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topasmc · Aug 10, 2016 · b1b41b0 · b1b41b0
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diff --git a/examples-docs/Basic/FlatteningFilter.rst b/examples-docs/Basic/FlatteningFilter.rst
@@ -0,0 +1,6 @@
+.. _example_basic_flatteningfilter:
+
+FlatteningFilter.txt
+--------------------
+
+.. literalinclude:: /examples/Basic/FlatteningFilter.txt
diff --git a/examples-docs/Basic/index.rst b/examples-docs/Basic/index.rst
@@ -8,6 +8,7 @@ Basic
 	DividedComponents
 	Emittance_Gaussian
 	Emittance_Twiss
+	FlatteningFilter
 	Isotope
 	LayeredMassGeometry
 	OneBox

diff --git a/examples-docs/PhaseSpace/WriteROOT.rst b/examples-docs/PhaseSpace/WriteROOT.rst
@@ -0,0 +1,6 @@
+.. _example_phsp_root_write:
+
+WriteROOT.txt
+--------------
+
+.. literalinclude:: /examples/PhaseSpace/WriteROOT.txt
diff --git a/examples-docs/PhaseSpace/index.rst b/examples-docs/PhaseSpace/index.rst
@@ -2,13 +2,14 @@ PhaseSpace
 ==========
 
 .. toctree::
-	:maxdepth: 1
+    :maxdepth: 1
 
-	MultiRun_Write_ASCII
-	ReadASCII
-	ReadBinary
-	ReadLimited
-	WriteASCII
-	WriteBinary
-	WriteIonsASCII
-	WriteLimited
+    MultiRun_Write_ASCII
+    ReadASCII
+    ReadBinary
+    ReadLimited
+    WriteASCII
+    WriteBinary
+    WriteIonsASCII
+    WriteLimited
+    WriteROOT
diff --git a/examples/Basic/DNAModelByRegions.txt b/examples/Basic/DNAModelByRegions.txt
@@ -8,7 +8,7 @@
 
 # A simple geometry. The material must be G4_WATER.
 s:Ge/Target/Parent   = "World"
-s:Ge/Target/Type     = "G4Box"
+s:Ge/Target/Type     = "TsBox"
 s:Ge/Target/Material = "G4_WATER"
 d:Ge/Target/HLX      = 0.5 um
 d:Ge/Target/HLY      = 0.5 um
@@ -24,7 +24,7 @@ s:Ge/World/Material = "G4_WATER"
 s:Ge/World/Color    = "blue"
 
 # Start with a physics list
-sv:Ph/Default/Modules = 7 "g4em-penelope" "g4h-phy_QGSP_BIC_HP" "g4decay" "g4ion-binarycascade" "g4h-elastic_HP" "g4stopping" "g4radioactivedecay"
+sv:Ph/Default/Modules = 6 "g4em-penelope" "g4h-phy_QGSP_BIC_HP" "g4decay" "g4ion-binarycascade" "g4h-elastic_HP" "g4stopping"
 # Set the regions where g4em-penelope is switch to g4-dna (opt1)
 sv:Ph/Default/ActiveG4DNAInRegionsNamed = 1 "target"
 s:Ph/Default/DNAModelName = "opt1" # Default is "opt0"
@@ -35,7 +35,7 @@ s:So/Example/Component                = "BeamPosition"
 s:So/Example/BeamParticle             = "proton"
 d:So/Example/BeamEnergy               = 5 MeV
 u:So/Example/BeamEnergySpread         = 0.757504
-s:So/Example/BeamPositionDistribution = "Point"
+s:So/Example/BeamPositionDistribution = "None"
 s:So/Example/BeamAngularDistribution  = "Gaussian"
 d:So/Example/BeamAngularCutoffX       = 90. deg
 d:So/Example/BeamAngularCutoffY       = 90. deg

diff --git a/examples/Basic/Emittance_Gaussian.txt b/examples/Basic/Emittance_Gaussian.txt
@@ -47,7 +47,7 @@ d:Ge/MyBeamSizeInX = 20.0 cm
 d:Ge/MyBeamSizeInY = 20.0 cm
 
 #--- Beam Box
-s:Ge/PlaneAtBeamPosition/Type      = "G4Box"
+s:Ge/PlaneAtBeamPosition/Type      = "TsBox"
 s:Ge/PlaneAtBeamPosition/Material  = "Vacuum"
 s:Ge/PlaneAtBeamPosition/Parent    = "World"
 d:Ge/PlaneAtBeamPosition/HLX       = 0.5 cm + Ge/MyBeamSizeInX

diff --git a/examples/Basic/FlatteningFilter.txt b/examples/Basic/FlatteningFilter.txt
@@ -0,0 +1,35 @@
+# This is not any particular actual flattening filter.
+# It just demonstrates the general principle of how to
+# combine two different kinds of polycones to create
+# a shape that no single polycone can represent.
+
+b:Ge/World/Invisible = "True"
+
+s:Gr/MyViewA/Type = "OpenGL"
+d:Gr/MyViewA/Phi = 45. deg
+d:Gr/MyViewA/Theta = 45. deg
+
+b:Ts/PauseBeforeQuit = "True"
+
+s:Ge/FlatteningFilter/Type = "Group"
+s:Ge/FlatteningFilter/Parent = "World"
+#d:Ge/FlatteningFilter/RotX = 90. deg
+
+# Inner section is implemented as a Solid Polycone
+s:Ge/InnerCone/Type              = "G4SPolycone"
+s:Ge/InnerCone/Parent            = "FlatteningFilter"
+s:Ge/InnerCone/Material          = "G4_Ti"
+s:Ge/InnerCone/Color             = "grey"
+s:Ge/InnerCone/DrawingStyle      = "Solid"
+dv:Ge/InnerCone/R                = 7 0 9 9 6 5 2  0 mm
+dv:Ge/InnerCone/Z                = 7 0 0 1 2 6 8 10 mm
+
+# Outer section is implemented as a Hollow Polycone
+s:Ge/OuterCone/Type              = "G4HPolycone"
+s:Ge/OuterCone/Parent            = "FlatteningFilter"
+s:Ge/OuterCone/Material          = "G4_Ti"
+s:Ge/OuterCone/Color             = "brown"
+s:Ge/OuterCone/DrawingStyle      = "Solid"
+dv:Ge/OuterCone/ROuter           = 4 15 15 15 15 mm
+dv:Ge/OuterCone/RInner           = 4  9  9 10 13 mm
+dv:Ge/OuterCone/Z                = 4  0  1  2  3 mm
diff --git a/examples/Basic/Isotope.txt b/examples/Basic/Isotope.txt
@@ -16,7 +16,7 @@ i:Is/U238/Z = 92
 i:Is/U238/N = 238
 d:Is/U238/A = 238.03 g/mole
 
-s:Ge/MyBox/Type     = "G4Box"
+s:Ge/MyBox/Type     = "TsBox"
 s:Ge/MyBox/Material = "MyUranium"
 s:Ge/MyBox/Parent   = "World"
 d:Ge/MyBox/HLX      = 2.5 m

diff --git a/examples/Basic/LayeredMassGeometry.txt b/examples/Basic/LayeredMassGeometry.txt
@@ -61,7 +61,7 @@ s:So/Example/BeamPositionDistribution = "Flat"
 s:So/Example/BeamPositionCutoffShape  = "Ellipse"
 d:So/Example/BeamPositionCutoffX      = 5 cm
 d:So/Example/BeamPositionCutoffY      = 20 cm
-s:So/Example/BeamAngularDistribution  = "Point"
+s:So/Example/BeamAngularDistribution  = "None"
 i:So/Example/NumberOfHistoriesInRun   = 10
 
 sv:Ph/Default/Modules = 1 "g4em-standard_opt0"

diff --git a/examples/Basic/OneBox.txt b/examples/Basic/OneBox.txt
@@ -1,7 +1,7 @@
 # Simplest TOPAS example.
 # A box in a beam with EM physics.
 
-s:Ge/MyBox/Type     = "G4Box"
+s:Ge/MyBox/Type     = "TsBox"
 s:Ge/MyBox/Material = "Air"
 s:Ge/MyBox/Parent   = "World"
 d:Ge/MyBox/HLX      = 2.5 m

diff --git a/examples/Basic/ShapeTestWithAllParameters.txt b/examples/Basic/ShapeTestWithAllParameters.txt
@@ -6,37 +6,37 @@
 # http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ch04.html#sect.Geom.Solids
 
 # Box
-s:Ge/DemoG4Box/Type                  = "G4Box"
-s:Ge/DemoG4Box/Parent                = "World"
-s:Ge/DemoG4Box/Material              = "Air"
-d:Ge/DemoG4Box/TransX                = 0 cm
-d:Ge/DemoG4Box/TransY                = 0 cm
-d:Ge/DemoG4Box/TransZ                = 0 cm
-d:Ge/DemoG4Box/RotX                  = 0 deg
-d:Ge/DemoG4Box/RotY                  = 0 deg
-d:Ge/DemoG4Box/RotZ                  = 0 deg
-d:Ge/DemoG4Box/HLX                   = 30. mm
-d:Ge/DemoG4Box/HLY                   = 40. mm
-d:Ge/DemoG4Box/HLZ                   = 60. mm
-s:Ge/DemoG4Box/Color                 = "white"
+s:Ge/DemoBox/Type                    = "TsBox"
+s:Ge/DemoBox/Parent                  = "World"
+s:Ge/DemoBox/Material                = "Air"
+d:Ge/DemoBox/TransX                  = 0 cm
+d:Ge/DemoBox/TransY                  = 0 cm
+d:Ge/DemoBox/TransZ                  = 0 cm
+d:Ge/DemoBox/RotX                    = 0 deg
+d:Ge/DemoBox/RotY                    = 0 deg
+d:Ge/DemoBox/RotZ                    = 0 deg
+d:Ge/DemoBox/HLX                     = 30. mm
+d:Ge/DemoBox/HLY                     = 40. mm
+d:Ge/DemoBox/HLZ                     = 60. mm
+s:Ge/DemoBox/Color                   = "white"
 
-# Tubs
-s:Ge/DemoTubs/Type                   = "G4Tubs"
-s:Ge/DemoTubs/Parent                 = "World"
-s:Ge/DemoTubs/Material               = "Air"
-d:Ge/DemoTubs/TransX                 = 0 cm
-d:Ge/DemoTubs/TransY                 = 0 cm
-d:Ge/DemoTubs/TransZ                 = 12 cm
-d:Ge/DemoTubs/RotX                   = 0 deg
-d:Ge/DemoTubs/RotY                   = 0 deg
-d:Ge/DemoTubs/RotZ                   = 0 deg
-d:Ge/DemoTubs/RMin                   = 10 mm
-d:Ge/DemoTubs/RMax                   = 15 mm
-d:Ge/DemoTubs/HL                     = 20 mm
-d:Ge/DemoTubs/SPhi                   = 1. rad
-d:Ge/DemoTubs/DPhi                   = 1.5 rad
-s:Ge/DemoTubs/Color                  = "lightblue"
-s:Ge/DemoTubs/DrawingStyle           = "FullWireFrame"
+# Cylinder
+s:Ge/DemoCylinder/Type               = "TsCylinder"
+s:Ge/DemoCylinder/Parent             = "World"
+s:Ge/DemoCylinder/Material           = "Air"
+d:Ge/DemoCylinder/TransX             = 0 cm
+d:Ge/DemoCylinder/TransY             = 0 cm
+d:Ge/DemoCylinder/TransZ             = 12 cm
+d:Ge/DemoCylinder/RotX               = 0 deg
+d:Ge/DemoCylinder/RotY               = 0 deg
+d:Ge/DemoCylinder/RotZ               = 0 deg
+d:Ge/DemoCylinder/RMin               = 10 mm
+d:Ge/DemoCylinder/RMax               = 15 mm
+d:Ge/DemoCylinder/HL                 = 20 mm
+d:Ge/DemoCylinder/SPhi               = 1. rad
+d:Ge/DemoCylinder/DPhi               = 1.5 rad
+s:Ge/DemoCylinder/Color              = "lightblue"
+s:Ge/DemoCylinder/DrawingStyle       = "FullWireFrame"
 
 # CutTubs
 s:Ge/DemoCutTubs/Type                = "G4CutTubs"
@@ -153,7 +153,7 @@ d:Ge/DemoGTrap/Alp2                  = 10 deg
 s:Ge/DemoGTrap/Color                 = "indigo"
 
 # Sphere
-s:Ge/DemoSphere/Type                 = "G4Sphere"
+s:Ge/DemoSphere/Type                 = "TsSphere"
 s:Ge/DemoSphere/Parent               = "World"
 s:Ge/DemoSphere/Material             = "Air"
 d:Ge/DemoSphere/TransX               = 0 cm
@@ -233,8 +233,8 @@ d:Ge/DemoSPolycone/RotY              = 0 deg
 d:Ge/DemoSPolycone/RotZ              = 0 deg
 d:Ge/DemoSPolycone/PhiStart          = 0.25 rad
 d:Ge/DemoSPolycone/PhiTotal          = 1.5 rad
-dv:Ge/DemoSPolycone/R                = 9 0 10 10 5 5 10 10 2 2 mm
-dv:Ge/DemoSPolycone/Z                = 9 5 7 9 11 25 27 29 31 35 mm
+dv:Ge/DemoSPolycone/R                = 10 0 10 10 5 5 10 10 2 2 0 mm
+dv:Ge/DemoSPolycone/Z                = 10 5 7 9 11 25 27 29 31 35 35 mm
 s:Ge/DemoSPolycone/Color             = "grey"
 s:Ge/DemoSPolycone/DrawingStyle      = "FullWireFrame"
 

diff --git a/examples/Basic/ShapeTestWithOnlyRequiredParameters.txt b/examples/Basic/ShapeTestWithOnlyRequiredParameters.txt
@@ -6,23 +6,23 @@
 # http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ch04.html#sect.Geom.Solids
 
 # Box
-s:Ge/DemoG4Box/Type                  = "G4Box"
-s:Ge/DemoG4Box/Parent                = "World"
-s:Ge/DemoG4Box/Material              = "Air"
-d:Ge/DemoG4Box/HLX                   = 30. mm
-d:Ge/DemoG4Box/HLY                   = 40. mm
-d:Ge/DemoG4Box/HLZ                   = 60. mm
-s:Ge/DemoG4Box/Color                 = "white"
+s:Ge/DemoBox/Type                    = "TsBox"
+s:Ge/DemoBox/Parent                  = "World"
+s:Ge/DemoBox/Material                = "Air"
+d:Ge/DemoBox/HLX                     = 30. mm
+d:Ge/DemoBox/HLY                     = 40. mm
+d:Ge/DemoBox/HLZ                     = 60. mm
+s:Ge/DemoBox/Color                   = "white"
 
 # Tubs
-s:Ge/DemoTubs/Type                   = "G4Tubs"
-s:Ge/DemoTubs/Parent                 = "World"
-s:Ge/DemoTubs/Material               = "Air"
-d:Ge/DemoTubs/TransZ                 = 12 cm
-d:Ge/DemoTubs/RMax                   = 15 mm
-d:Ge/DemoTubs/HL                     = 20 mm
-s:Ge/DemoTubs/Color                  = "lightblue"
-s:Ge/DemoTubs/DrawingStyle           = "FullWireFrame"
+s:Ge/DemoCylinder/Type               = "TsCylinder"
+s:Ge/DemoCylinder/Parent             = "World"
+s:Ge/DemoCylinder/Material           = "Air"
+d:Ge/DemoCylinder/TransZ             = 12 cm
+d:Ge/DemoCylinder/RMax               = 15 mm
+d:Ge/DemoCylinder/HL                 = 20 mm
+s:Ge/DemoCylinder/Color              = "lightblue"
+s:Ge/DemoCylinder/DrawingStyle       = "FullWireFrame"
 
 # CutTubs
 s:Ge/DemoCutTubs/Type                = "G4CutTubs"
@@ -122,7 +122,7 @@ d:Ge/DemoGTrap/Alp2                  = 10 deg
 s:Ge/DemoGTrap/Color                 = "indigo"
 
 # Sphere
-s:Ge/DemoSphere/Type                 = "G4Sphere"
+s:Ge/DemoSphere/Type                 = "TsSphere"
 s:Ge/DemoSphere/Parent               = "World"
 s:Ge/DemoSphere/Material             = "Air"
 d:Ge/DemoSphere/TransZ               = 124 cm
@@ -171,8 +171,8 @@ s:Ge/DemoSPolycone/Type              = "G4SPolycone"
 s:Ge/DemoSPolycone/Parent            = "World"
 s:Ge/DemoSPolycone/Material          = "Air"
 d:Ge/DemoSPolycone/TransZ            = 186 cm
-dv:Ge/DemoSPolycone/R                = 9 0 10 10 5 5 10 10 2 2 mm
-dv:Ge/DemoSPolycone/Z                = 9 5 7 9 11 25 27 29 31 35 mm
+dv:Ge/DemoSPolycone/R                = 10 0 10 10 5 5 10 10 2 2 0 mm
+dv:Ge/DemoSPolycone/Z                = 10 5 7 9 11 25 27 29 31 35 35 mm
 s:Ge/DemoSPolycone/Color             = "grey"
 s:Ge/DemoSPolycone/DrawingStyle      = "FullWireFrame"
 

diff --git a/examples/Basic/TwoBeams.txt b/examples/Basic/TwoBeams.txt
@@ -22,7 +22,7 @@ s:So/Imaging/BeamPositionCutoffShape  = "Ellipse"
 s:So/Imaging/BeamPositionDistribution = "Flat"
 d:So/Imaging/BeamPositionCutoffX      = 7. cm
 d:So/Imaging/BeamPositionCutoffY      = 21. cm
-s:So/Imaging/BeamAngularDistribution  = "Point"
+s:So/Imaging/BeamAngularDistribution  = "None"
 i:So/Imaging/NumberOfHistoriesInRun   = 5
 
 s:So/Therapy/Type                     = "Beam"

diff --git a/examples/DICOM/DoseTo4DCT.txt b/examples/DICOM/DoseTo4DCT.txt
@@ -78,7 +78,7 @@ s:So/Example/BeamPositionDistribution = "Flat"
 s:So/Example/BeamPositionCutoffShape  = "Ellipse"
 d:So/Example/BeamPositionCutoffX      = 0.5 cm
 d:So/Example/BeamPositionCutoffY      = 0.5 cm
-s:So/Example/BeamAngularDistribution  = "Point"
+s:So/Example/BeamAngularDistribution  = "None"
 i:So/Example/NumberOfHistoriesInRun   = 100
 
 sv:Ph/Default/Modules = 1 "g4em-standard_opt0"

diff --git a/examples/DICOM/DoseToCT.txt b/examples/DICOM/DoseToCT.txt
@@ -69,8 +69,8 @@ s:So/Example/BeamPositionDistribution = "Flat"
 s:So/Example/BeamPositionCutoffShape  = "Ellipse"
 d:So/Example/BeamPositionCutoffX      = 5. cm
 d:So/Example/BeamPositionCutoffY      = 20. cm
-s:So/Example/BeamAngularDistribution  = "Point"
-i:So/Example/NumberOfHistoriesInRun   = 10000
+s:So/Example/BeamAngularDistribution  = "None"
+i:So/Example/NumberOfHistoriesInRun   = 500
 
 # Uncomment to activate graphics
 s:Gr/ViewA/Type           = "OpenGL"
@@ -83,6 +83,6 @@ d:Gr/ViewA/Phi            = 10 deg
 # Extra graphics options to handle complex voxel geometries
 i:Gr/ShowOnlyOutlineIfVoxelCountExceeds = 210000000
 
-i:Ts/ShowHistoryCountAtInterval = 5000
+i:Ts/ShowHistoryCountAtInterval = 100
 
 b:Ts/PauseBeforeQuit = "True"
diff --git a/examples/DICOM/Implant.txt b/examples/DICOM/Implant.txt
@@ -67,7 +67,7 @@ s:So/Example/BeamPositionDistribution = "Flat"
 s:So/Example/BeamPositionCutoffShape  = "Ellipse"
 d:So/Example/BeamPositionCutoffX      = 5 cm
 d:So/Example/BeamPositionCutoffY      = 20 cm
-s:So/Example/BeamAngularDistribution  = "Point"
+s:So/Example/BeamAngularDistribution  = "None"
 i:So/Example/NumberOfHistoriesInRun   = Tf/Num/Value
 
 # Graphics

diff --git a/examples/Graphics/TestGraphics.txt b/examples/Graphics/TestGraphics.txt
@@ -1,6 +1,6 @@
 # Demonstrates a variety of Graphics options
 
-s:Ge/Box/Type         = "G4Box"
+s:Ge/Box/Type         = "TsBox"
 s:Ge/Box/Parent       = "World"
 s:Ge/Box/Material     = "G4_WATER"
 d:Ge/Box/HLX          = 1. m

diff --git a/examples/Graphics/TwoProjections.txt b/examples/Graphics/TwoProjections.txt
@@ -19,7 +19,7 @@ d:Gr/MyOGLb/PerspectiveAngle = 10. deg
 d:Gr/MyOGLb/Theta            = 45. deg
 d:Gr/MyOGLb/Phi              = 45. deg
 
-s:Ge/Box/Type     = "G4Box"
+s:Ge/Box/Type     = "TsBox"
 s:Ge/Box/Parent   = "World"
 s:Ge/Box/Material = "G4_WATER"
 d:Ge/Box/HLX      = 1. m

diff --git a/examples/Nozzle/ConstantsForNozzles.txt b/examples/Nozzle/ConstantsForNozzles.txt
@@ -70,15 +70,14 @@ s:Ma/CompensatorLucite/DefaultColor         = "grey"
 
 ########################################
 # Dummy beam
-# Point type beam
 ########################################
 s:So/Example/Type                     = "Beam"
 s:So/Example/Component                = "BeamPosition"
 s:So/Example/BeamParticle             = "proton"
 d:So/Example/BeamEnergy               = 160.0 MeV
 u:So/Example/BeamEnergySpread         = 0.0
-s:So/Example/BeamPositionDistribution = "Point"
-s:So/Example/BeamAngularDistribution  = "Point"
+s:So/Example/BeamPositionDistribution = "None"
+s:So/Example/BeamAngularDistribution  = "None"
 i:So/Example/NumberOfHistoriesInRun   = 10
 
 

diff --git a/examples/Nozzle/RasterScanningPattern.txt b/examples/Nozzle/RasterScanningPattern.txt
@@ -25,5 +25,5 @@ s:Tf/BField1st/Function = "Step"
 dv:Tf/BField1st/Times   = 4  0.25 0.5 0.75 1.0 s
 dv:Tf/BField1st/Values  = 4 -0.105 -0.035 0.035  0.105 tesla
 
-d:Ge/Dipole1/Strength = Tf/BField1st/Value tesla
-d:Ge/Dipole2/Strength = Tf/BField2nd/Value tesla
+d:Ge/Dipole1/MagneticFieldStrength = Tf/BField1st/Value tesla
+d:Ge/Dipole2/MagneticFieldStrength = Tf/BField2nd/Value tesla