[Run-Problem]: How to implement temperature scaling?

[jonahpeter]

Contact Details

jonahpeter@g.harvard.edu

What was the issue?

Hi all, I am trying to run a simulation with temperature scaling and am encountering strange behavior. As shown in the attached console output, many of my reaction rates are being set to 1 and many of my background reaction rates are being set negative.

I can see exactly where this is happening in TsIRTConfiguration.cc, but I don't understand why it was coded this way. For line 1300, it seems that temperature scaling is only available for a set of 10 hard-coded reactions. Is this accurate? If so, what is happening to my other reactions?

For instance, consider what happens when I set ApplyCorrectionScalingForTemperature=True. Based on lines 311 and 1471, this sets the variable fKick = True which multiplies the new reaction rate newKobs by an additional scaling factor. It seems to me that when this parameter is True, the reaction rates are scaled relative to the default rates, and when this parameter is False, the new rates are calculated from first principles based on the Arhenius function.

However this parameter also toggles whether the background reaction rates that are positive or negative! Therefore, it seems I will get completely unphysical results when this parameter is True (i.e., when the rates are negative) and completely unexpected results when this parameter is False (i.e., the rates are positive but haven't been scaled for temperature).

Could someone please clarify whether temperature scaling is meant to only be used for the 10 hard-coded reactions? If so, I guess this means it's not compatible with pH scaling or scavenging.

Thanks!

90_C.txt
PlanteReactions.txt

TOPAS-nBio category

Chemistry

Version

3.0

What Operative System (OS) are you running on?

MacOS

Relevant log output

Welcome to TOPAS, Tool for Particle Simulation (Version 4.0)
Loading parameters starting from: 90_C.txt

Geant4 Data directory has been specified by the
TOPAS_G4_DATA_DIR environment variable as /Applications/GEANT4/G4DATA

**************************************************************
 Geant4 version Name: geant4-11-01-patch-03 [MT]   (10-November-2023)
  << in Multi-threaded mode >> 
                       Copyright : Geant4 Collaboration
                      References : NIM A 506 (2003), 250-303
                                 : IEEE-TNS 53 (2006), 270-278
                                 : NIM A 835 (2016), 186-225
                             WWW : http://geant4.org/
**************************************************************

TOPAS is in MT mode, setting number of threads to: 4

TOPAS set the tolerances based on the World size to:
      Surface tolerance = 5 nm, and radial tolerance = 5 nm.
Checking overlaps for volume Phantom:0 (G4Box) ... OK! 

Checking for Unused Components.
These are Components that were never built even though they were at least
partially defined in some parameters. This is not necessarily an error.
It may be an intentional choice to have these Component definitions handy for later use.
To turn off this check, set Ge/CheckForUnusedComponents to False
  No unused components were found.

MyPhysics
-- Set scavenging capacity for molecule H of 2490 /s 
-- Set scavenging capacity for molecule H of 5.94 /s 
-- Set scavenging capacity for molecule  of 624 /s 
-- Set scavenging capacity for molecule OHm of 11100 /s 
-- Set scavenging capacity for molecule e_aq of 2090 /s 
-- Set scavenging capacity for molecule e_aq of 15.8 /s 
-- Branching ratio: All ionization states probability 1
-- Branching ratio: A1B1 Dissociative decay probability 0.65
-- Branching ratio: A1B1 Relaxation probability 0.35
-- Branching ratio: B1A1 Relaxation probability 0.3
-- Branching ratio: B1A1 Dissociative decay probability 0.15
-- Branching ratio: B1A1 Auto-ionization probability 0.55
-- Branching ratio: B1A1 Auto-ionization probability 0
-- Branching ratio: B1A1 Dissociative decay2 probability 0
-- Branching ratio: Rydberg states and diffuse bands auto-ionization probability 0.5
-- Branching ratio: Rydberg states and diffuse bands relaxation probability 0.5
-- Branching ratio: dissociative attachment probability 1
-- Branching ratio: H2O Electron Hole Recombination Dissociative decay1 probability 0.15
-- Branching ratio: H2O Electron Hole Recombination Dissociative decay2 probability 0.55
-- Branching ratio: H2O Electron Hole Recombination Dissociative decay3 probability 0
-- Branching ratio: H2O Electron Hole Recombination Dissociative decay4 probability 0.3
Solvation model selected: 11003
   1. Ritchie.
   2. Terrisol.
   3. Meesungnoen.
   4. Kreipl.
   5. Meesugnoen solid.
-- Diffusion coefficient for molecule: H used the value 7e-09 (m2/s) 
-- Diffusion coefficient for molecule: H2 used the value 4.8e-09 (m2/s) 
-- Diffusion coefficient for molecule: H2O2 used the value 2.3e-09 (m2/s) 
-- Diffusion coefficient for molecule: H3Op used the value 9e-09 (m2/s) 
-- Diffusion coefficient for molecule: OH used the value 2.8e-09 (m2/s) 
-- Diffusion coefficient for molecule: OHm used the value 5e-09 (m2/s) 
-- Diffusion coefficient for molecule: Product used the value 0 (m2/s) 
-- Diffusion coefficient for molecule: e_aq used the value 4.9e-09 (m2/s) 

### TsEmDNAPhysics Construct Processes 
Ts Rudd ionisation model is constructed 
 Re-set reaction kobs to : 1.006e+10/M/s
 Re-set reaction kobs to : 3.5e+07/M/s
 Re-set reaction kobs to : 2.51e+07/M/s
 Re-set reaction kobs to : 1.55e+10/M/s
 Re-set reaction kobs to : 2.5e+10/M/s
 Re-set reaction kobs to : 1.1e+10/M/s
 Re-set reaction kobs to : 1.13e+11/M/s
 Re-set reaction kobs to : 3.28e+07/M/s
 Re-set reaction kobs to : 5.5e+09/M/s
 Re-set reaction kobs to : 2.95e+10/M/s
 Re-set reaction kobs to : 2.11e+10/M/s
 Re-set reaction kobs to : 1.272e+10/M/s

========================================================================================================================
   TypeMolecules        Products                       Kobs (/M/s)    r (nm)        Preact       
========================================================================================================================
 I     O3P^0   + O3P^0   -> O2^0                    1              6.60708e-11   1            
 I     H^0     + O3P^0   -> OH^0                    1              4.44547e-12   1            
 I     H^0     + H^0     -> H_2^0                   5.40637e+10    0.257676      1            
 I     H^0     + O^-1    -> OH^-1                   1              4.44547e-12   1            
 I     H^0     + e_aq^-1 -> H_2^0 + OH^-1           6.86972e+10    0.186576      1            
 I     HO2^0   + O3P^0   -> O2^0 + OH^0             1              3.07306e-11   1            
 I     OH^0    + O3P^0   -> HO2^0                   1              1.32527e-11   1            

========================================================================================================================
Type   Molecules        Products                       Kobs (/M/s)    Kdif (/M/s)    Kact (/M/s)     r (nm)        Preact       alpha (/nm)   
========================================================================================================================
 II    HO2^-1  + O3P^0   -> O2^-1 + OH^0            1              1.15785e+10    1               0.45          3.38465e-11  2.22222       
 II    H_2^0   + O3P^0   -> H^0 + OH^0              1              4.79478e+10    1               0.34          9.60038e-12  2.94118       
 II    H_2^0   + O^-1    -> H^0 + OH^-1             1              5.4999e+10     1               0.39          7.75415e-12  2.5641        
 II    H^0     + H2O2^0  -> OH^0                    2.84495e+08    1.08051e+11    1.6386e+08      0.4           0.0011083    2.50379       
 II    H^0     + HO2^0   -> H2O2^0                  1              9.08874e+10    1               0.4           4.62429e-12  2.5           
 II    H^0     + OH^-1   -> e_aq^-1                 1              1.63194e+11    1               0.52          2.19385e-12  1.92308       
 II    H^0     + OH^0    -> None                    3.00282e+10    1.10752e+11    4.01027e+10     0.41          0.13353      3.32218       
 II    H^0     + O2^0    -> HO2^0                   1              8.20711e+10    1               0.36          5.43619e-12  2.77778       
 II    H^0     + O2^-1   -> HO2^-1                  1              9.14531e+10    1               0.41          4.53004e-12  2.43902       
 II    H2O2^0  + O3P^0   -> HO2^0 + OH^0            1              3.09372e+10    1               0.41          1.33912e-11  2.43902       
 II    H2O2^0  + OH^-1   -> HO2^-1                  1              8.87455e+10    1               0.54          3.93707e-12  1.85185       
 II    H2O2^0  + O^-1    -> HO2^0 + OH^-1           1              3.471e+10      1               0.46          1.11399e-11  2.17391       
 II    H2O2^0  + e_aq^-1 -> OH^-1 + OH^0            3.41493e+10    1.55279e+11    6.06624e+10     0.71          0.0755787    1.95869       
 II    HO2^0   + HO2^0   -> H2O2^0 + O2^0           1              7.31035e+09    1               0.42          5.5873e-11   2.38095       
 II    HO2^0   + O2^-1   -> HO2^-1 + O2^0           1              1.31791e+10    1               0.43          3.0562e-11   2.32558       
 II    OH^-1   + O3P^0   -> HO2^-1                  1              6.31536e+10    1               0.53          5.59998e-12  1.88679       
 II    OH^-1   + HO2^0   -> O2^-1                   1              6.55711e+10    1               0.54          5.32853e-12  1.85185       
 II    OH^0    + HO2^-1  -> HO2^0 + OH^-1           1              3.33305e+10    1               0.47          1.14483e-11  2.12766       
 II    OH^0    + H_2^0   -> H^0                     1              6.70352e+10    1               0.36          6.65551e-12  2.77778       
 II    OH^0    + H2O2^0  -> HO2^0                   1              5.18762e+10    1               0.43          7.7642e-12   2.32558       
 II    OH^0    + HO2^0   -> O2^0                    1              3.34225e+10    1               0.43          1.20511e-11  2.32558       
 II    OH^0    + OH^-1   -> O^-1                    1              9.0389e+10     1               0.55          3.81947e-12  1.81818       
 II    OH^0    + OH^0    -> H2O2^0                  1.09866e+10    2.65413e+10    1.87468e+10     0.44          0.219112     3.87801       
 II    OH^0    + O^-1    -> HO2^-1                  1              3.54646e+10    1               0.47          1.07594e-11  2.12766       
 II    OH^0    + e_aq^-1 -> OH^-1                   6.03333e+10    1.57466e+11    9.68918e+10     0.72          0.151355     2.2435        
 II    OH^0    + O2^-1   -> O2^0 + OH^-1            1              3.23684e+10    1               0.44          1.22731e-11  2.27273       
 II    OH^0    + O3^-1   -> O2^-1 + HO2^0           1              3.16917e+10    1               0.42          1.28882e-11  2.38095       
 II    O2^0    + O3P^0   -> O3^0                    1              1.23201e+10    1               0.37          3.56647e-11  2.7027        
 II    O2^0    + O^-1    -> O3^-1                   1              1.3985e+10     1               0.42          2.92063e-11  2.38095       
 II    e_aq^-1 + HO2^0   -> HO2^-1                  1              1.24812e+11    1               0.71          2.32349e-12  1.40845       
 II    e_aq^-1 + O2^0    -> O2^-1                   1              1.18288e+11    1               0.67          2.5538e-12   1.49254       

========================================================================================================================
Type   Molecules        Products                       Kobs (/M/s)    r (nm)        reff (nm)    Preact       
========================================================================================================================
 III   H3O^1   + OH^-1   -> None                    3.65972e+11    0.998515         1.44759         1               
 III   H3O^1   + O3^-1   -> OH^0 + O2^0             1              nan              6.10029e-12     1               
 III   e_aq^-1 + e_aq^-1 -> H_2^0 + OH^-1 + OH^-1   4.76366e+10    0.614571         0.300762        1               

========================================================================================================================
Type   Molecules        Products                       Kobs (/M/s)    Kdif (/M/s)    Kact (/M/s)     r (nm)        reff (nm)    reff1 (nm)    Preact       
========================================================================================================================
 IV    HO2^-1  + O^-1    -> O2^-1 + OH^-1           1              5.24638e+09    1               0.5           0.203901     3.88651e-11   1.05824e-10  
 IV    H3O^1   + HO2^-1  -> H2O2^0                  1              1.59054e+11    1               0.5           0.99792      6.27408e-12   1.2776e-12   
 IV    H3O^1   + O^-1    -> OH^0                    1              1.63586e+11    1               0.5           0.99792      6.10029e-12   1.24221e-12  
 IV    H3O^1   + O2^-1   -> HO2^0                   1              1.57792e+11    1               0.47          0.973814     6.17152e-12   1.29914e-12  
 IV    O^-1    + O^-1    -> H2O2^0 + OH^-1 + OH^-1  1              3.08611e+09    1               0.5           0.203901     3.30354e-11   1.799e-10    
 IV    O^-1    + O3^-1   -> O2^-1 + O2^-1           1              4.96746e+09    1               0.45          0.164102     3.30354e-11   1.21256e-10  
 IV    e_aq^-1 + HO2^-1  -> O^-1 + OH^-1            1              7.12708e+10    1               0.75          0.421768     5.91783e-12   5.49188e-12  
 IV    e_aq^-1 + H3O^1   -> H^0                     4.76908e+10    2.75462e+11    5.19729e+10     0.75          1.21579      0.148526      0.0367887    
 IV    e_aq^-1 + O^-1    -> OH^-1 + OH^-1           1              7.31858e+10    1               0.75          0.421768     5.76297e-12   5.34817e-12  
 IV    e_aq^-1 + O2^-1   -> H2O2^0 + OH^-1 + OH^-1  1              6.7712e+10     1               0.72          0.394524     5.8265e-12    5.99994e-12  
 IV    O2^-1   + O^-1    -> O2^0 + OH^-1 + OH^-1    1              5.10235e+09    1               0.47          0.179795     3.52377e-11   1.1421e-10   

========================================================================================================================
Type   Molecules        Products                       Kobs (/M/s)    r (nm)        reff (nm)    Preact       
========================================================================================================================

========================================================================================================================
Type   Molecules        Products                       Scavenging capacity /s
========================================================================================================================
 VI    O3P^0   + OH^-1   -> HO2^-1                  -41.6           Single factor 
 VI    O3P^0   + None    -> OH^0 + OH^0             -1900           Single factor 
 VI    HO2^-1  + H3O^1   -> H2O2^0                  -4980           Single factor 
 VI    HO2^-1  + None    -> H2O2^0 + OH^-1          -1.36e+06       Single factor 
 VI    H^0     + OH^-1   -> e_aq^-1                 -2490           Single factor 
 VI    H^0     + None    -> e_aq^-1 + H3O^1         -5.94           Single factor 
 VI    H2O2^0  + OH^-1   -> HO2^-1                  -466            Single factor 
 VI    HO2^0   + OH^-1   -> O2^-1                   -624            Single factor 
 VI    HO2^0   + None    -> H3O^1 + O2^-1           -715000         Single factor 
 VI    OH^-1   + H3O^1   -> None                    11100           Single factor 
 VI    OH^0    + OH^-1   -> O^-1                    -624            Single factor 
 VI    O^-1    + H3O^1   -> OH^0                    -4730           Single factor 
 VI    O^-1    + None    -> OH^0 + OH^-1            -1.36e+06       Single factor 
 VI    e_aq^-1 + H3O^1   -> H^0                     2090            Single factor 
 VI    e_aq^-1 + None    -> H^0 + OH^-1             -15.8           Single factor 
 VI    O2^-1   + H3O^1   -> HO2^0                   -4730           Single factor 
 VI    O2^-1   + None    -> HO2^0 + OH^-1           -0.15           Single factor 
 VI    O3^-1   + H3O^1   -> OH^0 + O2^0             -8910           Single factor 
 VI    O3^-1   + None    -> O^-1 + O2^0             -2660           Single factor 


 -------------- OpenTOPAS-nBio IRT Warning -------------
 -- SpinBehavior is ExplicitAssignament
 ----------------------------------------------

Visualization verbosity changed to quiet (0)
=======================================================================
======                 Electromagnetic Physics Parameters      ========
=======================================================================
LPM effect enabled                                 1
Enable creation and use of sampling tables         0
Apply cuts on all EM processes                     0
Use combined TransportationWithMsc                 Disabled
Use general process                                0
Enable linear polarisation for gamma               0
Enable photoeffect sampling below K-shell          1
Enable sampling of quantum entanglement            0
X-section factor for integral approach             0.8
Min kinetic energy for tables                      100 eV 
Max kinetic energy for tables                      100 TeV
Number of bins per decade of a table               7
Verbose level                                      1
Verbose level for worker thread                    0
Bremsstrahlung energy threshold above which 
  primary e+- is added to the list of secondary    100 TeV
Bremsstrahlung energy threshold above which primary
  muon/hadron is added to the list of secondary    100 TeV
Lowest triplet kinetic energy                      1 MeV
Enable sampling of gamma linear polarisation       0
5D gamma conversion model type                     0
5D gamma conversion model on isolated ion          0
Livermore data directory                           epics_2017
=======================================================================
======                 Ionisation Parameters                   ========
=======================================================================
Step function for e+-                              (0.2, 1 mm)
Step function for muons/hadrons                    (0.2, 0.1 mm)
Step function for light ions                       (0.2, 0.1 mm)
Step function for general ions                     (0.2, 0.1 mm)
Lowest e+e- kinetic energy                         1 keV
Lowest muon/hadron kinetic energy                  1 keV
Use ICRU90 data                                    0
Fluctuations of dE/dx are enabled                  1
Type of fluctuation model for leptons and hadrons  Universal
Use built-in Birks satuaration                     0
Build CSDA range enabled                           0
Use cut as a final range enabled                   0
Enable angular generator interface                 0
Max kinetic energy for CSDA tables                 1 GeV
Max kinetic energy for NIEL computation            0 eV 
Linear loss limit                                  0.01
Read data from file for e+e- pair production by mu 0
=======================================================================
======                 Multiple Scattering Parameters          ========
=======================================================================
Type of msc step limit algorithm for e+-           3
Type of msc step limit algorithm for muons/hadrons 0
Msc lateral displacement for e+- enabled           1
Msc lateral displacement for muons and hadrons     0
Urban msc model lateral displacement alg96         1
Range factor for msc step limit for e+-            0.04
Range factor for msc step limit for muons/hadrons  0.2
Geometry factor for msc step limitation of e+-     2.5
Safety factor for msc step limit for e+-           0.6
Skin parameter for msc step limitation of e+-      1
Lambda limit for msc step limit for e+-            1 mm
Use Mott correction for e- scattering              0
Factor used for dynamic computation of angular 
  limit between single and multiple scattering     1
Fixed angular limit between single 
  and multiple scattering                          3.1416 rad
Upper energy limit for e+- multiple scattering     100 MeV
Type of electron single scattering model           0
Type of nuclear form-factor                        1
Screening factor                                   1
=======================================================================
======                 Atomic Deexcitation Parameters          ========
=======================================================================
Fluorescence enabled                               1
Directory in G4LEDATA for fluorescence data files  fluor
Auger electron cascade enabled                     1
PIXE atomic de-excitation enabled                  0
De-excitation module ignores cuts                  1
Type of PIXE cross section for hadrons             Empirical
Type of PIXE cross section for e+-                 Livermore
=======================================================================
======                 DNA Physics Parameters                  ========
=======================================================================
Use fast sampling in DNA models                    0
Use Stationary option in DNA models                0
Use DNA with multiple scattering of e-             0
Use DNA e- solvation model type                    11003
=======================================================================

### ===  Deexcitation model UAtomDeexcitation is activated for 1 region:
          DefaultRegionForTheWorld  1  1  0
### ===  Auger flag: 1
### ===  Ignore cuts flag:   1
TsDNAELSEPAElasticModel: high energy limit decreased from 1e+08 MeV to 1 MeV
Rudd ionisation model is initialized 
Energy range: 0 eV - 1e+06 keV for proton

phot:  for gamma SubType=12 BuildTable=0
      LambdaPrime table from 200 keV to 100 TeV in 61 bins 
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
 LivermorePhElectric : Emin=    0 eV  Emax=  100 TeV  SauterGavrila Fluo

compt:  for gamma SubType=13 BuildTable=1
      Lambda table from 100 eV  to 1 MeV, 7 bins/decade, spline: 1
      LambdaPrime table from 1 MeV to 100 TeV in 56 bins 
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
    LivermoreCompton : Emin=    0 eV  Emax=  100 TeV Fluo

conv:  for gamma SubType=14 BuildTable=1
      Lambda table from 1.022 MeV to 100 TeV, 18 bins/decade, spline: 1
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
 LivermoreConversion : Emin=    0 eV  Emax=  100 TeV  ModifiedTsai

Rayl:  for gamma SubType=11 BuildTable=1
      Lambda table from 100 eV  to 150 keV, 7 bins/decade, spline: 0
      LambdaPrime table from 150 keV to 100 TeV in 62 bins 
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
   LivermoreRayleigh : Emin=    0 eV  Emax=  100 TeV  CullenGenerator

e-_G4DNAElastic:  for e- SubType=51 BuildTable=0
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
DNAELSEPAElasticModel : Emin=    0 eV  Emax=  100 TeV

e-_G4DNAExcitation:  for e- SubType=52 BuildTable=0
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
DNABornExcitationModel : Emin=    0 eV  Emax=    1 MeV

e-_G4DNAIonisation:  for e- SubType=53 BuildTable=0
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
DNABornIonisationModel : Emin=    0 eV  Emax=    1 MeV  deltaBorn Fluo

e-_G4DNAElectronSolvation:  for e- SubType=58 BuildTable=0
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
DNAOneStepThermalizationModel_Meesungnoen2002 : Emin=    0 eV  Emax=   10 eV 

e-_G4DNAVibExcitation:  for e- SubType=54 BuildTable=0
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
DNASancheExcitationModel : Emin=    0 eV  Emax=  100 eV 

e-_G4DNAAttachment:  for e- SubType=55 BuildTable=0
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
DNAMeltonAttachmentModel : Emin=    0 eV  Emax=   13 eV 

msc:  for e+  SubType= 10
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
            UrbanMsc : Emin=    0 eV  Emax=  100 TeV Nbins=84 100 eV  - 100 TeV
          StepLim=DistanceToBoundary Rfact=0.04 Gfact=2.5 Sfact=0.6 DispFlag:1 Skin=1 Llim=1 mm

eIoni:  for e+  XStype:3  SubType=2
      dE/dx and range tables from 100 eV  to 100 TeV in 84 bins
      Lambda tables from threshold to 100 TeV, 7 bins/decade, spline: 1
      StepFunction=(0.2, 1 mm), integ: 3, fluct: 1, linLossLim= 0.01
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
        MollerBhabha : Emin=    0 eV  Emax=  100 TeV
G4WT3 > Begin processing for Run: 0, History: 0
G4WT0 > Begin processing for Run: 0, History: 100
G4WT1 > Begin processing for Run: 0, History: 200
G4WT1 > Begin processing for Run: 0, History: 300
G4WT0 > Begin processing for Run: 0, History: 400

TOPAS run sequence complete.
Particle source Demo: Total number of histories: 0
Particle source MyBeam: Total number of histories: 500
######### Averaged IRT-execution-time per history (132 histories): 0.956288 s +/- 0.311303 s 

Note that TOPAS interrupted one or more histories during this session
due to errors reported by Geant4.
The total number of interrupted histories was: 111
For details on each of these errors, see the console log for "G4Exception"
If only a very small proportion of your histories were affected,
you may be able to still use the overall result,
but this is a judgement call you need to make for yourself.
You can set TOPAS to limit the number of messages about interrupted histories by setting
the parameter Ts/InterruptedHistoryMaxReports
You can set TOPAS to exit if it exceeds a given number of interrupted histories by setting
the parmameter Ts/MaxInterruptedHistories

Elapsed times:
Parameter Reading : User=0.010000s Real=0.003428s Sys=0.000000s [Cpu=291.8%]
    Initialization: User=0.030000s Real=0.030463s Sys=0.000000s [Cpu=98.5%]
         Execution: User=127.900000s Real=36.535374s Sys=0.740000s [Cpu=352.1%]
      Finalization: User=0.010000s Real=0.008455s Sys=0.010000s [Cpu=236.5%]
             Total: User=127.95s Real=36.5777s Sys=0.75s

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[jonahpeter]

Edited my question based on new understanding^^^

[JoseRamosMendez]

Temperature is hardcoded as TOPAS-nBio was validated for low-LET radiation at 0 < T < 90 C see here. At that "low-LET", only those reactions are relevant. You could try to incorporate scaling for other reactions in case you need to go high in LET (like Herve's paper).

[jonahpeter]

Hi Jose, many thanks for your continued help! Does this mean that the temperature scaling is not compatible with pH scaling? Or that it is, but only if the pH scaling can be implemented using those 10 reactions?