[Run issue]: Inquiry Regarding the "TsNucleus" Scorer and Distributed Source Compatibility

[aoliaodaxiaoguaishou]

Contact Details

banshengguazi@gmail.com

What was the issue?

Hello! I am currently measuring the damage score of the "TsNucleus" cell nucleus. The scorer used is the "ExampleNucleusDNADamage" scorer corresponding to this cell nucleus, and a distributed radiation source is used. However, a problem occurred during the simulation:

Reading geometry information file...
Reading copy number map file...
Reading chromosome-voxel map file...
Visualization verbosity changed to quiet (0)
Segmentation fault (core dumped)

I would like to ask if it is because the scoring module of the cell nucleus does not support the distributed type of particle source. If I want to implement the corresponding type support, do I have to modify the source code?
Your assistance and guidance would be greatly appreciated.
Thank you in advance for your time and help.
Best regards,
Lucy

TOPAS-nBio category

Scoring

Version

3.0

What Operative System (OS) are you running on?

Linux (Debian/Ubuntu)

Relevant log output

#### Physics and Chemistry ####
s:Ge/Nucleus/AssignToRegionNamed = "G4DNA"
sv:Ph/Default/Modules       = 4 "g4em-standard_opt4" "g4decay" "g4radioactivedecay" "TsEmDNAChemistry" 
s:Ph/Default/ForRegion/G4DNA/ActiveG4EmModelFromModule = "g4em-dna"


#### Source and runs ####
s:So/RadionuclideSource/Type                       = "Distributed"
s:So/RadionuclideSource/Component                  = "Cytoplasm"
s:So/RadionuclideSource/BeamParticle               = "GenericIon(89, 225)" # Ac-225
d:So/RadionuclideSource/BeamEnergy                 = 5.0 MeV
u:So/RadionuclideSource/BeamEnergySpread           = 0.
ic:So/RadionuclideSource/NumberOfHistoriesInRun    = 10
ic:So/RadionuclideSource/NumberOfSourcePoints      = 10
bc:So/RadionuclideSource/RedistributePointsOnNewRun = "False"


# 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

# -- Scorer --
includeFile									= ../../scorers/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
Ts/ShowHistoryCountAtInterval                       = 1

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