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update dosimetry/DNA example to use DNA Activator #74

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33 changes: 0 additions & 33 deletions dosimetry/DNA/output.mac
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47 changes: 0 additions & 47 deletions dosimetry/DNA/output/plot.C
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47 changes: 0 additions & 47 deletions dosimetry/DNA/plot.C
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0 dosimetry/DNA/GateMaterials.db → dosimetry/dna/GateMaterials.db
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17 changes: 9 additions & 8 deletions dosimetry/DNA/README → dosimetry/dna/README
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=======================================
GATE - mixedDNA
GATE - DNA physics lists and activator
=======================================

Authors: Q.T. Pham, Y. Perrot, L. Maigne*
Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France
* Corresponding author: maigne@clermont.in2p3.fr
Authors: L. Maigne, A. Pereda*
Laboratoire de Physique de Clermont, CNRS/IN2P3 - Université Clermont Auvergne, France
* Corresponding author: lydia.maigne@clermont.in2p3.fr


!! Be careful you must use the so-called "G4_WATER" material while using Geant4 DNA processes and models !!


---> Description

This example shows how to mix Standard and DNA physics list in the same simulation.
This example shows how to use standard and DNA physics list (in specific regions) in the same simulation.

---> Set-up

The geometry consists in a world volume made of liquid water (G4_WATER material) including three boxes Target1, Target2, Target3 made of liquid water (G4_WATER material) of thickness 50 micrometers aligned along the Z axis.
The geometry consists in a world volume made of liquid water (G4_WATER material) including three boxes Target1, Target2, Target3
made of liquid water (G4_WATER material) of thickness 50 micrometers aligned along the Z axis.
Monoenergetic protons of 8 MeV are shot along the Z axis at 10 micrometers of the face of the first box Target1.

---> Physics

Geant4 Standard option 3 physics list is assigned to the world volume with a cut of 4 micrometers (2.9 keV electrons in liquid water).
Geant4 DNA physics list is assigned to Target1 and Target3 (note that cut is not active using Geant4 DNA processes and models).
Geant4 Standard option 4 physics list is assigned to the world volume with a cut of 4 micrometers (2.9 keV electrons in liquid water).
Geant4 DNA physics list option 4 is assigned to Target1 and Target3 (note that cut is not active using Geant4 DNA processes and models).
A KillActor is used to kill electrons with kinetic energy below 8 eV. It prevents electrons to be trapped into single scattering.

---> Output
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0 dosimetry/DNA/geometry.mac → dosimetry/dna/geometry.mac
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4 changes: 2 additions & 2 deletions dosimetry/DNA/mixedDNA.mac → dosimetry/dna/main.mac
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Expand Up @@ -31,7 +31,7 @@
#=======================================================

/gate/run/initialize

/gate/physics/displayCuts

#=====================================================
# VISUALISATION
Expand All @@ -55,5 +55,5 @@
# SIMULTAION # START BEAMS
#=======================================================

/gate/application/setTotalNumberOfPrimaries 50
/gate/application/setTotalNumberOfPrimaries 2
/gate/application/start
33 changes: 33 additions & 0 deletions dosimetry/dna/output.mac
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#Energy Spectrum Target1

/gate/actor/addActor EnergySpectrumActor MyActor1
/gate/actor/MyActor1/save output/target1.root
/gate/actor/MyActor1/attachTo Target1
/gate/actor/MyActor1/energySpectrum/setEmin 0 eV
/gate/actor/MyActor1/energySpectrum/setEmax 10.0 keV
/gate/actor/MyActor1/energySpectrum/setNumberOfBins 50
/gate/actor/MyActor1/energyLossHisto/setEdepMin 0 eV
/gate/actor/MyActor1/energyLossHisto/setEdepMax 10.0 keV
/gate/actor/MyActor1/energyLossHisto/setNumberOfEdepBins 50

#Energy Spectrum Target2
/gate/actor/addActor EnergySpectrumActor MyActor2
/gate/actor/MyActor2/save output/target2.root
/gate/actor/MyActor2/attachTo Target2
/gate/actor/MyActor2/energySpectrum/setEmin 0 eV
/gate/actor/MyActor2/energySpectrum/setEmax 10.0 keV
/gate/actor/MyActor2/energySpectrum/setNumberOfBins 50
/gate/actor/MyActor1/energyLossHisto/setEdepMin 0 eV
/gate/actor/MyActor1/energyLossHisto/setEdepMax 10.0 keV
/gate/actor/MyActor1/energyLossHisto/setNumberOfEdepBins 50

#Energy Spectrum Target3
/gate/actor/addActor EnergySpectrumActor MyActor3
/gate/actor/MyActor3/save output/target3.root
/gate/actor/MyActor3/attachTo Target3
/gate/actor/MyActor3/energySpectrum/setEmin 0 eV
/gate/actor/MyActor3/energySpectrum/setEmax 10.0 keV
/gate/actor/MyActor3/energySpectrum/setNumberOfBins 50
/gate/actor/MyActor1/energyLossHisto/setEdepMin 0 eV
/gate/actor/MyActor1/energyLossHisto/setEdepMax 10.0 keV
/gate/actor/MyActor1/energyLossHisto/setNumberOfEdepBins 50
12 changes: 5 additions & 7 deletions dosimetry/DNA/physics.mac → dosimetry/dna/physics.mac
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# PHYSICS
#======================================================

/gate/physics/addPhysicsListMixed emstandard_opt3_mixed_emdna
#/gate/physics/addPhysicsListMixed emlivermore_mixed_emdna

/gate/physics/SetDNAInRegion Target1
/gate/physics/SetDNAInRegion Target3

/gate/physics/ConstructProcessMixed
/gate/physics/addPhysicsList emstandard_opt4
# possible values for the line after:
# DNA_Opt0, DNA_Opt2, DNA_Opt4, DNA_Opt4a, DNA_Opt6, DNA_Opt6a, DNA_Opt7
/process/em/AddDNARegion Target1 DNA_Opt4
/process/em/AddDNARegion Target3 DNA_Opt4

/gate/physics/Gamma/SetCutInRegion world 4 um
/gate/physics/Electron/SetCutInRegion world 4 um
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43 changes: 43 additions & 0 deletions dosimetry/dna/plot.C
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// *********************************************************************
// To execute this macro under ROOT,
// 1 - launch ROOT (usually type 'root' at your machine's prompt)
// 2 - type '.X plot.C' at the ROOT session prompt
// by Q.T.PHAM
// *********************************************************************
{
gROOT->Reset();
gStyle->SetPalette(1);
gROOT->SetStyle("Plain");
Double_t scale;

c1 = new TCanvas ("c1","graph",66,52,1000,500);

TFile* f =new TFile ("output/target1.root");
f->ls();

TH1F * h1 = (TH1F*)f->Get("energyEdepSpectrum");
h1->SetLineColor(kBlue);
h1->SetTitle("Production of Secondary Particles");
h1->GetXaxis()->SetTitle("Edep (MeV)");
h1->GetYaxis()->SetTitle("Frequency");
h1->GetXaxis()->SetRangeUser(0.001,0.007);
h1->SetStats(0);
h1->Draw("PE");

TFile* f2 =new TFile ("output/target2.root");
TH1F * h2 = (TH1F*)f2->Get("energyEdepSpectrum");
h2->SetLineColor(kRed);
h2->Draw("PESAME");

TFile* f3 =new TFile ("output/target3.root");
TH1F * h3 = (TH1F*)f3->Get("energyEdepSpectrum");
h3->SetLineColor(kGreen);
h3->Draw("PESAME");

leg = new TLegend(0.9,0.7,0.48,0.9);
leg->SetFillColor(kWhite);
leg->AddEntry(h1,"target1","l");
leg->AddEntry(h2,"target2","l");
leg->AddEntry(h3,"target3","l");
leg->Draw();
}
19 changes: 10 additions & 9 deletions dosimetry/DNA/readme.md → dosimetry/dna/readme.md
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Authors:
* Q.T. Pham, Y. Perrot, L. Maigne<br>
Laboratoire de Physique Corpusculaire de Clermont-Ferrand, CNRS/IN2P3 - Clermont University, France<br>
Corresponding author: maigne@clermont.in2p3.fr
Authors:
* L. Maigne, A. Pereda<br>
Laboratoire de Physique de Clermont, CNRS/IN2P3 - Université Clermont Auvergne, France<br>
Corresponding author: lydia.maigne@clermont.in2p3.fr

!! Be careful you must use the so-called "G4_WATER" material while using Geant4 DNA processes and models !!

## Description

This example shows how to **mix Standard and DNA physics list** in the same simulation.
This example shows how to use standard and DNA physics list (in specific regions) in the same simulation.

## Set-up

The geometry consists in a world volume made of liquid water (G4_WATER material) including three boxes Target1, Target2, Target3
The geometry consists in a world volume made of liquid water (G4_WATER material) including three boxes Target1, Target2, Target3
made of liquid water (G4_WATER material) of thickness 50 micrometers aligned along the Z axis.
Monoenergetic protons of 8 MeV are shot along the Z axis at 10 micrometers of the face of the first box Target1.

## Physics

Geant4 Standard option 3 physics list is assigned to the world volume with a cut of 4 micrometers (2.9 keV electrons in liquid water).
Geant4 DNA physics list is assigned to Target1 and Target3 (note that cut is not active using Geant4 DNA processes and models).
Geant4 Standard option 4 physics list is assigned to the world volume with a cut of 4 micrometers (2.9 keV electrons in liquid water).
Geant4 DNA physics list option 4 is assigned to Target1 and Target3 (note that cut is not active using Geant4 DNA processes and models).
A KillActor is used to kill electrons with kinetic energy below 8 eV. It prevents electrons to be trapped into single scattering.

## Output

The production of secondary particles is scored in each Target via EnergySpectrumActor.
To analyse the spectrum with ROOT, use the plot.C macro file.
One can check the correct production of secondaries: from 2.9 keV in Target2, whereas the Geant4 DNA models in Target1 and Target3 are able to produce secondaries below 2.9 keV.
One can check the correct production of secondaries: from 2.9 keV in Target2, whereas the Geant4 DNA models in
Target1 and Target3 are able to produce secondaries below 2.9 keV.
4 changes: 2 additions & 2 deletions dosimetry/DNA/source.mac → dosimetry/dna/source.mac
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/gate/source/addSource mybeam gps
/gate/source/mybeam/gps/particle proton
/gate/source/mybeam/gps/energy 8 MeV
/gate/source/mybeam/gps/energytype Mono
/gate/source/mybeam/gps/type Point
/gate/source/mybeam/gps/ene/type Mono
/gate/source/mybeam/gps/pos/type Point
/gate/source/mybeam/gps/direction 0 0 1
/gate/source/mybeam/gps/pos/centre 0. 0. -0.01 cm
0 dosimetry/DNA/verbose.mac → dosimetry/dna/verbose.mac
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0 dosimetry/DNA/visu.mac → dosimetry/dna/visu.mac
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