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Add all nBio classes for beta release.
 new file: examples/README.md new file: examples/geometry/cells/BloodCells/Basophil.txt new file: examples/geometry/cells/BloodCells/Eosinophil.txt new file: examples/geometry/cells/BloodCells/Lymphocyte.txt new file: examples/geometry/cells/BloodCells/Monocyte.txt new file: examples/geometry/cells/BloodCells/Neutrophil.txt new file: examples/geometry/cells/BloodCells/RedBloodCell.txt new file: examples/geometry/cells/BoneCells/Osteoblast.txt new file: examples/geometry/cells/BoneCells/Osteoclast.txt new file: examples/geometry/cells/BoneCells/Osteocyte.txt new file: examples/geometry/cells/CellCulture.txt new file: examples/geometry/cells/CuboidalCell.txt new file: examples/geometry/cells/EllipsoidCell.txt new file: examples/geometry/cells/FibroblastCell.txt new file: examples/geometry/cells/HexagonCell.txt new file: examples/geometry/cells/Neuron/NMO_00228.swc new file: examples/geometry/cells/Neuron/NMO_78177_glial.swc new file: examples/geometry/cells/Neuron/Neuron.txt new file: examples/geometry/cells/SphericalCell.txt new file: examples/geometry/dna/CharltonDNA.txt new file: examples/geometry/dna/CircularPlasmid.txt new file: examples/geometry/dna/DNAFabric/DNAFabricFile.txt new file: examples/geometry/dna/DNAFabric/DNAFiber.txt new file: examples/geometry/dna/DNAFabric/fiber.dnafab new file: examples/geometry/dna/FractalDNA/Fractal.txt new file: examples/geometry/dna/FractalDNA/FullGenome.dat new file: examples/geometry/dna/LinearDNA.txt new file: examples/geometry/dna/SimpleDNACylinders.txt new file: examples/geometry/dna/SolenoidFiber/BasePairScoring/ParametersFibre.txt new file: examples/geometry/dna/SolenoidFiber/BasePairScoring/Parameters_Beam.txt new file: examples/geometry/dna/SolenoidFiber/BasePairScoring/Parameters_Geometry.txt new file: examples/geometry/dna/SolenoidFiber/BasePairScoring/Parameters_Main.txt new file: examples/geometry/dna/SolenoidFiber/BasePairScoring/Parameters_Physics.txt new file: examples/geometry/dna/SolenoidFiber/BasePairScoring/Parameters_Scorer.txt new file: examples/geometry/dna/SolenoidFiber/BasePairScoring/Parameters_Vis.txt new file: examples/geometry/dna/SolenoidFiber/SpatialScoring/Parameters_Beam.txt new file: examples/geometry/dna/SolenoidFiber/SpatialScoring/Parameters_Geometry.txt new file: examples/geometry/dna/SolenoidFiber/SpatialScoring/Parameters_Main.txt new file: examples/geometry/dna/SolenoidFiber/SpatialScoring/Parameters_Physics.txt new file: examples/geometry/dna/SolenoidFiber/SpatialScoring/Parameters_Scorer.txt new file: examples/geometry/dna/SolenoidFiber/SpatialScoring/Parameters_Vis.txt new file: examples/geometry/dna/SupercoiledPlasmid/TsPlasmidSupercoiled.txt new file: examples/geometry/dna/SupercoiledPlasmid/pBR322_a.xyz new file: examples/geometry/dna/SupercoiledPlasmid/pBR322_b.xyz new file: examples/geometry/dna/wholeNucleus/DNA.txt new file: examples/geometry/dna/wholeNucleus/chromo1.dat new file: examples/geometry/dna/wholeNucleus/chromo10.dat new file: examples/geometry/dna/wholeNucleus/chromo11.dat new file: examples/geometry/dna/wholeNucleus/chromo12.dat new file: examples/geometry/dna/wholeNucleus/chromo13.dat new file: examples/geometry/dna/wholeNucleus/chromo14.dat new file: examples/geometry/dna/wholeNucleus/chromo15.dat new file: examples/geometry/dna/wholeNucleus/chromo16.dat new file: examples/geometry/dna/wholeNucleus/chromo17.dat new file: examples/geometry/dna/wholeNucleus/chromo18.dat new file: examples/geometry/dna/wholeNucleus/chromo19.dat new file: examples/geometry/dna/wholeNucleus/chromo2.dat new file: examples/geometry/dna/wholeNucleus/chromo20.dat new file: examples/geometry/dna/wholeNucleus/chromo21.dat new file: examples/geometry/dna/wholeNucleus/chromo22.dat new file: examples/geometry/dna/wholeNucleus/chromo3.dat new file: examples/geometry/dna/wholeNucleus/chromo4.dat new file: examples/geometry/dna/wholeNucleus/chromo5.dat new file: examples/geometry/dna/wholeNucleus/chromo6.dat new file: examples/geometry/dna/wholeNucleus/chromo7.dat new file: examples/geometry/dna/wholeNucleus/chromo8.dat new file: examples/geometry/dna/wholeNucleus/chromo9.dat new file: examples/geometry/dna/wholeNucleus/chromoX.dat new file: examples/geometry/dna/wholeNucleus/chromoY.dat new file: examples/geometry/other/Membrane.txt new file: examples/geometry/other/Mitochondria.txt new file: examples/geometry/other/generateRandomCylinders.txt new file: examples/geometry/other/readBackRandomCylindres.txt new file: examples/processes/ActiveChemistryDefault.txt new file: examples/processes/ActiveChemistryExtended.txt new file: examples/processes/ActiveChemistryRevised.txt new file: examples/processes/ActiveCustomizablePhysics.txt new file: examples/processes/G4DNAModelPerRegion.txt new file: examples/processes/RemoveChemicalSpeciesInVolume.txt new file: examples/processes/TOPASChemistry.txt new file: examples/processes/TOPASChemistry_Extended.txt new file: examples/scorers/1ZBB.pdb new file: examples/scorers/DBSCAN.txt new file: examples/scorers/DBSCAN_VRT.txt new file: examples/scorers/GvalueG4DNADefault.txt new file: examples/scorers/GvalueRevisedPhysicsChemistry.txt new file: examples/scorers/IonizationDetailInRandomCylinders.txt new file: examples/scorers/NumberOfChemicalSpeciesAtTime.txt new file: examples/scorers/PDB4DNA.txt new file: examples/scorers/PDB4DNA_VRT.txt new file: examples/scorers/particleTuple.txt new file: examples/scorers/randomCylinders_position_nm_rotation_deg.xyz new file: examples/scorers/simpleSSBandDSBInPlasmid.txt new file: examples/scorers/simpleSSBandDSBInPlasmidWithDBSCAN.txt new file: geometry/cells/BloodCells/TsBasophil.cc new file: geometry/cells/BloodCells/TsBasophil.hh new file: geometry/cells/BloodCells/TsEosinophil.cc new file: geometry/cells/BloodCells/TsEosinophil.hh new file: geometry/cells/BloodCells/TsLymphocyte.cc new file: geometry/cells/BloodCells/TsLymphocyte.hh new file: geometry/cells/BloodCells/TsMonocyte.cc new file: geometry/cells/BloodCells/TsMonocyte.hh new file: geometry/cells/BloodCells/TsNeutrophil.cc new file: geometry/cells/BloodCells/TsNeutrophil.hh new file: geometry/cells/BloodCells/TsRedBloodCell.cc new file: geometry/cells/BloodCells/TsRedBloodCell.hh new file: geometry/cells/BoneCells/TsOsteoblast.cc new file: geometry/cells/BoneCells/TsOsteoblast.hh new file: geometry/cells/BoneCells/TsOsteoclast.cc new file: geometry/cells/BoneCells/TsOsteoclast.hh new file: geometry/cells/BoneCells/TsOsteocyte.cc new file: geometry/cells/BoneCells/TsOsteocyte.hh new file: geometry/cells/CellCulture/TsCellCulture.cc new file: geometry/cells/CellCulture/TsCellCulture.hh new file: geometry/cells/CellCulture/TsNtupleForCulture.cc new file: geometry/cells/CellCulture/TsNtupleForCulture.hh new file: geometry/cells/Neuron/TsNeuroMorpho.cc new file: geometry/cells/Neuron/TsNeuroMorpho.hh new file: geometry/cells/Neuron/TsNtupleForNeuron.cc new file: geometry/cells/Neuron/TsNtupleForNeuron.hh new file: geometry/cells/TsCuboidalCell.cc new file: geometry/cells/TsCuboidalCell.hh new file: geometry/cells/TsEllipsoidCell.cc new file: geometry/cells/TsEllipsoidCell.hh new file: geometry/cells/TsFibroblastCell1.cc new file: geometry/cells/TsFibroblastCell1.hh new file: geometry/cells/TsFibroblastCell2.cc new file: geometry/cells/TsFibroblastCell2.hh new file: geometry/cells/TsFibroblastCell3.cc new file: geometry/cells/TsFibroblastCell3.hh new file: geometry/cells/TsHexagonCell.cc new file: geometry/cells/TsHexagonCell.hh new file: geometry/cells/TsSphericalCell.cc new file: geometry/cells/TsSphericalCell.hh new file: geometry/dna/CircularPlasmid/TsCircularPlasmid.cc new file: geometry/dna/CircularPlasmid/TsCircularPlasmid.hh new file: geometry/dna/CircularPlasmid/TsNtupleForPlasmid.cc new file: geometry/dna/CircularPlasmid/TsNtupleForPlasmid.hh new file: geometry/dna/DNAFabric/GeoCalculation.cc new file: geometry/dna/DNAFabric/GeoCalculation.hh new file: geometry/dna/DNAFabric/GeoManager.cc new file: geometry/dna/DNAFabric/GeoManager.hh new file: geometry/dna/DNAFabric/GeoVolume.cc new file: geometry/dna/DNAFabric/GeoVolume.hh new file: geometry/dna/DNAFabric/PhysGeoImport.cc new file: geometry/dna/DNAFabric/PhysGeoImport.hh new file: geometry/dna/DNAFabric/TsDNAFabric.cc new file: geometry/dna/DNAFabric/TsDNAFabric.hh new file: geometry/dna/DNAFabric/TsFiber.cc new file: geometry/dna/DNAFabric/TsFiber.hh new file: geometry/dna/FractalDNAModel/TsFractalDNA.cc new file: geometry/dna/FractalDNAModel/TsFractalDNA.hh new file: geometry/dna/Solenoid_Fiber/NtupleForBasePair/ClusterAlgoBasePair.cc new file: geometry/dna/Solenoid_Fiber/NtupleForBasePair/ClusterAlgoBasePair.hh new file: geometry/dna/Solenoid_Fiber/NtupleForBasePair/NtupleForBasePair.cc new file: geometry/dna/Solenoid_Fiber/NtupleForBasePair/NtupleForBasePair.hh new file: geometry/dna/Solenoid_Fiber/NtupleForBasePair/StartClusteringBasePair.cc new file: geometry/dna/Solenoid_Fiber/NtupleForBasePair/StartClusteringBasePair.hh new file: geometry/dna/Solenoid_Fiber/NtupleForBasePair/WriteDamageSpecBasePair.cc new file: geometry/dna/Solenoid_Fiber/NtupleForBasePair/WriteDamageSpecBasePair.hh new file: geometry/dna/Solenoid_Fiber/NtupleForSpatial/ClusterAlgoSpatial.cc new file: geometry/dna/Solenoid_Fiber/NtupleForSpatial/ClusterAlgoSpatial.hh new file: geometry/dna/Solenoid_Fiber/NtupleForSpatial/NtupleForSpatial.cc new file: geometry/dna/Solenoid_Fiber/NtupleForSpatial/NtupleForSpatial.hh new file: geometry/dna/Solenoid_Fiber/NtupleForSpatial/WriteDamageSpecSpatial.cc new file: geometry/dna/Solenoid_Fiber/NtupleForSpatial/WriteDamageSpecSpatial.hh new file: geometry/dna/Solenoid_Fiber/SharedClasses/AddChromosomeDomain.cc new file: geometry/dna/Solenoid_Fiber/SharedClasses/AddChromosomeDomain.hh new file: geometry/dna/Solenoid_Fiber/SharedClasses/Clusters.hh new file: geometry/dna/Solenoid_Fiber/SharedClasses/HitPoint.hh new file: geometry/dna/Solenoid_Fiber/SharedClasses/TsDamagePhaseSpaceStore.cc new file: geometry/dna/Solenoid_Fiber/SharedClasses/TsDamagePhaseSpaceStore.hh new file: geometry/dna/Solenoid_Fiber/TsSolenoidFiber/TsSolenoidFiber.cc new file: geometry/dna/Solenoid_Fiber/TsSolenoidFiber/TsSolenoidFiber.hh new file: geometry/dna/TsCharltonDNA.cc new file: geometry/dna/TsCharltonDNA.hh new file: geometry/dna/TsCylindericalChromatin.cc new file: geometry/dna/TsCylindericalChromatin.hh new file: geometry/dna/TsCylindericalDNA.cc new file: geometry/dna/TsCylindericalDNA.hh new file: geometry/dna/TsCylindericalNucleosome.cc new file: geometry/dna/TsCylindericalNucleosome.hh new file: geometry/dna/TsLinearDNA.cc new file: geometry/dna/TsLinearDNA.hh new file: geometry/dna/TsPlasmidSupercoiled/TsPlasmidSupercoiled.cc new file: geometry/dna/TsPlasmidSupercoiled/TsPlasmidSupercoiled.hh new file: geometry/dna/TsPlasmidSupercoiled/auxiliarClasses/DNA.hh new file: geometry/dna/TsPlasmidSupercoiled/auxiliarClasses/DNACoordinates.cc new file: geometry/dna/TsPlasmidSupercoiled/auxiliarClasses/DNACoordinates.hh new file: geometry/dna/wholeNucleus/ChromosomeParameterisation.cc new file: geometry/dna/wholeNucleus/ChromosomeParameterisation.hh new file: geometry/dna/wholeNucleus/TsDNA.cc new file: geometry/dna/wholeNucleus/TsDNA.hh new file: geometry/other/membrane/TsChannel.cc new file: geometry/other/membrane/TsChannel.hh new file: geometry/other/membrane/TsIonChannel.cc new file: geometry/other/membrane/TsIonChannel.hh new file: geometry/other/membrane/TsMembraneLayer.cc new file: geometry/other/membrane/TsMembraneLayer.hh new file: geometry/other/membrane/TsMembraneRing.cc new file: geometry/other/membrane/TsMembraneRing.hh new file: geometry/sampling/TsRandomCylindersInComponent.cc new file: geometry/sampling/TsRandomCylindersInComponent.hh new file: molecules/TsH2O2.cc new file: molecules/TsH2O2.hh new file: molecules/TsHO2.cc new file: molecules/TsHO2.hh new file: molecules/TsO2.cc new file: molecules/TsO2.hh new file: molecules/TsScavengerProduct.cc new file: molecules/TsScavengerProduct.hh new file: primary/TsGeneratorUniformlyRandomAtVolume.cc new file: primary/TsGeneratorUniformlyRandomAtVolume.hh new file: processes/TsDNAFirstOrderReaction.cc new file: processes/TsDNAFirstOrderReaction.hh new file: processes/TsDNAMolecularStepByStepModel.cc new file: processes/TsDNAMolecularStepByStepModel.hh new file: processes/TsDNAOneStepThermalizationModel.cc new file: processes/TsDNAOneStepThermalizationModel.hh new file: processes/TsDNAOneStepThermalizationModelh.hh new file: processes/TsDNARemoveInMaterial.cc new file: processes/TsDNARemoveInMaterial.hh new file: processes/TsDNARuddIonisationExtendedModel.cc new file: processes/TsDNARuddIonisationExtendedModel.hh new file: processes/TsDNASmoluchowskiReactionModel.cc new file: processes/TsDNASmoluchowskiReactionModel.hh new file: processes/TsEmDNAChemistry.cc new file: processes/TsEmDNAChemistry.hh new file: processes/TsEmDNAChemistryExtended.cc new file: processes/TsEmDNAChemistryExtended.hh new file: processes/TsEmDNAPhysics.cc new file: processes/TsEmDNAPhysics.hh new file: processes/TsSplitProcessG4DNA.cc new file: processes/TsSplitProcessG4DNA.hh new file: rundemos.csh new file: scorers/TsNtupleForCell.cc new file: scorers/TsNtupleForCell.hh new file: scorers/TsScoreDBSCAN.cc new file: scorers/TsScoreDBSCAN.hh new file: scorers/TsScoreGValue.cc new file: scorers/TsScoreGValue.hh new file: scorers/TsScoreMoleculeTuple.cc new file: scorers/TsScoreMoleculeTuple.hh new file: scorers/TsScoreNumberOfMoleculesAtTime.cc new file: scorers/TsScoreNumberOfMoleculesAtTime.hh new file: scorers/TsScorePDB4DNA.cc new file: scorers/TsScorePDB4DNA.hh new file: scorers/TsScoreSimpleSSBandDSB.cc new file: scorers/TsScoreSimpleSSBandDSB.hh new file: scorers/TsScoreSimpleSSBandDSBWithDBSCAN.cc new file: scorers/TsScoreSimpleSSBandDSBWithDBSCAN.hh new file: scorers/auxiliarClasses/ClusterSBPoints.cc new file: scorers/auxiliarClasses/ClusterSBPoints.hh new file: scorers/auxiliarClasses/ClusteringAlgo.cc new file: scorers/auxiliarClasses/ClusteringAlgo.hh new file: scorers/auxiliarClasses/PDBatom.cc new file: scorers/auxiliarClasses/PDBatom.hh new file: scorers/auxiliarClasses/PDBbarycenter.cc new file: scorers/auxiliarClasses/PDBbarycenter.hh new file: scorers/auxiliarClasses/PDBlib.cc new file: scorers/auxiliarClasses/PDBlib.hh new file: scorers/auxiliarClasses/PDBmolecule.cc new file: scorers/auxiliarClasses/PDBmolecule.hh new file: scorers/auxiliarClasses/PDBresidue.cc new file: scorers/auxiliarClasses/PDBresidue.hh new file: scorers/auxiliarClasses/SBPoint.cc new file: scorers/auxiliarClasses/SBPoint.hh
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‎examples/README.md

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# General information
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Run the demos with:
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source rundemos.csh
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In some examples, a pause before quit is enabled. Then, just write `exit` at the terminal.
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## Geometry examples
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### DNA models
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#### CharltonDNA.txt
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Simplified model of DNA. It is represented as a cylinder with base pairs assambled
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by two cylindrical segments of 0.34 nm length placed around a cylinder of 1 nm
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diameter that represents the base. The DNA diameter is 2.3 nm.
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#### DNA.txt
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DNA model representing a whole nuclear DNA. The example is taken from
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the Geant4 DNA example wholeNuclearDNA and implemented into TOPAS-nBio.
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#### Plasmid.txt
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A circular plasmid of 2000 base pairs. The DNA is cylidrical with 2.3 nm diameter.
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The bases are 0.34 nm length.
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### Cell models
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#### EllipsoidCell.txt
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#### FibroblastCell.txt
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#### SphericalCell.txt
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### Sampling geometries
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#### NikjooCylinders.txt
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#### generateRandomCylinders.txt
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Shows how to generate random cylinders enclosed by a user-defined TsSphere,
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TsCylinder or TsBox. In an iterative process, the algorithm generates randomly
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a cylinder and checks with existing cylinders for overlaps. It rejects the new cylinder
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if overlaps exists. The positions in nm and rotations in deg (6 columns) are stored
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in an ascii file. Accordingly, many warning messages about overlapping geometries are expected.
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#### readBackRandomCylindres.txt
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Shows how to read back the output ascii file from example
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`generateRandomCylinders.txt`. Users still need to set the shape and
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dimensions of the envelope geometry.
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## Processes examples
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### Physics
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#### ActiveCustomizablePhysics.txt
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Shows how to select the elastic/inelastic scattering models for e- and the elastic scattering
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model for protons.
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#### G4DNAModelPerRegion.txt
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Shows how to set the Geant4DNA track-structure physics per region and condensed history elsewhere.
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### Chemistry
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#### ActiveChemistryDefault.txt
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Shows how to activate the step-by-step transport of chemical species
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#### ActiveChemistryRevised.txt
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Shows how to set the chemistry parameters different than those provided by the Geant4-DNA default
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chemistry list.
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#### ActiveChemistryExtended.txt
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Shows how to customize the chemistry parameters using an extended list of reactions.
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#### RemoveChemicalSpeciesInVolume.txt
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Shows how to terminate the transport of chemical species in a user-defined volume with specific
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material.
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## Scorer examples
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#### DBSCAN.txt
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Shows how to calcualte single and double strand breaks in a homogeneous geometry using the DBSCAN algorithm
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#### DBSCAN_VRT.txt
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Shows how to calcualte single and double strand breaks in a homogeneous geometry using the DBSCAN algorithm
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with a variance reduction technique (particle splitting).
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#### PDB4DNA.txt
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Shows how to calculate single and double strand breaks using an overlaid geometry from a PDB file. The scoring
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method is inherited from the PDB4DNA example of Geant4-DNA.
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#### PDB4DNA_VRT.txt
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Shows how to calculate single and double strand breaks using an overlaid geometry from a PDB file and
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variance reduction (particle splitting). The scoring method is inherited from the PDB4DNA example of Geant4-DNA.
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#### NumberOfChemicalSpeciesAtTime.txt
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Shows how to calculate the number of chemical species as a function of time. Time is discretized in a log-scale way.
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#### GvalueG4DNADefault.txt
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Shows how to calcualte the G-value (number of chemical species per 100 eV of energy deposit)
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#### GvalueRevisedPhysicsChemistry.txt
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Shows how to calcualte the G-value (number of chemical species per 100 eV of energy deposit) using a revised set
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of chemistry parameters.
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#### particleTuple.txt
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Shows how to get the physical chemical track information. For the chemical track, the information is retrived only at
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TimeCut.
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#### IonizationDetailInRandomCylinders.txt
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Shows how to get the physical track information including only essential information.
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#### simpleSSBandDSBInPlasmid.txt
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Shows how to score SSB and DSB in a plasmid geometry using the simple definition of DSB (2 SSB separated within 10 bps).
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The classification of the DSB is performed via a PDB4DNA-like algorithm, example `PDB4DNA.txt`
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#### simpleSSBandDSBInPlasmidWithDBSCAN.txt
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Shows how to score SSB and DSB in a plasmid geometry using the simple definition of DSB (2 SSB separated within 10 bps).
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The classification of the DSB is performed via the DBSCAN algorithm.
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‎examples/geometry/cells/BloodCells/Basophil.txt

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# TOPAS-nBio example.
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#
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# White blood cell: Basophil
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#
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# Cell has a bi-lobed nucleus and has the option of containing granules
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#If users specify the number of granules in the cell, then overlap checking has to be set to false.
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#Note: Overlap checking is still done, but flag needs to be off to randomly place granules in the cell.
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b:Ge/QuitIfOverlapDetected="false"
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d:Ge/World/HLX=20. um
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d:Ge/World/HLY=20. um
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d:Ge/World/HLZ=20. um
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b:Ge/World/invisible = "true"
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s:Ge/MyCell/Type="TsBasophil"
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s:Ge/MyCell/Material="G4_WATER"
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s:Ge/MyCell/Parent="World"
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d:Ge/MyCell/BasophilRadius=7.0 um
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s:Ge/MyCell/Nucleus/Material="G4_WATER"
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s:Ge/MyCell/Nucleus/Color="purple"
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s:Ge/MyCell/Nucleus/DrawingStyle = "Solid"
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s:Ge/MyCell/Granule/Material="G4_WATER"
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s:Ge/MyCell/Granule/Color="blue"
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s:Ge/MyCell/Granule/DrawingStyle = "Solid"
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i:Ge/MyCell/Granule/NumberOfGranules = 50
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#Option to set the Granule radius if not set and granules are included, the default radius is 0.25 um
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#d:Ge/MyCell/Granule/GranuleRadius=0.1 um
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Ph/Default/Modules = 1 "g4em-penelope"
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# Set a source
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s:So/Example/Type = "Beam"
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s:So/Example/Component = "BeamPosition"
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s:So/Example/BeamParticle = "proton"
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d:So/Example/BeamEnergy = 2 MeV
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u:So/Example/BeamEnergySpread = 0.757504
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s:So/Example/BeamPositionDistribution = "None"
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s:So/Example/BeamAngularDistribution = "Gaussian"
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d:So/Example/BeamAngularCutoffX = 90. deg
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d:So/Example/BeamAngularCutoffY = 90. deg
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d:So/Example/BeamAngularSpreadX = 0.0032 rad
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d:So/Example/BeamAngularSpreadY = 0.0032 rad
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i:So/Example/NumberOfHistoriesInRun = 1000
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#Score dose in the Cell
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s:Sc/CellScorer/Quantity = "DoseToMedium"
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s:Sc/CellScorer/Component = "MyCell"
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b:Sc/CellScorer/OutputToConsole = "TRUE"
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b:Sc/CellScorer/PropagateToChildren = "true"
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s:Sc/CellScorer/IfOutputFileAlreadyExists = "overwrite"
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#Score energy deposited in Cell components
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s:Sc/OrganelleScorer/Quantity = "TsNtupleForCell"
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s:Sc/OrganelleScorer/Component = "MyCell"
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s:Sc/OrganelleScorer/IfOutputFileAlreadyExists = "Overwrite"
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s:Sc/OrganelleScorer/OutputType = "ASCII"
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s:Sc/OrganelleScorer/OutputFile = "EdepToOrganelles"
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#Visualization settings
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s:Gr/ViewA/Type = "OpenGL"
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i:Gr/ViewA/WindowSizeX = 1024
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i:Gr/ViewA/WindowSizeY = 768
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Ts/PauseBeforeQuit = "True"

‎examples/geometry/cells/BloodCells/Eosinophil.txt

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# TOPAS-nBio example
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#
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# White blood cell: Eosinophil
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#
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# Cell has a bi-lobed nucleus and has the option of containing granules.
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#If users specify the number of granules in the cell, then this check has to be set to false:
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#Overlap checking is still done.
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b:Ge/QuitIfOverlapDetected="false"
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d:Ge/World/HLX=20. um
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d:Ge/World/HLY=20. um
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d:Ge/World/HLZ=20. um
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b:Ge/World/invisible = "true"
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s:Ge/MyCell/Type="TsEosinophil"
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s:Ge/MyCell/Material="G4_WATER"
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s:Ge/MyCell/Parent="World"
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d:Ge/MyCell/EosinophilRadius=8.0 um
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s:Ge/MyCell/Color="white"
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#s:Ge/MyCell/DrawingStyle = "Solid"
22+
23+
s:Ge/MyCell/Nucleus/Material="G4_WATER"
24+
s:Ge/MyCell/Nucleus/Color="purple"
25+
s:Ge/MyCell/Nucleus/DrawingStyle = "Solid"
26+
27+
s:Ge/MyCell/Granule/Material="G4_WATER"
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s:Ge/MyCell/Granule/Color="blue"
29+
s:Ge/MyCell/Granule/DrawingStyle = "Solid"
30+
i:Ge/MyCell/Granule/NumberOfGranules = 100
31+
32+
#Option to set the Granule radius if not set and granules are included, the default radius is 0.25 um
33+
d:Ge/MyCell/Granule/GranuleRadius=0.1 um
34+
35+
Ph/Default/Modules = 1 "g4em-standard_opt0"
36+
37+
# Set a source
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s:So/Example/Type = "Beam"
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s:So/Example/Component = "BeamPosition"
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s:So/Example/BeamParticle = "proton"
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d:So/Example/BeamEnergy = 5 MeV
42+
u:So/Example/BeamEnergySpread = 0.757504
43+
s:So/Example/BeamPositionDistribution = "None"
44+
s:So/Example/BeamAngularDistribution = "Gaussian"
45+
d:So/Example/BeamAngularCutoffX = 90. deg
46+
d:So/Example/BeamAngularCutoffY = 90. deg
47+
d:So/Example/BeamAngularSpreadX = 0.0032 rad
48+
d:So/Example/BeamAngularSpreadY = 0.0032 rad
49+
i:So/Example/NumberOfHistoriesInRun = 200
50+
51+
#Score in the Cell
52+
s:Sc/CellScorer/Quantity = "DoseToMedium"
53+
s:Sc/CellScorer/Component = "MyCell"
54+
b:Sc/CellScorer/OutputToConsole = "TRUE"
55+
b:Sc/CellScorer/PropagateToChildren = "true"
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s:Sc/CellScorer/IfOutputFileAlreadyExists = "overwrite"
57+
58+
#Score energy deposited in Cell components
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s:Sc/OrganelleScorer/Quantity = "TsNtupleForCell"
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s:Sc/OrganelleScorer/Component = "MyCell"
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s:Sc/OrganelleScorer/IfOutputFileAlreadyExists = "Overwrite"
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s:Sc/OrganelleScorer/OutputType = "ASCII"
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s:Sc/OrganelleScorer/OutputFile = "EdepToOrganelles"
64+
65+
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s:Gr/ViewA/Type = "OpenGL"
67+
i:Gr/ViewA/WindowSizeX = 1024
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i:Gr/ViewA/WindowSizeY = 768
69+
70+
71+
Ts/PauseBeforeQuit = "True"

‎examples/geometry/cells/BloodCells/Lymphocyte.txt

+63
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,63 @@
1+
# TOPAS-nBio example.
2+
#
3+
# White blood cell: Lymphocyte
4+
#
5+
# Cell has a single large nucleus.
6+
7+
b:Ge/QuitIfOverlapDetected="true"
8+
9+
d:Ge/World/HLX=20. um
10+
d:Ge/World/HLY=20. um
11+
d:Ge/World/HLZ=20. um
12+
b:Ge/World/invisible = "true"
13+
14+
s:Ge/MyCell/Type="TsLymphocyte"
15+
s:Ge/MyCell/Material="G4_WATER"
16+
s:Ge/MyCell/Parent="World"
17+
d:Ge/MyCell/LymphocyteRadius=5.0 um
18+
s:Ge/MyCell/Color="white"
19+
#s:Ge/MyCell/DrawingStyle = "Solid"
20+
21+
s:Ge/MyCell/Nucleus/Material="G4_WATER"
22+
s:Ge/MyCell/Nucleus/Color="purple"
23+
s:Ge/MyCell/Nucleus/DrawingStyle = "Solid"
24+
25+
Ph/Default/Modules = 1 "g4em-standard_opt0"
26+
27+
s:So/Disk/Type = "Beam"
28+
s:So/Disk/Component = "BeamPosition"
29+
s:So/Disk/BeamParticle = "proton" #gamma
30+
d:So/Disk/BeamEnergy = 2 MeV
31+
u:So/Disk/BeamEnergySpread = 0
32+
s:So/Disk/BeamShape = "Rectangle"
33+
s:So/Disk/BeamPositionDistribution = "Flat"
34+
s:So/Disk/BeamAngularDistribution = "Gaussian"
35+
d:So/Disk/BeamAngularCutoffX = 10 deg
36+
d:So/Disk/BeamAngularCutoffY = 10 deg
37+
s:So/Disk/BeamPositionCutoffShape = "Rectangle"
38+
d:So/Disk/BeamPositionCutoffX = 10 um
39+
d:So/Disk/BeamPositionCutoffY = 10 um
40+
d:So/Disk/BeamAngularSpreadX = 0.01 deg
41+
d:So/Disk/BeamAngularSpreadY = 0.01 deg
42+
i:So/Disk/NumberOfHistoriesInRun=1000
43+
44+
#Score in the Cell
45+
s:Sc/CellScorer/Quantity = "DoseToMedium"
46+
s:Sc/CellScorer/Component = "MyCell"
47+
b:Sc/CellScorer/OutputToConsole = "True"
48+
b:Sc/CellScorer/PropagateToChildren = "true"
49+
s:Sc/CellScorer/IfOutputFileAlreadyExists = "overwrite"
50+
51+
#Score energy deposited in Cell components
52+
s:Sc/OrganelleScorer/Quantity = "TsNtupleForCell"
53+
s:Sc/OrganelleScorer/Component = "MyCell"
54+
s:Sc/OrganelleScorer/IfOutputFileAlreadyExists = "Overwrite"
55+
s:Sc/OrganelleScorer/OutputType = "ASCII"
56+
s:Sc/OrganelleScorer/OutputFile = "EdepToOrganelles"
57+
58+
59+
s:Gr/ViewA/Type = "OpenGL"
60+
i:Gr/ViewA/WindowSizeX = 1024
61+
i:Gr/ViewA/WindowSizeY = 768
62+
63+
Ts/PauseBeforeQuit = "True"

‎examples/geometry/cells/BloodCells/Monocyte.txt

+60
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,60 @@
1+
# TOPAS-nBio example.
2+
#
3+
# White blood cell: Monocyte
4+
#
5+
# Cell has a single large kidney-shaped nucleus.
6+
7+
b:Ge/QuitIfOverlapDetected="true"
8+
9+
d:Ge/World/HLX=30. um
10+
d:Ge/World/HLY=30. um
11+
d:Ge/World/HLZ=30. um
12+
b:Ge/World/invisible = "true"
13+
14+
s:Ge/MyCell/Type="TsMonocyte"
15+
s:Ge/MyCell/Material="G4_WATER"
16+
s:Ge/MyCell/Parent="World"
17+
d:Ge/MyCell/MonocyteRadius=10.0 um
18+
19+
s:Ge/MyCell/Nucleus/Material="G4_WATER"
20+
s:Ge/MyCell/Nucleus/Color="purple"
21+
s:Ge/MyCell/Nucleus/DrawingStyle = "Solid"
22+
23+
Ph/Default/Modules = 1 "g4em-dna"
24+
25+
s:So/Disk/Type = "Beam"
26+
s:So/Disk/Component = "BeamPosition"
27+
s:So/Disk/BeamParticle = "proton" #gamma
28+
d:So/Disk/BeamEnergy = 2 MeV
29+
u:So/Disk/BeamEnergySpread = 0
30+
s:So/Disk/BeamShape = "Rectangle"
31+
s:So/Disk/BeamPositionDistribution = "Flat"
32+
s:So/Disk/BeamAngularDistribution = "Gaussian"
33+
d:So/Disk/BeamAngularCutoffX = 10 deg
34+
d:So/Disk/BeamAngularCutoffY = 10 deg
35+
s:So/Disk/BeamPositionCutoffShape = "Rectangle"
36+
d:So/Disk/BeamPositionCutoffX = 10 um
37+
d:So/Disk/BeamPositionCutoffY = 10 um
38+
d:So/Disk/BeamAngularSpreadX = 0.01 deg
39+
d:So/Disk/BeamAngularSpreadY = 0.01 deg
40+
i:So/Disk/NumberOfHistoriesInRun=10
41+
42+
#Score in the Cell
43+
s:Sc/CellScorer/Quantity = "DoseToMedium"
44+
s:Sc/CellScorer/Component = "MyCell"
45+
b:Sc/CellScorer/OutputToConsole = "True"
46+
b:Sc/CellScorer/PropagateToChildren = "true"
47+
s:Sc/CellScorer/IfOutputFileAlreadyExists = "overwrite"
48+
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#Score energy deposited in Cell components
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s:Sc/OrganelleScorer/Quantity = "TsNtupleForCell"
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s:Sc/OrganelleScorer/Component = "MyCell"
52+
s:Sc/OrganelleScorer/IfOutputFileAlreadyExists = "Overwrite"
53+
s:Sc/OrganelleScorer/OutputType = "ASCII"
54+
s:Sc/OrganelleScorer/OutputFile = "EdepToOrganelles"
55+
56+
s:Gr/ViewA/Type = "OpenGL"
57+
i:Gr/ViewA/WindowSizeX = 1024
58+
i:Gr/ViewA/WindowSizeY = 768
59+
60+
Ts/PauseBeforeQuit = "True"

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