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Merged
JoseRamosMendez merged 8 commits into from
Feb 27, 2026
Merged

Release v4.1.0 #119

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79c7e22
Fix: Caught several bugs
Nov 21, 2025
70d083e
Fix: Changes for builging in Geant4-DNA v11.3.2
Dec 16, 2025
05c7939
Fix: reduced loop in map checking for finding particle names
Dec 16, 2025
912d55d
fix: code cleaning, roadmap for Geant4-DNA v11.3.2
Dec 17, 2025
dd980fe
Fix: background reactions at contact was not performing fine
Dec 18, 2025
0afad45
modified: geometry/dna/TsLinearDNA.cc
Dec 19, 2025
409e69b
Update Geant4 dataset versions in CI configuration
JoseRamosMendez Dec 22, 2025
2684821
Fixing inconsistencies in screen output
tmasilela Jan 15, 2026
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16 changes: 8 additions & 8 deletions .github/workflows/ci.yml
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Expand Up @@ -39,27 +39,27 @@ jobs:
uses: actions/cache@v4
with:
path: ${{ env.G4DATA_DIR }}
key: g4data-G4EMLOW-8.2-G4ENSDFSTATE-2.3
key: g4data-G4EMLOW-8.6.1-G4ENSDFSTATE-3.0

- name: Download Geant4 EMLOW & ENSDFSTATE datasets
if: steps.cache-g4data.outputs.cache-hit != 'true'
run: |
set -euo pipefail
mkdir -p "$G4DATA_DIR"
cd "$G4DATA_DIR"
curl -sSLO https://cern.ch/geant4-data/datasets/G4EMLOW.8.2.tar.gz
tar -xzf G4EMLOW.8.2.tar.gz
rm G4EMLOW.8.2.tar.gz
curl -sSLO https://cern.ch/geant4-data/datasets/G4ENSDFSTATE.2.3.tar.gz
tar -xzf G4ENSDFSTATE.2.3.tar.gz
rm G4ENSDFSTATE.2.3.tar.gz
curl -sSLO https://cern.ch/geant4-data/datasets/G4EMLOW.8.6.1.tar.gz
tar -xzf G4EMLOW.8.6.1.tar.gz
rm G4EMLOW.8.6.1.tar.gz
curl -sSLO https://cern.ch/geant4-data/datasets/G4ENSDFSTATE.3.0.tar.gz
tar -xzf G4ENSDFSTATE.3.0.tar.gz
rm G4ENSDFSTATE.3.0.tar.gz

- name: Pull OpenTOPAS Docker image
run: docker pull $TOPAS_DOCKER_IMAGE

- name: Download TOPAS docker launcher
run: |
curl -sSfL https://raw.githubusercontent.com/OpenTOPAS/OpenTOPAS/fix-bugs/docker/topas-docker -o docker-run
curl -sSfL https://raw.githubusercontent.com/OpenTOPAS/OpenTOPAS/main/docker/topas-docker -o docker-run
chmod +x docker-run

- name: Install nrtest tooling
Expand Down
2 changes: 1 addition & 1 deletion README.md
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@@ -1,4 +1,4 @@
# TOPAS-nBio
# TOPAS-nBio (Version 4.1.0)
This is the TOPAS-nBio extension repository, a Monte Carlo simulation framework for (sub-) cellular radiobiology.

TOPAS-nBio is described here: https://topas-nbio.readthedocs.io/.
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1 change: 0 additions & 1 deletion geometry/dna/TsLinearDNA.cc
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Expand Up @@ -12,7 +12,6 @@
// A strand of DNA.

#include "TsLinearDNA.hh"

#include "TsParameterManager.hh"

#include "G4VPhysicalVolume.hh"
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15 changes: 8 additions & 7 deletions processes/TsEmDNAPhysics.cc
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Expand Up @@ -241,7 +241,7 @@ void TsEmDNAPhysics::ConstructProcess()
G4DNAPTBElasticModel* modelDNAPTBElastic = new G4DNAPTBElasticModel("THF/TMP/PY", particle);

G4DNAModelInterface* e_elasticInteraction = new G4DNAModelInterface("e-_elastic_interaction");
e_elasticInteraction->RegisterModel(e_modelDNARutherfordElastic, particle);
e_elasticInteraction->RegisterModel(e_modelDNARutherfordElastic);
e_elasticInteraction->RegisterModel(modelDNAPTBElastic);
e_elasticInteraction->RegisterModel(new G4DNAVacuumModel());

Expand All @@ -255,7 +255,7 @@ void TsEmDNAPhysics::ConstructProcess()
G4DNAPTBElasticModel* modelDNAPTBElastic = new G4DNAPTBElasticModel("THF/TMP/PY", particle);

G4DNAModelInterface* e_elasticInteraction = new G4DNAModelInterface("e-_elastic_interaction");
e_elasticInteraction->RegisterModel(e_modelDNACPA100Model, particle);
e_elasticInteraction->RegisterModel(e_modelDNACPA100Model);
e_elasticInteraction->RegisterModel(modelDNAPTBElastic);
e_elasticInteraction->RegisterModel(new G4DNAVacuumModel());

Expand All @@ -270,7 +270,7 @@ void TsEmDNAPhysics::ConstructProcess()
G4DNAPTBElasticModel* modelDNAPTBElastic = new G4DNAPTBElasticModel("THF/TMP/PY", particle);

G4DNAModelInterface* e_elasticInteraction = new G4DNAModelInterface("e-_elastic_interaction");
e_elasticInteraction->RegisterModel(e_modelDNAUeharaScreenedRutherfordElastic, particle);
e_elasticInteraction->RegisterModel(e_modelDNAUeharaScreenedRutherfordElastic);
e_elasticInteraction->RegisterModel(modelDNAPTBElastic);
e_elasticInteraction->RegisterModel(new G4DNAVacuumModel());

Expand Down Expand Up @@ -347,7 +347,7 @@ void TsEmDNAPhysics::ConstructProcess()
G4DNAPTBExcitationModel* modelDNAPTBExcitation = new G4DNAPTBExcitationModel("THF/TMP/PY",particle);
G4DNAModelInterface* e_excitationInteraction = new G4DNAModelInterface("e-_excitation_interaction");

e_excitationInteraction->RegisterModel(e_modelDNAEmfietzoglouExcitation,particle);
e_excitationInteraction->RegisterModel(e_modelDNAEmfietzoglouExcitation);
e_excitationInteraction->RegisterModel(modelDNAPTBExcitation);
e_excitationInteraction->RegisterModel(new G4DNAVacuumModel());

Expand All @@ -360,7 +360,7 @@ void TsEmDNAPhysics::ConstructProcess()
G4DNAPTBExcitationModel* modelDNAPTBExcitation = new G4DNAPTBExcitationModel("THF/TMP/PY",particle);
G4DNAModelInterface* e_excitationInteraction = new G4DNAModelInterface("e-_excitation_interaction");

e_excitationInteraction->RegisterModel(e_modelDNABornExcitation,particle);
e_excitationInteraction->RegisterModel(e_modelDNABornExcitation);
e_excitationInteraction->RegisterModel(modelDNAPTBExcitation);
e_excitationInteraction->RegisterModel(new G4DNAVacuumModel());

Expand Down Expand Up @@ -454,7 +454,7 @@ void TsEmDNAPhysics::ConstructProcess()
G4DNAPTBIonisationModel* modelDNAPTBIonisation = new G4DNAPTBIonisationModel("THF/TMP/PY",particle);

G4DNAModelInterface* e_ionisationInteraction = new G4DNAModelInterface("e-_ionisation_interaction");
e_ionisationInteraction->RegisterModel(e_modelDNAEmfietzoglouIonisation,particle);
e_ionisationInteraction->RegisterModel(e_modelDNAEmfietzoglouIonisation);
e_ionisationInteraction->RegisterModel(modelDNAPTBIonisation);
e_ionisationInteraction->RegisterModel(new G4DNAVacuumModel());

Expand Down Expand Up @@ -482,7 +482,7 @@ void TsEmDNAPhysics::ConstructProcess()
G4DNAPTBIonisationModel* modelDNAPTBIonisation = new G4DNAPTBIonisationModel("THF/TMP/PY",particle);

G4DNAModelInterface* e_ionisationInteraction = new G4DNAModelInterface("e-_ionisation_interaction");
e_ionisationInteraction->RegisterModel(e_modelDNABornIonisation,particle);
e_ionisationInteraction->RegisterModel(e_modelDNABornIonisation);
e_ionisationInteraction->RegisterModel(modelDNAPTBIonisation);
e_ionisationInteraction->RegisterModel(new G4DNAVacuumModel());

Expand Down Expand Up @@ -904,3 +904,4 @@ void TsEmDNAPhysics::ConstructProcess()
G4LossTableManager::Instance()->SetAtomDeexcitation(de);
}


2 changes: 1 addition & 1 deletion processes/TsEmDNAPhysics.hh
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Expand Up @@ -36,4 +36,4 @@ private:
G4int verbose;
};

#endif
#endif
6 changes: 3 additions & 3 deletions processes/TsIRT.cc
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Expand Up @@ -26,7 +26,6 @@
#include <set>

TsIRT::TsIRT(TsParameterManager* pM, G4String parmName): TsVIRTProcedure(pM,parmName){
fReactionConf = new TsIRTConfiguration(parmName, pM);

fSpeciesIndex = 0;
fMoleculesName = fReactionConf->GetMoleculeNames();
Expand Down Expand Up @@ -123,7 +122,7 @@ void TsIRT::AddMolecule(G4Track* aTrack, G4double time, G4int moleculeID, G4Thre
TsIRTConfiguration::TsMolecule TsIRT::ConstructMolecule(G4Track* aTrack, G4double time, G4int moleculeID, G4ThreeVector offset) {
G4int pdg = -1;
G4ThreeVector position = aTrack->GetPosition();
const G4String& name = GetMolecule(aTrack)->GetName();
G4String name = fReactionConf->NormalizeMoleculeName(GetMolecule(aTrack)->GetName());
pdg = fMoleculesIDs[name];

TsIRTConfiguration::TsMolecule aMol;
Expand Down Expand Up @@ -371,7 +370,8 @@ void TsIRT::ConductReactions() {

} else {
fReactionConf->Diffuse(fChemicalSpecies[iM],irt-fChemicalSpecies[iM].time);
for ( int ip = 0; ip < 3; ip++ )
//positions = fReactionConf->GetBackgroundPositionOfProducts(fChemicalSpecies[iM], indexOfReaction);
for ( int ip = 0; ip < 3; ip++ )
positions.push_back(fChemicalSpecies[iM].position);

binReaction = fReactionConf->GetReaction(indexOfReaction);
Expand Down
2 changes: 0 additions & 2 deletions processes/TsIRT.hh
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Expand Up @@ -49,7 +49,6 @@ protected:
std::unordered_map<G4int,std::unordered_map<G4int,std::unordered_map<G4int,std::unordered_map<G4int,G4bool>>>> fSpaceBinned;
std::map<G4int, G4String> fMoleculesName;

TsIRTConfiguration* fReactionConf;
TsParameterManager* fPm;
G4String fName;

Expand All @@ -59,4 +58,3 @@ protected:

};
#endif

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