├── .gitignore ├── .readthedocs.yaml ├── .static └── dark_background.css ├── GUI ├── GUI.png └── Intro.rst ├── Makefile ├── README.md ├── conf.py ├── examples-docs ├── Basic │ ├── AllParameterForms.rst │ ├── BatchJob1.rst │ ├── BatchJob2.rst │ ├── BatchJobShared.rst │ ├── BoxRotatedAroundItsCorner.rst │ ├── DNAModelByRegions.rst │ ├── DistributedSourcePointsInShell.rst │ ├── DistributedSourcePointsInSphere.rst │ ├── DistributedSourcePointsInSphereGaussian.rst │ ├── DistributedSourcePointsInTwistedTubs.rst │ ├── DividedComponents.rst │ ├── EmModelByRegions.rst │ ├── Emittance_Gaussian.rst │ ├── Emittance_Twiss.rst │ ├── EnvironmentSource.rst │ ├── ExtraSequence1.rst │ ├── ExtraSequence2.rst │ ├── ExtraSequences.rst │ ├── FlatteningFilter.rst │ ├── Isotope.rst │ ├── LayeredMassGeometry.rst │ ├── OneBox.rst │ ├── OneBoxRotate.rst │ ├── OneBoxTranslate.rst │ ├── ParallelWorlds.rst │ ├── ParticleSourcesFromGroup.rst │ ├── PhysicsSetting.rst │ ├── QtShapeTest.rst │ ├── ShapeTestWithAllParameters.rst │ ├── ShapeTestWithOnlyRequiredParameters.rst │ ├── Spectrum.rst │ ├── TwoBeams.rst │ ├── VolumetricSource.rst │ ├── VoxelMaterialsInDividedComponents.rst │ └── index.rst ├── Brachytherapy │ ├── .DS_Store │ ├── COMSEyePlaque.rst │ ├── Cs131_IsoRay-CS-1-Rev2.rst │ ├── DoseTLE.rst │ ├── EyeModel.rst │ ├── HDRSource.rst │ ├── HDRSourceInApplicator.rst │ ├── I125_BardSTM1251.rst │ ├── I125_Best2301.rst │ ├── I125_IsoAid_IAI-125A.rst │ ├── I125_OncoSeed6711.rst │ ├── I125_SL-125.rst │ ├── I125_SelectSeed.rst │ ├── I125_Theragenic-AgX100.rst │ ├── Ir192_Flexisource.rst │ ├── Ir192_MicroSelectronV2.rst │ ├── Ir192_TG186.rst │ ├── LDRSource.rst │ ├── Pd103_Best2335.rst │ ├── Pd103_IAPd103A.rst │ ├── Pd103_Theraseed200Heavy.rst │ ├── Pd103_Theraseed200Light.rst │ ├── TG186Applicator.rst │ ├── index.rst │ └── intro.rst ├── Graphics │ ├── ColorByCharge.rst │ ├── ColorByCreatorProcess.rst │ ├── ColorByEnergy.rst │ ├── ColorByGeneration.rst │ ├── ColorByMomentum.rst │ ├── ColorByOriginComponent.rst │ ├── ColorByOriginComponentOrSubComponent.rst │ ├── ColorByOriginVolume.rst │ ├── ColorByParticleType.rst │ ├── ColorTest.rst │ ├── FilterByCreatorProcess.rst │ ├── FilterByEnergy.rst │ ├── FilterByMomentum.rst │ ├── FilterByOriginComponent.rst │ ├── FilterByOriginComponentOrSubcomonent.rst │ ├── FilterByOriginVolume.rst │ ├── FilterByParticleCharge.rst │ ├── FilterByParticleType.rst │ ├── NanoMeterScaleTest.rst │ ├── ParticleFlight.rst │ ├── QtTest.rst │ ├── SolidSphere.rst │ ├── TestGraphics.rst │ ├── TwoProjections.rst │ └── index.rst ├── MVLinac │ ├── Field.rst │ ├── FixedTxHead.rst │ ├── Flattener18MV.rst │ ├── Flattener6MV.rst │ ├── FullTxHeadField.rst │ ├── Jaws.rst │ ├── LinacDefaults.rst │ ├── MLC.rst │ ├── MainTxHead.rst │ ├── Monitor.rst │ ├── ParameterControlFiles.png │ ├── ScoreEnergyFluence.rst │ ├── ScoreEnergySpectrum.rst │ ├── ScorePhaseSpace.rst │ ├── TOPAS_IEC.png │ ├── Target.rst │ ├── TestComponent.rst │ ├── VRT_1.rst │ ├── VRT_2.rst │ ├── VRT_3.rst │ ├── VRT_HD.rst │ ├── WaterBox.rst │ ├── WaterPhantom.rst │ ├── index.rst │ └── intro.rst ├── Nozzle │ ├── ConstantsForNozzles.rst │ ├── RasterScanningPattern.rst │ ├── ScanningNozzle.rst │ ├── ScanningStationaryTarget.rst │ ├── ScanningTargetMovingHorizontal.rst │ ├── ScanningTargetMovingInDepth.rst │ ├── ScatteringNozzle.rst │ ├── ScatteringNozzle_QtTest.rst │ ├── ScatteringNozzle_run.rst │ ├── ScatteringNozzle_run_QtTest.rst │ ├── TargetInWaterPhantom.rst │ ├── TsAnalysisWaterPhantom.rst │ ├── Viewer.rst │ └── index.rst ├── Optical │ ├── OpticalMaterialSample.rst │ ├── OpticalPhotonCount.rst │ ├── PixelatedDetector.rst │ ├── PlasticScintillator.rst │ ├── Rotating_Surfaces.rst │ ├── Surfaces.rst │ ├── WavelengthShifter.rst │ └── index.rst ├── Outcome │ ├── CEModelBurman.rst │ ├── CVModelStavrev.rst │ ├── LKMModelBurman │ ├── Phantom.rst │ ├── PoissonModelOkunieff.rst │ ├── TestOutcomeModel.rst │ ├── TestRestoreModel.rst │ └── index.rst ├── Patient │ ├── .DS_Store │ ├── Applicator.rst │ ├── DicomCutaway.rst │ ├── DoseTo4DCT.rst │ ├── DoseToCT.rst │ ├── HUtoMaterialSchneider.rst │ ├── HUtoMaterialSchneider2.rst │ ├── Implant.rst │ ├── PatientInIEC_1.rst │ ├── PatientInIEC_2.rst │ ├── PatientInIEC_2_time_feature.rst │ ├── PatientInIEC_3.rst │ ├── TwoDicoms.rst │ ├── ViewAbdomen.rst │ ├── ViewAbdomen_rtdose.rst │ ├── XCAT.rst │ ├── XCAT_Materials.rst │ └── index.rst ├── PhaseSpace │ ├── MultiRun_Write_ASCII.rst │ ├── ReadASCII.rst │ ├── ReadBinary.rst │ ├── ReadElekta.rst │ ├── ReadLimited.rst │ ├── ReadVarian.rst │ ├── WriteASCII.rst │ ├── WriteBinary.rst │ ├── WriteIonsASCII.rst │ ├── WriteLimited.rst │ ├── WriteROOT.rst │ └── index.rst ├── Scoring │ ├── ChargeInSphere.rst │ ├── Complex.rst │ ├── DepthDose.rst │ ├── Dose.rst │ ├── DoseInVoxelMaterials.rst │ ├── DoseToMediumVsWater.rst │ ├── DoseVolumeHistogram.rst │ ├── EnergyAndDose.rst │ ├── EnergyDepositBinnedByEnergy.rst │ ├── EnergyDivisions.rst │ ├── EnergyInBinnedCylinder.rst │ ├── FilterByInteractionCount.rst │ ├── Filters.rst │ ├── FoilToBox.rst │ ├── FoilToCylinder.rst │ ├── FoilToSphere.rst │ ├── Gated.rst │ ├── GeometryDivisions.rst │ ├── Histograms.rst │ ├── Inactive.rst │ ├── Ion.rst │ ├── Origin.rst │ ├── OriginCount.rst │ ├── ParallelBoxRebinned.rst │ ├── SparsifyAndSingleIndex.rst │ ├── SplitByTimeFeature.rst │ ├── Surfaces.rst │ ├── VoxelMaterials.rst │ └── index.rst ├── SpecialComponents │ ├── CAD.rst │ ├── DipoleMagnet.rst │ ├── MultiLeafCollimator.rst │ ├── MultiLeafCollimator_sequence.rst │ ├── MultiWire_Chamber.rst │ ├── Propeller.rst │ ├── Propeller_ContinuousRotation.rst │ ├── Propeller_StepRotation.rst │ ├── PurgingMagnet_move.rst │ ├── QuadAndDipoleMagnets.rst │ ├── QuadInMovingNozzle.rst │ ├── QuadrupoleMagnet.rst │ ├── RangeModulator.rst │ ├── RangeModulator_ConstantBeam.rst │ ├── RangeModulator_CurrentModulatedBeam.rst │ ├── RidgeFilter.rst │ ├── RotatingMagnet.rst │ ├── UniformElectroMagneticField.rst │ └── index.rst ├── TimeFeature │ ├── BoxWithinBox.rst │ ├── CameraRotateAndZoom.rst │ ├── ChangingKEFilterByTimeFeature.rst │ ├── ColorChange.rst │ ├── CylinderGrowingInPhi.rst │ ├── Darkening.rst │ ├── Logo.rst │ ├── RasterScanOnMovingTarget.rst │ ├── RotateResizeRecolor.rst │ ├── RotatingCylinderWithPhiCut.rst │ ├── Rotation.rst │ ├── RunRandom_Mode.rst │ ├── RunSequential_Mode.rst │ └── index.rst ├── UCSFETF │ ├── UCSF_Beamline_Base.rst │ ├── UCSF_Beamline_Propeller10.rst │ ├── UCSF_Beamline_Propeller15.rst │ ├── UCSF_Beamline_Propeller20.rst │ ├── UCSF_Beamline_Propeller24.rst │ ├── UCSF_DefaultParameters.rst │ ├── UCSF_WaterPhantom.rst │ ├── User_BP_R28_WaterPhantom.rst │ ├── User_Beamline_WC_Viewer.rst │ ├── User_SOBP24_R28_WaterPhantom.rst │ ├── User_SOBP24_Viewer.rst │ ├── Viewer.rst │ └── index.rst └── VarianceReduction │ ├── AmbientDoseEquivalent.rst │ ├── CrossSectionEnhancement.rst │ ├── ForcedInteraction.rst │ ├── GeometricalParticleSplit.rst │ ├── ImportanceSampling.rst │ ├── ImportanceSamplingMassGeometry.rst │ ├── ImportanceSamplingSecondaryBiasing.rst │ ├── SecondaryBiasing.rst │ ├── WeightWindow.rst │ └── index.rst ├── examples ├── Basic │ ├── AllParameterForms.txt │ ├── BatchJob1.txt │ ├── BatchJob2.txt │ ├── BatchJobShared.txt │ ├── BoxRotatedAroundItsCorner.txt │ ├── DNAModelByRegions.txt │ ├── DistributedSourcePointsInShell.txt │ ├── DistributedSourcePointsInSphere.txt │ ├── DistributedSourcePointsInSphereGaussian.txt │ ├── DistributedSourcePointsInTwistedTubs.txt │ ├── DividedComponents.txt │ ├── EmModelByRegions.txt │ ├── Emittance_Gaussian.txt │ ├── Emittance_Twiss.txt │ ├── EnvironmentSource.txt │ ├── ExtraSequence1.txt │ ├── ExtraSequence2.txt │ ├── ExtraSequences.txt │ ├── FlatteningFilter.txt │ ├── Isotope.txt │ ├── LayeredMassGeometry.txt │ ├── OneBox.txt │ ├── OneBoxRotate.txt │ ├── OneBoxTranslate.txt │ ├── ParallelWorlds.txt │ ├── ParticleSourcesFromGroup.txt │ ├── PhysicsSetting.txt │ ├── QtShapeTest.txt │ ├── ShapeTestWithAllParameters.txt │ ├── ShapeTestWithOnlyRequiredParameters.txt │ ├── Spectrum.txt │ ├── TwoBeams.txt │ ├── VolumetricSource.txt │ └── VoxelMaterialsInDividedComponents.txt ├── Brachytherapy │ ├── COMSEyePlaque.txt │ ├── DoseTLE.txt │ ├── EyeModel.txt │ ├── HDR │ │ ├── Ir192_Flexisource.txt │ │ ├── Ir192_MicroSelectronV2.txt │ │ ├── Ir192_TG186.txt │ │ └── TG186Applicator.txt │ ├── HDRSource.txt │ ├── HDRSourceInApplicator.txt │ ├── LDR │ │ ├── Cs131_IsoRay-CS-1-Rev2.txt │ │ ├── I125_BardSTM1251.txt │ │ ├── I125_Best2301.txt │ │ ├── I125_IsoAid_IAI-125A.txt │ │ ├── I125_OncoSeed6711.txt │ │ ├── I125_SL-125.txt │ │ ├── I125_SelectSeed.txt │ │ ├── I125_Theragenic-AgX100.txt │ │ ├── Pd103_Best2335.txt │ │ ├── Pd103_IAPd103A.txt │ │ ├── Pd103_Theraseed200Heavy.txt │ │ └── Pd103_Theraseed200Light.txt │ ├── LDRSource.txt │ ├── Muen.dat │ ├── README.md │ └── README.pdf ├── Graphics │ ├── ColorByCharge.txt │ ├── ColorByCreatorProcess.txt │ ├── ColorByEnergy.txt │ ├── ColorByGeneration.txt │ ├── ColorByMomentum.txt │ ├── ColorByOriginComponent.txt │ ├── ColorByOriginComponentOrSubComponent.txt │ ├── ColorByOriginVolume.txt │ ├── ColorByParticleType.txt │ ├── ColorTest.txt │ ├── FilterByCreatorProcess.txt │ ├── FilterByEnergy.txt │ ├── FilterByMomentum.txt │ ├── FilterByOriginComponent.txt │ ├── FilterByOriginComponentOrSubComponent.txt │ ├── FilterByOriginVolume.txt │ ├── FilterByParticleCharge.txt │ ├── FilterByParticleType.txt │ ├── NanoMeterScaleTest.txt │ ├── ParticleFlight.txt │ ├── QtTest.txt │ ├── SolidSphere.txt │ ├── TestGraphics.txt │ └── TwoProjections.txt ├── MVLinac │ ├── Field.txt │ ├── FixedTxHead.txt │ ├── Flattener18MV.txt │ ├── Flattener6MV.txt │ ├── FullTxHeadField.txt │ ├── Jaws.txt │ ├── LinacDefaults.txt │ ├── MLC.txt │ ├── MainTxHead.txt │ ├── Monitor.txt │ ├── PrimaryCollimator.txt │ ├── ScoreEnergyFluence.txt │ ├── ScoreEnergySpectrum.txt │ ├── ScorePhaseSpace.txt │ ├── Target.txt │ ├── TestComponent.txt │ ├── VRT_1.txt │ ├── VRT_2.txt │ ├── VRT_3.txt │ ├── VRT_HD.txt │ ├── WaterBox.txt │ └── WaterPhantom.txt ├── Nozzle │ ├── ApertureFileIn.ap │ ├── CompensatorFileIn.rc │ ├── CompensatorFileInRowsDepths.rc │ ├── ConstantsForNozzles.txt │ ├── RasterScanningPattern.txt │ ├── ScanningNozzle.txt │ ├── ScanningStationaryTarget.txt │ ├── ScanningTargetMovingHorizontal.txt │ ├── ScanningTargetMovingInDepth.txt │ ├── ScatteringNozzle.txt │ ├── ScatteringNozzle_QtTest.txt │ ├── ScatteringNozzle_run.txt │ ├── ScatteringNozzle_run_QtTest.txt │ ├── TargetInWaterPhantom.txt │ ├── TsAnalysisWaterPhantom.txt │ └── Viewer.txt ├── Optical │ ├── OpticalMaterialSample.txt │ ├── OpticalPhotonCount.txt │ ├── PixelatedDetector.txt │ ├── PlasticScintillator.txt │ ├── Rotating_Surfaces.txt │ ├── Surfaces.txt │ └── WavelengthShifter.txt ├── Outcome │ ├── CEModelBurman.txt │ ├── CVModelStavrev.txt │ ├── DoseAtOAR1Saved.bin │ ├── DoseAtOAR1Saved.binheader │ ├── DoseAtOAR2Saved.bin │ ├── DoseAtOAR2Saved.binheader │ ├── DoseAtTargetSaved.bin │ ├── DoseAtTargetSaved.binheader │ ├── LKMModelBurman.txt │ ├── Phantom.txt │ ├── PoissonModelOkunieff.txt │ ├── TestOutcomeModel.txt │ └── TestRestoreModel.txt ├── Patient │ ├── Abdomen.zip │ ├── Applicator.txt │ ├── DICOM_Box.zip │ ├── DicomCutaway.txt │ ├── DoseTo4DCT.txt │ ├── DoseToCT.txt │ ├── HUtoMaterialSchneider.txt │ ├── HUtoMaterialSchneider2.txt │ ├── Implant.txt │ ├── PatientInIEC_1.txt │ ├── PatientInIEC_2.txt │ ├── PatientInIEC_2_time_feature.txt │ ├── PatientInIEC_3.txt │ ├── README.txt │ ├── TwoDicoms.txt │ ├── ViewAbdomen.txt │ ├── ViewAbdomen_rtdose.txt │ ├── XCAT.txt │ ├── XCAT_FullMouse_86x86x161_atn_1.bin │ ├── XCAT_FullMouse_86x86x161_atn_1.log │ ├── XCAT_Materials.txt │ ├── XIO_Example.dat │ └── synthetic_lung.tar.bz2 ├── PhaseSpace │ ├── MultiRun_Write_ASCII.txt │ ├── ReadASCII.txt │ ├── ReadBinary.txt │ ├── ReadElekta.txt │ ├── ReadLimited.txt │ ├── ReadVarian.txt │ ├── WriteASCII.txt │ ├── WriteBinary.txt │ ├── WriteIonsASCII.txt │ ├── WriteLimited.txt │ └── WriteROOT.txt ├── Scoring │ ├── ChargeInSphere.txt │ ├── Complex.txt │ ├── DepthDose.txt │ ├── Dose.txt │ ├── DoseInVoxelMaterials.txt │ ├── DoseToMediumVsWater.txt │ ├── DoseVolumeHistogram.txt │ ├── EnergyAndDose.txt │ ├── EnergyDepositBinnedByEnergy.txt │ ├── EnergyDivisions.txt │ ├── EnergyInBinnedCylinder.txt │ ├── FilterByInteractionCount.txt │ ├── Filters.txt │ ├── FoilToBox.txt │ ├── FoilToCylinder.txt │ ├── FoilToSphere.txt │ ├── Gated.txt │ ├── GeometryDivisions.txt │ ├── Histograms.txt │ ├── Inactive.txt │ ├── Ion.txt │ ├── Origin.txt │ ├── OriginCount.txt │ ├── ParallelBoxRebinned.txt │ ├── SparsifyAndSingleIndex.txt │ ├── SplitByTimeFeature.txt │ ├── Surfaces.txt │ └── VoxelMaterials.txt ├── SpecialComponents │ ├── Aperture_cm.ply │ ├── Aperture_cm.stl │ ├── CAD.txt │ ├── DipoleMagnet.txt │ ├── MultiLeafCollimator.txt │ ├── MultiLeafCollimator_sequence.txt │ ├── MultiWire_Chamber.txt │ ├── Propeller.txt │ ├── Propeller_ContinuousRotation.txt │ ├── Propeller_StepRotation.txt │ ├── PurgMag3D.TABLE │ ├── PurgingMagnet_move.txt │ ├── QuadAndDipoleMagnets.txt │ ├── QuadInMovingNozzle.txt │ ├── QuadrupoleMagnet.txt │ ├── RangeModulator.txt │ ├── RangeModulator_ConstantBeam.txt │ ├── RangeModulator_CurrentModulatedBeam.txt │ ├── RidgeFilter.txt │ ├── RotatingMagnet.txt │ └── UniformElectroMagneticField.txt ├── TimeFeature │ ├── BoxWithinBox.txt │ ├── CameraRotateAndZoom.txt │ ├── ChangingKEFilterByTimeFeature.txt │ ├── ColorChange.txt │ ├── CylinderGrowingInPhi.txt │ ├── Darkening.txt │ ├── Logo.txt │ ├── RasterScanOnMovingTarget.txt │ ├── RotateResizeRecolor.txt │ ├── RotatingCylinderWithPhiCut.txt │ ├── Rotation.txt │ ├── RunRandom_Mode.txt │ └── RunSequential_Mode.txt ├── UCSFETF │ ├── UCSF_Beamline_Base.txt │ ├── UCSF_Beamline_Propeller10.txt │ ├── UCSF_Beamline_Propeller15.txt │ ├── UCSF_Beamline_Propeller20.txt │ ├── UCSF_Beamline_Propeller24.txt │ ├── UCSF_DefaultParameters.txt │ ├── UCSF_WaterPhantom.txt │ ├── User_BP_R28_WaterPhantom.txt │ ├── User_Beamline_WC_Viewer.txt │ ├── User_SOBP24_R28_WaterPhantom.txt │ ├── User_SOBP24_Viewer.txt │ └── Viewer.txt └── VarianceReduction │ ├── AmbientDoseEquivalent.txt │ ├── CrossSectionEnhancement.txt │ ├── ForcedInteraction.txt │ ├── GeometricalParticleSplit.txt │ ├── ImportanceSampling.txt │ ├── ImportanceSamplingMassGeometry.txt │ ├── ImportanceSamplingSecondaryBiasing.txt │ ├── SecondaryBiasing.txt │ └── WeightWindow.txt ├── extension-docs ├── field.rst ├── filtering.rst ├── geometry.rst ├── imaging.rst ├── intro.rst ├── outcome.rst ├── physics.rst ├── scoring.rst ├── source.rst └── user_hook.rst ├── extensions ├── rbe.rst └── rbe_scorers.png ├── getting-started ├── README.txt ├── authors.rst ├── citation.rst ├── history │ ├── 1_0.rst │ ├── 2_0.rst │ ├── 3_0.rst │ ├── 3_1.rst │ ├── 3_2.rst │ ├── 3_3.rst │ ├── 3_4.rst │ ├── 3_5.rst │ ├── 3_6.rst │ ├── 3_7.rst │ ├── 3_8.rst │ └── index.rst ├── install.rst ├── intro.rst └── users.rst ├── index.rst ├── parameters ├── BasicOptLoop.svg ├── GUI.png ├── GUI.rst ├── IndexToParameters.rst ├── defaults.rst ├── geometry │ ├── Aperture_1.png │ ├── Applicator.png │ ├── CAD_1.png │ ├── CAD_2.png │ ├── Compensator_1.png │ ├── Eye.png │ ├── EyePlaque.png │ ├── Jaws.png │ ├── MLC_1.png │ ├── MLC_2.png │ ├── MWC_1.png │ ├── PixelatedDetector.png │ ├── Propeller_1.png │ ├── Propeller_2.png │ ├── RMW_1.png │ ├── RMW_2.png │ ├── RMW_3.png │ ├── RidgeFilter_1.png │ ├── RidgeFilter_2.png │ ├── SMC.png │ ├── dividable.png │ ├── dividable.rst │ ├── field.rst │ ├── generic.png │ ├── generic.rst │ ├── group.rst │ ├── index.rst │ ├── intro.rst │ ├── parallel_world.rst │ ├── patient.rst │ ├── placement.rst │ ├── rtdose_grid_option1.png │ ├── rtdose_grid_option2.png │ ├── rtdose_grid_option3.png │ ├── specialized.rst │ └── visualization.rst ├── graphics.rst ├── intro │ ├── batch_jobs.rst │ ├── design.rst │ ├── file_graphs.png │ ├── hierarchy.png │ ├── hierarchy.rst │ ├── index.rst │ ├── relative.rst │ ├── syntax.rst │ └── syntax_highlighting.rst ├── material.rst ├── outcome.rst ├── overall │ ├── index.rst │ ├── misc.rst │ ├── mode.rst │ ├── multithreading.rst │ ├── repeatsequenceuntil.rst │ └── seed.rst ├── parameter_optimization.rst ├── physics │ ├── index.rst │ ├── intro.rst │ ├── misc.rst │ ├── modular.rst │ ├── optical.rst │ └── reference.rst ├── scoring │ ├── filter.rst │ ├── index.rst │ ├── intro.rst │ ├── misc.rst │ ├── output.rst │ ├── phasespace.rst │ ├── surface.rst │ └── volume.rst ├── source │ ├── PhaseSpaceElectron.png │ ├── PhaseSpaceXRays.png │ ├── beam.rst │ ├── distributed.rst │ ├── emittance.rst │ ├── emittance_1.png │ ├── emittance_2.png │ ├── environment.rst │ ├── index.rst │ ├── intro.rst │ ├── isotropic.rst │ ├── misc.rst │ ├── phasespace.rst │ └── volumetric.rst ├── time.rst └── variance │ ├── crosssection_enhancement.png │ ├── crosssection_enhancement.rst │ ├── forced_interaction.png │ ├── forced_interaction.rst │ ├── geometrical_particle_split.rst │ ├── geometrical_splitting.png │ ├── importance_sampling.png │ ├── importance_sampling.rst │ ├── index.rst │ ├── intro.rst │ ├── secondary_biasing.png │ ├── secondary_biasing.rst │ ├── specific_particles.rst │ ├── split_geometry.png │ ├── weight_window.png │ └── weight_window.rst └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- 1 | .build 2 | __pycache__ 3 | _build 4 | .vscode -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- 1 | # .readthedocs.yaml 2 | # Read the Docs configuration file 3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details 4 | 5 | version: 2 6 | 7 | build: 8 | os: ubuntu-22.04 9 | tools: 10 | python: "3.10" 11 | 12 | sphinx: 13 | configuration: conf.py 14 | 15 | formats: all 16 | 17 | python: 18 | install: 19 | - requirements: requirements.txt 20 | -------------------------------------------------------------------------------- /.static/dark_background.css: -------------------------------------------------------------------------------- 1 | div[class^='highlight'] pre { 2 | background-color: #272822 !important; 3 | } 4 | 5 | .highlight .nc { 6 | font-weight: normal !important; 7 | } /* Name.Class */ 8 | 9 | .highlight .kc { 10 | font-weight: normal !important; 11 | } /* Keyword.Constant */ 12 | -------------------------------------------------------------------------------- /GUI/GUI.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/GUI/GUI.png -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # topas-docs 2 | 3 | The documentation is written in reStructuredText format (reST). It is hosted by [ReadTheDocs](https://docs.readthedocs.org). A good resource on reST is the [Sphinx documentation](http://www.sphinx-doc.org), but please note that not all features described there are supported by ReadTheDocs. It also describes some Python-only features, since that is its domain. 4 | 5 | If working on a Mac, I recommend installing Python with [Homebrew](http://brew.sh) to avoid messing up your system Python. 6 | 7 | To build and view the docs locally (recommended for substantial editing), you will need to 8 | 9 | pip install sphinx sphinx-autobuild sphinx_rtd_theme 10 | pip install -e git://github.com/davidchall/topas-pygments.git#egg=topas_pygments 11 | 12 | then, after your edits 13 | 14 | make clean 15 | make html 16 | open .build/html/index.html 17 | -------------------------------------------------------------------------------- /examples-docs/Basic/AllParameterForms.rst: -------------------------------------------------------------------------------- 1 | AllParameterForms.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/AllParameterForms.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/BatchJob1.rst: -------------------------------------------------------------------------------- 1 | BatchJob1.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/BatchJob1.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/BatchJob2.rst: -------------------------------------------------------------------------------- 1 | BatchJob2.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/BatchJob2.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/BatchJobShared.rst: -------------------------------------------------------------------------------- 1 | BatchJobShared.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/BatchJobShared.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/BoxRotatedAroundItsCorner.rst: -------------------------------------------------------------------------------- 1 | BoxRotatedAroundItsCorner.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/BoxRotatedAroundItsCorner.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/DNAModelByRegions.rst: -------------------------------------------------------------------------------- 1 | DNAModelByRegions.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/DNAModelByRegions.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/DistributedSourcePointsInShell.rst: -------------------------------------------------------------------------------- 1 | DistributedSourcePointsInShell.txt 2 | ---------------------------------- 3 | 4 | .. literalinclude:: /examples/Basic/DistributedSourcePointsInShell.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/DistributedSourcePointsInSphere.rst: -------------------------------------------------------------------------------- 1 | DistributedSourcePointsInSphere.txt 2 | ----------------------------------- 3 | 4 | .. literalinclude:: /examples/Basic/DistributedSourcePointsInSphere.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/DistributedSourcePointsInSphereGaussian.rst: -------------------------------------------------------------------------------- 1 | DistributedSourcePointsInSphereGaussian.txt 2 | ------------------------------------------- 3 | 4 | .. literalinclude:: /examples/Basic/DistributedSourcePointsInSphereGaussian.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/DistributedSourcePointsInTwistedTubs.rst: -------------------------------------------------------------------------------- 1 | DistributedSourcePointsInTwistedTubs.txt 2 | ---------------------------------------- 3 | 4 | .. literalinclude:: /examples/Basic/DistributedSourcePointsInTwistedTubs.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/DividedComponents.rst: -------------------------------------------------------------------------------- 1 | DividedComponents.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/DividedComponents.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/EmModelByRegions.rst: -------------------------------------------------------------------------------- 1 | EmModelByRegions.txt 2 | ---------------------- 3 | 4 | .. literalinclude:: /examples/Basic/EmModelByRegions.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/Emittance_Gaussian.rst: -------------------------------------------------------------------------------- 1 | .. _example_basic_emittance_gaussian: 2 | 3 | Emittance_Gaussian.txt 4 | ---------------------- 5 | 6 | .. literalinclude:: /examples/Basic/Emittance_Gaussian.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Basic/Emittance_Twiss.rst: -------------------------------------------------------------------------------- 1 | .. _example_basic_emittance_twiss: 2 | 3 | Emittance_Twiss.txt 4 | ------------------- 5 | 6 | .. literalinclude:: /examples/Basic/Emittance_Twiss.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Basic/EnvironmentSource.rst: -------------------------------------------------------------------------------- 1 | EnvironmentSource.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/EnvironmentSource.txt 5 | 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----------------------- 5 | 6 | .. literalinclude:: /examples/Basic/LayeredMassGeometry.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Basic/OneBox.rst: -------------------------------------------------------------------------------- 1 | OneBox.txt 2 | ---------- 3 | 4 | .. literalinclude:: /examples/Basic/OneBox.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/OneBoxRotate.rst: -------------------------------------------------------------------------------- 1 | OneBoxRotate.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/Basic/OneBoxRotate.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/OneBoxTranslate.rst: -------------------------------------------------------------------------------- 1 | OneBoxTranslate.txt 2 | ------------------- 3 | 4 | .. literalinclude:: /examples/Basic/OneBoxTranslate.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/ParallelWorlds.rst: -------------------------------------------------------------------------------- 1 | ParallelWorlds.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/ParallelWorlds.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/ParticleSourcesFromGroup.rst: -------------------------------------------------------------------------------- 1 | ParticleSourcesFromGroup.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/ParticleSourcesFromGroup.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/PhysicsSetting.rst: -------------------------------------------------------------------------------- 1 | PhysicsSetting.txt 2 | ------------------ 3 | 4 | .. literalinclude:: /examples/Basic/PhysicsSetting.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/QtShapeTest.rst: -------------------------------------------------------------------------------- 1 | QtShapeTest.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/QtShapeTest.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/ShapeTestWithAllParameters.rst: -------------------------------------------------------------------------------- 1 | .. _example_basic_shapesall: 2 | 3 | ShapeTestWithAllParameters.txt 4 | ------------------------------ 5 | 6 | .. literalinclude:: /examples/Basic/ShapeTestWithAllParameters.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Basic/ShapeTestWithOnlyRequiredParameters.rst: -------------------------------------------------------------------------------- 1 | ShapeTestWithOnlyRequiredParameters.txt 2 | --------------------------------------- 3 | 4 | .. literalinclude:: /examples/Basic/ShapeTestWithOnlyRequiredParameters.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/Spectrum.rst: -------------------------------------------------------------------------------- 1 | .. _example_basic_spectrum: 2 | 3 | Spectrum.txt 4 | ------------ 5 | 6 | .. literalinclude:: /examples/Basic/Spectrum.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Basic/TwoBeams.rst: -------------------------------------------------------------------------------- 1 | TwoBeams.txt 2 | ------------ 3 | 4 | .. literalinclude:: /examples/Basic/TwoBeams.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/VolumetricSource.rst: -------------------------------------------------------------------------------- 1 | VolumetricSource.txt 2 | ------------ 3 | 4 | .. literalinclude:: /examples/Basic/VolumetricSource.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/VoxelMaterialsInDividedComponents.rst: -------------------------------------------------------------------------------- 1 | VoxelMaterialsInDividedComponents.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Basic/VoxelMaterialsInDividedComponents.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Basic/index.rst: -------------------------------------------------------------------------------- 1 | Basic 2 | ===== 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | AllParameterForms 8 | BatchJob1 9 | BatchJob2 10 | BatchJobShared 11 | BoxRotatedAroundItsCorner 12 | DistributedSourcePointsInShell 13 | DistributedSourcePointsInSphereGaussian 14 | DistributedSourcePointsInSphere 15 | DistributedSourcePointsInTwistedTubs 16 | DividedComponents 17 | DNAModelByRegions 18 | Emittance_Gaussian 19 | Emittance_Twiss 20 | EmModelByRegions 21 | EnvironmentSource 22 | ExtraSequence1 23 | ExtraSequence2 24 | ExtraSequences 25 | FlatteningFilter 26 | Isotope 27 | LayeredMassGeometry 28 | OneBox 29 | OneBoxRotate 30 | OneBoxTranslate 31 | ParallelWorlds 32 | ParticleSourcesFromGroup 33 | PhysicsSetting 34 | QtShapeTest 35 | ShapeTestWithAllParameters 36 | ShapeTestWithOnlyRequiredParameters 37 | Spectrum 38 | TwoBeams 39 | VolumetricSource 40 | VoxelMaterialsInDividedComponents 41 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples-docs/Brachytherapy/.DS_Store -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /examples-docs/Brachytherapy/EyeModel.rst: -------------------------------------------------------------------------------- 1 | EyeModel.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/EyeModel.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/HDRSource.rst: -------------------------------------------------------------------------------- 1 | HDRSource.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/HDRSource.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/HDRSourceInApplicator.rst: -------------------------------------------------------------------------------- 1 | HDRSourceInApplicator.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/HDRSourceInApplicator.txt 5 | 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/examples/Brachytherapy/LDR/I125_IsoAid_IAI-125A.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/I125_OncoSeed6711.rst: -------------------------------------------------------------------------------- 1 | I125_OncoSeed6711.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/LDR/I125_OncoSeed6711.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/I125_SL-125.rst: -------------------------------------------------------------------------------- 1 | I125_SL-125.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/LDR/I125_SL-125.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/I125_SelectSeed.rst: -------------------------------------------------------------------------------- 1 | I125_SelectSeed.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/LDR/I125_SelectSeed.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/I125_Theragenic-AgX100.rst: -------------------------------------------------------------------------------- 1 | I125_Theragenic-AgX100.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/LDR/I125_Theragenic-AgX100.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/Ir192_Flexisource.rst: -------------------------------------------------------------------------------- 1 | Ir192_Flexisource.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/HDR/Ir192_Flexisource.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/Ir192_MicroSelectronV2.rst: -------------------------------------------------------------------------------- 1 | Ir192_MicroSelectronV2.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/HDR/Ir192_MicroSelectronV2.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/Ir192_TG186.rst: -------------------------------------------------------------------------------- 1 | Ir192_TG186.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/HDR/Ir192_TG186.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/LDRSource.rst: -------------------------------------------------------------------------------- 1 | LDRSource.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/LDRSource.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/Pd103_Best2335.rst: -------------------------------------------------------------------------------- 1 | Pd103_Best2335.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/LDR/Pd103_Best2335.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/Pd103_IAPd103A.rst: -------------------------------------------------------------------------------- 1 | Pd103_IAPd103A.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/LDR/Pd103_IAPd103A.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/Pd103_Theraseed200Heavy.rst: -------------------------------------------------------------------------------- 1 | Pd103_Theraseed200Heavy.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/LDR/Pd103_Theraseed200Heavy.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/Pd103_Theraseed200Light.rst: -------------------------------------------------------------------------------- 1 | Pd103_Theraseed200Light.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/LDR/Pd103_Theraseed200Light.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/TG186Applicator.rst: -------------------------------------------------------------------------------- 1 | TG186Applicator.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Brachytherapy/HDR/TG186Applicator.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Brachytherapy/index.rst: -------------------------------------------------------------------------------- 1 | Brachytherapy 2 | ============= 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | intro 8 | DoseTLE 9 | HDRSource 10 | HDRSourceInApplicator 11 | Ir192_Flexisource 12 | Ir192_MicroSelectronV2 13 | Ir192_TG186 14 | TG186Applicator 15 | LDRSource 16 | Cs131_IsoRay-CS-1-Rev2 17 | I125_BardSTM1251 18 | I125_Best2301 19 | I125_IsoAid_IAI-125A 20 | I125_OncoSeed6711 21 | I125_SelectSeed 22 | I125_SL-125 23 | I125_Theragenic-AgX100 24 | Pd103_Best2335 25 | Pd103_IAPd103A 26 | Pd103_Theraseed200Heavy 27 | Pd103_Theraseed200Light 28 | EyeModel 29 | COMSEyePlaque 30 | -------------------------------------------------------------------------------- /examples-docs/Graphics/ColorByCharge.rst: -------------------------------------------------------------------------------- 1 | ColorByCharge.txt 2 | -------------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/ColorByCharge.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/ColorByCreatorProcess.rst: -------------------------------------------------------------------------------- 1 | ColorByCreatorProcess.txt 2 | -------------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/ColorByCreatorProcess.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/ColorByEnergy.rst: -------------------------------------------------------------------------------- 1 | ColorByEnergy.txt 2 | ------------------ 3 | 4 | .. literalinclude:: /examples/Graphics/ColorByEnergy.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/ColorByGeneration.rst: -------------------------------------------------------------------------------- 1 | ColorByGeneration.txt 2 | ---------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/ColorByGeneration.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/ColorByMomentum.rst: -------------------------------------------------------------------------------- 1 | ColorByMomentum.txt 2 | -------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/ColorByMomentum.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/ColorByOriginComponent.rst: -------------------------------------------------------------------------------- 1 | ColorByOriginComponent.txt 2 | -------------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/ColorByOriginComponent.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/ColorByOriginComponentOrSubComponent.rst: -------------------------------------------------------------------------------- 1 | ColorByOriginComponentOrSubComponent.txt 2 | ----------------------------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/ColorByOriginComponentOrSubComponent.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/ColorByOriginVolume.rst: -------------------------------------------------------------------------------- 1 | ColorByOriginVolume.txt 2 | ------------------------ 3 | 4 | .. literalinclude:: /examples/Graphics/ColorByOriginVolume.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/ColorByParticleType.rst: -------------------------------------------------------------------------------- 1 | ColorByParticleType.txt 2 | ------------------------ 3 | 4 | .. literalinclude:: /examples/Graphics/ColorByParticleType.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/ColorTest.rst: -------------------------------------------------------------------------------- 1 | ColorTest.txt 2 | --------------- 3 | 4 | .. literalinclude:: /examples/Graphics/ColorTest.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/FilterByCreatorProcess.rst: -------------------------------------------------------------------------------- 1 | FilterByCreatorProcess.txt 2 | --------------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/FilterByCreatorProcess.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/FilterByEnergy.rst: -------------------------------------------------------------------------------- 1 | FilterByEnergy.txt 2 | ------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/FilterByEnergy.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/FilterByMomentum.rst: -------------------------------------------------------------------------------- 1 | FilterByMomentum.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/FilterByMomentum.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/FilterByOriginComponent.rst: -------------------------------------------------------------------------------- 1 | FilterByOriginComponent.txt 2 | ---------------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/FilterByOriginComponent.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/FilterByOriginComponentOrSubcomonent.rst: -------------------------------------------------------------------------------- 1 | FilterByOriginComponentOrSubComponent.txt 2 | ------------------------------------------ 3 | 4 | .. literalinclude:: /examples/Graphics/FilterByOriginComponentOrSubComponent.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/FilterByOriginVolume.rst: -------------------------------------------------------------------------------- 1 | FilterByOriginVolume.txt 2 | ------------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/FilterByOriginVolume.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/FilterByParticleCharge.rst: -------------------------------------------------------------------------------- 1 | FilterByParticleCharge.txt 2 | --------------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/FilterByParticleCharge.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/FilterByParticleType.rst: -------------------------------------------------------------------------------- 1 | FilterByParticleType.txt 2 | ------------------------- 3 | 4 | .. literalinclude:: /examples/Graphics/FilterByParticleType.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/NanoMeterScaleTest.rst: -------------------------------------------------------------------------------- 1 | NanoMeterScaleTest.txt 2 | ------------------ 3 | 4 | .. literalinclude:: /examples/Graphics/NanoMeterScaleTest.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/ParticleFlight.rst: -------------------------------------------------------------------------------- 1 | ParticleFlight.txt 2 | ------------------ 3 | 4 | .. literalinclude:: /examples/Graphics/ParticleFlight.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/QtTest.rst: -------------------------------------------------------------------------------- 1 | QtTest.txt 2 | --------------- 3 | 4 | .. literalinclude:: /examples/Graphics/QtTest.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/SolidSphere.rst: -------------------------------------------------------------------------------- 1 | SolidSphere.txt 2 | --------------- 3 | 4 | .. literalinclude:: /examples/Graphics/SolidSphere.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/TestGraphics.rst: -------------------------------------------------------------------------------- 1 | TestGraphics.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/Graphics/TestGraphics.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/TwoProjections.rst: -------------------------------------------------------------------------------- 1 | TwoProjections.txt 2 | ------------------ 3 | 4 | .. literalinclude:: /examples/Graphics/TwoProjections.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Graphics/index.rst: -------------------------------------------------------------------------------- 1 | Graphics 2 | ======== 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | ColorByCharge 8 | ColorByCreatorProcess 9 | ColorByEnergy 10 | ColorByGeneration 11 | ColorByMomentum 12 | ColorByOriginComponent 13 | ColorByOriginComponentOrSubComponent 14 | ColorByOriginVolume 15 | ColorByParticleType 16 | ColorTest 17 | FilterByCreatorProcess 18 | FilterByEnergy 19 | FilterByMomentum 20 | FilterByOriginComponent 21 | FilterByOriginComponentOrSubComponent 22 | FIlterByOriginVolume 23 | FilterByParticleCharge 24 | FilerByParticleType 25 | NanoMeterScaleTest 26 | ParticleFlight 27 | QtTest 28 | SolidSphere 29 | TestGraphics 30 | TwoProjections 31 | 32 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/Field.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_field: 2 | 3 | Field.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/Field.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/FixedTxHead.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_fixedtxhead: 2 | 3 | FixedTxHead.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/FixedTxHead.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/Flattener18MV.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_flattener18mv: 2 | 3 | Flattener18MV.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/Flattener18MV.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/Flattener6MV.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_flattener6mv: 2 | 3 | Flattener6MV.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/Flattener6MV.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/FullTxHeadField.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_fulltxhead: 2 | 3 | FullTxHeadField.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/FullTxHeadField.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/Jaws.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_jaws: 2 | 3 | Jaws.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/Jaws.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/LinacDefaults.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_linacdefaults: 2 | 3 | LinacDefaults.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/LinacDefaults.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/MLC.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_mlc: 2 | 3 | MLC.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/MLC.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/MainTxHead.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_maintxhead: 2 | 3 | MainTxHead.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/MainTxHead.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/Monitor.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_monitor: 2 | 3 | Monitor.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/Monitor.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/ParameterControlFiles.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples-docs/MVLinac/ParameterControlFiles.png -------------------------------------------------------------------------------- /examples-docs/MVLinac/ScoreEnergyFluence.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_scoreenergyfluence: 2 | 3 | ScoreEnergyFluence.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/ScoreEnergyFluence.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/ScoreEnergySpectrum.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_scoreenergyspectrum: 2 | 3 | ScoreEnergySpectrum.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/ScoreEnergySpectrum.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/ScorePhaseSpace.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_scorephasespace: 2 | 3 | ScorePhaseSpace.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/ScorePhaseSpace.txt 7 | -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- /examples-docs/MVLinac/VRT_1.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_vrt1: 2 | 3 | VRT_1b.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/VRT_1.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/VRT_2.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_vrt2: 2 | 3 | VRT_2.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/VRT_2.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/VRT_3.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_vrt3: 2 | 3 | VRT_3.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/VRT_3.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/VRT_HD.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_vrthd: 2 | 3 | VRT_HD.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/VRT_HD.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/WaterBox.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_waterbox: 2 | 3 | WaterBox.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/WaterBox.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/WaterPhantom.rst: -------------------------------------------------------------------------------- 1 | .. _example_linac_waterphantom: 2 | 3 | WaterPhantom.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/MVLinac/WaterPhantom.txt 7 | -------------------------------------------------------------------------------- /examples-docs/MVLinac/index.rst: -------------------------------------------------------------------------------- 1 | MVLinac 2 | ================= 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | intro 8 | Field 9 | FixedTxHead 10 | Flattener6MV 11 | Flattener18MV 12 | FullTxHeadField 13 | Jaws 14 | LinacDefaults 15 | MLC 16 | MainTxHead 17 | Monitor 18 | ScoreEnergyFluence 19 | ScoreEnergySpectrum 20 | ScorePhaseSpace 21 | Target 22 | TestComponent 23 | VRT_1 24 | VRT_2 25 | VRT_3 26 | VRT_HD 27 | WaterBox 28 | WaterPhantom 29 | 30 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/ConstantsForNozzles.rst: -------------------------------------------------------------------------------- 1 | ConstantsForNozzles.txt 2 | ------------------------ 3 | 4 | .. literalinclude:: /examples/Nozzle/ConstantsForNozzles.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/RasterScanningPattern.rst: -------------------------------------------------------------------------------- 1 | .. _example_nozzle_raster: 2 | 3 | RasterScanningPattern.txt 4 | ------------------------- 5 | 6 | .. literalinclude:: /examples/Nozzle/RasterScanningPattern.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/ScanningNozzle.rst: -------------------------------------------------------------------------------- 1 | .. _example_nozzle_scanning: 2 | 3 | ScanningNozzle.txt 4 | ------------------ 5 | 6 | .. literalinclude:: /examples/Nozzle/ScanningNozzle.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/ScanningStationaryTarget.rst: -------------------------------------------------------------------------------- 1 | .. _example_nozzle_scanning_stationary: 2 | 3 | ScanningStationaryTarget.txt 4 | ---------------------------- 5 | 6 | .. literalinclude:: /examples/Nozzle/ScanningStationaryTarget.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/ScanningTargetMovingHorizontal.rst: -------------------------------------------------------------------------------- 1 | .. _example_nozzle_scanning_horiz: 2 | 3 | ScanningTargetMovingHorizontal.txt 4 | ---------------------------------- 5 | 6 | .. literalinclude:: /examples/Nozzle/ScanningTargetMovingHorizontal.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/ScanningTargetMovingInDepth.rst: -------------------------------------------------------------------------------- 1 | .. _example_nozzle_scanning_depth: 2 | 3 | ScanningTargetMovingInDepth.txt 4 | ------------------------------- 5 | 6 | .. literalinclude:: /examples/Nozzle/ScanningTargetMovingInDepth.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/ScatteringNozzle.rst: -------------------------------------------------------------------------------- 1 | .. _example_nozzle_scattering: 2 | 3 | ScatteringNozzle.txt 4 | -------------------- 5 | 6 | .. literalinclude:: /examples/Nozzle/ScatteringNozzle.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/ScatteringNozzle_QtTest.rst: -------------------------------------------------------------------------------- 1 | ScanningNozzle_QtTest.txt 2 | -------------------------- 3 | 4 | .. literalinclude:: /examples/Nozzle/ScanningNozzle_QtTest.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/ScatteringNozzle_run.rst: -------------------------------------------------------------------------------- 1 | .. _example_nozzle_scattering_run: 2 | 3 | ScatteringNozzle_run.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/Nozzle/ScatteringNozzle_run.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/ScatteringNozzle_run_QtTest.rst: -------------------------------------------------------------------------------- 1 | ScanningNozzle_run_QtTest.txt 2 | ------------------------------ 3 | 4 | .. literalinclude:: /examples/Nozzle/ScanningNozzle_run_QtTest.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/TargetInWaterPhantom.rst: -------------------------------------------------------------------------------- 1 | TargetInWaterPhantom.txt 2 | ------------------------- 3 | 4 | .. literalinclude:: /examples/Nozzle/TargetInWaterPhantom.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/TsAnalysisWaterPhantom.rst: -------------------------------------------------------------------------------- 1 | TsAnalysisWaterPhantom.txt 2 | --------------------------- 3 | 4 | .. literalinclude:: /examples/Nozzle/TsAnalysisWaterPhantom.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/Viewer.rst: -------------------------------------------------------------------------------- 1 | Viewer.txt 2 | ----------- 3 | 4 | .. literalinclude:: /examples/Nozzle/Viewer.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Nozzle/index.rst: -------------------------------------------------------------------------------- 1 | Nozzle 2 | ====== 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | ConstantsForNozzles 8 | RasterScanningPattern 9 | ScanningNozzle 10 | ScanningStationaryTarget 11 | ScanningTargetMovingHorizontal 12 | ScanningTargetMovingInDepth 13 | ScatteringNozzle 14 | ScatteringNozzle_QtTest 15 | ScatteringNozzle_run 16 | ScatteringNozzle_run_QtTest 17 | TargetInWaterPhantom 18 | TsAnalysisWaterPhantom 19 | Viewer 20 | -------------------------------------------------------------------------------- /examples-docs/Optical/OpticalMaterialSample.rst: -------------------------------------------------------------------------------- 1 | OpticalMaterialSample.txt 2 | -------------------------- 3 | 4 | .. literalinclude:: /examples/Optical/OpticalMaterialSample.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Optical/OpticalPhotonCount.rst: -------------------------------------------------------------------------------- 1 | .. _example_optical_photoncount: 2 | 3 | OpticalPhotonCount.txt 4 | ---------------------- 5 | 6 | .. literalinclude:: /examples/Optical/OpticalPhotonCount.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Optical/PixelatedDetector.rst: -------------------------------------------------------------------------------- 1 | PixelatedDetector.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Optical/PixelatedDetector.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Optical/PlasticScintillator.rst: -------------------------------------------------------------------------------- 1 | PlasticScintillator.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Optical/PlasticScintillator.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Optical/Rotating_Surfaces.rst: -------------------------------------------------------------------------------- 1 | Rotating_Surfaces.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Optical/Rotating_Surfaces.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Optical/Surfaces.rst: -------------------------------------------------------------------------------- 1 | Surfaces.txt 2 | ------------ 3 | 4 | .. literalinclude:: /examples/Optical/Surfaces.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Optical/WavelengthShifter.rst: -------------------------------------------------------------------------------- 1 | WavelengthShifter.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Optical/WavelengthShifter.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Optical/index.rst: -------------------------------------------------------------------------------- 1 | Optical 2 | ======= 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | OpticalMaterialSample 8 | OpticalPhotonCount 9 | PixelatedDetector 10 | PlasticScintillator 11 | Rotating_Surfaces 12 | Surfaces 13 | WavelengthShifter 14 | -------------------------------------------------------------------------------- /examples-docs/Outcome/CEModelBurman.rst: -------------------------------------------------------------------------------- 1 | CEModelBurman.txt 2 | ------------------ 3 | 4 | .. literalinclude:: /examples/Outcome/CDModelBurman.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Outcome/CVModelStavrev.rst: -------------------------------------------------------------------------------- 1 | CVModelStavrev.txt 2 | ------------------- 3 | 4 | .. literalinclude:: /examples/Outcome/CVModelStavrev.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Outcome/LKMModelBurman: -------------------------------------------------------------------------------- 1 | LKMModelBurman.txt 2 | ------------------- 3 | 4 | .. literalinclude:: /examples/Outcome/LKMModelBurman.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Outcome/Phantom.rst: -------------------------------------------------------------------------------- 1 | Phantom.txt 2 | ------------ 3 | 4 | .. literalinclude:: /examples/Outcome/Phantom.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Outcome/PoissonModelOkunieff.rst: -------------------------------------------------------------------------------- 1 | PoissonModelOkuneff.txt 2 | ------------------------ 3 | 4 | .. literalinclude:: /examples/Outcome/PoissonModelOkunieff.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Outcome/TestOutcomeModel.rst: -------------------------------------------------------------------------------- 1 | .. _example_outcome_testoutcomemodel: 2 | 3 | TestOutcomeModel.txt 4 | ----------------------- 5 | 6 | .. literalinclude:: /examples/Outcome/TestOutcomeModel.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Outcome/TestRestoreModel.rst: -------------------------------------------------------------------------------- 1 | .. _example_outcome_testrestoremodel: 2 | 3 | TestRestoreModel.txt 4 | ----------------------- 5 | 6 | .. literalinclude:: /examples/Outcome/TestRestoreModel.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Outcome/index.rst: -------------------------------------------------------------------------------- 1 | .. _example_outcome: 2 | 3 | Outcome 4 | ======= 5 | 6 | .. toctree:: 7 | :maxdepth: 1 8 | 9 | CEModelBurman 10 | CVModelStavrev 11 | LKMModelBurman 12 | Phantom 13 | PoissonModelOkunieff 14 | TestOutcomeModel 15 | TestRestoreModel 16 | -------------------------------------------------------------------------------- /examples-docs/Patient/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples-docs/Patient/.DS_Store -------------------------------------------------------------------------------- /examples-docs/Patient/Applicator.rst: -------------------------------------------------------------------------------- 1 | Applicator.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Patient/Applicator.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/DicomCutaway.rst: -------------------------------------------------------------------------------- 1 | DicomCutaway.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Patient/DicomCutaway.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/DoseTo4DCT.rst: -------------------------------------------------------------------------------- 1 | .. _example_dicom_time: 2 | 3 | DoseTo4DCT.txt 4 | ----------------------- 5 | 6 | .. literalinclude:: /examples/Patient/DoseTo4DCT.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Patient/DoseToCT.rst: -------------------------------------------------------------------------------- 1 | .. _example_dicom: 2 | 3 | DoseToCT.txt 4 | ----------------------- 5 | 6 | .. literalinclude:: /examples/Patient/DoseToCT.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Patient/HUtoMaterialSchneider.rst: -------------------------------------------------------------------------------- 1 | HUtoMaterialSchneiber.txt 2 | -------------------------- 3 | 4 | .. literalinclude:: /examples/Patient/HUtoMaterialSchneider.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/HUtoMaterialSchneider2.rst: -------------------------------------------------------------------------------- 1 | HUtoMaterialSchneider2.txt 2 | --------------------------- 3 | 4 | .. literalinclude:: /examples/Patient/HUtoMaterialSchneider2.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/Implant.rst: -------------------------------------------------------------------------------- 1 | Implant.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Patient/Implant.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/PatientInIEC_1.rst: -------------------------------------------------------------------------------- 1 | PatientInIEC_1.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Patient/PatientInIEC_1.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/PatientInIEC_2.rst: -------------------------------------------------------------------------------- 1 | PatientInIEC_2.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Patient/PatientInIEC_2.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/PatientInIEC_2_time_feature.rst: -------------------------------------------------------------------------------- 1 | PatientInIEC_2_time_feature.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Patient/PatientInIEC_2_time_feature.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/PatientInIEC_3.rst: -------------------------------------------------------------------------------- 1 | PatientInIEC_3.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Patient/PatientInIEC_3.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/TwoDicoms.rst: -------------------------------------------------------------------------------- 1 | TwoDicoms.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Patient/TwoDicoms.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/ViewAbdomen.rst: -------------------------------------------------------------------------------- 1 | ViewAbdomen.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Patient/ViewAbdomen.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/ViewAbdomen_rtdose.rst: -------------------------------------------------------------------------------- 1 | .. _example_dicom_viewabdomen_rtdose: 2 | 3 | ViewAbdomen_rtdose.txt 4 | ----------------------- 5 | 6 | .. literalinclude:: /examples/Patient/ViewAbdomen_rtdose.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Patient/XCAT.rst: -------------------------------------------------------------------------------- 1 | .. _example_xcat: 2 | 3 | XCAT.txt 4 | ----------------------- 5 | 6 | .. literalinclude:: /examples/Patient/XCAT.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Patient/XCAT_Materials.rst: -------------------------------------------------------------------------------- 1 | XCAT_Materials.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Patient/XCAT_Materials.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Patient/index.rst: -------------------------------------------------------------------------------- 1 | Patient 2 | ======= 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | Applicator 8 | DicomCutaway 9 | DoseTo4DCT 10 | DoseToCT 11 | HUtoMaterialSchneider 12 | HUtoMaterialSchneider2 13 | Implant 14 | PatientInIEC_1 15 | PatientInIEC_2_time_feature 16 | PatientInIEC_2 17 | PatientInIEC_3 18 | TwoDicoms 19 | ViewAbdomen_rtdose 20 | ViewAbdomen 21 | XCAT_Materials 22 | XCAT 23 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/MultiRun_Write_ASCII.rst: -------------------------------------------------------------------------------- 1 | MultiRun_Write_ASCII.txt 2 | ------------------------ 3 | 4 | .. literalinclude:: /examples/PhaseSpace/MultiRun_Write_ASCII.txt 5 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/ReadASCII.rst: -------------------------------------------------------------------------------- 1 | ReadASCII.txt 2 | ------------- 3 | 4 | .. literalinclude:: /examples/PhaseSpace/ReadASCII.txt 5 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/ReadBinary.rst: -------------------------------------------------------------------------------- 1 | ReadBinary.txt 2 | -------------- 3 | 4 | .. literalinclude:: /examples/PhaseSpace/ReadBinary.txt 5 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/ReadElekta.rst: -------------------------------------------------------------------------------- 1 | ReadElekta.txt 2 | -------------- 3 | 4 | .. literalinclude:: /examples/PhaseSpace/ReadElekta.txt 5 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/ReadLimited.rst: -------------------------------------------------------------------------------- 1 | ReadLimited.txt 2 | --------------- 3 | 4 | .. literalinclude:: /examples/PhaseSpace/ReadLimited.txt 5 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/ReadVarian.rst: -------------------------------------------------------------------------------- 1 | ReadVarian.txt 2 | -------------- 3 | 4 | .. literalinclude:: /examples/PhaseSpace/ReadVarian.txt 5 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/WriteASCII.rst: -------------------------------------------------------------------------------- 1 | .. _example_phsp_ascii_write: 2 | 3 | WriteASCII.txt 4 | -------------- 5 | 6 | .. literalinclude:: /examples/PhaseSpace/WriteASCII.txt 7 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/WriteBinary.rst: -------------------------------------------------------------------------------- 1 | .. _example_phsp_binary_write: 2 | 3 | WriteBinary.txt 4 | --------------- 5 | 6 | .. literalinclude:: /examples/PhaseSpace/WriteBinary.txt 7 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/WriteIonsASCII.rst: -------------------------------------------------------------------------------- 1 | WriteIonsASCII.txt 2 | ------------------ 3 | 4 | .. literalinclude:: /examples/PhaseSpace/WriteIonsASCII.txt 5 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/WriteLimited.rst: -------------------------------------------------------------------------------- 1 | .. _example_phsp_limited_write: 2 | 3 | WriteLimited.txt 4 | ---------------- 5 | 6 | .. literalinclude:: /examples/PhaseSpace/WriteLimited.txt 7 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/WriteROOT.rst: -------------------------------------------------------------------------------- 1 | .. _example_phsp_root_write: 2 | 3 | WriteROOT.txt 4 | -------------- 5 | 6 | .. literalinclude:: /examples/PhaseSpace/WriteROOT.txt 7 | -------------------------------------------------------------------------------- /examples-docs/PhaseSpace/index.rst: -------------------------------------------------------------------------------- 1 | PhaseSpace 2 | ========== 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | MultiRun_Write_ASCII 8 | ReadASCII 9 | ReadBinary 10 | ReadLimited 11 | ReadElekta 12 | ReadVarian 13 | WriteASCII 14 | WriteBinary 15 | WriteIonsASCII 16 | WriteLimited 17 | WriteROOT 18 | -------------------------------------------------------------------------------- /examples-docs/Scoring/ChargeInSphere.rst: -------------------------------------------------------------------------------- 1 | ChargeInSphere.txt 2 | ------------------ 3 | 4 | .. literalinclude:: /examples/Scoring/ChargeInSphere.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/Complex.rst: -------------------------------------------------------------------------------- 1 | Complex.txt 2 | ----------- 3 | 4 | .. literalinclude:: /examples/Scoring/Complex.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/DepthDose.rst: -------------------------------------------------------------------------------- 1 | DepthDose.txt 2 | -------- 3 | 4 | .. literalinclude:: /examples/Scoring/DepthDose.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/Dose.rst: -------------------------------------------------------------------------------- 1 | Dose.txt 2 | -------- 3 | 4 | .. literalinclude:: /examples/Scoring/Dose.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/DoseInVoxelMaterials.rst: -------------------------------------------------------------------------------- 1 | .. _example_scoring_voxelmaterials: 2 | 3 | DoseInVoxelMaterials.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/Scoring/DoseInVoxelMaterials.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Scoring/DoseToMediumVsWater.rst: -------------------------------------------------------------------------------- 1 | DoseToMediumVsWater.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Scoring/DoseToMediumVsWater.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/DoseVolumeHistogram.rst: -------------------------------------------------------------------------------- 1 | .. _example_scoring_DVH: 2 | 3 | DoseVolumeHistogram.txt 4 | ----------------------- 5 | 6 | .. literalinclude:: /examples/Scoring/DoseVolumeHistogram.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Scoring/EnergyAndDose.rst: -------------------------------------------------------------------------------- 1 | EnergyAndDose.txt 2 | ----------------- 3 | 4 | .. literalinclude:: /examples/Scoring/EnergyAndDose.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/EnergyDepositBinnedByEnergy.rst: -------------------------------------------------------------------------------- 1 | EnergyDepositBinnedByEnergy.txt 2 | ----------------- 3 | 4 | .. literalinclude:: /examples/Scoring/EnergyDepositBinnedByEnergy.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/EnergyDivisions.rst: -------------------------------------------------------------------------------- 1 | EnergyDivisions.txt 2 | ------------------- 3 | 4 | .. literalinclude:: /examples/Scoring/EnergyDivisions.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/EnergyInBinnedCylinder.rst: -------------------------------------------------------------------------------- 1 | EnergyInBinnedCylinder.txt 2 | -------------------------- 3 | 4 | .. literalinclude:: /examples/Scoring/EnergyInBinnedCylinder.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/FilterByInteractionCount.rst: -------------------------------------------------------------------------------- 1 | .. _example_scoring_filter_by_interaction_count: 2 | 3 | FilterByInteractionCount.txt 4 | ---------------------------- 5 | 6 | .. literalinclude:: /examples/Scoring/FilterByInteractionCount.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Scoring/Filters.rst: -------------------------------------------------------------------------------- 1 | .. _example_scoring_filters: 2 | 3 | Filters.txt 4 | ----------- 5 | 6 | .. literalinclude:: /examples/Scoring/Filters.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Scoring/FoilToBox.rst: -------------------------------------------------------------------------------- 1 | FoilToBox.txt 2 | ------------- 3 | 4 | .. literalinclude:: /examples/Scoring/FoilToBox.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/FoilToCylinder.rst: -------------------------------------------------------------------------------- 1 | FoilToCylinder.txt 2 | ------------------ 3 | 4 | .. literalinclude:: /examples/Scoring/FoilToCylinder.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/FoilToSphere.rst: -------------------------------------------------------------------------------- 1 | FoilToSphere.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/Scoring/FoilToSphere.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/Gated.rst: -------------------------------------------------------------------------------- 1 | Gated.txt 2 | --------- 3 | 4 | .. literalinclude:: /examples/Scoring/Gated.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/GeometryDivisions.rst: -------------------------------------------------------------------------------- 1 | GeometryDivisions.txt 2 | --------------------- 3 | 4 | .. literalinclude:: /examples/Scoring/GeometryDivisions.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/Histograms.rst: -------------------------------------------------------------------------------- 1 | Histograms.txt 2 | -------------- 3 | 4 | .. literalinclude:: /examples/Scoring/Histograms.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/Inactive.rst: -------------------------------------------------------------------------------- 1 | Inactive.txt 2 | ------------ 3 | 4 | .. literalinclude:: /examples/Scoring/Inactive.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/Ion.rst: -------------------------------------------------------------------------------- 1 | Ion.txt 2 | ------- 3 | 4 | .. literalinclude:: /examples/Scoring/Ion.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/Origin.rst: -------------------------------------------------------------------------------- 1 | Origin.txt 2 | ---------- 3 | 4 | .. literalinclude:: /examples/Scoring/Origin.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/OriginCount.rst: -------------------------------------------------------------------------------- 1 | OriginCount.txt 2 | ---------- 3 | 4 | .. literalinclude:: /examples/Scoring/OriginCount.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/ParallelBoxRebinned.rst: -------------------------------------------------------------------------------- 1 | ParallelBoxRebinned.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/Scoring/ParallelBoxRebinned.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/SparsifyAndSingleIndex.rst: -------------------------------------------------------------------------------- 1 | SparsifyAndSingleIndex.txt 2 | ------------------ 3 | 4 | .. literalinclude:: /examples/Scoring/SparsifyAndSingleIndex.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/SplitByTimeFeature.rst: -------------------------------------------------------------------------------- 1 | .. _example_scoring_timefeature: 2 | 3 | SplitByTimeFeature.txt 4 | ---------------------- 5 | 6 | .. literalinclude:: /examples/Scoring/SplitByTimeFeature.txt 7 | -------------------------------------------------------------------------------- /examples-docs/Scoring/Surfaces.rst: -------------------------------------------------------------------------------- 1 | Surfaces.txt 2 | ------------ 3 | 4 | .. literalinclude:: /examples/Scoring/Surfaces.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/VoxelMaterials.rst: -------------------------------------------------------------------------------- 1 | VoxelMaterials.txt 2 | ------------------- 3 | 4 | .. literalinclude:: /examples/Scoring/VoxelMaterials.txt 5 | -------------------------------------------------------------------------------- /examples-docs/Scoring/index.rst: -------------------------------------------------------------------------------- 1 | Scoring 2 | ======= 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | ChargeInSphere 8 | Complex 9 | DepthDose 10 | Dose 11 | DoseInVoxelMaterials 12 | DoseToMediumVsWater 13 | DoseVolumeHistogram 14 | EnergyAndDose 15 | EnergyDepositBinnedByEnergy 16 | EnergyDivisions 17 | EnergyInBinnedCylinder 18 | FilterByInteractionCount 19 | Filters 20 | FoilToBox 21 | FoilToCylinder 22 | FoilToSphere 23 | Gated 24 | GeometryDivisions 25 | Histograms 26 | Inactive 27 | Ion 28 | Origin 29 | OriginCount 30 | ParallelBoxRebinned 31 | SparsifyAndSingleIndex 32 | SplitByTimeFeature 33 | Surfaces 34 | VoxelMaterials 35 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/CAD.rst: -------------------------------------------------------------------------------- 1 | CAD.txt 2 | ------- 3 | 4 | .. literalinclude:: /examples/SpecialComponents/CAD.txt 5 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/DipoleMagnet.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_dipole: 2 | 3 | DipoleMagnet.txt 4 | ---------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/DipoleMagnet.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/MultiLeafCollimator.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_mlc: 2 | 3 | MultiLeafCollimator.txt 4 | ----------------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/MultiLeafCollimator.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/MultiLeafCollimator_sequence.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_mlc_sequence: 2 | 3 | MultiLeafCollimator_sequence.txt 4 | -------------------------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/MultiLeafCollimator_sequence.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/MultiWire_Chamber.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_mwc: 2 | 3 | MultiWire_Chamber.txt 4 | --------------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/MultiWire_Chamber.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/Propeller.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_propeller: 2 | 3 | Propeller.txt 4 | ------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/Propeller.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/Propeller_ContinuousRotation.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_propeller_continuous: 2 | 3 | Propeller_ContinuousRotation.txt 4 | -------------------------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/Propeller_ContinuousRotation.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/Propeller_StepRotation.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_propeller_step: 2 | 3 | Propeller_StepRotation.txt 4 | -------------------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/Propeller_StepRotation.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/PurgingMagnet_move.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_purgingmagnet: 2 | 3 | PurgingMagnet_move.txt 4 | ---------------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/PurgingMagnet_move.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/QuadAndDipoleMagnets.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_quadanddipole: 2 | 3 | QuadAndDipoleMagnets.txt 4 | ------------------------ 5 | 6 | .. literalinclude:: /examples/SpecialComponents/QuadAndDipoleMagnets.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/QuadInMovingNozzle.rst: -------------------------------------------------------------------------------- 1 | QuadInMovingNozzle.txt 2 | ---------------------- 3 | 4 | .. literalinclude:: /examples/SpecialComponents/QuadInMovingNozzle.txt 5 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/QuadrupoleMagnet.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_quadrupole: 2 | 3 | QuadrupoleMagnet.txt 4 | -------------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/QuadrupoleMagnet.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/RangeModulator.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_rmw: 2 | 3 | RangeModulator.txt 4 | ------------------ 5 | 6 | .. literalinclude:: /examples/SpecialComponents/RangeModulator.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/RangeModulator_ConstantBeam.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_rmw_constant: 2 | 3 | RangeModulator_ConstantBeam.txt 4 | ------------------------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/RangeModulator_ConstantBeam.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/RangeModulator_CurrentModulatedBeam.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_rmw_modulated: 2 | 3 | RangeModulator_CurrentModulatedBeam.txt 4 | --------------------------------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/RangeModulator_CurrentModulatedBeam.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/RidgeFilter.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_ridgefilter: 2 | 3 | RidgeFilter.txt 4 | --------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/RidgeFilter.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/RotatingMagnet.rst: -------------------------------------------------------------------------------- 1 | RotatingMagnet.txt 2 | ------------------ 3 | 4 | .. literalinclude:: /examples/SpecialComponents/RotatingMagnet.txt 5 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/UniformElectroMagneticField.rst: -------------------------------------------------------------------------------- 1 | .. _example_special_electromagnet: 2 | 3 | UniformElectroMagneticField.txt 4 | ------------------------------- 5 | 6 | .. literalinclude:: /examples/SpecialComponents/UniformElectroMagneticField.txt 7 | -------------------------------------------------------------------------------- /examples-docs/SpecialComponents/index.rst: -------------------------------------------------------------------------------- 1 | SpecialComponents 2 | ================= 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | CAD 8 | DipoleMagnet 9 | MultiLeafCollimator 10 | MultiLeafCollimator_sequence 11 | MultiWire_Chamber 12 | Propeller_ContinuousRotation 13 | Propeller_StepRotation 14 | Propeller 15 | PurgingMagnet_move 16 | QuadAndDipoleMagnets 17 | QuadInMovingNozzle 18 | QuadrupoleMagnet 19 | RangeModulator_ConstantBeam 20 | RangeModulator_CurrentModulatedBeam 21 | RangeModulator 22 | RidgeFilter 23 | RotatingMagnet 24 | UniformElectroMagneticField 25 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/BoxWithinBox.rst: -------------------------------------------------------------------------------- 1 | BoxWithinBox.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/TimeFeature/BoxWithinBox.txt 5 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/CameraRotateAndZoom.rst: -------------------------------------------------------------------------------- 1 | CameraRotateAndZoom.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/TimeFeature/CameraRotateAndZoom.txt 5 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/ChangingKEFilterByTimeFeature.rst: -------------------------------------------------------------------------------- 1 | ChangingKEFilterByTimeFeature.txt 2 | --------------------------------- 3 | 4 | .. literalinclude:: /examples/TimeFeature/ChangingKEFilterByTimeFeature.txt 5 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/ColorChange.rst: -------------------------------------------------------------------------------- 1 | ColorChange.txt 2 | --------------- 3 | 4 | .. literalinclude:: /examples/TimeFeature/ColorChange.txt 5 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/CylinderGrowingInPhi.rst: -------------------------------------------------------------------------------- 1 | CylinderGrowingInPhi.txt 2 | ------------------------ 3 | 4 | .. literalinclude:: /examples/TimeFeature/CylinderGrowingInPhi.txt 5 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/Darkening.rst: -------------------------------------------------------------------------------- 1 | .. _example_timefeature_darkening: 2 | 3 | Darkening.txt 4 | ------------- 5 | 6 | .. literalinclude:: /examples/TimeFeature/Darkening.txt 7 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/Logo.rst: -------------------------------------------------------------------------------- 1 | Logo.txt 2 | -------- 3 | 4 | .. literalinclude:: /examples/TimeFeature/Logo.txt 5 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/RasterScanOnMovingTarget.rst: -------------------------------------------------------------------------------- 1 | RasterScanOnMovingTarget.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/TimeFeature/RasterScanOnMovingTarget.txt 5 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/RotateResizeRecolor.rst: -------------------------------------------------------------------------------- 1 | RotateResizeRecolor.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/TimeFeature/RotateResizeRecolor.txt 5 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/RotatingCylinderWithPhiCut.rst: -------------------------------------------------------------------------------- 1 | RotatingCylinderWithPhiCut.txt 2 | ----------------------- 3 | 4 | .. literalinclude:: /examples/TimeFeature/RotatingCylinderWithPhiCut.txt 5 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/Rotation.rst: -------------------------------------------------------------------------------- 1 | .. _example_timefeature_rotation: 2 | 3 | Rotation.txt 4 | ------------ 5 | 6 | .. literalinclude:: /examples/TimeFeature/Rotation.txt 7 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/RunRandom_Mode.rst: -------------------------------------------------------------------------------- 1 | .. _example_timefeature_random: 2 | 3 | RunRandom_Mode.txt 4 | ------------------ 5 | 6 | .. literalinclude:: /examples/TimeFeature/RunRandom_Mode.txt 7 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/RunSequential_Mode.rst: -------------------------------------------------------------------------------- 1 | .. _example_timefeature_sequential: 2 | 3 | RunSequential_Mode.txt 4 | ---------------------- 5 | 6 | .. literalinclude:: /examples/TimeFeature/RunSequential_Mode.txt 7 | -------------------------------------------------------------------------------- /examples-docs/TimeFeature/index.rst: -------------------------------------------------------------------------------- 1 | TimeFeature 2 | =========== 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | BoxWithinBox 8 | CameraRotateAndZoom 9 | ChangingKEFilterByTimeFeature 10 | ColorChange 11 | CylinderGrowingInPhi 12 | Darkening 13 | Logo 14 | RasterScanOnMovingTarget 15 | RotateResizeRecolor 16 | RotatingCylinderWithPhiCut 17 | Rotation 18 | RunRandom_Mode 19 | RunSequential_Mode 20 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/UCSF_Beamline_Base.rst: -------------------------------------------------------------------------------- 1 | UCSF_Beamline_Base.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/UCSF_Beamline_Base.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/UCSF_Beamline_Propeller10.rst: -------------------------------------------------------------------------------- 1 | UCSF_Beamline_Propeller10.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/UCSF_Beamline_Propeller10.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/UCSF_Beamline_Propeller15.rst: -------------------------------------------------------------------------------- 1 | UCSF_Beamline_Propeller15.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/UCSF_Beamline_Propeller15.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/UCSF_Beamline_Propeller20.rst: -------------------------------------------------------------------------------- 1 | UCSF_Beamline_Propeller20.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/UCSF_Beamline_Propeller20.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/UCSF_Beamline_Propeller24.rst: -------------------------------------------------------------------------------- 1 | UCSF_Beamline_Propeller24.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/UCSF_Beamline_Propeller24.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/UCSF_DefaultParameters.rst: -------------------------------------------------------------------------------- 1 | UCSF_DefaultParameters.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/UCSF_DefaultParameters.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/UCSF_WaterPhantom.rst: -------------------------------------------------------------------------------- 1 | UCSF_WaterPhantom.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/UCSF_WaterPhantom.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/User_BP_R28_WaterPhantom.rst: -------------------------------------------------------------------------------- 1 | User_BP_R28_WaterPhantom.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/User_BP_R28_WaterPhantom.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/User_Beamline_WC_Viewer.rst: -------------------------------------------------------------------------------- 1 | User_Beamline_WC_Viewer.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/User_Beamline_WC_Viewer.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/User_SOBP24_R28_WaterPhantom.rst: -------------------------------------------------------------------------------- 1 | User_SOBP24_R28_WaterPhantom.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/User_SOBP24_R28_WaterPhantom.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/User_SOBP24_Viewer.rst: -------------------------------------------------------------------------------- 1 | User_SOBP24_Viewer.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/User_SOBP24_Viewer.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/Viewer.rst: -------------------------------------------------------------------------------- 1 | Viewer.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/UCSFETF/Viewer.txt 5 | -------------------------------------------------------------------------------- /examples-docs/UCSFETF/index.rst: -------------------------------------------------------------------------------- 1 | UCSFETF 2 | =========== 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | UCSF_Beamline_Base 8 | UCSF_Beamline_Propeller10 9 | UCSF_Beamline_Propeller15 10 | UCSF_Beamline_Propeller20 11 | UCSF_Beamline_Propeller24 12 | UCSF_DefaultParameters.rst 13 | UCSF_WaterPhantom.rst 14 | User_Beamline_WC_Viewer 15 | User_BP_R28_WaterPhantom 16 | User_SOBP24_R28_WaterPhantom 17 | User_SOBP24_Viewer 18 | Viewer 19 | -------------------------------------------------------------------------------- /examples-docs/VarianceReduction/AmbientDoseEquivalent.rst: -------------------------------------------------------------------------------- 1 | AmbientDoseEquivalent.txt 2 | ------------------------- 3 | 4 | .. literalinclude:: /examples/VarianceReduction/AmbientDoseEquivalent.txt 5 | -------------------------------------------------------------------------------- /examples-docs/VarianceReduction/CrossSectionEnhancement.rst: -------------------------------------------------------------------------------- 1 | CrossSectionEnhancement.txt 2 | ------------------------- 3 | 4 | .. literalinclude:: /examples/VarianceReduction/CrossSectionEnhancement.txt 5 | -------------------------------------------------------------------------------- /examples-docs/VarianceReduction/ForcedInteraction.rst: -------------------------------------------------------------------------------- 1 | ForcedInteraction.txt 2 | ------------------------- 3 | 4 | .. literalinclude:: /examples/VarianceReduction/ForcedInteraction.txt 5 | -------------------------------------------------------------------------------- /examples-docs/VarianceReduction/GeometricalParticleSplit.rst: -------------------------------------------------------------------------------- 1 | GeometricalParticleSplit.txt 2 | ---------------------------- 3 | 4 | .. literalinclude:: /examples/VarianceReduction/GeometricalParticleSplit.txt 5 | -------------------------------------------------------------------------------- /examples-docs/VarianceReduction/ImportanceSampling.rst: -------------------------------------------------------------------------------- 1 | ImportanceSampling.txt 2 | ---------------------- 3 | 4 | .. literalinclude:: /examples/VarianceReduction/ImportanceSampling.txt 5 | -------------------------------------------------------------------------------- /examples-docs/VarianceReduction/ImportanceSamplingMassGeometry.rst: -------------------------------------------------------------------------------- 1 | ImportanceSamplingMassGeometry.txt 2 | ---------------------------------- 3 | 4 | .. literalinclude:: /examples/VarianceReduction/ImportanceSamplingMassGeometry.txt 5 | -------------------------------------------------------------------------------- /examples-docs/VarianceReduction/ImportanceSamplingSecondaryBiasing.rst: -------------------------------------------------------------------------------- 1 | ImportanceSamplingSecondaryBiasing.txt 2 | ---------------------------------- 3 | 4 | .. literalinclude:: /examples/VarianceReduction/ImportanceSamplingSecondaryBiasing.txt 5 | -------------------------------------------------------------------------------- /examples-docs/VarianceReduction/SecondaryBiasing.rst: -------------------------------------------------------------------------------- 1 | .. _example_vr_secondarybiasing: 2 | 3 | SecondaryBiasing.txt 4 | -------------------- 5 | 6 | .. literalinclude:: /examples/VarianceReduction/SecondaryBiasing.txt 7 | -------------------------------------------------------------------------------- /examples-docs/VarianceReduction/WeightWindow.rst: -------------------------------------------------------------------------------- 1 | WeightWindow.txt 2 | ---------------- 3 | 4 | .. literalinclude:: /examples/VarianceReduction/WeightWindow.txt 5 | -------------------------------------------------------------------------------- /examples-docs/VarianceReduction/index.rst: -------------------------------------------------------------------------------- 1 | VarianceReduction 2 | ================= 3 | 4 | .. toctree:: 5 | :maxdepth: 1 6 | 7 | AmbientDoseEquivalent 8 | CrossSectionEnhancement 9 | ForcedInteraction 10 | GeometricalParticleSplit 11 | ImportanceSampling 12 | ImportanceSamplingMassGeometry 13 | ImportanceSamplingSecondaryBiasing 14 | SecondaryBiasing 15 | WeightWindow 16 | -------------------------------------------------------------------------------- /examples/Basic/BatchJob1.txt: -------------------------------------------------------------------------------- 1 | # Demonstrates how to have two separate jobs share everything 2 | # except the seed and output file. 3 | 4 | includeFile = BatchJobShared.txt 5 | 6 | i:Ts/Seed = 1 7 | s:Sc/DoseAtPhantom/OutputFile = "DoseAtPhantomForSeed" + Ts/Seed 8 | -------------------------------------------------------------------------------- /examples/Basic/BatchJob2.txt: -------------------------------------------------------------------------------- 1 | # Demonstrates how to have two separate jobs share everything 2 | # except the seed and output file. 3 | 4 | includeFile = BatchJobShared.txt 5 | 6 | i:Ts/Seed = 2 7 | s:Sc/DoseAtPhantom/OutputFile = "DoseAtPhantomForSeed" + Ts/Seed 8 | -------------------------------------------------------------------------------- /examples/Basic/BoxRotatedAroundItsCorner.txt: -------------------------------------------------------------------------------- 1 | # Example demonsrating a box rotated around its corner 2 | # by placing the box inside of a Group and rotating that group. 3 | 4 | s:Ge/MyGroup/Type = "Group" 5 | s:Ge/MyGroup/Parent = "World" 6 | dc:Ge/MyGroup/RotX = 0. deg 7 | d:Ge/MyGroup/RotY = 0. deg 8 | d:Ge/MyGroup/RotZ = 0. deg 9 | d:Ge/MyGroup/TransZ = -2. m 10 | 11 | s:Ge/MyBox/Type = "TsBox" 12 | s:Ge/MyBox/Material = "G4_WATER" 13 | s:Ge/MyBox/Parent = "MyGroup" 14 | d:Ge/MyBox/HLX = 1.5 m 15 | d:Ge/MyBox/HLY = 1. m 16 | d:Ge/MyBox/HLZ = 1. m 17 | d:Ge/MyBox/TransX = Ge/MyBox/HLX m 18 | d:Ge/MyBox/TransY = Ge/MyBox/HLY m 19 | d:Ge/MyBox/TransZ = Ge/MyBox/HLZ m 20 | dc:Ge/MyBox/RotX = 20. deg 21 | d:Ge/MyBox/RotY = 20. deg 22 | d:Ge/MyBox/RotZ = 20. deg 23 | s:Ge/MyBox/Color = "blue" 24 | s:Ge/MyBox/DrawingStyle = "WireFrame" 25 | 26 | s:Ge/BoxCorner/Type = "TsBox" 27 | s:Ge/BoxCorner/Material = "G4_WATER" 28 | s:Ge/BoxCorner/Parent = "MyBox" 29 | d:Ge/BoxCorner/HLX = .2 m 30 | d:Ge/BoxCorner/HLY = .2 m 31 | d:Ge/BoxCorner/HLZ = .2 m 32 | d:Ge/BoxCorner/TransX = Ge/BoxCorner/HLX - Ge/MyBox/HLX m 33 | d:Ge/BoxCorner/TransY = Ge/BoxCorner/HLY - Ge/MyBox/HLY m 34 | d:Ge/BoxCorner/TransZ = Ge/BoxCorner/HLZ - Ge/MyBox/HLZ m 35 | s:Ge/BoxCorner/Color = "magenta" 36 | s:Ge/BoxCorner/DrawingStyle = "Solid" 37 | 38 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 39 | 40 | s:Gr/ViewA/Type = "OpenGL" 41 | b:Gr/ViewA/IncludeAxes = "True" 42 | d:Gr/ViewA/AxesSize = 4. m 43 | 44 | Ts/UseQt = "True" 45 | -------------------------------------------------------------------------------- /examples/Basic/DistributedSourcePointsInSphere.txt: -------------------------------------------------------------------------------- 1 | s:Ge/World/Material = "G4_W" 2 | d:Ge/World/HLX = 2.0 m 3 | d:Ge/World/HLY = 2.0 m 4 | d:Ge/World/HLZ = 2.0 m 5 | b:Ge/World/Invisible = "True" 6 | 7 | s:Ge/DemoSphere/Type = "TsSphere" 8 | s:Ge/DemoSphere/Parent = "World" 9 | s:Ge/DemoSphere/Material = "Vacuum" 10 | d:Ge/DemoSphere/RMax = 120 mm 11 | 12 | s:Ge/DemoTwistedTubs/Type = "G4TwistedTubs" 13 | #s:Ge/DemoTwistedTubs/Parent = "World" 14 | s:Ge/DemoTwistedTubs/Material = "Vacuum" 15 | d:Ge/DemoTwistedTubs/Twist = 60 deg 16 | d:Ge/DemoTwistedTubs/EndInnerRad = 10 mm 17 | d:Ge/DemoTwistedTubs/EndOuterRad = 15 mm 18 | d:Ge/DemoTwistedTubs/HLZ = 20 mm 19 | d:Ge/DemoTwistedTubs/Phi = 90 deg 20 | s:Ge/DemoTwistedTubs/Color = "brown" 21 | s:Ge/DemoTwistedTubs/DrawingStyle = "FullWireFrame" 22 | 23 | s:So/Example/Type = "Distributed" 24 | s:So/Example/Component = "DemoSphere" 25 | s:So/Example/BeamParticle = "gamma" 26 | d:So/Example/BeamEnergy = 10. keV 27 | u:So/Example/BeamEnergySpread = 0. 28 | ic:So/Example/NumberOfHistoriesInRun = 5 29 | ic:So/Example/NumberOfSourcePoints = 4 30 | bc:So/Example/RedistributePointsOnNewRun = "False" 31 | 32 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 33 | 34 | i:Ts/ShowHistoryCountAtInterval = 100 35 | b:Ts/PauseBeforeQuit = "True" 36 | 37 | s:Gr/ViewA/Type = "OpenGL" 38 | Ts/UseQt = "T" 39 | -------------------------------------------------------------------------------- /examples/Basic/DistributedSourcePointsInSphereGaussian.txt: -------------------------------------------------------------------------------- 1 | s:Ge/World/Material = "G4_W" 2 | d:Ge/World/HLX = 2.0 m 3 | d:Ge/World/HLY = 2.0 m 4 | d:Ge/World/HLZ = 2.0 m 5 | b:Ge/World/Invisible = "True" 6 | 7 | s:Ge/DemoSphere/Type = "TsSphere" 8 | s:Ge/DemoSphere/Parent = "World" 9 | s:Ge/DemoSphere/Material = "G4_WATER" 10 | d:Ge/DemoSphere/RMax = 120 mm 11 | 12 | s:Ge/DemoTwistedTubs/Type = "G4TwistedTubs" 13 | #s:Ge/DemoTwistedTubs/Parent = "World" 14 | s:Ge/DemoTwistedTubs/Material = "Vacuum" 15 | d:Ge/DemoTwistedTubs/Twist = 60 deg 16 | d:Ge/DemoTwistedTubs/EndInnerRad = 10 mm 17 | d:Ge/DemoTwistedTubs/EndOuterRad = 15 mm 18 | d:Ge/DemoTwistedTubs/HLZ = 20 mm 19 | d:Ge/DemoTwistedTubs/Phi = 90 deg 20 | s:Ge/DemoTwistedTubs/Color = "brown" 21 | s:Ge/DemoTwistedTubs/DrawingStyle = "FullWireFrame" 22 | 23 | s:So/Example/Type = "Distributed" 24 | s:So/Example/Component = "DemoSphere" 25 | s:So/Example/BeamParticle = "gamma" 26 | d:So/Example/BeamEnergy = 10. keV 27 | u:So/Example/BeamEnergySpread = 0. 28 | ic:So/Example/NumberOfHistoriesInRun = 5 29 | ic:So/Example/NumberOfSourcePoints = 4 30 | bc:So/Example/RedistributePointsOnNewRun = "False" 31 | s:So/Example/PointDistribution = "Flat" # default to "Flat" 32 | dc:So/Example/PointDistributionSigma = 20. mm 33 | 34 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 35 | 36 | i:Ts/ShowHistoryCountAtInterval = 100 37 | b:Ts/PauseBeforeQuit = "True" 38 | 39 | s:Gr/ViewA/Type = "OpenGL" 40 | Ts/UseQt = "T" 41 | -------------------------------------------------------------------------------- /examples/Basic/DistributedSourcePointsInTwistedTubs.txt: -------------------------------------------------------------------------------- 1 | s:Ge/World/Material = "G4_W" 2 | d:Ge/World/HLX = 2.0 m 3 | d:Ge/World/HLY = 2.0 m 4 | d:Ge/World/HLZ = 2.0 m 5 | b:Ge/World/Invisible = "True" 6 | 7 | s:Ge/DemoSphere/Type = "TsSphere" 8 | #s:Ge/DemoSphere/Parent = "World" 9 | s:Ge/DemoSphere/Material = "Vacuum" 10 | d:Ge/DemoSphere/RMax = 120 mm 11 | 12 | s:Ge/InnerSphere/Type = "TsSphere" 13 | s:Ge/InnerSphere/Parent = "DemoSphere" 14 | s:Ge/InnerSphere/Material = "Vacuum" 15 | d:Ge/InnerSphere/RMax = 100 mm 16 | 17 | s:Ge/DemoTwistedTubs/Type = "G4TwistedTubs" 18 | s:Ge/DemoTwistedTubs/Parent = "World" 19 | s:Ge/DemoTwistedTubs/Material = "Vacuum" 20 | d:Ge/DemoTwistedTubs/Twist = 60 deg 21 | d:Ge/DemoTwistedTubs/EndInnerRad = 10 mm 22 | d:Ge/DemoTwistedTubs/EndOuterRad = 15 mm 23 | d:Ge/DemoTwistedTubs/HLZ = 20 mm 24 | d:Ge/DemoTwistedTubs/Phi = 90 deg 25 | s:Ge/DemoTwistedTubs/Color = "brown" 26 | s:Ge/DemoTwistedTubs/DrawingStyle = "FullWireFrame" 27 | 28 | s:So/Example/Type = "Distributed" 29 | s:So/Example/Component = "DemoTwistedTubs" 30 | s:So/Example/BeamParticle = "gamma" 31 | d:So/Example/BeamEnergy = 10. keV 32 | u:So/Example/BeamEnergySpread = 0. 33 | ic:So/Example/NumberOfHistoriesInRun = 5 34 | ic:So/Example/NumberOfSourcePoints = 4 35 | bc:So/Example/RedistributePointsOnNewRun = "False" 36 | 37 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 38 | 39 | i:Ts/ShowHistoryCountAtInterval = 100 40 | b:Ts/PauseBeforeQuit = "True" 41 | 42 | s:Gr/ViewA/Type = "OpenGL" 43 | Ts/UseQt = "T" 44 | -------------------------------------------------------------------------------- /examples/Basic/EmModelByRegions.txt: -------------------------------------------------------------------------------- 1 | # Demonstrates having electromagnetic model defined in specific regions. 2 | # While only one electromagnetic model can be used in a given TOPAS 3 | # physics list, you are free to define a electromagnetic model in 4 | # a user specific region. 5 | # The em models currently supported are: g4em-livermore, g4em-polarized 6 | # g4em-lowep, g4em-penelope and g4em-standard_opt(0-4) 7 | 8 | # A simple geometry. The material must be G4_WATER. 9 | s:Ge/Target/Parent = "World" 10 | s:Ge/Target/Type = "TsBox" 11 | s:Ge/Target/Material = "G4_WATER" 12 | d:Ge/Target/HLX = 0.5 cm 13 | d:Ge/Target/HLY = 0.5 cm 14 | d:Ge/Target/HLZ = 0.25 cm 15 | s:Ge/Target/Color = "grass" 16 | # Assign a region 17 | s:Ge/Target/AssignToRegionNamed = "target" 18 | 19 | d:Ge/World/HLX = Ge/Target/HLX um 20 | d:Ge/World/HLY = Ge/Target/HLY um 21 | d:Ge/World/HLZ = 1.5 * Ge/Target/HLZ um 22 | s:Ge/World/Material = "G4_WATER" 23 | s:Ge/World/Color = "blue" 24 | 25 | # Start with a physics list 26 | sv:Ph/Default/Modules = 6 "g4em-penelope" "g4h-phy_QGSP_BIC_HP" "g4decay" "g4ion-binarycascade" "g4h-elastic_HP" "g4stopping" 27 | s:Ph/Default/ForRegion/target/ActiveG4EmModelFromModule = "g4em-livermore" 28 | 29 | # Set a source 30 | s:So/Example/Type = "Beam" 31 | s:So/Example/Component = "BeamPosition" 32 | s:So/Example/BeamParticle = "proton" 33 | d:So/Example/BeamEnergy = 80 MeV 34 | u:So/Example/BeamEnergySpread = 0.757504 35 | s:So/Example/BeamPositionDistribution = "None" 36 | s:So/Example/BeamAngularDistribution = "Gaussian" 37 | d:So/Example/BeamAngularCutoffX = 90. deg 38 | d:So/Example/BeamAngularCutoffY = 90. deg 39 | d:So/Example/BeamAngularSpreadX = 0.0032 rad 40 | d:So/Example/BeamAngularSpreadY = 0.0032 rad 41 | i:So/Example/NumberOfHistoriesInRun = 10 42 | 43 | s:Gr/view/Type = "OpenGl" 44 | b:Ts/PauseBeforeQuit = "True" 45 | -------------------------------------------------------------------------------- /examples/Basic/Emittance_Twiss.txt: -------------------------------------------------------------------------------- 1 | includeFile = Emittance_Gaussian.txt 2 | 3 | #!!! You can choose one from these three options 4 | s:So/Example/Distribution = "twiss_gaussian" 5 | #s:So/Example/Distribution = "twiss_kv" 6 | #s:So/Example/Distribution = "twiss_waterbag" 7 | 8 | u:So/Example/AlphaX = 0.2 9 | d:So/Example/BetaX = 600.0 mm # 10 | d:So/Example/EmittanceX = 0.01 mm #we don't multiply pi 11 | 12 | u:So/Example/AlphaY = 2.5 13 | d:So/Example/BetaY = 1400.0 mm 14 | d:So/Example/EmittanceY = 0.02 mm 15 | 16 | #+ twiss gaussian option only 17 | #0.9 means that 90 % particles will be included in ellipse circle 18 | u:So/Example/ParticleFractionX = 0.90 19 | u:So/Example/ParticleFractionY = 0.90 20 | 21 | s:Sc/Beam/OutputFile = "BeamTwiss" 22 | -------------------------------------------------------------------------------- /examples/Basic/ExtraSequence1.txt: -------------------------------------------------------------------------------- 1 | dc:Ge/BeamExitWindow/TransX = 0. cm 2 | dc:Ge/BeamExitWindow/TransY = -200. cm 3 | dc:Ge/BeamExitWindow/TransZ = 0. cm 4 | dc:Ge/BeamExitWindow/RotX = 90. deg 5 | dc:Ge/BeamExitWindow/RotY = 0. deg 6 | dc:Ge/BeamExitWindow/RotZ = 0. deg 7 | 8 | dc:So/Example/BeamEnergy = 50. MeV 9 | ic:So/Example/NumberOfHistoriesInRun = 500 10 | -------------------------------------------------------------------------------- /examples/Basic/ExtraSequence2.txt: -------------------------------------------------------------------------------- 1 | dc:Ge/BeamExitWindow/TransX = 0. cm 2 | dc:Ge/BeamExitWindow/TransY = -100. cm 3 | dc:Ge/BeamExitWindow/TransZ = -100. cm 4 | dc:Ge/BeamExitWindow/RotX = 45. deg 5 | dc:Ge/BeamExitWindow/RotY = 0. deg 6 | dc:Ge/BeamExitWindow/RotZ = 0. deg 7 | 8 | dc:So/Example/BeamEnergy = 100. MeV 9 | ic:So/Example/NumberOfHistoriesInRun = 1000 10 | -------------------------------------------------------------------------------- /examples/Basic/FlatteningFilter.txt: -------------------------------------------------------------------------------- 1 | # This is not any particular actual flattening filter. 2 | # It just demonstrates the general principle of how to 3 | # combine two different kinds of polycones to create 4 | # a shape that no single polycone can represent. 5 | 6 | b:Ge/World/Invisible = "True" 7 | 8 | s:Gr/MyViewA/Type = "OpenGL" 9 | d:Gr/MyViewA/Phi = 45. deg 10 | d:Gr/MyViewA/Theta = 45. deg 11 | 12 | b:Ts/PauseBeforeQuit = "True" 13 | 14 | s:Ge/FlatteningFilter/Type = "Group" 15 | s:Ge/FlatteningFilter/Parent = "World" 16 | #d:Ge/FlatteningFilter/RotX = 90. deg 17 | 18 | # Inner section is implemented as a Solid Polycone 19 | s:Ge/InnerCone/Type = "G4SPolycone" 20 | s:Ge/InnerCone/Parent = "FlatteningFilter" 21 | s:Ge/InnerCone/Material = "G4_Ti" 22 | s:Ge/InnerCone/Color = "grey" 23 | s:Ge/InnerCone/DrawingStyle = "Solid" 24 | dv:Ge/InnerCone/R = 7 0 9 9 6 5 2 0 mm 25 | dv:Ge/InnerCone/Z = 7 0 0 1 2 6 8 10 mm 26 | 27 | # Outer section is implemented as a Hollow Polycone 28 | s:Ge/OuterCone/Type = "G4HPolycone" 29 | s:Ge/OuterCone/Parent = "FlatteningFilter" 30 | s:Ge/OuterCone/Material = "G4_Ti" 31 | s:Ge/OuterCone/Color = "brown" 32 | s:Ge/OuterCone/DrawingStyle = "Solid" 33 | dv:Ge/OuterCone/ROuter = 4 15 15 15 15 mm 34 | dv:Ge/OuterCone/RInner = 4 9 9 10 13 mm 35 | dv:Ge/OuterCone/Z = 4 0 1 2 3 mm 36 | -------------------------------------------------------------------------------- /examples/Basic/OneBox.txt: -------------------------------------------------------------------------------- 1 | # Simplest TOPAS example. 2 | # A box in a beam with EM physics. 3 | 4 | s:Ge/MyBox/Type = "TsBox" 5 | s:Ge/MyBox/Material = "Air" 6 | s:Ge/MyBox/Parent = "World" 7 | d:Ge/MyBox/HLX = 2.5 m 8 | d:Ge/MyBox/HLY = 2. m 9 | d:Ge/MyBox/HLZ = 1. m 10 | d:Ge/MyBox/TransX = 2. m 11 | d:Ge/MyBox/TransY = 0. m 12 | d:Ge/MyBox/TransZ = 0. m 13 | d:Ge/MyBox/RotX = 0. deg 14 | d:Ge/MyBox/RotY = 0. deg 15 | d:Ge/MyBox/RotZ = 0. deg 16 | 17 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 18 | 19 | s:Gr/ViewA/Type = "OpenGL" 20 | i:Gr/ViewA/WindowSizeX = 1024 21 | i:Gr/ViewA/WindowSizeY = 768 22 | b:Gr/ViewA/IncludeAxes = "True" 23 | d:Gr/ViewA/Theta = 55 deg 24 | d:Gr/ViewA/Phi = 20 deg 25 | s:Gr/ViewA/Projection = "Perspective" 26 | d:Gr/ViewA/PerspectiveAngle = 30 deg 27 | u:Gr/ViewA/Zoom = 2. 28 | 29 | b:Ts/PauseBeforeQuit = "True" 30 | -------------------------------------------------------------------------------- /examples/Basic/OneBoxRotate.txt: -------------------------------------------------------------------------------- 1 | # Demonstrates use of includeFile. 2 | # Overrides the RotX value from OneBox.txt 3 | 4 | includeFile = OneBox.txt 5 | 6 | d:Ge/MyBox/RotX = 45. deg 7 | -------------------------------------------------------------------------------- /examples/Basic/OneBoxTranslate.txt: -------------------------------------------------------------------------------- 1 | # Demonstrates use of includeFile. 2 | # Translates box by a value of -0.5 times the value 3 | # of TransX that was inherited from the includeFile. 4 | 5 | includeFile = OneBox.txt 6 | 7 | d:Ge/MyBox/TransX = inheritedValue m * -0.5 8 | -------------------------------------------------------------------------------- /examples/Basic/ParallelWorlds.txt: -------------------------------------------------------------------------------- 1 | # Demonstrates use of parallel worlds. 2 | 3 | d:Ge/World/HLX = 2.0 m 4 | d:Ge/World/HLY = 2.0 m 5 | d:Ge/World/HLZ = 2.0 m 6 | b:Ge/World/Invisible = "True" 7 | 8 | s:Ge/BoxInMassWorld/Parent = "World" 9 | s:Ge/BoxInMassWorld/Type = "TsBox" 10 | sc:Ge/BoxInMassWorld/Material = "G4_WATER" 11 | dc:Ge/BoxInMassWorld/HLX = 7.0 cm 12 | dc:Ge/BoxInMassWorld/HLY = 7.0 cm 13 | dc:Ge/BoxInMassWorld/HLZ = 9.0 cm 14 | sc:Ge/BoxInMassWorld/DrawingStyle = "WireFrame" 15 | ic:Ge/BoxInMassWorld/XBins = 2 16 | ic:Ge/BoxInMassWorld/YBins = 2 17 | ic:Ge/BoxInMassWorld/ZBins = 2 18 | sc:Ge/BoxInMassWorld/Color = "Blue" 19 | 20 | s:Ge/BoxInParallelWorld/Parent = "World" 21 | s:Ge/BoxInParallelWorld/Type = "TsBox" 22 | b:Ge/BoxInParallelWorld/IsParallel = "True" 23 | dc:Ge/BoxInParallelWorld/HLX = 7.0 cm 24 | dc:Ge/BoxInParallelWorld/HLY = 7.0 cm 25 | dc:Ge/BoxInParallelWorld/HLZ = 9.0 cm 26 | sc:Ge/BoxInParallelWorld/DrawingStyle = "WireFrame" 27 | ic:Ge/BoxInParallelWorld/XBins = 3 28 | ic:Ge/BoxInParallelWorld/YBins = 3 29 | ic:Ge/BoxInParallelWorld/ZBins = 3 30 | sc:Ge/BoxInParallelWorld/Color = "Magenta" 31 | 32 | s:Ge/Sphere/Parent = "World" 33 | s:Ge/Sphere/Type = "TsSphere" 34 | b:Ge/Sphere/IsParallel = "True" 35 | dc:Ge/Sphere/RMax = 2.0 cm 36 | sc:Ge/Sphere/DrawingStyle = "WireFrame" 37 | ic:Ge/Sphere/XBins = 3 38 | ic:Ge/Sphere/YBins = 3 39 | ic:Ge/Sphere/ZBins = 3 40 | dc:Ge/Sphere/TransX = 3. cm 41 | dc:Ge/Sphere/TransY = 3. cm 42 | dc:Ge/Sphere/TransZ = 3. cm 43 | sc:Ge/Sphere/Color = "Green" 44 | 45 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 46 | 47 | s:Gr/ViewA/Type = "OpenGL" 48 | 49 | Ts/UseQt = "True" 50 | -------------------------------------------------------------------------------- /examples/Basic/Spectrum.txt: -------------------------------------------------------------------------------- 1 | # Demonstrates use of EnergySpectrum. 2 | # Resulting particles can be seen in ASCIIOutput.phsp 3 | 4 | s:Ge/World/Material = "Vacuum" 5 | 6 | s:So/Example/BeamEnergySpectrumType = "Continuous" 7 | dv:So/Example/BeamEnergySpectrumValues = 3 50. 100. 150. MeV 8 | uv:So/Example/BeamEnergySpectrumWeights = 3 .20 .60 .20 9 | 10 | s:Ge/VacFilm/Type = "TsBox" 11 | s:Ge/VacFilm/Parent = "World" 12 | s:Ge/VacFilm/Material = "Vacuum" 13 | d:Ge/VacFilm/HLX = 50.0 cm 14 | d:Ge/VacFilm/HLY = 50.0 cm 15 | d:Ge/VacFilm/HLZ = 1.0 cm 16 | 17 | s:Sc/PhaseSpaceAtVacFilm/Quantity = "PhaseSpace" 18 | b:Sc/PhaseSpaceAtVacFilm/OutputToConsole = "True" 19 | s:Sc/PhaseSpaceAtVacFilm/Surface = "VacFilm/ZMinusSurface" 20 | s:Sc/PhaseSpaceAtVacFilm/OutputType = "ASCII" # ASCII, Binary or Limited 21 | s:Sc/PhaseSpaceAtVacFilm/OutputFile = "ASCIIOutput" 22 | s:Sc/PhaseSpaceAtVacFilm/IfOutputFileAlreadyExists = "Overwrite" 23 | 24 | s:So/Example/Type = "Beam" 25 | s:So/Example/Component = "BeamPosition" 26 | s:So/Example/BeamParticle = "proton" 27 | s:So/Example/BeamPositionDistribution = "Gaussian" 28 | s:So/Example/BeamPositionCutoffShape = "Ellipse" 29 | d:So/Example/BeamPositionCutoffX = 10. cm 30 | d:So/Example/BeamPositionCutoffY = 10. cm 31 | d:So/Example/BeamPositionSpreadX = 0.65 cm 32 | d:So/Example/BeamPositionSpreadY = 0.65 cm 33 | s:So/Example/BeamAngularDistribution = "Gaussian" 34 | d:So/Example/BeamAngularCutoffX = 90. deg 35 | d:So/Example/BeamAngularCutoffY = 90. deg 36 | d:So/Example/BeamAngularSpreadX = 0.0032 rad 37 | d:So/Example/BeamAngularSpreadY = 0.0032 rad 38 | i:So/Example/NumberOfHistoriesInRun = 1000 39 | 40 | i:Ts/ShowHistoryCountAtInterval = 10 41 | -------------------------------------------------------------------------------- /examples/Brachytherapy/HDRSource.txt: -------------------------------------------------------------------------------- 1 | # # 2 | # Example: HDR source # 3 | # # 4 | # # 5 | # Latest version - May 2021 # 6 | # Author: Francisco Berumen # 7 | # Contact - fberumenm@gmail.com # 8 | # https://doi.org/10.1016/j.brachy.2020.12.007 # 9 | # # 10 | 11 | ##### Import one of the following HDR sources ##### 12 | includeFile = ./HDR/Ir192_TG186.txt 13 | #includeFile = ./HDR/Ir192_MicroSelectronV2.txt 14 | #includeFile = ./HDR/Ir192_Flexisource.txt 15 | 16 | ##### Water phantom of 50 cm side ##### 17 | d:Ge/World/HLX = 25 cm 18 | d:Ge/World/HLY = 25 cm 19 | d:Ge/World/HLZ = 25 cm 20 | s:Ge/World/Material = "G4_WATER" 21 | 22 | ##### Physics ##### 23 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 24 | 25 | ##### Graphics ##### 26 | b:Gr/Enable = "T" 27 | b:Ts/PauseBeforeQuit = "T" 28 | 29 | s:Gr/View/Type = "OpenGL" 30 | u:Gr/View/Zoom = 75. 31 | d:Gr/View/Phi = 20 deg 32 | d:Gr/View/Theta = 90 deg 33 | b:Gr/View/IncludeAxes = "T" 34 | d:Gr/View/AxesSize = 5 mm 35 | -------------------------------------------------------------------------------- /examples/Brachytherapy/HDRSourceInApplicator.txt: -------------------------------------------------------------------------------- 1 | # # 2 | # Example: TG186 source inside the TG186 applicator # 3 | # # 4 | # # 5 | # Latest version - May 2021 # 6 | # Author: Francisco Berumen # 7 | # Contact - fberumenm@gmail.com # 8 | # https://doi.org/10.1016/j.brachy.2020.12.007 # 9 | # # 10 | 11 | ##### Import the source and applicator ##### 12 | includeFile = ./HDR/Ir192_TG186.txt 13 | includeFile = ./HDR/TG186Applicator.txt 14 | 15 | ## Since the TG186 source must be inside the applicator, 16 | ## the parent of the "Capsule" group component (TG186 source) 17 | ## is the "AirCylinder" applicator's geometry component. 18 | s:Ge/Capsule/Parent = "AirCylinder" 19 | 20 | ## See the effect of the shielded applicator with more photons 21 | i:So/Source/NumberOfHistoriesInRun = 150 22 | 23 | ##### Water phantom of 50 cm side ##### 24 | d:Ge/World/HLX = 25 cm 25 | d:Ge/World/HLY = 25 cm 26 | d:Ge/World/HLZ = 25 cm 27 | s:Ge/World/Material = "G4_WATER" 28 | 29 | ##### Physics ##### 30 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 31 | 32 | ##### Graphics ##### 33 | b:Gr/Enable = "T" 34 | b:Ts/PauseBeforeQuit = "T" 35 | 36 | s:Gr/View/Type = "OpenGL" 37 | u:Gr/View/Zoom = 4.5 38 | d:Gr/View/Phi = 90 deg 39 | d:Gr/View/Theta = 91 deg 40 | b:Gr/View/IncludeAxes = "F" 41 | d:Gr/View/AxesSize = 10 cm 42 | -------------------------------------------------------------------------------- /examples/Brachytherapy/README.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples/Brachytherapy/README.pdf -------------------------------------------------------------------------------- /examples/Graphics/NanoMeterScaleTest.txt: -------------------------------------------------------------------------------- 1 | # This example demonstrates an issue that occurs when there 2 | # is a very large zoom factor and how to work around that issue. 3 | # You will see that the display is not exactly centered on the 4 | # desired component, and that, if you try to adjust the Theta or Phi, 5 | # the change is not smooth but instead has discontinuities. 6 | # The issue is resolved if one makes the world invisible, 7 | # as this means the initial extent of the displayed scene only 8 | # contains the nm scale components, so little or no zoom is required. 9 | 10 | d:Ge/World/HLX = 20. cm 11 | d:Ge/World/HLY = 20. cm 12 | d:Ge/World/HLZ = 20. cm 13 | #b:Ge/World/Invisible = "True" # Uncomment to solve zoom issue 14 | 15 | s:Ge/CenterBox/Type = "TsBox" 16 | s:Ge/CenterBox/Material = "Air" 17 | s:Ge/CenterBox/Parent = "World" 18 | d:Ge/CenterBox/HLX = 2.5 nm 19 | d:Ge/CenterBox/HLY = 2. nm 20 | d:Ge/CenterBox/HLZ = 1. nm 21 | s:Ge/CenterBox/Color = "White" 22 | 23 | s:Ge/PlusXBox/Type = "TsBox" 24 | s:Ge/PlusXBox/Material = "Air" 25 | s:Ge/PlusXBox/Parent = "World" 26 | d:Ge/PlusXBox/HLX = 2.5 nm 27 | d:Ge/PlusXBox/HLY = 2. nm 28 | d:Ge/PlusXBox/HLZ = 1. nm 29 | d:Ge/PlusXBox/TransX = 10. nm 30 | s:Ge/PlusXBox/Color = "Blue" 31 | 32 | s:Ge/PlusYBox/Type = "TsBox" 33 | s:Ge/PlusYBox/Material = "Air" 34 | s:Ge/PlusYBox/Parent = "World" 35 | d:Ge/PlusYBox/HLX = 2.5 nm 36 | d:Ge/PlusYBox/HLY = 2. nm 37 | d:Ge/PlusYBox/HLZ = 1. nm 38 | d:Ge/PlusYBox/TransY = 10. nm 39 | s:Ge/PlusYBox/Color = "Red" 40 | 41 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 42 | 43 | s:Gr/ViewA/Type = "OpenGL" 44 | uv:Gr/ViewA/Scale = 3 1000 1000 1000 # Comment out to solve zoom issue 45 | u:Gr/ViewA/Zoom = 40000 # Comment out to solve zoom issue 46 | d:Gr/ViewA/Theta = 45. deg 47 | d:Gr/ViewA/Phi = 45. deg 48 | 49 | s:Gr/ViewA/CenterOn = "PlusYBox" 50 | 51 | b:Ts/PauseBeforeQuit = "True" 52 | -------------------------------------------------------------------------------- /examples/Graphics/QtTest.txt: -------------------------------------------------------------------------------- 1 | # Qt example. 2 | # Parameters marked Changeable with the "c:" syntax appear in GUI 3 | 4 | s:Ge/MyBox/Type = "TsBox" 5 | sc:Ge/MyBox/Material = "G4_WATER" 6 | s:Ge/MyBox/Parent = "World" 7 | dc:Ge/MyBox/HLX = 1.5 m 8 | dc:Ge/MyBox/HLY = 1. m 9 | dc:Ge/MyBox/HLZ = 1. m 10 | dc:Ge/MyBox/TransX = 0. m 11 | dc:Ge/MyBox/TransY = 0. m 12 | dc:Ge/MyBox/TransZ = 1.5 m 13 | dc:Ge/MyBox/RotX = 0. deg 14 | dc:Ge/MyBox/RotY = 0. deg 15 | dc:Ge/MyBox/RotZ = 0. deg 16 | ic:Ge/MyBox/XBins = 1 17 | ic:Ge/MyBox/YBins = 1 18 | ic:Ge/MyBox/ZBins = 1 19 | sc:Ge/MyBox/Color = "blue" 20 | sc:Ge/MyBox/DrawingStyle = "WireFrame" 21 | bc:Ge/MyBox/Invisible = "False" 22 | 23 | s:So/Therapy/Type = "Beam" 24 | sc:So/Therapy/Component = "BeamPosition" 25 | sc:So/Therapy/BeamParticle = "e-" 26 | dc:So/Therapy/BeamEnergy = 169.23 MeV 27 | uc:So/Therapy/BeamEnergySpread = 0.757504 28 | sc:So/Therapy/BeamPositionDistribution = "Gaussian" 29 | sc:So/Therapy/BeamPositionCutoffShape = "Ellipse" 30 | dc:So/Therapy/BeamPositionCutoffX = 10. cm 31 | dc:So/Therapy/BeamPositionCutoffY = 10. cm 32 | dc:So/Therapy/BeamPositionSpreadX = 0.65 cm 33 | dc:So/Therapy/BeamPositionSpreadY = 0.65 cm 34 | sc:So/Therapy/BeamAngularDistribution = "Gaussian" 35 | dc:So/Therapy/BeamAngularCutoffX = 90. deg 36 | dc:So/Therapy/BeamAngularCutoffY = 90. deg 37 | dc:So/Therapy/BeamAngularSpreadX = 0.0032 rad 38 | dc:So/Therapy/BeamAngularSpreadY = 0.0032 rad 39 | ic:So/Therapy/NumberOfHistoriesInRun = 10 40 | 41 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 42 | 43 | s:Gr/ViewA/Type = "OpenGL" 44 | 45 | Ts/UseQt = "True" 46 | -------------------------------------------------------------------------------- /examples/MVLinac/Jaws.txt: -------------------------------------------------------------------------------- 1 | # Jaws for Siemens Oncor: Uses TOPAS component Jaws 2 | # Reference for geometry: Jabbari et al, J Med Signal Sens 3(3):172-179 3 | 4 | ############################# Parameter Descriptions ################################# 5 | # SAD: Source axis distance (nominal distance from x-ray target to gantry rotation axis) 6 | # SourceToUpstreamSurfaceDistance: Distance from x-ray target to jaw 7 | # PositiveFieldSetting: Positive jaw position projected to isocenter 8 | # NegativeFieldSetting: NegativeFieldSetting <= PositiveFieldSetting 9 | ####################################################################################### 10 | 11 | includeFile = LinacDefaults.txt #Values in LinacDafaults.txt may be overriden 12 | 13 | dc:Ge/Jaw/PositiveFieldSetting = 20 cm 14 | dc:Ge/Jaw/NegativeFieldSetting = -20 cm 15 | 16 | s:Ge/Jaw/Parent = "IEC_B" 17 | s:Ge/Jaw/Type = "TsJaws" 18 | s:Ge/Jaw/Material = "G4_W" 19 | 20 | d:Ge/Jaw/LX = 20. cm # Actual jaw width along JawTravelAxis 21 | d:Ge/Jaw/LY = 20. cm # Actual jaw length perpendicular to JawTravelAxis 22 | d:Ge/Jaw/LZ = 7.80 cm # Jaw thickness along IEC Zb axis 23 | dc:Ge/Jaw/SourceToUpstreamSurfaceDistance = 19.73 cm #Distance from x-ray target to jaw 24 | d:Ge/Jaw/SAD = Ge/SAD cm 25 | 26 | d:Ge/Jaw/DistSourceToSAD = Ge/Jaw/SAD - Ge/Jaw/SourceToUpstreamSurfaceDistance cm 27 | d:Ge/Jaw/HalfThickness = 0.5 * Ge/Jaw/LZ cm 28 | d:Ge/Jaw/TransZ = Ge/Jaw/DistSourceToSAD - Ge/Jaw/HalfThickness cm 29 | 30 | d:Ge/Jaw/TravelAxisX = 0. deg # Constant to help remember angle for X Axis Travel 31 | d:Ge/Jaw/TravelAxisY = 90. deg # Constant to help remember angle for Y Axis Travel 32 | d:Ge/Jaw/RotZ = Ge/Jaw/TravelAxisX deg # Set to one of the above two constants 33 | 34 | s:Ge/Jaw/DrawingStyle = "Solid" 35 | -------------------------------------------------------------------------------- /examples/MVLinac/LinacDefaults.txt: -------------------------------------------------------------------------------- 1 | # The LinacDefaults parameter control file is the final includeFile in the chain 2 | # Parameters provided in this file are intended to be overridden 3 | # See FullTxHead.txt, FixedTxHead.txt, and Field.txt 4 | # 5 | ############################# Parameter Descriptions ################################# 6 | # Linac geometry fixed components 7 | # SAD: Source axis distance (distance from nominal source position to isocenter) 8 | ####################################################################################### 9 | 10 | d:Ge/SAD = 100. cm 11 | -------------------------------------------------------------------------------- /examples/MVLinac/ScoreEnergyFluence.txt: -------------------------------------------------------------------------------- 1 | # Scorer - Energy fluence distribution on plane through isocenter 2 | 3 | #################### Key Parameters In ScoreEnergyFluence.txt ######################## 4 | # HLX/Y/Z: Half lengths of voxels used for scoring 5 | # X/YBins: Number of bins in IEC_G Xg and Yg 6 | # TransZ: Distance from isocenter to center of scoring region along IEC_G Zg 7 | ####################################################################################### 8 | 9 | s:Sc/EnergyFluence/Quantity = "EnergyFluence" 10 | s:Sc/EnergyFluence/Component= "Isocenter" 11 | s:Sc/EnergyFluence/IfOutputFileAlreadyExists = "Exit" # "Exit", "Overwrite" or "Increment" 12 | s:Sc/EnergyFluence/OutputType = "binary" 13 | 14 | # Isocenter 15 | s:Ge/Isocenter/Parent = "IEC_G" 16 | s:Ge/Isocenter/Type = "TsBox" 17 | s:Ge/Isocenter/Material = "air" 18 | d:Ge/Isocenter/HLX = 30 cm 19 | d:Ge/Isocenter/HLY = 30 cm 20 | d:Ge/Isocenter/HLZ = 0.05 cm 21 | i:Ge/Isocenter/XBins = 60 22 | i:Ge/Isocenter/YBins = 60 23 | d:Ge/Isocenter/TransZ = 0 cm 24 | s:Ge/Isocenter/DrawingStyle = "Solid" 25 | s:Ge/Isocenter/Color = "skyblue" 26 | 27 | -------------------------------------------------------------------------------- /examples/MVLinac/ScoreEnergySpectrum.txt: -------------------------------------------------------------------------------- 1 | # Scorer - Energy spectrum in 10 cm x 10 cm region at isocenter 2 | 3 | #################### Key Parameters In ScoreEnergySpectrum.txt ######################## 4 | # Ebins: Number of energy bins to be scored 5 | # EBinMin/Max: Minimum and maximum energy to be scored 6 | # EBinLog: Scoring bins logarithmically spaced if true, linearily spaced if false 7 | # HLX/Y/Z: Half lengths of voxels used for scoring 8 | # X/YBins: Number of bins in IEC_G Xg and Yg 9 | # TransZ: Distance from isocenter to center of scoring region along IEC_G Zg 10 | ####################################################################################### 11 | 12 | s:Sc/EnergySpectrum/Quantity = "Fluence" 13 | s:Sc/EnergySpectrum/Component= "Isocenter" 14 | s:Sc/EnergySpectrum/IfOutputFileAlreadyExists = "Exit" # "Exit", "Overwrite" or "Increment" 15 | s:Sc/EnergySpectrum/OutputType = "CSV" 16 | 17 | sv:Sc/EnergySpectrum/OnlyIncludeParticlesNamed = 1 "gamma" 18 | 19 | i:Sc/EnergySpectrum/EBins = 50 20 | d:Sc/EnergySpectrum/EBinMin = 0 MeV 21 | d:Sc/EnergySpectrum/EBinMax = 10 MeV 22 | # If you need log scale... 23 | #b:Sc/EnergySpectrum/EBinLog = “True” 24 | 25 | # Isocenter scoring volume (thin plane for scoring spectrum) 26 | s:Ge/Isocenter/Parent = "IEC_G" 27 | s:Ge/Isocenter/Type = "TsBox" 28 | s:Ge/Isocenter/Material = "air" 29 | d:Ge/Isocenter/HLX = 5 cm 30 | d:Ge/Isocenter/HLY = 5 cm 31 | d:Ge/Isocenter/HLZ = 0.01 cm 32 | i:Ge/Isocenter/XBins = 1 33 | i:Ge/Isocenter/YBins = 1 34 | d:Ge/Isocenter/TransZ = 0 cm 35 | s:Ge/Isocenter/DrawingStyle = "Solid" 36 | s:Ge/Isocenter/Color = "skyblue" 37 | 38 | 39 | -------------------------------------------------------------------------------- /examples/MVLinac/ScorePhaseSpace.txt: -------------------------------------------------------------------------------- 1 | # Phase space scored on plane perpendicular to beam axis Zg 2 | 3 | ##################### Key Parameters In ScorePhaseSpace.txt ########################## 4 | # Parameters marked with "^" are set to be changeable in the TOPAS GUI 5 | # ^Pos: Distance along beam axis Zg from the nominal target position (defined by SAD) 6 | # HLX/Y/Z: Half lengths of voxels used for scoring 7 | # X/YBins: Number of bins in IEC_G Xg and Yg 8 | # TransX/Y/Z: Distance from IEC_G origin to center of scoring region in Xg, Yg, Zg 9 | # RotX/Y/Z: Rotation of scoring region in Xg, Yg, Zg 10 | ###################################################################################### 11 | 12 | includeFile = LinacDefaults.txt #Values in LinacDafaults.txt overriden in Field.txt 13 | 14 | s:Ge/VacFilm/Type = "TsBox" 15 | s:Ge/VacFilm/Parent = "IEC_G" 16 | s:Ge/VacFilm/Material = "G4_AIR" 17 | d:Ge/VacFilm/HLX = 10.0 cm 18 | d:Ge/VacFilm/HLY = 10.0 cm 19 | d:Ge/VacFilm/HLZ = 0.05 cm 20 | d:Ge/VacFilm/TransX = 0. cm 21 | d:Ge/VacFilm/TransY = 0. cm 22 | dc:Ge/VacFilm/Pos = 19.0 cm 23 | d:Ge/VacFilm/TransZ = Ge/SAD - Ge/VacFilm/Pos cm 24 | d:Ge/VacFilm/RotX = 0. deg 25 | d:Ge/VacFilm/RotY = 0. deg 26 | d:Ge/VacFilm/RotZ = 0. deg 27 | s:Ge/VacFilm/Color = "skyblue" 28 | 29 | s:Sc/PhaseSpaceAtVacFilm/Quantity = "PhaseSpace" 30 | b:Sc/PhaseSpaceAtVacFilm/OutputToConsole = "False" 31 | s:Sc/PhaseSpaceAtVacFilm/Surface = "VacFilm/ZPlusSurface" 32 | s:Sc/PhaseSpaceAtVacFilm/OutputType = "ASCII" # ASCII, Binary, Limited or ROOT 33 | s:Sc/PhaseSpaceAtVacFilm/IfOutputFileAlreadyExists = "Exit" # "Exit", "Overwrite" or "Increment" 34 | s:Sc/PhaseSpaceAtVacFilm/OutputFile = "PhaseSpaceFixed" 35 | i:Sc/PhaseSpaceAtVacFilm/OutputBufferSize = 1000 36 | 37 | -------------------------------------------------------------------------------- /examples/MVLinac/TestComponent.txt: -------------------------------------------------------------------------------- 1 | # Parameter control file for testing individual components 2 | # Components are displayed in the GUI 3 | b:Gr/Enable = "True" 4 | b:Ts/UseQT = "True" 5 | 6 | # Components are situated relative to the SAD 7 | # For viewing components in the GUI, set SAD small, i.e., to 0 cm 8 | # Note: SAD needs to be set properly for jaw and MLC leaf positions, i.e., to 100 cm 9 | d:Ge/SAD = 0. cm 10 | #d:Ge/SAD = 100. cm 11 | 12 | # Comment out includeFile files that you want to be left out of the GUI 13 | includeFile = Target.txt 14 | includeFile = PrimaryCollimator.txt 15 | #includeFile = Flattener6MV.txt #Comment out at least one of the flatteners 16 | includeFile = Flattener18MV.txt #Comment out at least one of the flatteners 17 | #includeFile = Monitor.txt 18 | #includeFile = Jaws.txt #Comment out at least one of the secondary collimators 19 | #includeFile = MLC.txt #Comment out at least one of the secondary collimators 20 | #includeFile = WaterBox.txt #Comment out at least one of the dose scoring regions 21 | #includeFile = WaterPhantom.txt #Comment out at least one of the dose scoring regions 22 | 23 | 24 | -------------------------------------------------------------------------------- /examples/MVLinac/VRT_1.txt: -------------------------------------------------------------------------------- 1 | # This is the top-level TOPAS parameter control file. The following files are all also read to set the simulation parameters. 2 | 3 | includeFile = MainTxHead.txt 4 | 5 | s:Sc/phaseSpace/OutputFile = "particleSplit" 6 | 7 | # Activate VRT 8 | b:Vr/UseVarianceReduction = "True" 9 | 10 | # Uniform split 11 | b:Vr/ParticleSplit1/Active = "True" 12 | s:Vr/ParticleSplit/Type = "secondarybiasing" 13 | svc:Vr/ParTicleSplit/ForRegion/target/processesNamed = 1 "eBrem" 14 | uvc:Vr/ParticleSplit/ForRegion/target/SplitNumber = 1 1.0 15 | dv:Vr/ParticleSplit/ForRegion/target/MaximumEnergies = 1 10.0 MeV 16 | 17 | bc:Vr/ParticleSplit/UseDirectionalSplitting = "False" 18 | d:Vr/ParticleSplit/TransX = 0 cm 19 | d:Vr/ParticleSplit/TransY = 0 cm 20 | dc:Vr/ParticleSplit/TransZ = 0 cm 21 | dc:Vr/ParticleSplit/RMax = 10 cm 22 | 23 | ic:So/electronBeam/NumberOfHistoriesInRun = 100 24 | 25 | i:Ts/ShowHistoryCountAtInterval = 100 26 | b:Ts/ShowCPUTime = "True" 27 | 28 | -------------------------------------------------------------------------------- /examples/MVLinac/VRT_3.txt: -------------------------------------------------------------------------------- 1 | includeFile = VRT_2.txt 2 | 3 | b:Sc/phaseSpace/KillAfterPhaseSpace = "True" 4 | Sc/phaseSpace/OutputFile = "limitRegion" 5 | 6 | s:Ge/VrtParallelWorld/Parent = "World" 7 | s:Ge/VrtParallelWorld/Type = "TsBox" 8 | b:Ge/VrtParallelWorld/IsParallel = "True" 9 | d:Ge/VrtParallelWorld/HLX = Ge/World/HLX cm 10 | d:Ge/VrtParallelWorld/HLY = Ge/World/HLY cm 11 | d:Ge/VrtParallelWorld/HLZ = Ge/World/HLZ cm 12 | 13 | s:Ge/impCell1/Parent = "VrtParallelWorld" 14 | s:Ge/impCell1/Type = "TsBox" 15 | b:Ge/impCell1/IsParallel = "True" 16 | d:Ge/impCell1/HLX = Ge/World/HLX cm 17 | d:Ge/impCell1/HLY = Ge/World/HLY cm 18 | d:Ge/impCell1/HLZ = Ge/World/HLZ cm 19 | 20 | d:Ge/impCell2/PhiStart = 0. deg 21 | d:Ge/impCell2/PhiTotal = 360 deg 22 | d:Ge/impCell2/RotX = 0. deg 23 | d:Ge/impCell2/RotY = 0. deg 24 | d:Ge/impCell2/RotZ = 45 deg 25 | d:Ge/impCell2/TransX = 0. mm 26 | d:Ge/impCell2/TransY = 0. mm 27 | d:Ge/impCell2/TransZ = 0. mm 28 | dv:Ge/impCell2/ROuter = 4 Ge/World/HLX Ge/World/HLX Ge/World/HLX Ge/World/HLX mm 29 | dv:Ge/impCell2/RInner = 4 240 240 45 45 mm 30 | dv:Ge/impCell2/Z = 4 -400 803 896 Ge/World/HLZ mm 31 | i:Ge/impCell2/NSides = 4 32 | s:Ge/impCell2/Parent = "impCell1" 33 | s:Ge/impCell2/Type = "G4HPolyhedra" 34 | s:Ge/impCell2/Color = "transparentred" 35 | s:Ge/impCell2/DrawingStyle = "Solid" 36 | b:Ge/impCell2/IsParallel = "True" 37 | 38 | iv:Gr/Color/TransparentRed = 4 255 0 0 100 39 | 40 | # Importance sampling 41 | b:Vr/ImportanceSampling/Active = "true" 42 | sv:Vr/ImportanceSampling/ParticleName = 2 "gamma" "e-" 43 | s:Vr/ImportanceSampling/Component = "VrtParallelWorld" 44 | sv:Vr/ImportanceSampling/SubComponents = 2 "impCell1" "impCell2" 45 | s:Vr/ImportanceSampling/Type = "ImportanceSampling" 46 | uvc:Vr/ImportanceSampling/ImportanceValues = 2 1 1 47 | 48 | b:Ts/ShowCPUTime = "True" 49 | 50 | -------------------------------------------------------------------------------- /examples/MVLinac/WaterBox.txt: -------------------------------------------------------------------------------- 1 | # Rectangular parallelopiped filled with water, aligned with IEC fixed Z axis Zf 2 | ####################################################################################### 3 | 4 | includeFile = LinacDefaults.txt #Values in LinacDafaults.txt may be overriden 5 | 6 | s:Ge/WaterPhantom/Parent = "IEC_S" 7 | s:Ge/WaterPhantom/Type = "TsBox" 8 | s:Ge/WaterPhantom/Material = "G4_WATER" 9 | d:Ge/WaterPhantom/HLX = 20. cm 10 | d:Ge/WaterPhantom/HLY = 20. cm 11 | d:Ge/WaterPhantom/HLZ = 20. cm 12 | i:Ge/WaterPhantom/XBins = 1 13 | i:Ge/WaterPhantom/YBins = 1 14 | i:Ge/WaterPhantom/ZBins = 1 15 | d:Ge/WaterPhantom/TransZ = -20. cm 16 | s:Ge/WaterPhantom/DrawingStyle = "Solid" 17 | s:Ge/WaterPhantom/Color = "skyblue" 18 | -------------------------------------------------------------------------------- /examples/MVLinac/WaterPhantom.txt: -------------------------------------------------------------------------------- 1 | # Rectangular parallelopiped filled with water, aligned with IEC fixed Z axis Zf. 2 | # WaterPhantom has voxels for scoring. 3 | ####################################################################################### 4 | 5 | includeFile = LinacDefaults.txt #Values in LinacDafaults.txt overriden in Field.txt 6 | 7 | # Scorer - Dose distribution in 40 cm x 40 cm x 40 cm water box at 100 cm SSD 8 | s:Sc/Dose/Quantity = "DoseToWater" 9 | s:Sc/Dose/Component = "WaterPhantom" 10 | s:Sc/Dose/IfOutputFileAlreadyExists = "Exit" # "Exit", "Overwrite" or "Increment" 11 | s:Sc/Dose/OutputType = "CSV" 12 | 13 | 14 | # Isocenter scoring volume (thin plane for scoring fluence) 15 | s:Ge/WaterPhantom/Parent = "IEC_S" 16 | s:Ge/WaterPhantom/Type = "TsBox" 17 | s:Ge/WaterPhantom/Material = "G4_WATER" 18 | d:Ge/WaterPhantom/HLX = 20. cm 19 | d:Ge/WaterPhantom/HLY = 20. cm 20 | d:Ge/WaterPhantom/HLZ = 20. cm 21 | i:Ge/WaterPhantom/XBins = 80 22 | i:Ge/WaterPhantom/YBins = 80 23 | i:Ge/WaterPhantom/ZBins = 80 24 | d:Ge/WaterPhantom/TransZ = -20. cm 25 | s:Ge/WaterPhantom/DrawingStyle = "Solid" 26 | s:Ge/WaterPhantom/Color = "skyblue" 27 | -------------------------------------------------------------------------------- /examples/Nozzle/ApertureFileIn.ap: -------------------------------------------------------------------------------- 1 | 9 2 | -23.5, -20 3 | -20., -21.2 4 | -2, -20.5 5 | 13.5, -14.2 6 | 15.1, 7.5 7 | 12.5, 21.3 8 | 10.1, 24.2 9 | -3.6, 8.3 10 | -21.5, 2 11 | -------------------------------------------------------------------------------- /examples/Nozzle/CompensatorFileIn.rc: -------------------------------------------------------------------------------- 1 | SomeCompensatorFile DO NOT FABRICATE! 2 | 7 3 | 0.0 0.0 0.0 0.0 4 | 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 5 | 0.46188 6 | 4 0.4 -0.6 1.1 7 | 0.2 0.5 0.6 0.4 8 | 5 -0.4 0.8 0.7536 9 | 0.55 0.6 0.65 0.7 0.4 10 | 7 0.4 -1.0 0.4072 11 | 0.7 0.78 0.8 0.8 0.8 0.6 0.4 12 | 7 -0.4 1.2 0.0608 13 | 0.7 0.78 0.8 0.8 0.8 0.6 0.4 14 | 6 0.4 -1.0 -0.2856 15 | 0.5 0.6 0.66 0.8 0.8 0.6 16 | 5 -0.4 0.8 -0.632 17 | 0.5 0.6 0.7 0.7 0.5 18 | 2 0.4 -0.2 -0.9784 19 | 0.4 0.5 20 | 0 21 | -------------------------------------------------------------------------------- /examples/Nozzle/CompensatorFileInRowsDepths.rc: -------------------------------------------------------------------------------- 1 | 7 2 | 25.4 3 | 11.7318 4 | 4 10.16 -15.24 27.94 5 | 5.08 12.7 15.24 10.16 6 | 5 -10.16 20.32 19.1414 7 | 13.97 15.24 16.51 17.78 10.16 8 | 7 10.16 -25.4 10.3429 9 | 17.78 19.812 20.32 20.32 20.32 15.24 10.16 10 | 7 -10.16 30.48 1.54432 11 | 17.78 19.812 20.32 20.32 20.32 15.24 10.16 12 | 6 10.16 -25.4 -7.25424 13 | 12.7 15.24 16.764 20.32 20.32 15.24 14 | 5 -10.16 20.32 -16.0528 15 | 12.7 15.24 17.78 17.78 12.7 16 | 2 10.16 -5.08 -24.8514 17 | 10.16 12.7 18 | 0 0 -------------------------------------------------------------------------------- /examples/Nozzle/RasterScanningPattern.txt: -------------------------------------------------------------------------------- 1 | # Defines a raster scanning pattern used in some demonstrations. 2 | 3 | includeFile = ScanningNozzle.txt 4 | 5 | # Time Features for Scanning Magnets 6 | d:Ge/BFieldX_max = 0.15 tesla 7 | d:Ge/BFieldX_min = Ge/BFieldX_max tesla * -1.0 8 | d:Ge/BFieldX_range = Ge/BFieldX_max tesla * 2.0 9 | 10 | s:Tf/BField2nd/Function = "Step" 11 | dv:Tf/BField2nd/Times = 2 125.0 250.0 ms 12 | dv:Tf/BField2nd/Values = 2 Tf/BField2ndLeft/Value Tf/BField2ndRight/Value tesla 13 | 14 | s:Tf/BField2ndLeft/Function = "Linear tesla" 15 | d:Tf/BField2ndLeft/RepetitionInterval = 125.0 ms 16 | d:Tf/BField2ndLeft/Rate = 0.0024 tesla/ms 17 | d:Tf/BField2ndLeft/StartValue = Ge/BFieldX_min tesla 18 | 19 | s:Tf/BField2ndRight/Function = "Linear tesla" 20 | d:Tf/BField2ndRight/RepetitionInterval = 125.0 ms 21 | d:Tf/BField2ndRight/Rate = -0.0024 tesla/ms 22 | d:Tf/BField2ndRight/StartValue = Ge/BFieldX_max tesla 23 | 24 | s:Tf/BField1st/Function = "Step" 25 | dv:Tf/BField1st/Times = 4 0.25 0.5 0.75 1.0 s 26 | dv:Tf/BField1st/Values = 4 -0.105 -0.035 0.035 0.105 tesla 27 | 28 | d:Ge/Dipole1/MagneticFieldStrength = Tf/BField1st/Value tesla 29 | d:Ge/Dipole2/MagneticFieldStrength = Tf/BField2nd/Value tesla 30 | -------------------------------------------------------------------------------- /examples/Nozzle/ScanningStationaryTarget.txt: -------------------------------------------------------------------------------- 1 | # Use scanning nozzle to paint stationary target 2 | 3 | includeFile = RasterScanningPattern.txt TargetInWaterPhantom.txt Viewer.txt 4 | 5 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 6 | 7 | b:Ts/PauseBeforeQuit = "False" 8 | 9 | i:So/Example/NumberOfHistoriesInRun = 5 10 | d:So/Example/BeamEnergy = 145.00 MeV 11 | 12 | d:Tf/TimelineEnd = 1 s 13 | i:Tf/NumberOfSequentialTimes = 100 14 | 15 | -------------------------------------------------------------------------------- /examples/Nozzle/ScanningTargetMovingHorizontal.txt: -------------------------------------------------------------------------------- 1 | # Use scanning nozzle to paint target that is moving horizontally 2 | 3 | includeFile = RasterScanningPattern.txt TargetInWaterPhantom.txt Viewer.txt 4 | 5 | i:Tf/Verbosity = 1 6 | 7 | sv:Ph/Default/Modules = 1 "g4em-standard_opt0" 8 | 9 | d:Ge/X_max = 1.5 cm 10 | d:Ge/X_min = Ge/X_max cm * -1.0 11 | d:Ge/X_range = Ge/X_max cm * 2.0 12 | 13 | # 1. Motion for Target 14 | s:Tf/HorizontalMoveSine/Function = "Sine" 15 | d:Tf/HorizontalMoveSine/RepetitionInterval = 1.0 s 16 | d:Tf/HorizontalMoveSine/Rate = 0.36 deg/ms 17 | d:Tf/HorizontalMoveSine/StartValue = 0.0 deg 18 | 19 | d:Tf/HorizontalMove/Value = 2.0 cm * Tf/HorizontalMoveSine/Value 20 | d:Tf/HorizontalScan/Value = 0.15 tesla * Tf/HorizontalMoveSine/Value 21 | 22 | # 2. Compensated BField 23 | d:Tf/BField2ndTrackingField/Value = Tf/HorizontalScan/Value + Tf/BField2nd/Value tesla 24 | 25 | i:Tf/NumberOfSequentialTimes = 100 26 | d:Tf/TimelineEnd = 1 s 27 | 28 | d:Ge/PlaneAtR80/TransX = Tf/HorizontalMove/Value cm 29 | d:Ge/Dipole2/MagneticFieldStrength = Tf/BField2ndTrackingField/Value tesla 30 | 31 | Ts/UseQt = "True" -------------------------------------------------------------------------------- /examples/Nozzle/ScatteringNozzle_run.txt: -------------------------------------------------------------------------------- 1 | # Use scattering nozzle to generate spread out Bragg peak 2 | 3 | includeFile = ScatteringNozzle.txt TsAnalysisWaterPhantom.txt 4 | 5 | d:Ge/RMW_1/RotZ = Tf/RMW_Rotation/Value deg 6 | 7 | i:So/Example/NumberOfHistoriesInRun = 3 8 | 9 | d:Tf/TimelineEnd = 100.0 ms 10 | i:Tf/NumberOfSequentialTimes = 100 11 | 12 | s:Tf/RMW_Rotation/Function = "Linear deg" 13 | d:Tf/RMW_Rotation/Rate = 3.6 deg/ms 14 | d:Tf/RMW_Rotation/StartValue = 0.0 deg 15 | d:Tf/RMW_Rotation/RepetitionInterval = 100. ms 16 | 17 | b:Ts/PauseBeforeQuit = "False" 18 | i:Ts/ShowHistoryCountAtInterval = 0 19 | 20 | # Setting first scatterers: 21 | s:Tf/Scatterer1/L1/Function = "Step" 22 | dv:Tf/Scatterer1/L1/Times = 5 20 40 60 80 100 ms 23 | dv:Tf/Scatterer1/L1/Values = 5 Ge/Scatterer1/RotZ_OutOfBeam Ge/Scatterer1/RotZ_InBeam Ge/Scatterer1/RotZ_OutOfBeam Ge/Scatterer1/RotZ_InBeam Ge/Scatterer1/RotZ_OutOfBeam deg 24 | 25 | s:Tf/Scatterer1/L2/Function = "Step" 26 | dv:Tf/Scatterer1/L2/Times = 2 30 100 ms 27 | dv:Tf/Scatterer1/L2/Values = 2 Ge/Scatterer1/RotZ_InBeam Ge/Scatterer1/RotZ_OutOfBeam deg 28 | 29 | s:Tf/Scatterer1/L3/Function = "Step" 30 | dv:Tf/Scatterer1/L3/Times = 4 20 40 80 100 ms 31 | dv:Tf/Scatterer1/L3/Values = 4 Ge/Scatterer1/RotZ_InBeam Ge/Scatterer1/RotZ_OutOfBeam Ge/Scatterer1/RotZ_InBeam Ge/Scatterer1/RotZ_OutOfBeam deg 32 | 33 | Ge/Scatterer1/Lollipop1 = Tf/Scatterer1/L1/Value deg 34 | Ge/Scatterer1/Lollipop2 = Tf/Scatterer1/L2/Value deg 35 | Ge/Scatterer1/Lollipop3 = Tf/Scatterer1/L3/Value deg 36 | 37 | # Setting second scatterer: 38 | s:Tf/Scatterer2/Function = "Step" 39 | dv:Tf/Scatterer2/Times = 2 50 100 ms 40 | dv:Tf/Scatterer2/Values = 2 Ge/Scatterer2/RotZForS2 Ge/Scatterer2/RotZForS1 deg 41 | 42 | d:Ge/Scatterer2/Holder/RotZ = Tf/Scatterer2/Value deg 43 | 44 | # Show time feature steps on console 45 | i:Tf/Verbosity = 1 46 | -------------------------------------------------------------------------------- /examples/Nozzle/ScatteringNozzle_run_QtTest.txt: -------------------------------------------------------------------------------- 1 | # Use scattering nozzle to generate spread out Bragg peak 2 | 3 | includeFile = ScatteringNozzle_QtTest.txt TsAnalysisWaterPhantom.txt 4 | 5 | d:Ge/RMW_1/RotZ = Tf/RMW_Rotation/Value deg 6 | 7 | i:So/Example/NumberOfHistoriesInRun = 3 8 | 9 | d:Tf/TimelineEnd = 100.0 ms 10 | i:Tf/NumberOfSequentialTimes = 100 11 | 12 | s:Tf/RMW_Rotation/Function = "Linear deg" 13 | d:Tf/RMW_Rotation/Rate = 3.6 deg/ms 14 | d:Tf/RMW_Rotation/StartValue = 0.0 deg 15 | d:Tf/RMW_Rotation/RepetitionInterval = 100. ms 16 | 17 | i:Ts/ShowHistoryCountAtInterval = 0 18 | 19 | # Setting first scatterers: 20 | s:Tf/Scatterer1/L1/Function = "Step" 21 | dv:Tf/Scatterer1/L1/Times = 5 20 40 60 80 100 ms 22 | dv:Tf/Scatterer1/L1/Values = 5 Ge/Scatterer1/RotZ_OutOfBeam Ge/Scatterer1/RotZ_InBeam Ge/Scatterer1/RotZ_OutOfBeam Ge/Scatterer1/RotZ_InBeam Ge/Scatterer1/RotZ_OutOfBeam deg 23 | 24 | s:Tf/Scatterer1/L2/Function = "Step" 25 | dv:Tf/Scatterer1/L2/Times = 2 30 100 ms 26 | dv:Tf/Scatterer1/L2/Values = 2 Ge/Scatterer1/RotZ_InBeam Ge/Scatterer1/RotZ_OutOfBeam deg 27 | 28 | s:Tf/Scatterer1/L3/Function = "Step" 29 | dv:Tf/Scatterer1/L3/Times = 4 20 40 80 100 ms 30 | dv:Tf/Scatterer1/L3/Values = 4 Ge/Scatterer1/RotZ_InBeam Ge/Scatterer1/RotZ_OutOfBeam Ge/Scatterer1/RotZ_InBeam Ge/Scatterer1/RotZ_OutOfBeam deg 31 | 32 | Ge/Scatterer1/Lollipop1 = Tf/Scatterer1/L1/Value deg 33 | Ge/Scatterer1/Lollipop2 = Tf/Scatterer1/L2/Value deg 34 | Ge/Scatterer1/Lollipop3 = Tf/Scatterer1/L3/Value deg 35 | 36 | # Setting second scatterer: 37 | s:Tf/Scatterer2/Function = "Step" 38 | dv:Tf/Scatterer2/Times = 2 50 100 ms 39 | dv:Tf/Scatterer2/Values = 2 Ge/Scatterer2/RotZForS2 Ge/Scatterer2/RotZForS1 deg 40 | 41 | d:Ge/Scatterer2/Holder/RotZ = Tf/Scatterer2/Value deg 42 | 43 | # Show time feature steps on console 44 | i:Tf/Verbosity = 1 45 | 46 | b:Ts/UseQt = "True" 47 | -------------------------------------------------------------------------------- /examples/Nozzle/TargetInWaterPhantom.txt: -------------------------------------------------------------------------------- 1 | # Target used in some demonstrations. 2 | 3 | includeFile = ConstantsForNozzles.txt 4 | 5 | s:Ge/WaterPhantom/Type = "TsBox" 6 | s:Ge/WaterPhantom/Parent = "World" 7 | s:Ge/WaterPhantom/Material = "G4_WATER" 8 | d:Ge/WaterPhantom/HLX = 8.0 cm 9 | d:Ge/WaterPhantom/HLY = 8.0 cm 10 | d:Ge/WaterPhantom/HLZ = 10.0 cm 11 | d:Ge/WaterPhantom/MinusHLZ = Ge/WaterPhantom/HLZ cm * -1.0 12 | d:Ge/WaterPhantom/TransX = 0. cm 13 | d:Ge/WaterPhantom/TransY = 0. cm 14 | d:Ge/WaterPhantom/TransZ = Ge/WaterPhantom/MinusHLZ cm 15 | d:Ge/WaterPhantom/RotX = 0. deg 16 | d:Ge/WaterPhantom/RotY = 0. deg 17 | d:Ge/WaterPhantom/RotZ = 0. deg 18 | s:Ge/WaterPhantom/Color = "white" 19 | 20 | #Value for placing a target. 21 | #146.25 mm is the R80 for about 141 MeV proton 22 | d:Ge/R80 = -146.25 mm 23 | 24 | s:Ge/PlaneAtR80/Type = "TsBox" 25 | s:Ge/PlaneAtR80/Parent = "WaterPhantom" 26 | s:Ge/PlaneAtR80/Material = "G4_WATER" 27 | d:Ge/PlaneAtR80/HLX = 5.0 cm 28 | d:Ge/PlaneAtR80/HLY = 5.0 cm 29 | d:Ge/PlaneAtR80/HLZ = 0.5 cm 30 | d:Ge/PlaneAtR80/TransX = 0. cm 31 | d:Ge/PlaneAtR80/TransY = 0. cm 32 | d:Ge/PlaneAtR80/TransZ = Ge/WaterPhantom/HLZ + Ge/R80 cm 33 | d:Ge/PlaneAtR80/RotX = 0.0 deg 34 | d:Ge/PlaneAtR80/RotY = 0.0 deg 35 | d:Ge/PlaneAtR80/RotZ = 0.0 deg 36 | s:Ge/PlaneAtR80/Color = "red" 37 | i:Ge/PlaneAtR80/XBins = 1 38 | i:Ge/PlaneAtR80/YBins = 1 39 | i:Ge/PlaneAtR80/ZBins = 1 40 | -------------------------------------------------------------------------------- /examples/Nozzle/TsAnalysisWaterPhantom.txt: -------------------------------------------------------------------------------- 1 | # WaterPhantom used in some demonstrations. 2 | # 40cm long, 20 cm in x, 20 cm in y 3 | 4 | includeFile = ConstantsForNozzles.txt 5 | 6 | # Water Tank / Phantom 7 | s:Ge/WaterPhantom/Parent = "Gantry" 8 | s:Ge/WaterPhantom/Type = "TsBox" 9 | s:Ge/WaterPhantom/Material = "G4_WATER" 10 | d:Ge/WaterPhantom/HLX = 10.0 cm 11 | d:Ge/WaterPhantom/HLY = 10.0 cm 12 | d:Ge/WaterPhantom/HLZ = 20.0 cm 13 | d:Ge/WaterPhantom/TransX = 0.0 cm 14 | d:Ge/WaterPhantom/TransY = 0.0 cm 15 | d:Ge/WaterPhantom/TransZ = 0.0 cm 16 | d:Ge/WaterPhantom/RotX = 0. deg 17 | d:Ge/WaterPhantom/RotY = 0. deg 18 | d:Ge/WaterPhantom/RotZ = 0. deg 19 | d:Ge/WaterPhantom/MaxStepSize = 0.5 mm 20 | 21 | s:Ge/ScoringCylinder3cm/Parent = "WaterPhantom" 22 | s:Ge/ScoringCylinder3cm/Type = "TsCylinder" 23 | s:Ge/ScoringCylinder3cm/Material = "G4_WATER" 24 | d:Ge/ScoringCylinder3cm/RMin = 0.0 cm 25 | d:Ge/ScoringCylinder3cm/RMax = 3.0 cm 26 | d:Ge/ScoringCylinder3cm/HL = Ge/WaterPhantom/HLZ cm 27 | d:Ge/ScoringCylinder3cm/SPhi = 0. deg 28 | d:Ge/ScoringCylinder3cm/DPhi = 360. deg 29 | d:Ge/ScoringCylinder3cm/TransX = 0. cm 30 | d:Ge/ScoringCylinder3cm/TransY = 0. cm 31 | d:Ge/ScoringCylinder3cm/TransZ = 0. cm 32 | d:Ge/ScoringCylinder3cm/RotX = 0. deg 33 | d:Ge/ScoringCylinder3cm/RotY = 0.0 deg 34 | d:Ge/ScoringCylinder3cm/RotZ = 180. deg 35 | s:Ge/ScoringCylinder3cm/Color = "blue" 36 | i:Ge/ScoringCylinder3cm/RBins = 1 37 | i:Ge/ScoringCylinder3cm/PhiBins = 1 38 | i:Ge/ScoringCylinder3cm/ZBins = 200 39 | 40 | s:Sc/ScoringCylinder3cm/Quantity = "DoseToMedium" 41 | s:Sc/ScoringCylinder3cm/Component = "ScoringCylinder3cm" 42 | b:Sc/ScoringCylinder3cm/OutputToConsole = "False" 43 | s:Sc/ScoringCylinder3cm/IfOutputFileAlreadyExists = "Overwrite" 44 | 45 | -------------------------------------------------------------------------------- /examples/Nozzle/Viewer.txt: -------------------------------------------------------------------------------- 1 | # Graphics settings used in some demonstrations. 2 | 3 | includeFile = ConstantsForNozzles.txt 4 | 5 | s:Gr/ViewA/Type = "OpenGL" 6 | i:Gr/ViewA/WindowSizeX = 768 7 | i:Gr/ViewA/WindowSizeY = 768 8 | d:Gr/ViewA/Theta = 25 deg 9 | d:Gr/ViewA/Phi = 14 deg 10 | s:Gr/ViewA/Projection = "Perspective" 11 | d:Gr/ViewA/PerspectiveAngle = 20 deg 12 | u:Gr/ViewA/Zoom = 10 13 | b:Gr/ViewA/HiddenLineRemovalForTrajectories = "False" 14 | b:Gr/ViewA/IncludeAxes = "True" 15 | s:Gr/ViewA/AxesComponent = "World" 16 | d:Gr/ViewA/AxesSize = 0.1 m 17 | 18 | #b:Gr/ViewA/CopyOpenGLToEPS = "True" 19 | b:Gr/ViewA/IncludeTrajectories = "True" 20 | 21 | s:Gr/ViewA/ColorBy = "Charge" 22 | s:Gr/ViewA/ChargeColors = "red green cyan" 23 | -------------------------------------------------------------------------------- /examples/Optical/Rotating_Surfaces.txt: -------------------------------------------------------------------------------- 1 | # Demonstrates optical behavior on rotating surfaces 2 | 3 | includeFile = Surfaces.txt 4 | 5 | i:Ts/SequenceVerbosity = 0 6 | 7 | i:Tf/Verbosity = 0 8 | d:Tf/TimelineEnd = 60.0 ms 9 | i:Tf/NumberOfSequentialTimes = 40 10 | 11 | i:So/Example/NumberOfHistoriesInRun = 20 12 | 13 | d:Ge/Splitter/RotX = Tf/SplitterRot/Value deg 14 | 15 | s:Tf/SplitterRot/Function = "Linear deg" 16 | d:Tf/SplitterRot/Rate = 1. deg/ms 17 | d:Tf/SplitterRot/StartValue = -57.0 deg 18 | d:Tf/SplitterRot/RepetitionInterval = 60. ms 19 | 20 | d:Ge/Mirror/RotX = Tf/MirrorRot/Value deg 21 | 22 | s:Tf/MirrorRot/Function = "Linear deg" 23 | d:Tf/MirrorRot/Rate = -1. deg/ms 24 | d:Tf/MirrorRot/StartValue = 100.0 deg 25 | d:Tf/MirrorRot/RepetitionInterval = 60. ms 26 | -------------------------------------------------------------------------------- /examples/Outcome/CVModelStavrev.txt: -------------------------------------------------------------------------------- 1 | #Parameter obtained from Stavrev et. al. Physica Medica, Vol 17(2) (2001). 2 | # Table 1. 3 | # Organ mu_cr std sigma std D50_FSU std Gamma50_FSU std 4 | uv:Sc/CriticalVolumeValues/Lung = 8 0.08 0.02 0.02 0.01 220 51 0.3 0.02 # Pneumonitis 5 | uv:Sc/CriticalVolumeValues/Liver = 8 0.04 0.01 0.01 0.003 181 20 0.5 0.02 # Liver failure 6 | uv:Sc/CriticalVolumeValues/Brain = 8 0.08 0.02 0.05 0.02 104 7.9 1 0.1 # Necrosis 7 | uv:Sc/CriticalVolumeValues/Heart = 8 0.14 0.07 0.05 0.02 83 22 0.8 0.2 # Pericarditis 8 | uv:Sc/CriticalVolumeValues/Kidney = 8 0.22 0.06 0.05 0.01 59 14 0.4 0.06 # Clinical nephritis 9 | uv:Sc/CriticalVolumeValues/Esophagus = 8 0.01 0.02 0.02 0.03 97 14 2.4 0.8 # Clincial stricture, perforation 10 | uv:Sc/CriticalVolumeValues/Stomach = 8 0.02 0.01 0.03 0.01 94 7.1 2.2 0.5 # Ulceration, perforation 11 | uv:Sc/CriticalVolumeValues/BrachialPlexus = 8 0.01 0.03 0.05 0.1 86 9.9 6 4 # Clinically apparent nerve damage 12 | uv:Sc/CriticalVolumeValues/Bladder = 8 0.26 0.11 0.11 0.02 108 24 0.8 0.2 # Symptomatic bladder contraction and volume loss 13 | uv:Sc/CriticalVolumeValues/TMJointMandible= 8 0.07 0.06 0.09 0.07 86 7.4 3.1 1 # Marked limitation of joint function 14 | uv:Sc/CriticalVolumeValues/BrainStem = 8 0.12 0.06 0.08 0.04 97 12 1.2 0.2 # Necrosis 15 | uv:Sc/CriticalVolumeValues/Larynx = 8 0.07 0.08 0.08 0.05 108 22 1.9 0.5 # Cartilage necrosis perforation 16 | uv:Sc/CriticalVolumeValues/SmallIntestine = 8 0.04 0.05 0.04 0.04 97 28 1.2 0.3 # Obstruction, perforation 17 | uv:Sc/CriticalVolumeValues/Colon = 8 0.03 0.02 0.02 0.01 108 16 1.1 0.1 # Obstruction, perforation 18 | uv:Sc/CriticalVolumeValues/SpinalCord = 8 0.08 0.09 0.16 0.15 81 12 2.6 1 # Myelitis necrosis 19 | uv:Sc/CriticalVolumeValues/Skin = 8 0.11 0.05 0.09 0.05 93 8.5 1.7 0.3 # Necrosis, ulceration 20 | -------------------------------------------------------------------------------- /examples/Outcome/DoseAtOAR1Saved.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples/Outcome/DoseAtOAR1Saved.bin -------------------------------------------------------------------------------- /examples/Outcome/DoseAtOAR1Saved.binheader: -------------------------------------------------------------------------------- 1 | # TOPAS Version: 1.2_expanded 2 | # Parameter File: TestOutcomeModel.txt 3 | # Results for scorer OAR1 4 | # Scored in component: WaterPhantom/OAR1 5 | # X in 20 bins of 0.1 cm 6 | # Y in 20 bins of 0.1 cm 7 | # Z in 44 bins of 0.1 cm 8 | # DoseToMedium ( Gy ) : Sum 9 | # Binary file: DoseAtOAR1.bin 10 | -------------------------------------------------------------------------------- /examples/Outcome/DoseAtOAR2Saved.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples/Outcome/DoseAtOAR2Saved.bin -------------------------------------------------------------------------------- /examples/Outcome/DoseAtOAR2Saved.binheader: -------------------------------------------------------------------------------- 1 | # TOPAS Version: 1.2_expanded 2 | # Parameter File: TestOutcomeModel.txt 3 | # Results for scorer OAR2 4 | # Scored in component: WaterPhantom/OAR2 5 | # X in 24 bins of 0.1 cm 6 | # Y in 24 bins of 0.1 cm 7 | # Z in 24 bins of 0.1 cm 8 | # DoseToMedium ( Gy ) : Sum 9 | # Binary file: DoseAtOAR2.bin 10 | -------------------------------------------------------------------------------- /examples/Outcome/DoseAtTargetSaved.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples/Outcome/DoseAtTargetSaved.bin -------------------------------------------------------------------------------- /examples/Outcome/DoseAtTargetSaved.binheader: -------------------------------------------------------------------------------- 1 | # TOPAS Version: 1.2_expanded 2 | # Parameter File: TestOutcomeModel.txt 3 | # Results for scorer Target 4 | # Scored in component: WaterPhantom/Target 5 | # X in 20 bins of 0.1 cm 6 | # Y in 20 bins of 0.1 cm 7 | # Z in 44 bins of 0.1 cm 8 | # DoseToMedium ( Gy ) : Sum 9 | # Binary file: DoseAtTarget.bin 10 | -------------------------------------------------------------------------------- /examples/Patient/Abdomen.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples/Patient/Abdomen.zip -------------------------------------------------------------------------------- /examples/Patient/DICOM_Box.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples/Patient/DICOM_Box.zip -------------------------------------------------------------------------------- /examples/Patient/DicomCutaway.txt: -------------------------------------------------------------------------------- 1 | # Demonstrates use of graphical cutaway planes. 2 | # You must unzip DICOM_Box.zip before you run this example. 3 | 4 | includeFile = HUtoMaterialSchneider.txt 5 | 6 | s:Ge/World/Material = "Vacuum" 7 | b:Ge/World/Invisible = "TRUE" 8 | 9 | s:Ge/Patient/Parent = "World" 10 | s:Ge/Patient/Material = "G4_WATER" 11 | s:Ge/Patient/Type = "TsDicomPatient" 12 | s:Ge/Patient/DicomDirectory = "DICOM_Box" 13 | 14 | s:So/Example/Type = "Beam" 15 | s:So/Example/Component = "BeamPosition" 16 | s:So/Example/BeamParticle = "proton" 17 | d:So/Example/BeamEnergy = 30. MeV 18 | u:So/Example/BeamEnergySpread = 0.757504 19 | s:So/Example/BeamPositionDistribution = "Flat" 20 | s:So/Example/BeamPositionCutoffShape = "Ellipse" 21 | d:So/Example/BeamPositionCutoffX = 5. cm 22 | d:So/Example/BeamPositionCutoffY = 20. cm 23 | s:So/Example/BeamAngularDistribution = "None" 24 | i:So/Example/NumberOfHistoriesInRun = 5 25 | 26 | s:Gr/ViewA/Type = "OpenGL" 27 | sv:Gr/ViewA/VisibleWorlds = 1 "All" 28 | i:Gr/ViewA/WindowSizeX = 900 29 | i:Gr/ViewA/WindowSizeY = 900 30 | d:Gr/ViewA/Theta = 70 deg 31 | d:Gr/ViewA/Phi = 10 deg 32 | 33 | i:Gr/ViewA/nCutawayPlanes = 2 34 | d:Gr/ViewA/CutawayPlane/1/XPos = 0. cm 35 | d:Gr/ViewA/CutawayPlane/1/YPos = 0. cm 36 | d:Gr/ViewA/CutawayPlane/1/ZPos = 0. cm 37 | u:Gr/ViewA/CutawayPlane/1/XDir = -1. 38 | u:Gr/ViewA/CutawayPlane/1/YDir = -1. 39 | u:Gr/ViewA/CutawayPlane/1/ZDir = 0. 40 | 41 | d:Gr/ViewA/CutawayPlane/2/XPos = 0. cm 42 | d:Gr/ViewA/CutawayPlane/2/YPos = 0. cm 43 | d:Gr/ViewA/CutawayPlane/2/ZPos = 0. cm 44 | u:Gr/ViewA/CutawayPlane/2/XDir = -1. 45 | u:Gr/ViewA/CutawayPlane/2/YDir = 0. 46 | u:Gr/ViewA/CutawayPlane/2/ZDir = 0. 47 | 48 | # Extra graphics options to handle complex voxel geometries 49 | i:Gr/ShowOnlyOutlineIfVoxelCountExceeds = 210000000 50 | 51 | b:Ts/PauseBeforeQuit = "True" 52 | -------------------------------------------------------------------------------- /examples/Patient/PatientInIEC_2.txt: -------------------------------------------------------------------------------- 1 | # PatientInIEC_2 : we place a patient to treatment room. 2 | 3 | # Fix for iso-center 4 | # Fix for DICOM to IEC 5 | # Fix for Gantry rotation : 60 deg 6 | # Fix for Couch rotation : 90 deg 7 | 8 | includeFile = PatientInIEC_1.txt 9 | 10 | # step 1 11 | Ge/patient/TransX = -1.0 * Ge/patient_iso/TransX mm 12 | Ge/patient/TransY = -1.0 * Ge/patient_iso/TransY mm 13 | Ge/patient/TransZ = -1.0 * Ge/patient_iso/TransZ mm 14 | 15 | Ge/DICOM_to_IEC/RotX = 90.0 deg # step 2: 90.0 deg 16 | 17 | Ge/IEC_G/RotY = 60.0 deg # step3: 60 deg ? 18 | 19 | # Couch (patient support) 20 | Ge/IEC_S/RotZ = 45.0 deg # step4: 90 deg ? 21 | 22 | s:Sc/DoseAtPhantom1/Quantity = "DoseToWater" 23 | s:Sc/DoseAtPhantom1/Component = "patient_rleg" 24 | s:Sc/DoseAtPhantom1/IfOutputFileAlreadyExists = "Overwrite" 25 | b:Sc/DoseAtPhantom1/OutputAfterRun = "True" 26 | -------------------------------------------------------------------------------- /examples/Patient/PatientInIEC_2_time_feature.txt: -------------------------------------------------------------------------------- 1 | # PatientInIEC_2_time_feature : we rotate patient and gantry simulatenously using TimeFeature 2 | 3 | includeFile = PatientInIEC_2.txt 4 | 5 | # Gantry 6 | s:Tf/rotation/Function = "Linear deg" 7 | d:Tf/rotation/Rate = 5 deg/ms 8 | d:Tf/rotation/StartValue = 0.0 deg 9 | d:Tf/rotation/RepetitionInterval = 60. ms 10 | 11 | Ge/IEC_G/RotY = Tf/rotation/Value deg 12 | Ge/IEC_S/RotZ = Tf/rotation/Value deg # step3: 60 deg ? 13 | 14 | d:Tf/TimelineEnd = 60.0 ms 15 | i:Tf/NumberOfSequentialTimes = 60 16 | -------------------------------------------------------------------------------- /examples/Patient/PatientInIEC_3.txt: -------------------------------------------------------------------------------- 1 | # PatientInIEC_3 : we place a beam to DICOM 2 | 3 | includeFile = PatientInIEC_1.txt 4 | 5 | # step 1 : Fix patient to world 6 | 7 | Ge/patient/Parent = "World" 8 | 9 | # step 2 : place IEC_G on IEC_S 10 | 11 | Ge/DICOM_to_IEC/Parent = "World" 12 | Ge/IEC_S/Parent = "DICOM_to_IEC" 13 | Ge/IEC_G/Parent = "IEC_S" 14 | 15 | # step 3 : Gantry 16 | Ge/IEC_G/RotY = 60.0 deg # 60 deg ? 17 | 18 | # step 4 Couch (patient support) 19 | Ge/IEC_S/RotZ = -45.0 deg # -90 deg ? 20 | 21 | # step 5 rotation 22 | Ge/DICOM_to_IEC/RotX = -90 deg 23 | 24 | # step 6 translational movement 25 | Ge/DICOM_to_IEC/TransX = Ge/patient_iso/TransX mm 26 | Ge/DICOM_to_IEC/TransY = Ge/patient_iso/TransY mm 27 | Ge/DICOM_to_IEC/TransZ = Ge/patient_iso/TransZ mm 28 | -------------------------------------------------------------------------------- /examples/Patient/README.txt: -------------------------------------------------------------------------------- 1 | You must unzip the compressed DICOM files in this directory 2 | before you try these examples (the .zip and .bz2 files). 3 | -------------------------------------------------------------------------------- /examples/Patient/XCAT_FullMouse_86x86x161_atn_1.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples/Patient/XCAT_FullMouse_86x86x161_atn_1.bin -------------------------------------------------------------------------------- /examples/Patient/XIO_Example.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples/Patient/XIO_Example.dat -------------------------------------------------------------------------------- /examples/Patient/synthetic_lung.tar.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples/Patient/synthetic_lung.tar.bz2 -------------------------------------------------------------------------------- /examples/PhaseSpace/ReadASCII.txt: -------------------------------------------------------------------------------- 1 | # Read phase space in TOPAS ASCII form 2 | 3 | b:Ge/World/Invisible = "TRUE" 4 | 5 | s:Ge/VacFilm/Type = "TsBox" 6 | s:Ge/VacFilm/Parent = "World" 7 | s:Ge/VacFilm/Material = "G4_WATER" 8 | d:Ge/VacFilm/HLX = 50.0 cm 9 | d:Ge/VacFilm/HLY = 50.0 cm 10 | d:Ge/VacFilm/HLZ = 1.0 cm 11 | d:Ge/VacFilm/TransX = 0. cm 12 | d:Ge/VacFilm/TransY = 0. cm 13 | d:Ge/VacFilm/TransZ = 0. cm 14 | d:Ge/VacFilm/RotX = 0. deg 15 | d:Ge/VacFilm/RotY = 0. deg 16 | d:Ge/VacFilm/RotZ = 0. deg 17 | s:Ge/VacFilm/Color = "skyblue" 18 | 19 | s:So/Example/Type = "PhaseSpace" 20 | s:So/Example/PhaseSpaceFileName = "ASCIIOutput" 21 | s:So/Example/Component = "World" 22 | #i:So/Example/PhaseSpaceMultipleUse = 2 23 | b:So/Example/PhaseSpaceIncludeEmptyHistories = "True" 24 | 25 | # Graphics 26 | s:Gr/ViewA/Type = "OpenGL" 27 | i:Gr/ViewA/WindowSizeX = 900 28 | i:Gr/ViewA/WindowSizeY = 900 29 | d:Gr/ViewA/Theta = 55 deg 30 | d:Gr/ViewA/Phi = 20 deg 31 | s:Gr/ViewA/Projection = "Perspective" 32 | d:Gr/ViewA/PerspectiveAngle = 30 deg 33 | u:Gr/ViewA/Zoom = 1.3 34 | b:Gr/ViewA/HiddenLineRemovalForTrajectories = "True" 35 | 36 | i:Ts/ShowHistoryCountAtInterval = 10 37 | b:Ts/PauseBeforeQuit = "True" 38 | -------------------------------------------------------------------------------- /examples/PhaseSpace/ReadBinary.txt: -------------------------------------------------------------------------------- 1 | # Read phase space in TOPAS Binary form 2 | 3 | b:Ge/World/Invisible = "TRUE" 4 | 5 | s:Ge/VacFilm/Type = "TsBox" 6 | s:Ge/VacFilm/Parent = "World" 7 | s:Ge/VacFilm/Material = "G4_WATER" 8 | d:Ge/VacFilm/HLX = 50.0 cm 9 | d:Ge/VacFilm/HLY = 50.0 cm 10 | d:Ge/VacFilm/HLZ = 1.0 cm 11 | d:Ge/VacFilm/TransX = 0. cm 12 | d:Ge/VacFilm/TransY = 0. cm 13 | d:Ge/VacFilm/TransZ = 0. cm 14 | d:Ge/VacFilm/RotX = 0. deg 15 | d:Ge/VacFilm/RotY = 0. deg 16 | d:Ge/VacFilm/RotZ = 0. deg 17 | s:Ge/VacFilm/Color = "skyblue" 18 | 19 | s:So/Example/Type = "PhaseSpace" 20 | s:So/Example/PhaseSpaceFileName = "BinaryOutput" 21 | s:So/Example/Component = "World" 22 | #i:So/Example/PhaseSpaceMultipleUse = 2 23 | b:So/Example/PhaseSpaceIncludeEmptyHistories = "True" 24 | 25 | # Graphics 26 | s:Gr/ViewA/Type = "OpenGL" 27 | i:Gr/ViewA/WindowSizeX = 900 28 | i:Gr/ViewA/WindowSizeY = 900 29 | d:Gr/ViewA/Theta = 55 deg 30 | d:Gr/ViewA/Phi = 20 deg 31 | s:Gr/ViewA/Projection = "Perspective" 32 | d:Gr/ViewA/PerspectiveAngle = 30 deg 33 | u:Gr/ViewA/Zoom = 1.3 34 | b:Gr/ViewA/HiddenLineRemovalForTrajectories = "True" 35 | 36 | i:Ts/ShowHistoryCountAtInterval = 10 37 | b:Ts/PauseBeforeQuit = "True" 38 | -------------------------------------------------------------------------------- /examples/PhaseSpace/ReadLimited.txt: -------------------------------------------------------------------------------- 1 | # Read phase space in Limited form 2 | 3 | b:Ge/World/Invisible = "TRUE" 4 | 5 | s:Ge/VacFilm/Type = "TsBox" 6 | s:Ge/VacFilm/Parent = "World" 7 | s:Ge/VacFilm/Material = "G4_WATER" 8 | d:Ge/VacFilm/HLX = 50.0 cm 9 | d:Ge/VacFilm/HLY = 50.0 cm 10 | d:Ge/VacFilm/HLZ = 1.0 cm 11 | d:Ge/VacFilm/TransX = 0. cm 12 | d:Ge/VacFilm/TransY = 0. cm 13 | d:Ge/VacFilm/TransZ = 0. cm 14 | d:Ge/VacFilm/RotX = 0. deg 15 | d:Ge/VacFilm/RotY = 0. deg 16 | d:Ge/VacFilm/RotZ = 0. deg 17 | s:Ge/VacFilm/Color = "skyblue" 18 | 19 | s:So/Example/Type = "PhaseSpace" 20 | s:So/Example/PhaseSpaceFileName = "LimitedOutput" 21 | s:So/Example/Component = "World" 22 | #i:So/Example/PhaseSpaceMultipleUse = 2 23 | b:So/Example/PhaseSpaceIncludeEmptyHistories = "True" 24 | 25 | # Graphics 26 | s:Gr/ViewA/Type = "OpenGL" 27 | i:Gr/ViewA/WindowSizeX = 900 28 | i:Gr/ViewA/WindowSizeY = 900 29 | d:Gr/ViewA/Theta = 55 deg 30 | d:Gr/ViewA/Phi = 20 deg 31 | s:Gr/ViewA/Projection = "Perspective" 32 | d:Gr/ViewA/PerspectiveAngle = 30 deg 33 | u:Gr/ViewA/Zoom = 1.3 34 | b:Gr/ViewA/HiddenLineRemovalForTrajectories = "True" 35 | 36 | i:Ts/ShowHistoryCountAtInterval = 10 37 | b:Ts/PauseBeforeQuit = "True" 38 | -------------------------------------------------------------------------------- /examples/Scoring/ChargeInSphere.txt: -------------------------------------------------------------------------------- 1 | # Score charge in a sphere 2 | 3 | s:Ge/World/Material = "Vacuum" 4 | d:Ge/World/HLX = 2.0 m 5 | d:Ge/World/HLY = 2.0 m 6 | d:Ge/World/HLZ = 2.0 m 7 | b:Ge/World/Invisible = "TRUE" 8 | 9 | s:Ge/Sphere/Type = "TsSphere" 10 | s:Ge/Sphere/Parent = "World" 11 | s:Ge/Sphere/Material = "Air" 12 | d:Ge/Sphere/RMax = 55.0 cm 13 | s:Ge/Sphere/DrawingStyle = "FullWireFrame" 14 | 15 | s:Sc/Charge/Quantity = "Charge" 16 | s:Sc/Charge/Component = "Sphere" 17 | b:Sc/Charge/OutputToConsole = "TRUE" 18 | s:Sc/Charge/IfOutputFileAlreadyExists = "Overwrite" 19 | sv:Sc/Charge/OnlyIncludeParticlesNamed = 1 "proton" 20 | #s:Sc/Charge/OnlyIncludeParticlesOfGeneration = "secondary" 21 | 22 | s:Gr/ViewA/Type = "OpenGL" 23 | 24 | s:So/Example/Type = "Beam" 25 | s:So/Example/Component = "BeamPosition" 26 | s:So/Example/BeamParticle = "proton" 27 | d:So/Example/BeamEnergy = 169.23 MeV 28 | u:So/Example/BeamEnergySpread = 0.757504 29 | s:So/Example/BeamPositionDistribution = "Gaussian" 30 | s:So/Example/BeamPositionCutoffShape = "Ellipse" 31 | d:So/Example/BeamPositionCutoffX = 10. cm 32 | d:So/Example/BeamPositionCutoffY = 10. cm 33 | d:So/Example/BeamPositionSpreadX = 0.65 cm 34 | d:So/Example/BeamPositionSpreadY = 0.65 cm 35 | s:So/Example/BeamAngularDistribution = "Gaussian" 36 | d:So/Example/BeamAngularCutoffX = 90. deg 37 | d:So/Example/BeamAngularCutoffY = 90. deg 38 | d:So/Example/BeamAngularSpreadX = 0.0032 rad 39 | d:So/Example/BeamAngularSpreadY = 0.0032 rad 40 | i:So/Example/NumberOfHistoriesInRun = 500 41 | 42 | i:Ts/ShowHistoryCountAtInterval = 10 43 | b:Ts/PauseBeforeQuit = "True" 44 | -------------------------------------------------------------------------------- /examples/Scoring/DepthDose.txt: -------------------------------------------------------------------------------- 1 | s:Ge/Phantom/Type = "TsBox" 2 | s:Ge/Phantom/Parent = "World" 3 | s:Ge/Phantom/Material = "G4_WATER" 4 | d:Ge/Phantom/HLX = 10.0 cm 5 | d:Ge/Phantom/HLY = 10.0 cm 6 | d:Ge/Phantom/HLZ = 20.0 cm 7 | i:Ge/Phantom/ZBins = 20 8 | 9 | # Rotate Phantom so that the bin numbered 0 will be the 10 | # first bin hit. 11 | # Alternately, one could have adjusted the demo source 12 | # so that the beam pointed in from the other side of the world. 13 | d:Ge/Phantom/RotX = 180. deg 14 | 15 | s:Sc/DoseAtPhantom/Quantity = "DoseToMedium" 16 | s:Sc/DoseAtPhantom/Component = "Phantom" 17 | s:Sc/DoseAtPhantom/IfOutputFileAlreadyExists = "Overwrite" 18 | b:Sc/DoseAtPhantom/OutputToConsole = "True" 19 | 20 | i:So/Demo/NumberOfHistoriesInRun = 1000 21 | 22 | i:Ts/ShowHistoryCountAtInterval = 100 -------------------------------------------------------------------------------- /examples/Scoring/Inactive.txt: -------------------------------------------------------------------------------- 1 | # Demonstrate effect of setting a scorer inactive 2 | 3 | s:Ge/Box/Type = "TsBox" 4 | s:Ge/Box/Parent = "World" 5 | s:Ge/Box/Material = "G4_WATER" 6 | d:Ge/Box/HLX = 1. m 7 | d:Ge/Box/HLY = 1. m 8 | d:Ge/Box/HLZ = .4 m 9 | 10 | s:Sc/WasActive/Quantity = "Fluence" 11 | s:Sc/WasActive/Component = "Box" 12 | s:Sc/WasActive/IfOutputFileAlreadyExists = "Overwrite" 13 | b:Sc/WasActive/OutputToConsole = "True" 14 | 15 | s:Sc/WasInActive/Quantity = "Fluence" 16 | s:Sc/WasInActive/Component = "Box" 17 | s:Sc/WasInActive/IfOutputFileAlreadyExists = "Overwrite" 18 | b:Sc/WasInActive/OutputToConsole = "True" 19 | b:Sc/WasInActive/Active = "False" 20 | 21 | s:Gr/MyOGL/Type = "OpenGL" 22 | i:Gr/MyOGL/WindowSizeX = 600 23 | i:Gr/MyOGL/WindowSizeY = 600 24 | i:Gr/MyOGL/WindowPosX = 0 25 | i:Gr/MyOGL/WindowPosY = 0 26 | 27 | s:So/Example/Type = "Beam" 28 | s:So/Example/Component = "BeamPosition" 29 | s:So/Example/BeamParticle = "proton" 30 | d:So/Example/BeamEnergy = 169.23 MeV 31 | u:So/Example/BeamEnergySpread = 0.757504 32 | s:So/Example/BeamPositionDistribution = "Gaussian" 33 | s:So/Example/BeamPositionCutoffShape = "Ellipse" 34 | d:So/Example/BeamPositionCutoffX = 10. cm 35 | d:So/Example/BeamPositionCutoffY = 10. cm 36 | d:So/Example/BeamPositionSpreadX = 0.65 cm 37 | d:So/Example/BeamPositionSpreadY = 0.65 cm 38 | s:So/Example/BeamAngularDistribution = "Gaussian" 39 | d:So/Example/BeamAngularCutoffX = 90. deg 40 | d:So/Example/BeamAngularCutoffY = 90. deg 41 | d:So/Example/BeamAngularSpreadX = 0.0032 rad 42 | d:So/Example/BeamAngularSpreadY = 0.0032 rad 43 | i:So/Example/NumberOfHistoriesInRun = 100 44 | 45 | i:Ts/ShowHistoryCountAtInterval = 10 46 | b:Ts/PauseBeforeQuit = "True" 47 | -------------------------------------------------------------------------------- /examples/SpecialComponents/Aperture_cm.stl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/examples/SpecialComponents/Aperture_cm.stl -------------------------------------------------------------------------------- /examples/SpecialComponents/Propeller_ContinuousRotation.txt: -------------------------------------------------------------------------------- 1 | # Propeller with continuous rotation 2 | 3 | includeFile = Propeller.txt 4 | 5 | b:Ts/PauseBeforeQuit = "False" 6 | 7 | d:Ge/PropellerA/RotZ = Tf/PropellerRot/Value deg 8 | 9 | s:Tf/PropellerRot/Function = "Linear deg" 10 | d:Tf/PropellerRot/Rate = 3.6 deg/ms 11 | d:Tf/PropellerRot/StartValue = 0.0 deg 12 | d:Tf/PropellerRot/RepetitionInterval = 100.0 ms 13 | 14 | d:Tf/TimelineEnd = 100.0 ms 15 | i:Tf/NumberOfSequentialTimes = 100 16 | i:Tf/Verbosity = 1 17 | -------------------------------------------------------------------------------- /examples/SpecialComponents/Propeller_StepRotation.txt: -------------------------------------------------------------------------------- 1 | # Propeller with step rotation 2 | 3 | includeFile = Propeller.txt 4 | 5 | b:Ts/PauseBeforeQuit = "False" 6 | 7 | d:Ge/PropellerA/RotZ = Tf/PropellerRot/Value deg 8 | 9 | s:Tf/PropellerRot/Function = "Step" 10 | dv:Tf/PropellerRot/Times = 10 10 20 30 40 50 60 70 80 90 100 ms 11 | dv:Tf/PropellerRot/Values = 10 0 36 72 108 144 180 216 252 288 324 deg 12 | 13 | d:Tf/TimelineEnd = 100.0 ms 14 | i:Tf/NumberOfSequentialTimes = 100 15 | i:So/Example/NumberOfHistoriesInRun = 10 16 | i:Tf/Verbosity = 1 17 | -------------------------------------------------------------------------------- /examples/SpecialComponents/RangeModulator_ConstantBeam.txt: -------------------------------------------------------------------------------- 1 | # Range modulator wheel in constant current beam 2 | 3 | includeFile = RangeModulator.txt 4 | 5 | d:Ge/RangeModulatorA/Rotz = Tf/RMW_Rotation/Value deg 6 | 7 | i:So/Example/NumberOfHistoriesInRun = 3 8 | 9 | d:Tf/TimelineEnd = 12.0 ms 10 | i:Tf/NumberOfSequentialTimes = 20 11 | 12 | s:Tf/RMW_Rotation/Function = "Linear deg" 13 | d:Tf/RMW_Rotation/Rate = 3.6 deg/ms 14 | d:Tf/RMW_Rotation/StartValue = 0.0 deg 15 | d:Tf/RMW_Rotation/RepetitionInterval = 100. ms 16 | 17 | b:Ts/PauseBeforeQuit = "False" 18 | i:Ts/ShowHistoryCountAtInterval = 0 19 | 20 | # Show time feature steps on console 21 | i:Tf/Verbosity = 1 22 | 23 | b:Gr/ViewA/CopyOpenGLToEPS = "False" 24 | -------------------------------------------------------------------------------- /examples/SpecialComponents/RangeModulator_CurrentModulatedBeam.txt: -------------------------------------------------------------------------------- 1 | # Range modulator wheel in modulated current beam 2 | 3 | includeFile = RangeModulator_ConstantBeam.txt 4 | 5 | s:Tf/BeamCurrent/Function = "Step" 6 | dv:Tf/BeamCurrent/Times = 1 10 ms 7 | iv:Tf/BeamCurrent/Values = 1 10 8 | 9 | s:Tf/BeamWeight/Function = "Step" 10 | dv:Tf/BeamWeight/Times = 10 1 2 3 4 5 6 7 8 9 10 ms 11 | iv:Tf/BeamWeight/Values = 10 1 4 1 1 2 5 2 3 2 1 12 | 13 | i:So/Example/NumberOfHistoriesInRun = Tf/BCM_1/Value 14 | 15 | i:Tf/BCM_1/Value = Tf/BeamWeight/Value * Tf/BeamCurrent/Value 16 | -------------------------------------------------------------------------------- /examples/TimeFeature/RunRandom_Mode.txt: -------------------------------------------------------------------------------- 1 | includeFile = RunSequential_Mode.txt 2 | 3 | #============================================================================# 4 | #--- Timeline setting 5 | #============================================================================# 6 | b:Tf/RandomizeTimeDistribution = "True" 7 | 8 | #============================================================================# 9 | #--- Time Feature for Probability 10 | #============================================================================# 11 | s:Tf/Weights/Function = "Step" 12 | dv:Tf/Weights/Times = 5 1 2 3 4 5 s 13 | uv:Tf/Weights/Values = 5 1.0 0.8 0.6 0.4 0.2 14 | 15 | 16 | #============================================================================# 17 | #--- Assign particles 18 | #============================================================================# 19 | #Same number of total particles in RunSequential_Mode.txt 20 | i:So/Example/NumberOfHistoriesInRandomJob = 3000 21 | 22 | u:So/Example/ProbabilityOfUsingAGivenRandomTime = Tf/Weights/Value 23 | i:Ts/ShowHistoryCountAtInterval = 0 24 | 25 | #============================================================================# 26 | #--- Dose for DoseGrid 27 | #============================================================================# 28 | s:Sc/dose/OutputFile = "Dose_Rand" 29 | -------------------------------------------------------------------------------- /examples/UCSFETF/UCSF_Beamline_Propeller10.txt: -------------------------------------------------------------------------------- 1 | includeFile = UCSF_Beamline_Base.txt 2 | 3 | #2. Propeller 10. 4 | s:Ge/Propeller/Parent = "Nozzle" 5 | s:Ge/Propeller/Type = "TsPropeller" 6 | s:Ge/Propeller/Material = "World" 7 | d:Ge/Propeller/TransX = 0.0 mm 8 | d:Ge/Propeller/TransY = Ge/PropellerConstant/YShift mm 9 | d:Ge/Propeller/TransZ = Ge/PropellerConstant/ZPosition mm 10 | d:Ge/Propeller/RotX = 0.0 deg 11 | d:Ge/Propeller/RotY = 0.0 deg 12 | d:Ge/Propeller/RotZ = Tf/Rotation/Value deg 13 | b:Ge/Propeller/Invisible = "True" 14 | b:Ge/Propeller/Include = "True" 15 | s:Ge/Propeller/Message = "UCSFETF::Propeller10 is constructed!" 16 | 17 | 18 | i:Ge/Propeller/NbOfBlades = Ge/PropellerConstant/NbBlades 19 | d:Ge/Propeller/Rin = Ge/PropellerConstant/Rin mm 20 | d:Ge/Propeller/Rout = Ge/PropellerConstant/Rout mm 21 | 22 | s:Ge/Propeller/Blade/Material = "World" 23 | s:Ge/Propeller/Blade/Color = "skyblue" 24 | s:Ge/Propeller/Blade/DrawingStyle = "Solid" 25 | d:Ge/Propeller/Blade/MaxStepSize = Ge/PropellerConstant/MaxStepSize mm 26 | 27 | #Becareful the order of file up the pieces 28 | #bottom -> top 29 | dv:Ge/Propeller/Thickness= 9 30 | 1.03 1.03 1.03 1.03 1.03 31 | 1.03 1.03 1.03 1.03 mm 32 | 33 | #bottom -> top (ver03) 34 | #v:Ge/Propeller/Angles= 9 35 | #8.36 15.58 22.80 30.02 37.24 44.46 36 | #51.68 58.90 66.12 deg 37 | 38 | #edited by j.shin (4May 2011): ver04 39 | #Also chosen (19Dec 2011) 40 | dv:Ge/Propeller/Angles= 9 41 | 11.36 17.00 26.00 33.02 40.24 47.46 42 | 53.68 61.90 70.12 deg 43 | 44 | sv:Ge/Propeller/Materials=9 45 | "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" 46 | "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" 47 | -------------------------------------------------------------------------------- /examples/UCSFETF/UCSF_Beamline_Propeller15.txt: -------------------------------------------------------------------------------- 1 | includeFile = UCSF_Beamline_Base.txt 2 | 3 | #2. Propeller 15. 4 | s:Ge/Propeller/Parent = "Nozzle" 5 | s:Ge/Propeller/Type = "TsPropeller" 6 | s:Ge/Propeller/Material = "World" 7 | d:Ge/Propeller/TransX = 0.0 mm 8 | d:Ge/Propeller/TransY = Ge/PropellerConstant/YShift mm 9 | d:Ge/Propeller/TransZ = Ge/PropellerConstant/ZPosition cm 10 | d:Ge/Propeller/RotX = 0.0 deg 11 | d:Ge/Propeller/RotY = 0.0 deg 12 | d:Ge/Propeller/RotZ = Tf/Rotation/Value deg 13 | b:Ge/Propeller/Invisible = "True" 14 | s:Ge/Propeller/Message = "UCSFETF::Propeller15 is constructed!" 15 | 16 | i:Ge/Propeller/NbOfBlades = Ge/PropellerConstant/NbBlades 17 | d:Ge/Propeller/Rin = Ge/PropellerConstant/Rin mm 18 | d:Ge/Propeller/Rout = Ge/PropellerConstant/Rout mm 19 | 20 | s:Ge/Propeller/Blade/Material = "World" 21 | s:Ge/Propeller/Blade/Color = "skyblue" 22 | s:Ge/Propeller/Blade/DrawingStyle = "FullWireFrame" 23 | d:Ge/Propeller/Blade/MaxStepSize = Ge/PropellerConstant/MaxStepSize mm 24 | 25 | #Becareful the order of file up the pieces 26 | #bottom -> top 27 | dv:Ge/Propeller/Thickness = 9 28 | 1.54 1.54 1.54 1.54 1.54 29 | 1.54 1.54 1.54 1.54 mm 30 | 31 | #tuned (4 May 2011) 32 | dv:Ge/Propeller/Angles= 9 33 | 13.07 19.64 28.21 33.78 43.35 34 | 47.92 59.49 66.06 72.63 deg 35 | 36 | sv:Ge/Propeller/Materials=9 37 | "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" 38 | "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" 39 | -------------------------------------------------------------------------------- /examples/UCSFETF/UCSF_Beamline_Propeller20.txt: -------------------------------------------------------------------------------- 1 | includeFile = UCSF_Beamline_Base.txt 2 | 3 | #Propeller 20. 4 | s:Ge/Propeller/Parent = "Nozzle" 5 | s:Ge/Propeller/Type = "TsPropeller" 6 | s:Ge/Propeller/Material = "World" 7 | d:Ge/Propeller/TransX = 0.0 mm 8 | d:Ge/Propeller/TransY = Ge/PropellerConstant/YShift mm 9 | d:Ge/Propeller/TransZ = Ge/PropellerConstant/ZPosition mm 10 | d:Ge/Propeller/RotX = 0.0 deg 11 | d:Ge/Propeller/RotY = 0.0 deg 12 | d:Ge/Propeller/RotZ = Tf/Rotation/Value deg 13 | b:Ge/Propeller/Invisible = "True" 14 | s:Ge/Propeller/Message = "UCSFETF::Propeller20 is constructed!" 15 | 16 | i:Ge/Propeller/NbOfBlades = Ge/PropellerConstant/NbBlades 17 | d:Ge/Propeller/Rin = Ge/PropellerConstant/Rin mm 18 | d:Ge/Propeller/Rout = Ge/PropellerConstant/Rout mm 19 | 20 | s:Ge/Propeller/Blade/Material = "World" 21 | s:Ge/Propeller/Blade/Color = "skyblue" 22 | s:Ge/Propeller/Blade/DrawingStyle = "FullWireFrame" 23 | d:Ge/Propeller/Blade/MaxStepSize = Ge/PropellerConstant/MaxStepSize mm 24 | 25 | #Becareful the order of file up the pieces 26 | #bottom -> top 27 | dv:Ge/Propeller/Thickness =11 28 | 1.54 1.54 1.54 1.54 1.54 29 | 1.54 1.54 1.54 1.54 1.54 30 | 1.54 mm 31 | 32 | #bottom -> top 33 | dv:Ge/Propeller/Angles=11 34 | 9.16 15.70 22.24 28.78 35.32 35 | 41.86 48.40 54.94 61.48 68.02 36 | 74.56 deg 37 | 38 | sv:Ge/Propeller/Materials=11 39 | "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" 40 | "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" 41 | "G4_PLEXIGLASS" 42 | -------------------------------------------------------------------------------- /examples/UCSFETF/UCSF_Beamline_Propeller24.txt: -------------------------------------------------------------------------------- 1 | includeFile = UCSF_Beamline_Base.txt 2 | 3 | #4. Propeller 24. 4 | s:Ge/Propeller/Parent = "Nozzle" 5 | s:Ge/Propeller/Type = "TsPropeller" 6 | s:Ge/Propeller/Material = "World" 7 | d:Ge/Propeller/TransX = 0.0 mm 8 | d:Ge/Propeller/TransY = Ge/PropellerConstant/YShift mm 9 | d:Ge/Propeller/TransZ = Ge/PropellerConstant/ZPosition cm 10 | d:Ge/Propeller/RotX = 0.0 deg 11 | d:Ge/Propeller/RotY = 0.0 deg 12 | d:Ge/Propeller/RotZ = Tf/Rotation/Value deg 13 | b:Ge/Propeller/Invisible= "True" 14 | s:Ge/Propeller/Message = "UCSFETF::Propeller24 is constructed!" 15 | 16 | i:Ge/Propeller/NbOfBlades = Ge/PropellerConstant/NbBlades 17 | d:Ge/Propeller/Rin = Ge/PropellerConstant/Rin mm 18 | d:Ge/Propeller/Rout = Ge/PropellerConstant/Rout mm 19 | 20 | s:Ge/Propeller/Blade/Material = "World" 21 | s:Ge/Propeller/Blade/Color = "skyblue" 22 | s:Ge/Propeller/Blade/DrawingStyle = "Solid" 23 | d:Ge/Propeller/Blade/MaxStepSize = Ge/PropellerConstant/MaxStepSize mm 24 | 25 | #Becareful the order of file up the pieces 26 | #bottom -> top 27 | dv:Ge/Propeller/Thickness =13 28 | 1.8 1.8 1.8 1.8 1.8 29 | 1.8 1.8 1.8 1.8 1.8 30 | 1.8 1.8 1.8 mm 31 | 32 | #bottom -> top 33 | dv:Ge/Propeller/Angles=13 34 | 1.042 1.4 8.12 16.41 24.80 35 | 33.09 40.08 47.67 54.86 61.05 36 | 66.94 72.73 78.2 deg 37 | 38 | sv:Ge/Propeller/Materials= 13 39 | "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" 40 | "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" 41 | "G4_PLEXIGLASS" "G4_PLEXIGLASS" "G4_PLEXIGLASS" 42 | -------------------------------------------------------------------------------- /examples/UCSFETF/User_BP_R28_WaterPhantom.txt: -------------------------------------------------------------------------------- 1 | includeFile = UCSF_Beamline_Base.txt UCSF_WaterPhantom.txt 2 | 3 | # ===============================================# 4 | # WaterColumn thickness adjustment to define Range 5 | # ===============================================# 6 | Ge/WaterColumn/Thickness = 4.0 mm 7 | 8 | # ===============================================# 9 | # Execution mode setting. non-4D 10 | # ===============================================# 11 | i:So/Default/NumberOfHistoriesInRun = 15625 12 | 13 | b:Ts/ShowCPUTime = "True" 14 | 15 | Ts/PauseBeforeQuit = "False" 16 | 17 | # ===============================================# 18 | # Water phantom. voxelization for scoring 19 | # Scoring option 20 | # ===============================================# 21 | i:Ge/WaterPhantom/XBins=1 22 | i:Ge/WaterPhantom/YBins=1 23 | i:Ge/WaterPhantom/ZBins=80 24 | 25 | s:Sc/DoseAtWaterPhantom/Quantity = "DoseToMedium" 26 | s:Sc/DoseAtWaterPhantom/Component = "WaterPhantom" 27 | s:Sc/DoseAtWaterPhantom/OutputFile = "BP_R28" 28 | s:Sc/DoseAtWaterPhantom/OutputType = "binary" 29 | b:Sc/DoseAtWaterPhantom/OutputToConsole = "False" 30 | b:Sc/DoseAtWaterPhantom/Visualize = "True" 31 | s:Sc/DoseAtWaterPhantom/IfOutputFileAlreadyExists = "Overwrite" 32 | -------------------------------------------------------------------------------- /examples/UCSFETF/User_SOBP24_R28_WaterPhantom.txt: -------------------------------------------------------------------------------- 1 | includeFile = UCSF_Beamline_Propeller24.txt UCSF_WaterPhantom.txt 2 | 3 | # ===============================================# 4 | # WaterColumn thickness adjustment to define Range 5 | # ===============================================# 6 | Ge/WaterColumn/Thickness = 4.0 mm 7 | 8 | # ===============================================# 9 | # Execution mode setting (RandomJob & SequentialJob) 10 | # ===============================================# 11 | Tf/TimelineEnd = Tf/TimeOfPropellerRotation ms 12 | Tf/NumberOfSequentialTimes = Tf/UCSF_NbTimes 13 | 14 | b:Tf/RandomizeTimeDistribution = "True" 15 | 16 | So/Default/NumberOfHistoriesInRun = 100 * Tf/UCSF_NbHistoriesInRun 17 | i:So/Default/NumberOfHistoriesInRandomJob = 15625 18 | b:Ts/ShowCPUTime = "True" 19 | 20 | Ts/PauseBeforeQuit = "False" 21 | 22 | # ===============================================# 23 | # Water phantom. voxelization for scoring 24 | # Scoring option 25 | # ===============================================# 26 | i:Ge/WaterPhantom/XBins=1 27 | i:Ge/WaterPhantom/YBins=1 28 | i:Ge/WaterPhantom/ZBins=80 29 | 30 | s:Sc/DoseAtWaterPhantom/Quantity = "DoseToMedium" 31 | s:Sc/DoseAtWaterPhantom/Component = "WaterPhantom" 32 | s:Sc/DoseAtWaterPhantom/OutputFile = "SOBP24_R28" 33 | s:Sc/DoseAtWaterPhantom/OutputType = "binary" 34 | b:Sc/DoseAtWaterPhantom/OutputToConsole = "False" 35 | b:Sc/DoseAtWaterPhantom/Visualize = "True" 36 | s:Sc/DoseAtWaterPhantom/IfOutputFileAlreadyExists = "Overwrite" 37 | -------------------------------------------------------------------------------- /examples/UCSFETF/User_SOBP24_Viewer.txt: -------------------------------------------------------------------------------- 1 | includeFile = UCSF_Beamline_Propeller24.txt Viewer.txt 2 | 3 | Ge/WaterColumn/Thickness = 0.0 mm 4 | b:Ge/World/Invisible = "True" 5 | 6 | Tf/TimelineEnd = Tf/TimeOfPropellerRotation ms 7 | Tf/NumberOfSequentialTimes = Tf/UCSF_NbTimes 8 | So/Default/NumberOfHistoriesInRun = 2 * Tf/UCSF_NbHistoriesInRun 9 | 10 | Gr/ViewA/Zoom =3. 11 | u:Gr/ViewA/TransX = -0.2 12 | Ts/PauseBeforeSequence = "False" 13 | Ph/Default/Modules =1 "g4em-standard_opt0" 14 | 15 | Ge/Nozzle/TransZ = -150.0 cm 16 | 17 | i:Gr/ViewA/WindowSizeX = 1024 18 | i:Gr/ViewA/WindowSizeY = 768 19 | d:Gr/ViewA/Theta = 40 deg 20 | d:Gr/ViewA/Phi = 15 deg 21 | b:Gr/ViewA/CopyOpenGLToEPS = "False" 22 | -------------------------------------------------------------------------------- /examples/UCSFETF/Viewer.txt: -------------------------------------------------------------------------------- 1 | includeFile = UCSF_DefaultParameters.txt 2 | ## Graphics 3 | s:Gr/ViewA/Type = "OpenGL" 4 | i:Gr/ViewA/WindowSizeX = 768 5 | i:Gr/ViewA/WindowSizeY = 768 6 | d:Gr/ViewA/Theta = 25 deg 7 | d:Gr/ViewA/Phi = 14 deg 8 | s:Gr/ViewA/Projection = "Perspective" 9 | d:Gr/ViewA/PerspectiveAngle = 20 deg 10 | u:Gr/ViewA/Zoom = 10 11 | b:Gr/ViewA/HiddenLineRemovalForTrajectories = "False" 12 | b:Gr/ViewA/IncludeAxes="True" 13 | s:Gr/ViewA/AxesComponent = "World" 14 | d:Gr/ViewA/AxesSize= 0.1 m 15 | 16 | #b:Gr/ViewA/CopyOpenGLToEPS = "True" 17 | b:Gr/ViewA/IncludeTrajectories = "True" 18 | 19 | s:Gr/ViewA/ColorBy = "Charge" 20 | s:Gr/ViewA/ChargeColors = "red green cyan" 21 | -------------------------------------------------------------------------------- /extension-docs/field.rst: -------------------------------------------------------------------------------- 1 | .. _extension_fields: 2 | 3 | Custom Fields 4 | ============= 5 | 6 | .. highlight:: c++ 7 | 8 | While an ElectroMagnetic Field can have just an electric field, just a magnetic field, or a combination of the two, Geant4's architecture does not provide any base class for a purely electric field, but instead provides one base class for purely Magnetic fields and another for combined ElectroMagnetic fields. To allow you to use all features of both Geant4 classes, TOPAS emulates this curious aspect of Geant4's design. 9 | 10 | If you want to create a purely magnetic field, the first line of the cc file should be of the form:: 11 | 12 | // Magnetic Field for MyField1 13 | 14 | If you want to create a purely electric field, or a combined electromagnetic field, the first line of the cc file should be of the form:: 15 | 16 | // ElectroMagnetic Field for MyField1 17 | 18 | and then if what you really wanted was just an electric field, you implement the magnetic field strength as just zero. 19 | 20 | Geant4 will call your GetFieldValue every time it needs to query the field. For reasons that are not clear to this author, Geant4 will sometimes query your field for points outside of your intended geometry component, so make sure to return at least some value (at least a zero) for every possible point. 21 | 22 | Parameter lookups should be done in ResolveParameters. Call ResolveParameters directly from your constructor, and then you can also rely on TOPAS to re-call this method any time one of this field class's parameters is changed. 23 | -------------------------------------------------------------------------------- /extension-docs/outcome.rst: -------------------------------------------------------------------------------- 1 | .. _extension_outcome: 2 | 3 | Custom Outcome Models 4 | ===================== 5 | 6 | .. highlight:: c++ 7 | 8 | First line of the cc file must be of the form:: 9 | 10 | // Outcome Model for MyOutcomeModel1 11 | 12 | Your custom outcome model can perform whatever analysis you wish from a TOPAS DVH. 13 | The work is all in your Initialize method. 14 | 15 | See ExtensionsExamples/MyOutcomeModel1 16 | -------------------------------------------------------------------------------- /extension-docs/physics.rst: -------------------------------------------------------------------------------- 1 | .. _extension_physics: 2 | 3 | Custom Physics Lists and Physics Modules 4 | ======================================== 5 | 6 | .. highlight:: c++ 7 | 8 | First line of the cc file must be of the form:: 9 | 10 | // Physics List for MyPhysicsList1 11 | or 12 | // Physics Module for MyPhysicsModule1 13 | 14 | You can supply your own physics list or physics module. Note however that this option is not recommended unless you have significant Geant4 expertise. Even most long-time Geant4 users get into difficultly writing their own physics lists and physics modules. Wherever possible, you should try to use one of the Reference physics list or the Modular physics list with pre-written Geant4 physics modules. 15 | 16 | The example physics list and physics module provided in topas/extensions/MyPhysicsList1 and MyPhysicsModule include pointers to the TOPAS parameter manager as their arguments. This is not required, but allows you to use TOPAS parameters to adjust options within your list or modules. 17 | -------------------------------------------------------------------------------- /extension-docs/user_hook.rst: -------------------------------------------------------------------------------- 1 | .. _extension_hooks: 2 | 3 | Additional User Hooks 4 | ===================== 5 | 6 | .. highlight:: c++ 7 | 8 | Six additional hooks are provided in TsExtensionManager for you to attach your own code. 9 | 10 | * BeginSession 11 | * BeginRun 12 | * BeginHistory 13 | * EndHistory 14 | * EndRun 15 | * EndSession 16 | 17 | First line of the cc file must be of the form:: 18 | 19 | // BeginSession for TOPAS 20 | // BeginRun for TOPAS 21 | // BeginHistory for TOPAS 22 | // EndHistory for TOPAS 23 | // EndRun for TOPAS 24 | // EndSession for TOPAS 25 | 26 | There are no particular constraints on what you can do in these methods. They are provided simply to give you more flexibility in the design of your extensions. 27 | -------------------------------------------------------------------------------- /extensions/rbe_scorers.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/extensions/rbe_scorers.png -------------------------------------------------------------------------------- /getting-started/authors.rst: -------------------------------------------------------------------------------- 1 | Authors 2 | ======= 3 | 4 | 5 | TOPAS Software 6 | ~~~~~~~~~~~~~~ 7 | 8 | * Joseph Perl 9 | * Jungwook Shin 10 | * Jan Schuemann 11 | * Bruce Faddegon 12 | * Harald Paganetti 13 | * Jose Ramos 14 | * Aimee McNamara 15 | * David Hall 16 | 17 | 18 | 19 | 20 | TOPAS Documentation 21 | ~~~~~~~~~~~~~~~~~~~ 22 | 23 | ==================== ============================ 24 | Website Creator David Hall 25 | Lead Author Joseph Perl 26 | Additional Authors * Jungwook Shin 27 | * Jan Schuemann 28 | * Jose Ramos 29 | * David Hall 30 | Editors * Joseph Perl 31 | * David Hall 32 | User Contributions * Aleksandra Biegun 33 | * Fada Guan 34 | ==================== ============================ 35 | -------------------------------------------------------------------------------- /getting-started/citation.rst: -------------------------------------------------------------------------------- 1 | Citation 2 | ======== 3 | 4 | If you use TOPAS, please be sure to cite the following paper (`PubMed `_): 5 | 6 | Perl J, Shin J, Schumann J, Faddegon B, Paganetti H. TOPAS: an innovative proton Monte Carlo platform for research and clinical applications. Med Phys. 2012; 39(11):6818-37. 7 | 8 | and the follow-up paper emphasizing the latest developments: 9 | 10 | Faddegon B, Ramos-Mendez J, Schuemann J, McNamara A, Shin J, Perl J, Paganetti H, The TOPAS Tool for Particle Simulation, a Monte Carlo Simulation Tool for Physics, Biology and Clinical Research, Physica Medica, doi:10.1016/j.ejmp.2020.03.019.Here is a BibTeX entry to aid use within LaTeX: 11 | 12 | To discover the Geant4 version used by a specific version of TOPAS, please consult the :ref:`history`. 13 | 14 | .. code-block:: plain 15 | 16 | @article{TOPAS, 17 | author = {Perl, J. and Shin, J. and Schumann, J. and Faddegon, B. and Paganetti, H.}, 18 | title = {{TOPAS: An innovative proton Monte Carlo platform for research and clinical applications}}, 19 | journal = {Medical Physics}, 20 | pages = {6818}, 21 | volume = {39}, 22 | year = {2012}, 23 | pmid = {23127075}, 24 | doi = {10.1118/1.4758060} 25 | } 26 | 27 | @article{TOPAS, 28 | author = {Faddegon, B. and Ramos-Mendez, J. and Schuemann, J. and McNamara, A. and Shin, J. and Perl, J. and Paganetti H.}, 29 | title = {{The TOPAS Tool for Particle Simulation, a Monte Carlo Simulation Tool for Physics, Biology and Clinical Research}}, 30 | journal = {Physica Medica}, 31 | year = {2020}, 32 | doi = {10.1016} 33 | } 34 | -------------------------------------------------------------------------------- /getting-started/history/3_5.rst: -------------------------------------------------------------------------------- 1 | 3.5 Series 2 | ---------- 3 | 4 | This release is almost exactly the same TOPAS code as TOPAS Version 3.4, but with a new underlying Geant4 version. TOPAS 3.5 uses Geant4.10.06.p1, whereas TOPAS 3.4 used Geant4.10.05.p2. Our tests show no major difference in patient dose calculations, however, as this is a new Geant4 version, you should be on the lookout for changes that may affect your simulations. Our intention is that by comparing your TOPAS 3.5 simulation against a TOPAS 3.4 simulation, you can see how your results are affected by the underlying Geant4 version. There is one new feature: 5 | 6 | 7 | 8 | 3.5.0 (2020-06-21) 9 | ~~~~~~~~~~~~~~~~~~~ 10 | 11 | *Added:* Users of Topas 3.5 can take advantage of a new Drawing Style 12 | This new drawing style represents a solid as a random cloud of points within the solid:: 13 | 14 | S:Ge/MyComponent/DrawingStyle = "Cloud" # Previous options were "WireFrame", "FullWireFrame" and "Solid" 15 | 16 | It can be particularly useful in visualization of Boolean solids, as such solids are not always handled correctly by the polygon-generator underlying the other drawing styles. By default, the point cloud will be made of ten thousand points. You can adjust this by setting the new optional parameter:: 17 | 18 | i:Ge/MyComponent/NumberOfCloudPoints 19 | -------------------------------------------------------------------------------- /getting-started/history/index.rst: -------------------------------------------------------------------------------- 1 | .. _history: 2 | 3 | History 4 | ======= 5 | 6 | TOPAS_ wraps and extends the `Geant4 Simulation Toolkit`_. Geant4 is built directly into TOPAS (the user does not need to themselves install Geant4). The following table lists which Geant4 version is built into each TOPAS version. 7 | 8 | =============== ======================== 9 | TOPAS version Geant4 version 10 | =============== ======================== 11 | 3.8.0 10.07.p03 12 | 3.7.0 10.06.p03 13 | 3.6.0 10.06.p03 14 | 3.5.0 10.06.p01 15 | 3.4.0 10.05.p02 16 | 3.3.0 10.05.p01 17 | 3.2.0 10.05.p01 18 | 3.1.0 10.03.p01 19 | 3.0.0 10.02.p01 20 | 2.0.0 10.01.p02 21 | 1.0.0 9.06.4 22 | =============== ======================== 23 | 24 | 25 | A detailed list of changes introduced by each TOPAS version can be found below: 26 | 27 | .. toctree:: 28 | :maxdepth: 2 29 | 30 | 3_8 31 | 3_7 32 | 3_6 33 | 3_5 34 | 3_4 35 | 3_3 36 | 3_2 37 | 3_1 38 | 3_0 39 | 2_0 40 | 1_0 41 | 42 | Prior to the release of version 1.0, TOPAS had a long public beta phase. 43 | 44 | .. _TOPAS: http://www.topasmc.org 45 | .. _Geant4 Simulation Toolkit: https://geant4.web.cern.ch 46 | -------------------------------------------------------------------------------- /getting-started/install.rst: -------------------------------------------------------------------------------- 1 | Installation instructions for the latest TOPAS version are provided at the top of the `Code Repository `_ page of the TOPAS web site. 2 | This page is accessible only to licensed TOPAS users. 3 | -------------------------------------------------------------------------------- /getting-started/intro.rst: -------------------------------------------------------------------------------- 1 | Introduction to TOPAS 2 | ===================== 3 | 4 | TOPAS_ wraps and extends the `Geant4 Simulation Toolkit`_ to provide an easier-to-use application for the medical physicist. TOPAS's unique parameter control system lets you assemble and control a rich library of simulation objects (geometry components, particle sources, scorers, etc.) with no need to write C++ code. 5 | 6 | Advanced users remain free to implement their own simulation objects in C++ code, and add them to TOPAS via an :ref:`extension mechanism `. While user-written objects benefit from underlying functionality of TOPAS base classes and the TOPAS parameter system, they can exploit the full flexibility of Geant4. 7 | 8 | To discover the Geant4 version used by a specific version of TOPAS, please consult the :ref:`history`. 9 | 10 | .. note:: Users should carefully read the :ref:`parameters_intro`, as well as the introductory parts of the sections :ref:`geometry`, :ref:`source`, :ref:`physics` and :ref:`scoring`. The rest of the documentation provides a detailed reference that you may just want to skim initially. 11 | 12 | 13 | .. _TOPAS: http://www.topasmc.org 14 | .. _Geant4 Simulation Toolkit: https://geant4.web.cern.ch 15 | -------------------------------------------------------------------------------- /getting-started/users.rst: -------------------------------------------------------------------------------- 1 | User Support and Contributions 2 | ============================== 3 | 4 | User Support 5 | ------------ 6 | 7 | Help can be requested from TOPAS developers and other users at the `User Forum `_. Note that you must login as a registered user before you can access the forums. 8 | 9 | 10 | 11 | User Contributions 12 | ------------------ 13 | 14 | * Feedback and feature requests are best communicated via the User Forum described above. 15 | * If you would like to share your TOPAS :ref:`extensions ` or parameter files with other users, please get in touch 16 | * Contributions to this documentation website are also most welcome, but does require a GitHub account: 17 | 18 | * Click "Edit on GitHub" in the top-right corner of the page you wish to edit 19 | * This takes you to the page source at GitHub.com 20 | * Click the pencil icon to `fork the repository `_ and edit the page source 21 | * The source format is `reStructuredText `_ 22 | * After making your changes, open a `pull request `_ 23 | -------------------------------------------------------------------------------- /parameters/GUI.png: -------------------------------------------------------------------------------- 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s:Ge/MyGroup/Type="Group" 10 | s:Ge/MyGroup/Parent = "World" 11 | d:Ge/MyGroup/TransX=2. m 12 | d:Ge/MyGroup/TransY=2. m 13 | d:Ge/MyGroup/TransZ=0. m 14 | d:Ge/MyGroup/RotX=0. deg 15 | d:Ge/MyGroup/RotY=0. deg 16 | d:Ge/MyGroup/RotZ=30. deg 17 | 18 | The following example shows how a Group Component, ``Jaws``, placed in a nozzle, allows one to position two individual movable collimator blocks, ``Jaw_Upper`` and ``Jaw_Lower``, without the creation of an extraneous mother volume:: 19 | 20 | s:Ge/Jaws/Type = "Group" 21 | s:Ge/Jaws/Parent = "Nozzle" 22 | d:Ge/Jaws/TransZ = 0. m 23 | ... 24 | s:Ge/Jaw_Upper/Type = "TsBox" 25 | s:Ge/Jaw_Upper/Parent = "Jaws" 26 | s:Ge/Jaw_Upper/Material = "Tungsten" 27 | d:Ge/Aperture/TransY = 2. cm 28 | ... 29 | s:Ge/Jaw_Lower/Type = "TsBox" 30 | s:Ge/Jaw_Lower/Parent = "Jaws" 31 | s:Ge/Jaw_Lower/Material = "Tungsten" 32 | d:Ge/Aperture/TransY = -2. cm 33 | ... 34 | -------------------------------------------------------------------------------- /parameters/geometry/index.rst: -------------------------------------------------------------------------------- 1 | .. _geometry: 2 | 3 | Geometry Components 4 | =================== 5 | 6 | .. toctree:: 7 | :maxdepth: 2 8 | 9 | intro 10 | placement 11 | parallel_world 12 | field 13 | visualization 14 | dividable 15 | generic 16 | group 17 | specialized 18 | patient 19 | -------------------------------------------------------------------------------- /parameters/geometry/rtdose_grid_option1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/geometry/rtdose_grid_option1.png -------------------------------------------------------------------------------- /parameters/geometry/rtdose_grid_option2.png: -------------------------------------------------------------------------------- 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set other visualization attributes:: 9 | 10 | s:Ge/MyComponent/Color = "red" 11 | s:Ge/MyComponent/DrawingStyle = "Solid" # "Solid", "Wireframe" or "FullWireFrame" 12 | i:Ge/MyComponent/VisSegsPerCircle = 100 # Number of line segments to use to approximate a circle, defaults to 24 13 | b:Ge/MyComponent/Invisible = "True" # defaults to False meaning visible 14 | 15 | ``FullWireFrame`` includes drawing of additional edge lines that Geant4 calls "soft edges" - on many graphics devices ``WireFrame`` and ``FullWireFrame`` give the same result. 16 | 17 | Increase ``VisSegsPerCircle`` if you want a smoother curve. 18 | -------------------------------------------------------------------------------- /parameters/intro/batch_jobs.rst: -------------------------------------------------------------------------------- 1 | .. _parameters_batch: 2 | 3 | Controlling Multiple Batch Jobs 4 | ------------------------------- 5 | 6 | The hierarchical nature of parameter files makes it easy to control multiple batch jobs. 7 | 8 | Make up a parameter file (or hierarchy of files) that has most of your settings: 9 | 10 | * MostOfMySettings.txt 11 | 12 | Then make small additional parameter files for each job you want to submit: 13 | 14 | * Job1.txt 15 | * Job2.txt 16 | * Job3.txt 17 | 18 | where each of these files has:: 19 | 20 | includeFile = MostOfMySettings.txt 21 | Ts/Seed = 1 # Set this differently for each of Job1, Job2, Job3, ... 22 | Sc/MyScorer/OutputFile = "Job1Output" # Set this differently for each of Job1, Job2, Job3, 23 | 24 | Each job will thus have a unique starting random number seed (and hence produce a statistically distinct sample) and a unique output file specification, but all other aspects of the simulation will be identical from one job to the next. 25 | -------------------------------------------------------------------------------- /parameters/intro/file_graphs.png: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | .. _parameters_relative: 2 | 3 | Relative Parameters 4 | ------------------- 5 | 6 | TOPAS supports "relative parameters", wherein one parameter may be set relative to another, as in:: 7 | 8 | s:Ge/Phantom/Material = SomeOtherParameterName 9 | 10 | .. note:: 11 | 12 | The many uses of this relative parameter syntax become more clear once one understands the entirety of the TOPAS design, including :ref:`hierarchical control ` files and :ref:`time features `. 13 | 14 | With relative dimensioned double parameters, we must protect against a user setting a parameter relative to some other parameter that does not have appropriate units. The solution is to insist that a unit be included on the right side of the expression. In the example below, the unit of ``cm`` indicates that SomeOtherParameter must itself have units of length. If that other parameter’s unit is of the entirely wrong unit category (mass, angle, etc.), TOPAS will refuse to run. If the unit is of the right category but a different exact unit (m, mm, etc.), TOPAS will perform appropriate unit conversion:: 15 | 16 | d:Ge/Phantom/HLX = SomeOtherParameterName cm 17 | 18 | TOPAS has a grammar for operations such as adding or multiplying parameters:: 19 | 20 | Ge/Compensator/TransZ = Ge/Aperture/DistalEdge + Ge/Compensator/HLZ mm 21 | 22 | .. warning:: 23 | 24 | Note that there must be a space before and after the plus sign. 25 | 26 | Relative parameters allow only a limited number of functions, intentionally not a full math library, since other math functions may be ambiguous, requiring too much prior understanding of the mathematical syntax. The complete set of allowed syntax for any one parameter line is shown :ref:`here `. 27 | -------------------------------------------------------------------------------- /parameters/intro/syntax_highlighting.rst: -------------------------------------------------------------------------------- 1 | 2 | Syntax highlighting 3 | ------------------- 4 | 5 | It can be very useful to have a text editor capable of performing syntax highlighting. 6 | The following editors currently support topas syntax highlighting: 7 | 8 | - `Atom `_: 9 | Go to Packages >> Settings View >> Install Packages/Themes, and search for topas. This package should recognise both *.tps and *.topas files and highlight them automatically. Otherwise you have to manually turn on syntax highlighting in the bottom right of your screen 10 | - `Sublime text `_ 11 | open the Command Palette (cmd+shift+p on Mac, ctrl+shift+p on Linux/Windows) 12 | select Package Control: Install Package 13 | search for Topas Syntax 14 | - `Vim `_ 15 | see `here `_ for instructions 16 | -------------------------------------------------------------------------------- /parameters/overall/index.rst: -------------------------------------------------------------------------------- 1 | .. _overall: 2 | 3 | Overall Control 4 | =============== 5 | 6 | .. toctree:: 7 | :maxdepth: 2 8 | 9 | mode 10 | multithreading 11 | seed 12 | repeatsequenceuntil 13 | misc 14 | -------------------------------------------------------------------------------- /parameters/overall/multithreading.rst: -------------------------------------------------------------------------------- 1 | .. _multithreading: 2 | 3 | Multithreading 4 | -------------- 5 | 6 | TOPAS fully supports the Multi-Threaded simulation capability of Geant4. 7 | 8 | By default, TOPAS will occupy just one CPU thread. To use more, adjust:: 9 | 10 | i:Ts/NumberOfThreads = 4 # defaults to 1 11 | 12 | * If set to a positive integer, TOPAS will use that number of threads 13 | * If set to 0, TOPAS will use all of your computer's threads. This may be number of hardware cores or number of virtual cores (which includes hyper-threading cores) depending on your hardware architecture. 14 | * If set to a negative number, TOPAS will use all BUT this number of threads, leaving you some threads reserved for other tasks (email, web browsing, etc.). 15 | 16 | By default, console output from various threads will be interleaved. Output from each worker thread will have a distinctive prefix, such as: 17 | 18 | .. code-block:: plain 19 | 20 | G4WT0 > 21 | G4WT1 > 22 | 23 | To instead make Geant4 buffer the output, showing first everything from one thread and then everything from another thread, set:: 24 | 25 | b:Ts/BufferThreadOutput = "True" # Causes console output to be show one thread at a time 26 | -------------------------------------------------------------------------------- /parameters/parameter_optimization.rst: -------------------------------------------------------------------------------- 1 | .. _parameters_optimization: 2 | 3 | Parameter Optimization 4 | ====================== 5 | 6 | Any parameter (or set of parameters) in a topas simulation can be subject to formal mathematical optimisation according to a user-defined objective function using the third party library `TopasOpt `_. Some examples of situations where you may wish to optimize parameters include: 7 | 8 | - you have some measured data and you wish to tune some parameters model to best match the measurement 9 | - you are trying to speed up your topas runs and you want to optimise the physics settings to achieve faster runs with minimal change to simulation results 10 | - you are trying to design a new device and want to maximize some performance criteria. 11 | 12 | To get started with TopasOpt, start with the `worked examples `_ 13 | 14 | .. image:: BasicOptLoop.svg 15 | :alt: Basic Optimisation Loop -------------------------------------------------------------------------------- /parameters/physics/index.rst: -------------------------------------------------------------------------------- 1 | .. _physics: 2 | 3 | Physics 4 | ======= 5 | 6 | .. toctree:: 7 | :maxdepth: 2 8 | 9 | intro 10 | modular 11 | reference 12 | optical 13 | misc 14 | -------------------------------------------------------------------------------- /parameters/physics/reference.rst: -------------------------------------------------------------------------------- 1 | .. _physics_reference: 2 | 3 | Reference Physics Lists 4 | ----------------------- 5 | 6 | Reference physics lists are pre-made, complete lists provided by Geant4. 7 | 8 | One complication with reference lists is that they do not support use of :ref:`geometry_parallel`. This means that you cannot place components into a parallel world, and, for the :ref:`geometry_dividable` (TsBox, TsCylinder and TsSphere), you cannot score with a different set of divisions than you have set for the component itself (we handle such complex scoring by creating parallel worlds). TOPAS will give an error if you attempt to use a reference list in a situation where parallel worlds are needed. In such situations, use :ref:`physics_modular`. 9 | 10 | The names of the reference physics lists, and their detailed descriptions, are `here 11 | `_. 12 | 13 | To use a reference physics list, specify the list name in the ``Type`` parameter, such as:: 14 | 15 | s:Ph/Default/Type = "QGSP_BERT_HP" 16 | 17 | Reference physics lists allow only one additional option:: 18 | 19 | d:Ph/Default/CutForAllParticles = 0.05 mm # single range cut to use for all particles 20 | -------------------------------------------------------------------------------- /parameters/scoring/index.rst: -------------------------------------------------------------------------------- 1 | .. _scoring: 2 | 3 | Scoring 4 | ======= 5 | 6 | .. toctree:: 7 | :maxdepth: 2 8 | 9 | intro 10 | volume 11 | surface 12 | phasespace 13 | filter 14 | output 15 | misc 16 | -------------------------------------------------------------------------------- /parameters/scoring/intro.rst: -------------------------------------------------------------------------------- 1 | Introduction 2 | ------------ 3 | 4 | There are two basic classes of scorers: 5 | 6 | * :ref:`scoring_volume` (e.g. Energy or Dose) 7 | * :ref:`scoring_surface` (e.g. Track Count or Phase Space) 8 | 9 | Most scorers output overall quantities that are accumulated over many particles (counts and averages), but other scorers can output specific information per particle (in an n-tuple format). 10 | 11 | You can have any number of scorers. A scorer is defined when you have a line that ends with ``Quantity``, such as:: 12 | 13 | s:Sc/MyScorer/Quantity = "DoseToMedium" 14 | 15 | When your scoring component is the Parent of other components, you have the option to set scoring to record particles not only in the parent component, but also in its children:: 16 | 17 | b:Sc/MyScorer/PropagateToChildren = "True" 18 | 19 | This action is recursive to all levels of subcomponents. 20 | 21 | You may write your own additional scorers (see :ref:`extension_scoring`). 22 | -------------------------------------------------------------------------------- /parameters/source/PhaseSpaceElectron.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/source/PhaseSpaceElectron.png -------------------------------------------------------------------------------- /parameters/source/PhaseSpaceXRays.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/source/PhaseSpaceXRays.png -------------------------------------------------------------------------------- /parameters/source/distributed.rst: -------------------------------------------------------------------------------- 1 | .. _source_distributed: 2 | 3 | Distributed Source 4 | ------------------ 5 | 6 | The Distributed source represents radioactive material randomly distributed within other material. 7 | The user specifies how many random source points to sample within the component. 8 | The particle generator will then start equal numbers of histories from each of these source points. 9 | 10 | The Distributed Source is in many ways similar to the Volumetric Source. 11 | But whereas the Volumetric Source samples a new point every time it generates a particle 12 | (to simulate random activity within a volume of radioactive material), 13 | the Distributed Source does this sampling only a the construction phase 14 | (to simulate a random distribution of radioactive particles within some other material). 15 | 16 | Specify source type as:: 17 | 18 | s:So/Example/Type = "Volumetric" 19 | 20 | Additional required Parameters for the Distributed Source are:: 21 | 22 | s:So/Example/Component = "DemoSphere" 23 | i:So/Example/NumberOfHistoriesInRun = 5 24 | i:So/Example/NumberOfSourcePoints = 4 25 | b:So/Example/RedistributePointsOnNewHistory = "False" 26 | s:So/Example/PointDistribution = "Gaussian" # default to "Flat" 27 | d:So/Example/PointDistributionSigma = 20. mm 28 | 29 | And then the usual other parameters to control particle type, energy, etc., such as: 30 | 31 | s:So/Example/BeamParticle = "gamma" 32 | d:So/Example/BeamEnergy = 10. keV 33 | u:So/Example/BeamEnergySpread = 0. 34 | 35 | Examples that use this source can be found in: 36 | 37 | * examples/Basic/DistributedSourcePointsInShell.txt 38 | * examples/Basic/DistributedSourcePointsInSphere.txt 39 | * examples/Basic/DistributedSourcePointsInSphereGaussian.txt 40 | * examples/Basic/DistributedSourcePointsInTwistedTubs.txt 41 | -------------------------------------------------------------------------------- /parameters/source/emittance_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/source/emittance_1.png -------------------------------------------------------------------------------- /parameters/source/emittance_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/source/emittance_2.png -------------------------------------------------------------------------------- /parameters/source/index.rst: -------------------------------------------------------------------------------- 1 | .. _source: 2 | 3 | Particle Sources 4 | ================ 5 | 6 | .. toctree:: 7 | :maxdepth: 2 8 | 9 | intro 10 | beam 11 | distributed 12 | emittance 13 | environment 14 | isotropic 15 | volumetric 16 | phasespace 17 | misc 18 | -------------------------------------------------------------------------------- /parameters/source/isotropic.rst: -------------------------------------------------------------------------------- 1 | .. _source_isotropic: 2 | 3 | Isotropic Sources 4 | ~~~~~~~~~~~~~~~~~ 5 | 6 | Isotropic sources emit particles uniformly from the center of the specified ``Component``. 7 | 8 | Specify source type as:: 9 | 10 | s:So/MySource/Type = "Isotropic" 11 | 12 | The energies and species of the emitted particles can be specified using the same parameters available to the :ref:`source_beam`. 13 | -------------------------------------------------------------------------------- /parameters/source/volumetric.rst: -------------------------------------------------------------------------------- 1 | .. _source_volumetric: 2 | 3 | Volumetric Source 4 | ----------------- 5 | 6 | The Volumetric source emit particles from randomly sampled starting positions from within the radioactive volume of a given component. 7 | 8 | This source type has been designed for Brachytherapy applications (though there may be other applications as well). 9 | 10 | Specify source type as:: 11 | 12 | s:So/MySource/Type = "Volumetric" 13 | 14 | And then add an additional required parameter: 15 | 16 | s:So/MySource/ActiveMaterial 17 | 18 | to specify which material within the given component should be considered radioactive. 19 | 20 | So, for example, if you have: 21 | 22 | s:So/MySource/Type = "Volumetric" 23 | s:So/MySource/Component = "ActiveSource" 24 | sc:So/MySource/ActiveMaterial = "G4_Ir" 25 | 26 | particles will start from randomly sampled positions within the Iridium parts of the component named ActiveSource. 27 | 28 | Examples that use this source can be found in: 29 | 30 | * examples/Brachytherapy 31 | * examples/Basic/VolumetricSource.txt 32 | 33 | The energies and species of the emitted particles can be specified using the same parameters available to the :ref:`source_beam`. 34 | -------------------------------------------------------------------------------- /parameters/variance/crosssection_enhancement.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/variance/crosssection_enhancement.png -------------------------------------------------------------------------------- /parameters/variance/crosssection_enhancement.rst: -------------------------------------------------------------------------------- 1 | .. _vr_crosssection_enhancement: 2 | 3 | Cross section enhancement 4 | ------------------------- 5 | 6 | In this technique, particle's interaction in a material is enhanced by rescaling the cross-section of a process provided by the user. 7 | 8 | This technique is applied at every interaction of the particle. The user needs to provide a unitless scaling factor and the physical processes of interest:: 9 | 10 | s:Vr/CrossSectionEnhancement/Type = "CrossSectionEnhancement" 11 | sv:Vr/CrossSectionEnhancement/ProcessesNamed = 1 "eBrem" 12 | uv:Vr/CrossSectionEnhancement/EnhancementFactor = 1 20 13 | 14 | .. image:: crosssection_enhancement.png 15 | -------------------------------------------------------------------------------- /parameters/variance/forced_interaction.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/variance/forced_interaction.png -------------------------------------------------------------------------------- /parameters/variance/forced_interaction.rst: -------------------------------------------------------------------------------- 1 | .. _vr_forced_interaction: 2 | 3 | Forced interaction 4 | ------------------- 5 | 6 | In this technique, photons are forced to interact by resampling the interaction probability using an scaling distance factor. 7 | 8 | .. warning:: 9 | 10 | The distance must be smaller than the thickness of the component assigned to the region. 11 | 12 | This technique is applied per region, then the user is responsable to create and assign the components desired to a region. In addition, a scaling distance and physical process needs to be provided:: 13 | 14 | s:Vr/PhotonInteractionForcing/Type = "ForcedInteraction" 15 | sv:Vr/PhotonInteractionForcing/ForRegion/BiasingRegion/ProcessesNamed = 1 "compt" 16 | dv:Vr/PhotonInteractionForcing/ForRegion/BiasingRegion/ForcedDistances = 1 0.1 mm 17 | 18 | .. image:: forced_interaction.png 19 | -------------------------------------------------------------------------------- /parameters/variance/geometrical_particle_split.rst: -------------------------------------------------------------------------------- 1 | .. _vr_geometrical_splitting: 2 | 3 | Geometrical Particle Splitting 4 | ------------------------------ 5 | 6 | TOPAS variance reduction is further described in: 7 | 8 | Ramos-Mendez et al, “Geometrical splitting technique to improve the computational efficiency in Monte Carlo calculations for proton therapy,” Med. Phys. 40, 041718 (2013) 9 | 10 | This technique was designed for heavy charged particles. In this implementation, you must specify whether the beam entering into the sub-component has cylindrical symmetry or not. This is because the particles may or may not be randomly redistributed around the ``SplitAxis``. 11 | 12 | The Russian roulette is applied in a particular direction. That is, at the split plane and prior to being split, the particle is subject to the Russian roulette if its direction does not point towards a Region of Interest (ROI). Then the radius of the ROI and its position on the ``SplitAxis`` must to be defined too. Further, the Russian roulette can be turned on/off at specific surfaces between sub-components. 13 | 14 | .. code:: 15 | 16 | s:Vr/ParticleSplit/Type = "GeometricalParticleSplit" 17 | s:Vr/ParticleSplit/SplitAxis = "zaxis" 18 | d:Vr/ParticleSplit/RussianRoulette/ROIRadius = 7.8 cm 19 | d:Vr/ParticleSplit/RussianRoulette/ROITrans = 10 cm 20 | bv:Vr/ParticleSplit/RussianRoulette = 2 "false" "true" 21 | 22 | To set whether the region at each sub-component is symmetric or not and to define the corresponding split number:: 23 | 24 | bv:Vr/ParticleSplit/Symmetric = 2 "false" "true" 25 | uv:Vr/ParticleSplit/SplitNumber = 2 8 8 26 | 27 | .. image:: geometrical_splitting.png 28 | 29 | In addition for this technique, geometrical Russian roulette will be played if a particle leaves the component or the world in a scheme similar to the :ref:`vr_importance_sampling` technique. 30 | -------------------------------------------------------------------------------- /parameters/variance/geometrical_splitting.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/variance/geometrical_splitting.png -------------------------------------------------------------------------------- /parameters/variance/importance_sampling.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/variance/importance_sampling.png -------------------------------------------------------------------------------- /parameters/variance/importance_sampling.rst: -------------------------------------------------------------------------------- 1 | .. _vr_importance_sampling: 2 | 3 | Importance Sampling 4 | ------------------- 5 | 6 | In this technique, an importance value is assigned to each sub-component. If a particle is transported into a sub-component with a higher importance, then the particle is split. If it is transported into a sub-component with a lower importance, then Russian roulette is played. By default an importance value of 1 is automatically assigned to the parent component and to the world. 7 | 8 | .. warning:: 9 | 10 | It is desirable for the thickness of the sub-components to be similar to the mean free path of the physical process to be biased. 11 | 12 | The sub-component importance values are defined by hand. For example, to split the particles by a factor of 2 between subsequent sub-components, one must to define:: 13 | 14 | s:Vr/ParticleSplit/Type = "ImportanceSampling" 15 | uv:Vr/ParticleSplit/ImportanceValues = 5 1 2 4 8 16 16 | 17 | .. image:: importance_sampling.png 18 | -------------------------------------------------------------------------------- /parameters/variance/index.rst: -------------------------------------------------------------------------------- 1 | .. _variance: 2 | 3 | Variance Reduction 4 | ================== 5 | 6 | .. toctree:: 7 | :maxdepth: 2 8 | 9 | intro 10 | geometrical_particle_split 11 | importance_sampling 12 | weight_window 13 | specific_particles 14 | secondary_biasing 15 | forced_interaction 16 | crosssection_enhancement 17 | -------------------------------------------------------------------------------- /parameters/variance/secondary_biasing.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/variance/secondary_biasing.png -------------------------------------------------------------------------------- /parameters/variance/specific_particles.rst: -------------------------------------------------------------------------------- 1 | Tracking Only Specific Particles 2 | -------------------------------- 3 | 4 | In this option the particles are eliminated just after they were created. The user can choose which particles will be tracked in all components. Nevertheless, the user can specify if a component is going to be neglected. That is, all particles are tracked in such components. This option can be useful when the contribution of certain particles is negligible to the final scored quantity. But it must to be used with caution. This option is not a variance reduction. 5 | 6 | To eliminate particles other than protons and electrons in all components but in component named ``WaterPhantom``:: 7 | 8 | b:Vr/KillOtherParticles/Active = "True" 9 | sv:Vr/KillOtherParticles/HaveNoEffectInComponentsNamed = 1 "WaterPhantom" 10 | sv:Vr/KillOtherParticles/OnlyTrackParticlesNamed = 2 "proton" "e-" 11 | -------------------------------------------------------------------------------- /parameters/variance/split_geometry.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/variance/split_geometry.png -------------------------------------------------------------------------------- /parameters/variance/weight_window.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/topasmc/topas-docs/21ad23da4ab698ddc6196ca2a17780d0f3b4296d/parameters/variance/weight_window.png -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | Sphinx>=1.4.2 2 | docutils==0.17.1 3 | sphinx-rtd-theme 4 | git+https://github.com/davidchall/topas-pygments.git#egg=topas_pygments 5 | --------------------------------------------------------------------------------