[Gate-users] Radiotherapy and physics lists question

Lana Beck lana.beck at bristol.ac.uk
Thu Jan 30 14:33:58 CET 2020 

Dear David,

Thanks for your response.

Printing the processes used in emstandard_opt3 gives:
* e-
    - msc
    - eIoni
    - eBrem
    - ePairProd
  * gamma
    - phot
    - compt
    - conv
    - Rayl

Hence where eBrem has been used before with setSecBiasing, compt should instead be used to enhance the production of contamination electrons from the linac. So in the file main-write-PhS.mac if I add
/process/em/setSecBiasing compt linac 100 100 MeV (*)
this should produce 100 times the electrons as it does for gammas and eBrem.

However it does not. Using the deprecated command does work:
/gate/physics/addProcess Compton
/gate/physics/processes/Compton/setModel StandardModel gamma
/gate/physics/processes/Compton/activateSplitting gamma 100
/gate/physics/processes/Compton/addFilter         volumeFilter secondaries
/gate/physics/processes/Compton/secondaries/volumeFilter/addVolume        linac

(I am just using the full linac volume for this example).
I've attached the full code at the end just incase of confusion.

Many thanks,
Lana

On Tue, Jan 28, 2020 at 7:27 PM Lana Beck <lana.beck at bristol.ac.uk> wrote:

> Dear Dr Sarrut,
>
> I have a question about the example in your gitbook:
> https://dsarrut.gitbooks.io/gate-exercises/content/exercise4-linac.html
> and the associated code here:
>
> https://gitlab.in2p3.fr/davidsarrut/gate-exercices/blob/master/linac/mac/main-write-PhS.mac
>

the gitbook link is no more maintained, please use:
https://davidsarrut.pages.in2p3.fr/gate-exercices-site/ (for the moment it
is essentially the same).


> If you prefer I can send my question to the gate-users list but as it
> pertained to your gitbook particularly I thought I should email you first.
>

yes I prefer to copy the gate-user list please.


> I was wondering about the line (110) in the example:
> /process/em/setSecBiasing eBrem target 100 100 MeV
>
> However, in the Section 5.2.1.1 in the gate manual it says to use:
> /gate/physics/processes/Bremsstrahlung/activateSplitting e- 100
>
> https://opengate.readthedocs.io/en/latest/cut_and_variance_reduction_technics.html
> and then I guess filters could be used for volume and energy.
>
> Is there a difference in these two methods? Of course the latter one
> requires using:
> /gate/physics/addProcess Bremsstrahlung
> /gate/physics/processes/Bremsstrahlung/setModel StandardModel e-
> /gate/physics/processes/Bremsstrahlung/setModel StandardModel e+
> in order for activateSplitting to work. However I'm not really sure what
> happens when adding the Bremsstrahlung process since eBrem is already
> included in the initialised methods of emstandard_opt3.
>
>
the opengate doc is wrong here and should be updated. Please use the first
macro "setSecBiasing". The second sets of macros are now deprecated and
should not be used.



> I am interested in the electron contamination from the linac head and I
> need a large sample. Hence, I wanted to do something similar for Compton
> Scattering and I'm not sure which method to use.
>

For Compton Scattering, use the same setSecBiasing command but with the
Compton process name. You should find the name of the Compton somewhere in
the Geant4 document, sorry, dont know where ...

David


>
> Any advice would be greatly appreciated.
>
> Kind regards,
> Lana



#=====================================================
# VERBOSITY
#=====================================================

/control/execute mac/verbose.mac

#=====================================================
# VISUALISATION
#=====================================================

/control/execute mac/visu.mac

# =====================================================
# GEOMETRY
# =====================================================

/gate/geometry/setMaterialDatabase data/GateMaterials.db


# WORLD
/gate/world/setMaterial            Air
/gate/world/geometry/setXLength    1.0 m
/gate/world/geometry/setYLength    1.0 m
/gate/world/geometry/setZLength    1.0 m
/gate/world/vis/setVisible 1

# LINAC HEAD
# World origin is in the center of the beam e- source (not the real
# isocenter of the gantry room)
/gate/geometry/setMaterialDatabase data/LinacMaterials.db
/control/execute mac/linac_head.mac

# VIRTUAL PLANE FOR PHASE SPACE
/gate/linac/daughters/name               PhS_Plane
/gate/linac/daughters/insert             cylinder
/gate/PhS_Plane/setMaterial              Vacuum
/gate/PhS_Plane/geometry/setRmin         0 mm
/gate/PhS_Plane/geometry/setRmax         40 mm
/gate/PhS_Plane/geometry/setHeight       1 nm
/gate/PhS_Plane/placement/setTranslation 0.0 0.0 -297 mm
/gate/PhS_Plane/vis/setColor             white
/gate/PhS_Plane/vis/setVisible           1

# =====================================================
# PHYSICS
# =====================================================

/gate/physics/addPhysicsList emstandard_opt3

/gate/physics/Gamma/SetCutInRegion      world 1 mm
/gate/physics/Electron/SetCutInRegion   world 1 mm
/gate/physics/Positron/SetCutInRegion   world 1 mm

# /gate/physics/addProcess Compton
# /gate/physics/processes/Compton/setModel StandardModel gamma
# /gate/physics/processes/Compton/activateSplitting gamma 100
# /gate/physics/processes/Compton/addFilter         volumeFilter secondaries
# /gate/physics/processes/Compton/secondaries/volumeFilter/addVolume        linac

#=====================================================
# DETECTORS
#=====================================================

# ----------------------------------------------------
# Kill actor to stop particles when they go inside a region

/gate/actor/addActor          KillActor killer0
/gate/actor/killer0/attachTo  kill_box_top
/gate/actor/addActor          KillActor killer1
/gate/actor/killer1/attachTo  kill_box_bottom
/gate/actor/addActor          KillActor killer2
/gate/actor/killer2/attachTo  kill_box_bottom2

# ----------------------------------------------------
# the following actor regularly store the current number of
# event/track/step in a file

/gate/actor/addActor               SimulationStatisticActor stat
/gate/actor/stat/save              output/output-writePhS-stat.txt
/gate/actor/stat/saveEveryNSeconds 20

# ----------------------------------------------------
# Phase space storage (a PhS for gamma, another for e-)

/gate/actor/addActor                         PhaseSpaceActor PhS_g
/gate/actor/PhS_g/attachTo                   PhS_Plane
/gate/actor/PhS_g/save                     output/output-PhS-g.root
/gate/actor/PhS_g/enableParticleName         false
/gate/actor/PhS_g/enableProductionVolume     false
/gate/actor/PhS_g/enableProductionProcess    false
/gate/actor/PhS_g/useVolumeFrame             true
/gate/actor/PhS_g/addFilter                  particleFilter
/gate/actor/PhS_g/particleFilter/addParticle gamma
/gate/actor/PhS_g/enableZPosition            true
#/gate/actor/PhS_g/saveEveryNSeconds          20

# /gate/actor/addActor                         PhaseSpaceActor PhS_e
# /gate/actor/PhS_e/attachTo                   PhS_Plane
# /gate/actor/PhS_e/save               output/output-PhS-e.root
# /gate/actor/PhS_e/enableParticleName         false
# /gate/actor/PhS_e/enableProductionVolume     false
# /gate/actor/PhS_e/enableProductionProcess    false
# /gate/actor/PhS_e/useVolumeFrame             true
# /gate/actor/PhS_e/addFilter                  particleFilter
# /gate/actor/PhS_e/particleFilter/addParticle e-
# /gate/actor/PhS_e/enableZPosition            false
# /gate/actor/PhS_e/saveEveryNSeconds          20

#=====================================================
# INITIALISATION
#=====================================================

/gate/run/initialize

# Bremsstrahlung splitting : generate 100 photon (if below 100 MeV) with weight 1/100
/process/em/setSecBiasing eBrem target 100 100 MeV
/process/em/setSecBiasing compt linac 100 100 MeV

#=====================================================
# BEAMS
#=====================================================

/gate/source/addSource                mybeam gps
/gate/source/mybeam/gps/particle      e-
/gate/source/mybeam/gps/pos/type      Beam
/gate/source/mybeam/gps/pos/rot1      0 1 0
/gate/source/mybeam/gps/pos/rot2      1 0 0
/gate/source/mybeam/gps/pos/shape     Circle
/gate/source/mybeam/gps/pos/centre    0. 0. 0.6 mm
/gate/source/mybeam/gps/pos/sigma_x   1.274 mm
/gate/source/mybeam/gps/pos/sigma_y   1.274 mm
/gate/source/mybeam/gps/ang/rot1      1 0 0
/gate/source/mybeam/gps/ang/rot2      0 1 0
/gate/source/mybeam/gps/ang/type      beam1d
/gate/source/mybeam/gps/ang/sigma_r   0 deg
/gate/source/mybeam/gps/ene/type      Gauss
/gate/source/mybeam/gps/ene/mono      6.7 MeV
/gate/source/mybeam/gps/ene/sigma     0.077 MeV
/gate/source/mybeam/gps/direction     0 0 -1

#=====================================================
# START BEAMS
#=====================================================

/gate/random/setEngineName MersenneTwister
# /gate/random/setEngineSeed auto
/gate/random/setEngineSeed 123456

/gate/application/noGlobalOutput

#/tracking/verbose 2

/gate/application/setTotalNumberOfPrimaries 10
/gate/application/start

/gate/physics/processList Enabled
/gate/physics/processList Initialized
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