[Run issue]:Issue with TsEmDNAChemistryExtended and IRTCummulative Implementation

[Edgarchen666]

Contact Details

2101110329@stu.pku.edu.cn

What was the issue?

Dear TOPAS-nBio Community,

I am encountering an issue while attempting to use the TsEmDNAChemistryExtended reaction list with the IRTCummulative functionality in TOPAS-nBio. Despite following the documentation, the chemistry model does not initialize as expected when combined with IRT tracking.
Could anyone advise if:
a) Specific syntax adjustments are required for TsEmDNAChemistryExtended in IRT contexts?
b) Additional scorer declarations might resolve this compatibility issue?

Thank you for your expertise. Let me know if further details would be helpful.

TOPAS-nBio category

Geometry

Version

3.0

What Operative System (OS) are you running on?

Windows (WSL)

Relevant log output

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

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

i:Ts/Seed = 1234

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

sv:Ph/Default/Modules = 2 "g4em-dna" "TsEmDNAChemistryExtended"
s:Ph/Default/Electron/SetElasticScatteringModel = "CPA100"
#s:Ch/ChemistryName = "Plante"
#includeFile  = PlanteReactions.txt
#includeFile  = PlanteTypeVI.txt
#includeFile  = PlanteTypeVI-O2-.txt
s:Ch/ChemistryName = "TOPASChemistry"
includeFile  = TOPASChemistry_Extended.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



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

d:Ge/World/HLX= 3 um 
d:Ge/World/HLY= 3 um 
d:Ge/World/HLZ= 1 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      = 1 um
d:Ge/target/HLY      = 1 um
d:Ge/target/HLZ      = 1 um

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

s:So/Example/Type                     = "Volumetric"
s:So/Example/ActiveMaterial           = "G4_WATER"
s:So/Example/Component                = "target" 
s:So/Example/BeamParticle             = "proton"
d:So/Example/BeamEnergy               = 55.0 MeV 
u:So/Example/BeamEnergySpread         = 0
ic:So/Example/NumberOfHistoriesInRun  = 500000

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

s:Sc/gvalue/Quantity     = "TsIRTInterPulse" 
s:Sc/gvalue/Component    = "target"
#s:Sc/gvalue/OutputFile   = "Proton_100MeV_20 Gy_continues pulse_insD_550_averD_80_72.8MHz"
#s:Sc/gvalue/OutputFile   = "reactiontest-Proton_55MeV_5 Gy_5 continues pulse_1e5Hz_interval_10us_yuanlaidefanying"
s:Sc/gvalue/OutputFile   = "test"
s:Sc/gvalue/IfOutputFileAlreadyExists = "Overwrite"
s:Sc/gvalue/OutputType   = "ascii"
i:Sc/gvalue/TimeBins     = 5000
d:Sc/gvalue/TimeLower    = 1.0e0 ps
d:Sc/gvalue/TimeUpper    = 1e4 us 
i:Sc/gvalue/NumberOfPulses = 5
d:Sc/gvalue/PulsesFrequency = 1e5 /s
d:Sc/gvalue/PrescribedDose    = 1 Gy 
s:Sc/gvalue/PulseDistribution = "Gaussian"
d:Sc/gvalue/PulseTimeMean     = 0.0 us 
d:Sc/gvalue/PulseTimeFWHM     = 0.1 us 
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"

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


###The following is TsEmDNAChemistryExtended.txt
# Diffusion coefficients
sv:Ch/TOPASChemistry/DiffusionCoefficients/Molecules = 11 "SolvatedElectron" "Hydroxyl"  "Hydrogen"  "Hydronium" "DyHydrogen" "Hydroxide" "HydrogenPeroxide" "Oxygen" "SuperoxideAnion" "Hydroperoxy" "Dioxidanide"
dv:Ch/TOPASChemistry/DiffusionCoefficients/Values    = 11  4.90022052437e9 2.2e9 7e9 9.4601846875e9 4.8e9 5.3032890625e9 2.3e9 2.1e-9 2.1e-9 2.0e-9 2.0e-9 nm2/s

b:Ch/TOPASChemistry/SetWaterMolecularConfiguration = "False"

# Reaction rates
sv:Ch/TOPASChemistry/Reaction/SolvatedElectron/SolvatedElectron/Products    = 3 "Hydroxide" "Hydroxide" "Dyhydrogen"
d:Ch/TOPASChemistry/Reaction/SolvatedElectron/SolvatedElectron/ReactionRate = 0.647e10  /M/s

sv:Ch/TOPASChemistry/Reaction/SolvatedElectron/Hydroxyl/Products            = 1 "Hydroxide"
d:Ch/TOPASChemistry/Reaction/SolvatedElectron/Hydroxyl/ReactionRate         = 2.953e10  /M/s

sv:Ch/TOPASChemistry/Reaction/SolvatedElectron/Hydrogen/Products            = 2 "Hydroxide" "Dyhydrogen"
d:Ch/TOPASChemistry/Reaction/SolvatedElectron/Hydrogen/ReactionRate         = 2.652e10 /M/s

sv:Ch/TOPASChemistry/Reaction/SolvatedElectron/Hydronium/Products           = 1 "Hydrogen"
d:Ch/TOPASChemistry/Reaction/SolvatedElectron/Hydronium/ReactionRate        = 2.109e10 /M/s

sv:Ch/TOPASChemistry/Reaction/SolvatedElectron/HydrogenPeroxide/Products    = 2 "Hydroxide" "Hydroxyl"
d:Ch/TOPASChemistry/Reaction/SolvatedElectron/HydrogenPeroxide/ReactionRate = 1.405e10 /M/s

sv:Ch/TOPASChemistry/Reaction/Hydroxyl/Hydroxyl/Products                    = 1 "HydrogenPeroxide"
d:Ch/TOPASChemistry/Reaction/Hydroxyl/Hydroxyl/ReactionRate                 = 0.475e10 /M/s

sv:Ch/TOPASChemistry/Reaction/Hydroxyl/Hydrogen/Products                    = 1 "None"
d:Ch/TOPASChemistry/Reaction/Hydroxyl/Hydrogen/ReactionRate                 = 1.438e10 /M/s

sv:Ch/TOPASChemistry/Reaction/Hydrogen/Hydrogen/Products                    = 1 "Dyhydrogen"
d:Ch/TOPASChemistry/Reaction/Hydrogen/Hydrogen/ReactionRate                 = 0.503e10 /M/s

sv:Ch/TOPASChemistry/Reaction/Hydronium/Hydroxide/Products                  = 1 "None"
d:Ch/TOPASChemistry/Reaction/Hydronium/Hydroxide/ReactionRate               = 11.031e10 /M/s

###
sv:Ch/TOPASChemistry/Reaction/DyHydrogen/Hydroxyl/Products                   = 1 "Hydrogen"
d:Ch/TOPASChemistry/Reaction/DyHydrogen/Hydroxyl/ReactionRate                = 0.0045e10 /M/s

sv:Ch/TOPASChemistry/Reaction/Hydroxyl/HydrogenPeroxide/Products            = 1 "Hydroperoxy" 
d:Ch/TOPASChemistry/Reaction/Hydroxyl/HydrogenPeroxide/ReactionRate         = 0.0023e10 /M/s

sv:Ch/TOPASChemistry/Reaction/Hydroxyl/Hydroperoxy/Products                 = 1 "Oxygen"
d:Ch/TOPASChemistry/Reaction/Hydroxyl/Hydroperoxy/ReactionRate              = 1.0e10 /M/s

sv:Ch/TOPASChemistry/Reaction/Hydroxyl/SuperoxideAnion/Products             = 2 "Oxygen" "Hydroxide"
d:Ch/TOPASChemistry/Reaction/Hydroxyl/SuperoxideAnion/ReactionRate          = 0.9e10  /M/s

sv:Ch/TOPASChemistry/Reaction/Hydroxyl/Dioxidanide/Products                 = 2 "Hydroperoxy" "Hydroxide"
d:Ch/TOPASChemistry/Reaction/Hydroxyl/Dioxidanide/ReactionRate              = 0.9e10  /M/s

sv:Ch/TOPASChemistry/Reaction/SolvatedElectron/Hydroperoxy/Products         = 1 "Dioxidanide"
d:Ch/TOPASChemistry/Reaction/SolvatedElectron/Hydroperoxy/ReactionRate      = 2.0e10 /M/s

sv:Ch/TOPASChemistry/Reaction/SolvatedElectron/Oxygen/Products              = 1 "SuperoxideAnion"
d:Ch/TOPASChemistry/Reaction/SolvatedElectron/Oxygen/ReactionRate           = 1.9e10  /M/s

sv:Ch/TOPASChemistry/Reaction/SolvatedElectron/SuperoxideAnion/Products     = 2 "Hydroxide" "Dioxidanide"
d:Ch/TOPASChemistry/Reaction/SolvatedElectron/SuperoxideAnion/ReactionRate  = 1.3e10  /M/s

sv:Ch/TOPASChemistry/Reaction/Hydrogen/HydrogenPeroxide/Products            = 1 "Hydroxyl" 
d:Ch/TOPASChemistry/Reaction/Hydrogen/HydrogenPeroxide/ReactionRate         = 0.01e10  /M/s

sv:Ch/TOPASChemistry/Reaction/Hydrogen/Hydroperoxy/Products                 = 1 "HydrogenPeroxide"
d:Ch/TOPASChemistry/Reaction/Hydrogen/Hydroperoxy/ReactionRate              = 2e10  /M/s

sv:Ch/TOPASChemistry/Reaction/Hydrogen/Oxygen/Products                      = 1 "Hydroperoxy"
d:Ch/TOPASChemistry/Reaction/Hydrogen/Oxygen/ReactionRate                   = 2e10  /M/s

sv:Ch/TOPASChemistry/Reaction/Hydrogen/Hydroxide/Products                   = 1 "SolvatedElectron"
d:Ch/TOPASChemistry/Reaction/Hydrogen/Hydroxide/ReactionRate                = 0.002e10  /M/s

sv:Ch/TOPASChemistry/Reaction/Hydrogen/SuperoxideAnion/Products             = 1 "Dioxidanide"
d:Ch/TOPASChemistry/Reaction/Hydrogen/SuperoxideAnion/ReactionRate          = 2.0e10  /M/s

sv:Ch/TOPASChemistry/Reaction/Hydronium/SuperoxideAnion/Products            = 1 "Hydroperoxy"
d:Ch/TOPASChemistry/Reaction/Hydronium/SuperoxideAnion/ReactionRate         = 3.0e10  /M/s

sv:Ch/TOPASChemistry/Reaction/Hydronium/Dioxidanide/Products                = 1 "HydrogenPeroxide"
d:Ch/TOPASChemistry/Reaction/Hydronium/Dioxidanide/ReactionRate             = 2.0e10  /M/s

sv:Ch/TOPASChemistry/Reaction/Hydroperoxy/Hydroperoxy/Products              = 2 "HydrogenPeroxide" "Oxygen"
d:Ch/TOPASChemistry/Reaction/Hydroperoxy/Hydroperoxy/ReactionRate           = 0.000076e10 /M/s

sv:Ch/TOPASChemistry/Reaction/Hydroperoxy/SuperoxideAnion/Products          = 2 "Oxygen" "Dioxidanide"
d:Ch/TOPASChemistry/Reaction/Hydroperoxy/SuperoxideAnion/ReactionRate       = 0.0085e10 /M/s

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