Monoenergetic photon pencil beam

== <span style="color:#000080"> Introduction </span> ==

This example shows the dose distribution in water along the incident photon beam. The beam hits the water cube surface and deposits a dose under the surface of the water. The volume of the water cube is divided into slices perpendicular to the incident beam. At each slice the deposited dose and energy is computed. 

The slices are created using class '''G4PVReplica'''. The energy and dose are scored using classes '''G4UserSteppingAction''' and '''G4UserRunAction'''. Photons are generated using '''G4ParticleGun''' class. There is an option to chose among several EM physics lists.

== <span style="color:#000080"> Setting up the environment </span> == 

; Connect to HEP cluster and create folder PhotonPBFolder in your area

<pre style="color: #800000; background-color: #dcdcdc">
ssh -X username@plus1.hep.ucl.ac.uk 

password: type your password here

cd /home/username/ 

mkdir PhotonPBFolder 

cd PhotonPBFolder  
</pre>

; Setup your environment

<pre style="color: #800000; background-color: #dcdcdc">
source /unix/pbt/software/dev/bin/pbt-dev.sh  
</pre>

== <span style="color:#000080"> How to get the code </span> ==

; Copy the code to your working directory and rename it

<pre style="color: #800000; background-color: #dcdcdc">
cp -r /unix/pbt/tutorials/basic/PhotonPB .
  
mv PhotonPB PhotonPB_source
</pre>

== <span style="color:#000080"> How to run the code </span> == 

; Inside /home/username/PhotonPBFolder/ create a directory

<pre style="color: #800000; background-color: #dcdcdc">
mkdir PhotonPB_build  
</pre>

; To compile the code enter this directory and run cmake and make 

<pre style="color: #800000; background-color: #dcdcdc">
cd PhotonPB_build 

cmake -DGeant4_DIR=/unix/pbt/software/dev /home/username/PhotonPBFolder/PhotonPB_source 

make  
</pre>

; Run macro gamma.mac. The macro generates 10000 events.

<pre style="color: #800000; background-color: #dcdcdc">
./photonPB gamma.mac
</pre>
 
== <span style="color:#000080"> How to analyze data </span> ==

The macro produces root file '''Gamma.root''' with a histogram showing the energy deposition in 
water box along the beam line. It also produces text files: '''DoseFile.txt''' with 
energy and dose deposited in each slice and '''PlotDose.txt''' with dose deposited in each slice. 

=== <span style="color:#000080"> Text files </span> ===

This is output from '''DoseFile.txt''' with physics process '''emstandard_opt0''' and incident photon energy of '''20 MeV'''. Use your favorite editor '''pico''', '''vi''', '''emacs''' etc to open text files. For example, use editor pico:

<pre style="color: #800000; background-color: #dcdcdc">
pico DoseFile.txt
</pre>

<pre style="color: #800000; background-color: #dcdcdc">
 Layers :	 x[mm] 	Edep   	      Edep/Ebeam[%] 	     Dose 	Dose/MaxDose[%]
 layer 1: 	10	513.656 MeV	0.428046	5.14354e-09 Gy	32.1047	
 layer 2: 	20	800.659 MeV	0.667216	8.01749e-09 Gy	50.0432	
 layer 3: 	30	996.867 MeV	0.830722	9.98223e-09 Gy	62.3066	
 layer 4: 	40	1.23773 GeV	1.03144	        1.23942e-08 Gy	77.3614	
 layer 5: 	50	1.29582 GeV	1.07985	        1.29758e-08 Gy	80.9917	
 layer 6: 	60	1.43647 GeV	1.19706	        1.43843e-08 Gy	89.7831	
 layer 7: 	70	1.59565 GeV	1.32971	        1.59782e-08 Gy	99.7318	
 layer 8: 	80	1.59994 GeV	1.33328	        1.60211e-08 Gy	100	
 layer 9: 	90	1.53239 GeV	1.27699	        1.53448e-08 Gy	95.7783	
 layer 10: 	100	1.52627 GeV	1.27189	        1.52834e-08 Gy	95.3955	
 layer 11: 	110	1.49511 GeV	1.24592	        1.49714e-08 Gy	93.4478	
 layer 12: 	120	1.46007 GeV	1.21672	        1.46206e-08 Gy	91.2579	
 layer 13: 	130	1.44794 GeV	1.20662	        1.44991e-08 Gy	90.4998	
 layer 14: 	140	1.40362 GeV	1.16968	        1.40553e-08 Gy	87.7295	
 layer 15: 	150	1.44033 GeV	1.20028	        1.44229e-08 Gy	90.0244	
 layer 16: 	160	1.42336 GeV	1.18613	        1.42529e-08 Gy	88.9634	
 layer 17: 	170	1.28793 GeV	1.07327	        1.28968e-08 Gy	80.4985	
 layer 18: 	180	1.26477 GeV	1.05397	        1.26649e-08 Gy	79.051	
 layer 19: 	190	1.24786 GeV	1.03989	        1.24956e-08 Gy	77.9945	
 layer 20: 	200	5.30499e-307 eV 4.42082e-316	0 Gy	         0	


 The run consists of 6000 gamma of 20 MeV through 20 cm  of Water (density: 1 g/cm3 ) divided into 20 slices.

 Edep is the deposited energy in every slice.
 Total incident energy(Ebeam)= 120 GeV
 Total energy deposit= 25.169 GeV
 Dose is the deposited dose in every slice.
 MaxDose is the highest dose value from all slices.
</pre>

This is '''PlotDose.txt'''. These values can be analyzed with MATLAB and ROOT .

<pre style="color: #800000; background-color: #dcdcdc">  
10	32.1047	
20	50.0432	
30	62.3066	
40	77.3614	
50	80.9917	
60	89.7831	
70	99.7318	
80	100	
90	95.7783	
100	95.3955	
110	93.4478	
120	91.2579	
130	90.4998	
140	87.7295	
150	90.0244	
160	88.9634	
170	80.4985	
180	79.051	
190	77.9945	
200	0	
</pre>

=== <span style="color:#000080"> Root file </span> ===

Open '''Gamma.root''' file in the following way:

<pre style="color: #800000; background-color: #dcdcdc">
root -l Gamma.root

new TBrowser

Select ROOT files and Gamma.root
</pre>

The histogram inside Gamma.root shows the energy deposition in water box:
 
http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/PhotonPB/Edep_PhotonB.png 

To exit the ROOT terminal type 

<pre style="color: #800000; background-color: #dcdcdc">
.q
</pre>

You can plot the dose deposition along the depth of the absorber ('''PlotDose.txt''') using script '''PlotSimulation.C''' from folder '''PhotonPB_source'''. Copy this script to your current '''PhotonPB_build''' directory:

<pre style="color: #800000; background-color: #dcdcdc">
cp /home/username/PhotonPBFolder/PhotonPB_source/PlotSimulation.C .
</pre>  

Then run the script:

<pre style="color: #800000; background-color: #dcdcdc">
root -l 

.x PlotSimulation.C

</pre>

This will create '''Simulation.root''' file. Open the root file:

<pre style="color: #800000; background-color: #dcdcdc">
root -l Simulation.root

new TBrowser

Select ROOT files and Gamma.root
</pre>
 
This is the result:

http://www.hep.ucl.ac.uk/pbt/RadiotherapyWorkbook/skins/common/images/PhotonPB/DoseDeposition.png   

=== <span style="color:#000080"> Changes in macro gamma.mac </span> ===

You can change the physics process, incident photon energy, phantom material, number of slices etc. by
modifying the macro gamma.mac. Open the macro with editor pico:

<pre style="color: #800000; background-color: #dcdcdc">
pico gamma.mac
</pre>   

This is the content of the macro:

<pre style="color: #800000; background-color: #dcdcdc">
# gamma.mac
#
/control/verbose 2
/run/verbose 2
/tracking/verbose 0
/run/particle/verbose 1
/run/particle/dumpList
#
# set geometry and material
/photonPB/det/setMat Water
#/photonPB/det/setMat Lead
/photonPB/det/setSizeX  20 cm
/photonPB/det/setSizeYZ 20 cm
/photonPB/det/setSliceSizeYZ 4 cm
/photonPB/det/sliceNumber 20 
#
# set physics process
/photonPB/phys/addPhysics emstandard_opt0
#photonPB/phys/addPhysics emlivermore
#/photonPB/phys/addPhysics empenelope
#
# production tresholds (range cut off-
# not bigger than 10% of slice thickness)
/photonPB/phys/setCuts 1 mm
#/photonPB/phys/setGCut 1 um
#/photonPB/phys/setECut 1 um
#/photonPB/phys/setPCut 1 um
#
# initialize
/run/initialize
#
# particle gun properties (type of 
#particle and energy)
/gun/particle gamma
#/gun/particle e-
/gun/energy 20 MeV
#
# beam size
#/photonPB/gun/rndm 3 mm
#
# step limit (not bigger than 5% of 
# slice thickness)
/photonPB/stepMax 0.5 mm
#
/photonPB/event/printModulo 50
#
# output root file
/analysis/setFileName Gamma
#
# number of events
/run/beamOn 6000
</pre>

'''Change the physics process'''

The default physics process is '''emstandard_opt0'''. This package is used in high energy experiments. In gamma.mac change

<pre style="color: #800000; background-color: #dcdcdc">
/photonPB/phys/addPhysics emstandard_opt0
</pre>

to 

<pre style="color: #800000; background-color: #dcdcdc">
/photonPB/phys/addPhysics emlivermore
</pre>

The process '''emlivermore''' is used in low energy physics experiments. 

'''Change the incident particle energy'''

The default energy is 20 MeV. It is a typical energy used in radiotherapy. In gamma.mac you can change the value of 20 MeV 

<pre style="color: #800000; background-color: #dcdcdc">
/gun/energy 20 MeV
</pre>

to, for example, 10 MeV

<pre style="color: #800000; background-color: #dcdcdc">
/gun/energy 10 MeV
</pre>


Keep in mind that the primary particle generation is done at /PhotonPB_source/src/PrimaryGeneratorAction.cc.
This is part of the PrimaryGeneratorAction.cc:

<pre style="color: #800000; background-color: #dcdcdc">
fParticleGun  = new G4ParticleGun(1);
G4ParticleDefinition* particle = G4ParticleTable::GetParticleTable()->FindParticle("proton");
fParticleGun->SetParticleDefinition(particle);
fParticleGun->SetParticleEnergy(160*MeV);  
fParticleGun->SetParticleMomentumDirection(G4ThreeVector(1.,0.,0.));
     
...

G4double x0 = -0.5*(fDetector->GetAbsorSizeX());
G4double y0 = 0.*cm, z0 = 0.*cm;

...

fParticleGun->SetParticlePosition(G4ThreeVector(x0,y0,z0));
</pre>

The line 

<pre style="color: #800000; background-color: #dcdcdc">
fParticleGun  = new G4ParticleGun(1);
</pre>

means that only one particle is generated, incident from (x0,y0,z0). The default number of
events is set to 6000. Therefore, 6000 particles are incident to the water box. 

'''Change the diameter of the beam'''

You can set the diameter of the beam with the command:

<pre style="color: #800000; background-color: #dcdcdc">
/photonPB/gun/rndm 3 mm
</pre>

'''Change the material'''

In this example we compute the energy deposition of photons in water box. However,
there is an option to change the box material from water to lead. 

In gamma.mac change 

<pre style="color: #800000; background-color: #dcdcdc">
/photonPB/det/setMat Water
</pre>

to 

<pre style="color: #800000; background-color: #dcdcdc">
/photonPB/det/setMat Lead
</pre>

'''Change the type of incident particle'''

In gamma.mac change the photon 

<pre style="color: #800000; background-color: #dcdcdc">
/gun/particle gamma
</pre>

to electron

<pre style="color: #800000; background-color: #dcdcdc">
/gun/particle e-
</pre>

'''Change the number of slices'''

You can change the number of slices. The default number is 20. Keep in mind that 
if you want to have bigger number of slices you need to modify the file DetectorConstruction.hh in
/PhotonPB_source/include/.

In DetectorConstruction.hh set MaxLayer to a value which is bigger then the number of your slices. The default number is MaxLayer=30. For example, if you want your box to be divided to 35 slices you need to set the value of MaxLayer to ,for example, 40 then in gamma.mac you need to change the number of slices:

<pre style="color: #800000; background-color: #dcdcdc">
/photonPB/det/sliceNumber 35 
</pre>

Every time you modify files in directory PhotonPB_source you need to compile your code. In directory PhotonPB_build do

<pre style="color: #800000; background-color: #dcdcdc">
make 
</pre>

then run the macro

<pre style="color: #800000; background-color: #dcdcdc">
./photonPB gamma.mac
</pre>

=== <span style="color:#000080"> Visualisation </span> ===

Under construction (problems with OpenGL installed on plus1)

== <span style="color:#000080"> Files </span> ==

[[List of monoenergetic photon pencil beam files with brief description]]