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TOPAS-nBio v3.0

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@JoseRamosMendez JoseRamosMendez released this 03 Jun 22:54
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The TOPAS-nBio Collaboration.

Release notes June 3, 2024.

TOPAS-nBio v3.0 includes the first release of qc-nbio-testsuite, a continuous integration test suit for assisting user’s benchmarks and new adds to TOPAS-nBio. Additionally, results from a comprehensive regression test for accuracy evaluation are provided in a PDF document. The current release is only compatible with OpenTOPAS v.4.0 (https://opentopas.github.io/) build on top of Geant4/Geant4-DNA v11.1.3.

Details in TOPAS-nBio v3.0 accuracy can be found at the regression system

Processes.

  • TsDNAWaterDissociationDisplacer::GetProductsDisplacement()
    -- The adjustable displacement parameters of water dissociations have been changed (3 Rs -> 2 Rs).
    -- The displacement of B1A1 dissociation H2O->H2+2OH has been changed consistent with momentum conservation.

  • TsDNAELSEPAElasticModel
    -- TsDNAELSEPAElasticModel from G4DNAELSEPAElasticModel has been implemented with some changes in order to use density-scaling.

  • TsIRT::contactReactions
    -- A double sampling of contact reactions has been corrected.
    -- The boundary condition of contact reaction is now based on reactionRadius instead of effectiveReactionRadius.

  • TsIRTConfiguration::SampleIRTPartiallyDiffusionControlled()
    -- Sampling partially diffusion-controlled reactions for type II and type IV reactions now uses the acceptance-rejection method instead of the Brents function.

  • TsIRTConfiguration::ResolveRemainerReactionParameters()
    -- Calculation of reaction velocity v and effectivetildeReactionRadius σ_eff^'' has been corrected.

  • TsIRTConfiguration::CalculateContactProbabilities()
    -- The reaction probabilities of partially diffusion-controlled reactions have been corrected.

  • TsIRTConfiguration::ContactFirstOrderAndBackgroundReactions()
    -- The contact first order reaction has been rewritten for the correct unit.
    -- The reaction radius for the contact first-order reaction is left to further discussion.

  • IRT: Reaction rates and diffusion scale automatically by setting the temperature in Celsius (unitless). Water density scaling must be set manually.

  • TsIRT::TsIRT()
    -- Corrected the default time steps for G-value scoring from 0.1 ps to 1 ps. This was causing the first bin of G-value to always be 0
    -- First implementation of physical processes for interactions with gold material. It only supports electrons and gammas.
    -- It can be activated with

    s:Ph/Default/Modules = 1 “TsEmDNAPhysics”
b:Ph/Default/PhysicsForGold/Active = “True”
s:Ph/Default/PhysicsForGold/Region = “MyRegion”

Scorers.

  • scorers/TsScoreClusterSizeInRandomCylinders.cc/hh
    -- New ionization detail scorer for the calculation of cluster size. Generates a .phsp file with 4 columns of data containing the cluster size, ionization cluster frequency, excitation cluster frequency, and total cluster frequency

  • scorers/IRTTemperature/
    -- G-value calculation in pure liquid water with temperature variation from 20 C to 90 C

  • TsScoreClusterSizeInRandomCylinders::TsScoreClusterSizeInRandomCylinders()
    -- Added support for single volumes

  • A new example for process in Gold: examples/processes/GoldNanoParticle.txt

  • Updated DAMARIS for TOPAS-nBio 3.0

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