[Run issue]: TsIRTInterPulse: The number of generated free radicals < 0.

[Vacuoler]

Contact Details

sunjianhan@stu.pku.edu.cn

What was the issue?

Respected expert,

Hello!

When I used TsIRTInterPulse to simulate the free radicals generated by pulsed beams, the number of generated free radicals was less than 0 over time, just like the data below. The chemical reactions I used are the default PlanteReactions.txt and several type VI reactions added by Jose Ramos Mendez in problem IRTcummulative Example #7, PlanteTypeVI.txt. I don't know where the problem is.

My code and the cited chemical reactions are listed as follows:

2MeV_1ps_1Hz_1pulses_10Gy.txt
PlanteReactions.txt
PlanteTypeVI.txt

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

TOPAS Parameters

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

i:Ts/Verbosity = 1
i:Ts/ShowHistoryCountAtInterval = 260
Ts/NumberOfThreads = 1
b:Ts/BufferThreadOutput = "True"
b:Ts/ShowCPUTime = "True"

i:Ts/Seed = 1234

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

Physics & Chemistry

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

#sv:Ph/Default/Modules = 4 "TsEmDNAPhysics" "TsEmDNAChemistry" "g4em-dna_opt2" "g4em-dna-chemistry"
sv:Ph/Default/Modules = 2 "g4em-dna_opt2" "TsEmDNAChemistry"

s:Ph/Default/Electron/SetElasticScatteringModel = "CPA100"
s:Ph/Default/Electron/SetExcitationModel = "Emfietzoglou"
s:Ph/Default/Electron/SetIonisationModel = "Emfietzoglou"
b:Ph/Default/Electron/ActiveVibExcitation = "True"
b:Ph/Default/Electron/ActiveAttachment = "True"
s:Ch/ChemistryName = "Plante"
includeFile = PlanteReactions.txt
includeFile = PlanteTypeVI.txt
b:Sc/gvalue/EnableHighTimeScavengers = "True"

b:Ch/Plante/ChemicalStageTransportActive = "True"
d:Ch/Plante/ChemicalStageTimeEnd = 200e6 ps
#dv:Ch/Plante/ChemicalStageTimeStepsHighEdges = 1 200e6 ps
#dv:Ch/Plante/ChemicalStageTimeStepsResolutions = 1 2 ps

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

Geometry

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

d:Ge/World/HLX= 10 um
d:Ge/World/HLY= 10 um
d:Ge/World/HLZ= 10 um
s:Ge/World/Material ="G4_WATER"

s:Ge/target/Parent = "World"
s:Ge/target/Material = "G4_WATER"
s:Ge/target/Type = "TsBox"
d:Ge/target/HLX = 10 um
d:Ge/target/HLY = 10 um
d:Ge/target/HLZ = 10 um

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

s:So/Example/Type = "Volumetric"
s:So/Example/ActiveMaterial = "G4_WATER"
s:So/Example/Component = "target"
s:So/Example/BeamParticle = "e-"
d:So/Example/BeamEnergy = 2 MeV
u:So/Example/BeamEnergySpread = 0
ic:So/Example/NumberOfHistoriesInRun = 1000000

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

s:Sc/gvalue/Quantity = "TsIRTInterPulse"
s:Sc/gvalue/Component = "target"
s:Sc/gvalue/OutputFile = "2MeV_100ps_1Hz_1pulses_10Gy"
s:Sc/gvalue/IfOutputFileAlreadyExists = "Overwrite"
s:Sc/gvalue/OutputType = "ascii"
i:Sc/gvalue/TimeBins = 500
d:Sc/gvalue/TimeLower = 1.0e0 ps
d:Sc/gvalue/TimeUpper = 10 us
i:Sc/gvalue/NumberOfPulses = 1
d:Sc/gvalue/PulsesFrequency = 1e0 /s
d:Sc/gvalue/PrescribedDose = 10 Gy
s:Sc/gvalue/PulseDistribution = "Gaussian"
d:Sc/gvalue/PulseTimeMean = 50 ps
d:Sc/gvalue/PulseTimeFWHM = 100 ps
sv:Sc/gvalue/ReportMoleculesNamed = 10 "OH^0" "e_aq^-1" "H3O^1" "H2O2^0" "H^0" "H_2^0" "OH^-1" "O2^-1" "HO2^0" "O2^0"
s:Sc/gvalue/SensitiveVolumeName = "target"
b:Sc/gvalue/ForceLowTimeCutTo1ps = "True"

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

Thank you very much.

TOPAS-nBio category

Chemistry

Version

3.0

What Operative System (OS) are you running on?

No response

Relevant log output

No response

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Attestation

• I testify that I have fully read the bug reporting guideline beforehand.

[tmasilela]

Hi,

Are you sure you're using the latest version of TOPAS (OpenTOPAS v4.0.0) and TOPAS-nBio (v3.0)? This is a known issue that I posted about in the previous forum but should be fixed in the latest version of the software.

Hope that fixes your issue.

All the best,

Thongchai

[Vacuoler]

Excuse me, how can I install TOPAS nbio v3.0 separately? I am unable to determine whether the version I installed is this one. I downloaded topas-nbio on September 1, 2024.

Thank you very much.