[Run issue]: Inconsistent temperature scaling at 25 C

[jonahpeter]

Contact Details

No response

What was the issue?

Hi all,

It seems that setting u:Ch/TOPASChemistry/Temperature = 25 is not consistent with itself. There should be no scaling for this value, but for default reactions 4, 5, 7, 8, 10 the computed reaction rates are not equal to the default values. I wonder if this stems from a rounding error inside SmoluchowskiFunction or WaterDiffusionRate (or their arguments).

The errors are not too large, aside from reaction 7 which returns 1.78e10 instead of 1.56e10 (a ~14% error which feels significant). The log output is attached below.

TOPAS-nBio category

Chemistry

Version

3.0

What Operative System (OS) are you running on?

MacOS

Relevant log output

========================================================================================================================
   TypeMolecules        Products                      Kobs (/M/s)    r (nm)        Preact       
========================================================================================================================
 I     H^0     + H^0     -> H_2^0                  1.77533e+10    0.257676      1            
 I     H^0     + e_aq^-1 -> H_2^0 + OH^-1          2.5e+10        0.235995      1            

========================================================================================================================
Type   Molecules        Products                      Kobs (/M/s)    Kdif (/M/s)    Kact (/M/s)     r (nm)        Preact       alpha (/nm)   
========================================================================================================================
 II    H^0     + H2O2^0  -> OH^0                   9e+07          3.54815e+10    5.18344e+07     0.4           0.00106765   2.50365       
 II    H^0     + OH^0    -> None                   1.64488e+10    3.63686e+10    2.89779e+10     0.41          0.254897     4.3824        
 II    H2O2^0  + e_aq^-1 -> OH^-1 + OH^0           1.11716e+10    4.03588e+10    2.2076e+10      0.71          0.0999102    2.17887       
 II    OH^0    + OH^0    -> H2O2^0                 5.9236e+09     8.71557e+09    1.84915e+10     0.44          0.457363     7.09468       
 II    OH^0    + e_aq^-1 -> OH^-1                  3.09969e+10    4.09272e+10    1.24749e+11     0.72          0.472644     5.62232       

========================================================================================================================
Type   Molecules        Products                      Kobs (/M/s)    r (nm)        reff (nm)    Preact       
========================================================================================================================
 III   H3O^1   + OH^-1   -> None                   1.43e+11       0.898963         1.30327         1               
 III   e_aq^-1 + e_aq^-1 -> H_2^0 + OH^-1 + OH^-1  1.1e+10        0.583175         0.297004        1               

========================================================================================================================
Type   Molecules        Products                      Kobs (/M/s)    Kdif (/M/s)    Kact (/M/s)     r (nm)        reff (nm)    reff1 (nm)    Preact       
========================================================================================================================
 IV    e_aq^-1 + H3O^1   -> H^0                    2.3e+10        8.65948e+10    2.78743e+10     0.75          1.16337      0.212426      0.0646192    

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

========================================================================================================================
Type   Molecules        Products                      Scavenging capacity /s
========================================================================================================================
 VI    HO2^0   + OH^-1   -> O2^-1                  -624            Single factor 
 VI    OH^-1   + H3O^1   -> None                   11100           Single factor 
 VI    e_aq^-1 + H3O^1   -> H^0                    2090            Single factor

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[JoseRamosMendez]

Good question Jonah! Also thanks for the testing!
That depends on how (and which country) room, ambient and standard temperatures are defined. So, for water radiolysis (G-value validation and no temperature scaling), the kobs are those tested for accuracy and consistency at NIST. For temperature-dependence, keep in mind that those come from a fitted curve to measured data with some degree of sparsity.

[jonahpeter]

But if the temperature scaling is scaling relative to the default values (that is, when ApplyCorrectionScalingForTemperature =True), shouldn't scaling by a factor of 1 (simulations at 25 C) return the original default values?

[JoseRamosMendez]

Good point. Is 25C the reference value? or is it 22C or room-temperature (depends on location)? The kobs provided for water also have uncertainties as those are measured, besides the scaling is a regression fit from data obtained at higher temperatures in environments with added scavengers. So, I won't expect a one-to-one relationship at "original" values.