[Run issue]: Unable to Generate .dnadamage file

[alfiafazimah]

Contact Details

alfiafaizaazimah@gmail.com

What was the issue?

Hello TOPAS-nBio experts.
I'm having some troubles in running the examples/scorers/TsScoreDNADamage.txt, with TsIRTStrandBreaks scorer. It supposed to generate the .phsp, .header, and .dnadamaged files. But the .dnadamaged file is empty as shown in the pictures.

The run log shown as follow:

4WT0 > Begin processing for Run: 0, History: 0
G4WT0 > -- Direct SSB [[[ ]]]
G4WT0 >  --- IRT begins for total histories 1343
G4WT0 >  ---   Read dna information 
G4WT0 >  ---   Running IRT for 26850 dna and 0 chemical species
G4WT0 >  --- IRT ends 1343
G4WT0 >  -- total SSB: 0
G4WT0 > =========== Total direct SSB        : 0
G4WT0 > =========== Total indirect SSB      : 0
G4WT0 > =========== Total dose in envelope  : 50.018 Gy 
G4WT0 > =========== Total edep in envelope  : 0.16346 MeV 
G4WT0 > =========== SSB in plasmid       /Gy: 0 /Gy
G4WT0 > =========== SSB in plasmid    /Gy/Da: 0 /Gy/Da
G4WT0 > =========== SSB in plasmid    /100eV: 0 /100 eV
G4WT0 > =========== SSB in plasmid    umol/J: 0 umol/J
G4WT0 > =========== Total events to reach a dose of 50 (Gy) = 1343
G4WT0 > 
G4WT0 > Scorer: plasmid
G4WT0 > Header   has been written to file: TOPAS_IRT_StrandBreak.header
G4WT0 > Contents has been written to file: TOPAS_IRT_StrandBreak.phsp
G4WT0 > Scored in component: plasmid

TOPAS run sequence complete.
Particle source Demo: Total number of histories: 1344

Scorer: plasmid
Header   has been written to file: TOPAS_IRT_StrandBreak.header
Contents has been written to file: TOPAS_IRT_StrandBreak.phsp
Scored in component: plasmid

The code for the TsScoreDNADamage.txt as follow:

###### TOPAS Parameters #####
#############################

Ts/NumberOfThreads = 1
i:Ts/Verbosity = 3
Ts/ShowHistoryCountAtInterval  = 10000

#############################
#### Physics & Chemistry ####
#############################

sv:Ph/Default/Modules = 2 "TsEmDNAPhysics" "TsEmDNAChemistry"
s:Ph/Default/Electron/SetElasticScatteringModel = "CPA100"

s:Ch/ChemistryName = "TOPASChemistry"

includeFile = TOPASDNAReactions.txt 
b:Ch/TOPASChemistry/ChemicalStageTransportActive = "True"
d:Ch/TOPASChemistry/ChemicalStageTimeEnd = 1.00001 ps
dv:Ch/TOPASChemistry/ChemicalStageTimeStepsHighEdges = 1 999999 ps
dv:Ch/TOPASChemistry/ChemicalStageTimeStepsResolutions = 1 0.5 ps

#############################
#### Scavenger Molecules ####
#############################

s:Mo/DMSO/Symbol = "DMSO"
d:Mo/DMSO/DiffusionCoefficient = 0 nm2/s
u:Mo/DMSO/Charge = 0
d:Mo/DMSO/Radius = 0.3 nm

s:Mo/OHDMSOProduct/Symbol = "OHDMSOProduct"
d:Mo/OHDMSOProduct/DiffusionCoefficient = 0 nm2/s
u:Mo/OHDMSOProduct/Charge = 0
d:Mo/OHDMSOProduct/Radius = 0.3 nm

d:Ch/TOPASChemistry/Reaction/Hydroxyl/Deoxyribose/ReactionRate = 4.8689e9 /M/s

sv:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/Products = 1 "OHDMSOProduct"
d:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/ReactionRate = 7.1e9 /M/s
d:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/Concentration = 1e-1 M 
s:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/ScavengingModel = "ExponentialSingleFactor" 
b:Ch/TOPASChemistry/BackgroundReaction/hydroxyl/DMSO/CompatibleWithStepByStep = "False" 

#############################
######### Geometry ##########
#############################

Ge/World/HLX = 1.0 um
Ge/World/HLY = 1.0 um
Ge/World/HLZ = 1.0 um
Ge/World/Material = "G4_WATER"

includeFile = PlasmidGeometry.txt
d:Ge/plasmid/R = 0.5 um
i:Ge/plasmid/NumberOfPlasmids = 5
s:Ge/plasmid/InputFile = "pUC19_20C_3Sigma_ALP_Corrected.fab2g4dna"
s:Ge/plasmid/EnvelopeFileName = "Plasmid_50ugg_Sphere_1um_diameter_envelopes.xyz"

#############################
########## Scorer ###########
#############################

s:Sc/plasmid/Quantity       = "TsIRTStrandBreaks"
s:Sc/plasmid/Component      = "plasmid"
d:Sc/plasmid/PrescribedDose = 50 Gy
s:Sc/plasmid/IfOutputFileAlreadyExists = "Overwrite"
s:Sc/plasmid/OutputFile     = "TOPAS_IRT_StrandBreak"
s:Sc/plasmid/InputFile      = "Plasmid_50ugg_Sphere_1um_diameter_plasmids.xyz"
s:Sc/plasmid/OutputType     = "ASCII"
b:Sc/plasmid/PropagateToChildren = "True"
d:Sc/plasmid/TimeLower      = 1 ps
d:Sc/plasmid/TimeUpper      = 100 us
i:Sc/plasmid/TimeBins       = 200
iv:Sc/plasmid/OnlyUseDNAMoleculesWithID = 1 104
sv:Sc/plasmid/ReportMoleculesNamed = 7 "OH^0" "e_aq^-1" "H2O2^0" "H^0" "H_2^0" "DeoxyriboseDamaged" "Deoxyribose"
b:Sc/plasmid/HighTimeScavenger = "True"

#############################
########## Source ###########
#############################

So/Demo/Type              = "Volumetric"
So/Demo/Component         = "plasmid"
sc:So/Demo/ActiveMaterial = “G4_WATER”
s:So/Demo/BeamParticle    = "e-"
s:So/Demo/BeamEnergySpectrumType = "Discrete"
dv:So/Demo/BeamEnergySpectrumValues = 19 0.0144 0.0432 0.072  0.1008 
                                         0.1296 0.1584 0.1872 0.216 
                                         0.2448 0.2736 0.3024 0.3312 
                                         0.36   0.3888 0.4176 0.4464 
                                         0.4752 0.504  0.5328 MeV
uv:So/Demo/BeamEnergySpectrumWeights = 19 0.030134946933679106 0.041924794698170294 0.04768765307592566
                                          0.05258608269701772  0.05515535705710032  0.05568361907506123
                                          0.05681217884070499  0.05722038130912933  0.0583729529846804
                                          0.05604379772367094  0.05395476156173462  0.05229793977812995
                                          0.04970465350814004  0.042861259184555536 0.03522547183402968
                                          0.20890361619363204  0.045382509724823515 2.4011909907314027e-05
                                          2.4011909907314027e-05 

i:So/Demo/NumberOfHistoriesInRun = 100000

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

s:Gr/ViewA/Type = "OpenGL"
d:Gr/ViewA/Theta = 45 deg
d:Gr/ViewA/Phi   = 45 deg
i:Gr/ViewA/WindowSizeX = 900
i:Gr/ViewA/WindowSizeY = 700

Ts/PauseBeforeQuit = "False"
b:Ts/ShowCPUTime = "True"

Anyone can help how to fix this problem?

TOPAS-nBio category

Scoring

Version

3.0

What Operative System (OS) are you running on?

No response

Relevant log output

No response

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Attestation

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[wgshin]

Hi, this bug has been solved in discussion #73 and Pull request (#107)