s:Ge/Nucleus/Voxel/Material             = "G4_WATER"
b:Ge/Nucleus/ShowDNAVoxels              = "false"
s:Ge/Nucleus/ChromatinFiber/Material    = "G4_WATER"
b:Ge/Nucleus/ShowChromatinCylinders     = "false"
s:Ge/Nucleus/Histone/Material           = "G4_HistoneMaterial"
b:Ge/Nucleus/OnlyBuildOneHistone        = "false"
b:Ge/Nucleus/HistoneAsScavenger         = "true"
b:Ge/Nucleus/AddBases                   = "true"
s:Ge/Nucleus/Base1/Material             = "G4_BaseMaterial"
s:Ge/Nucleus/Base2/Material             = "G4_BaseMaterial"
b:Ge/Nucleus/AddBackbones               = "true"
s:Ge/Nucleus/Backbone1/Material         = "G4_BackboneMaterial"
s:Ge/Nucleus/Backbone2/Material         = "G4_BackboneMaterial"
b:Ge/Nucleus/AddHydrationShell          = "true"
s:Ge/Nucleus/HydrationShell1/Material   = "G4_WATER_MODIFIED"
s:Ge/Nucleus/HydrationShell2/Material   = "G4_WATER_MODIFIED"

# -- Materials
s:Ma/G4_HistoneMaterial/CloneFromMaterial   = "G4_WATER"
d:Ma/G4_HistoneMaterial/CloneWithDensity    = 1.407 g/cm3
s:Ma/G4_BaseMaterial/CloneFromMaterial      = "G4_WATER"
d:Ma/G4_BaseMaterial/CloneWithDensity       = 1.0 g/cm3
s:Ma/G4_BackboneMaterial/CloneFromMaterial  = "G4_WATER"
d:Ma/G4_BackboneMaterial/CloneWithDensity   = 1.0 g/cm3
s:Ma/G4_WATER_MODIFIED/CloneFromMaterial    = "G4_WATER"
d:Ma/G4_WATER_MODIFIED/CloneWithDensity     = 1.0 g/cm3

# -- Physics and Chemistry
#sv:Ph/Default/Modules                      		= 1 "g4em-dna"
sv:Ph/Default/Modules								= 2 "g4em-dna" "TsEmDNAChemistry" 	# OR	 physics and chemistry
includeFile											= supportFiles/TOPASDefaultReactions.txt
s:Ch/ChemistryName									= "TOPASChemistry"
b:Ch/TOPASChemistry/ChemicalStageTransportActive    = "True"
d:Ch/TOPASChemistry/ChemicalStageTimeEnd             	= 1.0 ns 
dv:Ch/TOPASChemistry/ChemicalStageTimeStep           	= 2 10.0 1000.0 ps 
dv:Ch/TOPASChemistry/ChemicalStageTimeStepResolution 	= 2 0.1 1.0 ps 
i:Ph/Verbosity 						= 0
#i:Ph/Verbosity                          			= 0

# -- Source and runs
s:So/ParticleGun/Type                               = "Beam"
s:So/ParticleGun/Component                          = "BeamPosition"
d:Ge/BeamPosition/TransZ                            = 5.00 um
s:So/ParticleGun/BeamParticle                       = "proton"
s:So/ParticleGun/BeamPositionDistribution           = "none"					# EITHER single track position
#s:So/ParticleGun/BeamPositionDistribution			= "Flat"					# OR 	 disk source
s:So/ParticleGun/BeamPositionCutoffShape			= "Ellipse"
d:So/ParticleGun/BeamPositionCutoffX 				= Ge/Nucleus/NucleusRadius um
d:So/ParticleGun/BeamPositionCutoffY 				= Ge/Nucleus/NucleusRadius um
s:So/ParticleGun/BeamAngularDistribution            = "none"
d:So/ParticleGun/BeamEnergy                         = 1 MeV
i:So/ParticleGun/NumberOfHistoriesInRun             = 14
b:Ge/Nucleus/RotateNucleusForEachRun				= "false"
d:Ge/Nucleus/RotX = 174.0 deg
d:Ge/Nucleus/RotY = -6.0 deg
d:Ge/Nucleus/RotZ = -40.0 deg
# Producing separate runs instead of separate histories if rotation enabled
#d:Tf/TimelineStart 			 					= 0. s
#d:Tf/TimelineEnd   			 					= 10. s
#i:Tf/NumberOfSequentialTimes 						= 5 # Number of runs

# -- Scorer --
includeFile									= ../DNAScorerStepByStep.txt
s:Sc/DNADamageScorer/Quantity				= "DNADamageNucleusStepByStep"
s:Sc/DNADamageScorer/Component 				= "Nucleus"
i:Sc/DNADamageScorer/NumberOfHistoriesInRun = So/ParticleGun/NumberOfHistoriesInRun
d:Sc/DNADamageScorer/ScoringRadius			= Ge/Nucleus/NucleusRadius um
i:Sc/DNADamageScorer/BasePairPositionAtGeometricHierarchy = 0
sv:Sc/DNADamageScorer/Strand1MaterialNames  = 4 "G4_WATER_MODIFIED" "G4_BackboneMaterial" "G4_BaseMaterial" "G4_HistoneMaterial"
sv:Sc/DNADamageScorer/Strand2MaterialNames  = 3 "G4_WATER_MODIFIED" "G4_BackboneMaterial" "G4_BaseMaterial"
s:Sc/DNADamageScorer/PrimaryParticle		= So/ParticleGun/BeamParticle
d:Sc/DNADamageScorer/MeanEnergy				= So/ParticleGun/BeamEnergy MeV
#d:Sc/DNADamageScorer/StopTrackingAtDose		= 0.5 gray
d:Sc/DNADamageScorer/ImageXMinPosition		= 0 um - Ge/Nucleus/NucleusRadius
d:Sc/DNADamageScorer/ImageXMaxPosition		= Ge/Nucleus/NucleusRadius um
d:Sc/DNADamageScorer/ImageYMinPosition		= 0 um - Ge/Nucleus/NucleusRadius
d:Sc/DNADamageScorer/ImageYMaxPosition		= Ge/Nucleus/NucleusRadius um
d:Sc/DNADamageScorer/ImageZMinPosition		= 0 um - Ge/Nucleus/NucleusRadius
d:Sc/DNADamageScorer/ImageZMaxPosition		= Ge/Nucleus/NucleusRadius um

# Geometry file for Nucleus scorer
s:Sc/DNADamageScorer/GeometryInfo			= "supportFiles/Geoinfo.txt"
s:Sc/DNADamageScorer/FileVoxelCopyNumbersInsideNucleus = "supportFiles/CopyNoTable.txt"
s:Sc/DNADamageScorer/MapChromosomeVoxelsFile = "supportFiles/signedCHVoxel.txt"

Ts/ShowHistoryCountAtInterval                       = 1

# -- Visualization
#s:Gr/view/Type                          = "OpenGL"
#i:Gr/view/WindowSizeX                   = 800
#i:Gr/view/WindowSizeY                   = 800
#d:Gr/view/Theta                         = 45 deg
#d:Gr/view/Phi                           = 30 deg
#s:Gr/view/ColorBy                       = "ParticleType"
#sv:Gr/view/ColorByParticleTypeNames     = 4 "e-" "alpha" "proton" "neutron"
#sv:Gr/view/ColorByParticleTypeColors    = 4 "green" "red" "blue" "grass"
#s:Gr/view/BackgroundColor               = "White"

i:Ts/Seed = 2581

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