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--- cn:csn5:isolpharm_ag:computing:geant4_list_of_commands [2018/09/17 09:20] – [Isotope Diffusion] bagli@infn.it
+++ cn:csn5:isolpharm_ag:computing:geant4_list_of_commands [2018/09/17 09:21] (current) – [Isotope Diffusion] bagli@infn.it
@@ Line 1: / Line 1: @@
+====== Geant4 List of Commands ======
+===== Introduction =====
+The Geant4 application EF10 contained in the docker image permits a two-steps simulation:
+  - The generation of isotopes
+  - The diffusion of isotopes
+The application can be launched via the command
+<code>./eff10_mod [macro_file] [--primaries] [physics_list_name]</code>
+where
+''[macro_file]'' is the name of the macro with the setup commands
+''[--primaries]'' is the option to switch to the simulation of isotopes production
+''[physics_list_name]'' is the optional name of the list of physics processes you want to use for the simulation of isotopes production
+===== List of Commands =====
+==== Physics List ====
+The physics list can be modified at the command launch.
+The default physics list is ''FTFP_BERT''
+The available physics lists are:
+<code>
+FTFP_BERT
+FTFP_BERT_TRV
+FTFP_BERT_ATL
+FTFP_BERT_HP
+FTFQGSP_BERT
+FTFP_INCLXX
+FTFP_INCLXX_HP
+FTF_BIC
+LBE
+QBBC
+QGSP_BERT
+QGSP_BERT_HP
+QGSP_BIC
+QGSP_BIC_HP
+QGSP_BIC_AllHP
+QGSP_FTFP_BERT
+QGSP_INCLXX
+QGSP_INCLXX_HP
+QGS_BIC
+Shielding
+ShieldingLEND
+ShieldingM
+NuBeam
+</code>
+At the end of the physics list name, the following suffixes change the electromagnetic part of the physics list, e.g. ''QGSP_INCLXX_EMX'':
+<code>
+_EMV
+_EMX
+_EMY
+_EMZ
+_LIV
+_PEN
+__GS
+__SS
+</code>
+The descriptions of the hadronic and electromagnetic models used in the physics list can be retrieved from the [[https://github.com/Geant4/geant4|Geant4 source code]] or the [[http://geant4-userdoc.web.cern.ch/geant4-userdoc/UsersGuides/PhysicsReferenceManual/html/index.html|Geant4 user guide]]
+==== Target ====
+Several target parameters can be modified via macro commands. Those commands affect all the simulations.
+== Temperature ==
+<code>/det/setTemperature [double] [unit]</code>
+Set the temperature of the target.
+Kelvin is the standard unit of measure.
+== Disk Material ==
+<code>/det/setTargetMaterial [string]</code>
+Set the target material.
+''UCx'' is the default material. Otherwise, a material in the [[http://geant4-userdoc.web.cern.ch/geant4-userdoc/UsersGuides/ForApplicationDeveloper/html/Appendix/materialNames.html#g4matrdb|Geant4 NIST]] database can be used. Other materials will be added in future releases.
+== Number of Disks ==
+<code>/det/setNumberOfDisks [int]</code>
+By default, the number of the disks is ''7''.
+Set the number of disk in the target
+== Disk Density ==
+<code>/det/setTargetDensity [double] [unit]</code>
+Set the disk material density. Default unit is g/cm3.
+By default, the disk material density is ''4.0 g/cm3''.
+== Box Starting Point ==
+<code>/det/setBoxInit [double] [unit]</code>
+Set the starting point of the envelope box. Default unit is cm.
+By default, the starting point of the envelope box is ''-10.702 cm''.
+== Box Ending Point ==
+<code>/det/setBoxEnd [double] [unit]</code>
+Set the ending point of the envelope box. Default unit is cm.
+By default, the starting point of the envelope box is ''9.448 cm''.
+== Disk Radius ==
+<code>/det/setTargetRadius [double] [unit]</code>
+Set the disk radius. The radius is the same for each disk. Default unit is cm.
+By default, the disk radius is ''2.00 cm''.
+== Disk Position ==
+<code>/det/setDiskPositionX [double] [unit]</code>
+Set the position of the ''X'' disk, where ''X'' spans from ''1'' to the number of disk set. Default unit is cm.
+By default, the positions of the disks are:
+<code>
+-6.682 cm
+-5.052 cm
+-3.322 cm
+-1.592 cm
++0.938 cm
++3.568 cm
++5.498 cm
+</code>
+== Disk Thickness ==
+<code>/det/setDiskThicknessX [double] [unit]</code>
+Set the thickness of the ''X'' disk, where ''X'' spans from ''1'' to the number of disk set. Default unit is cm.
+By default, the thickness for all the disks is ''0.08 cm''.
+==== Beam ====
+The beam parameters affect only the simulation of isotopes production.
+The [[http://geant4-userdoc.web.cern.ch/geant4-userdoc/UsersGuides/ForApplicationDeveloper/html/GettingStarted/generalParticleSource.html|Geant4 General Particle Source (GPS) commands]] can be used to setup the beam.
+===== Examples =====
+==== Primary Generation ====
+<code>
+#set the number of thread to be used in the calculation
+/run/numberOfThreads 1
+#set the random seeds
+/random/setSeeds 8904138 1546569
+#set the temperature of the disks
+/det/setTemperature 2000 kelvin
+#set the number of disks
+/det/setNumberOfDisks 7
+#set the disk material
+/det/setTargetMaterial UC4
+#set the density of the target material
+/det/setTargetDensity 4.0 g/cm3
+#set the init of the envelope
+/det/setBoxInit -10.702 cm
+#set the end of the envelope
+/det/setBoxEnd 9.448 cm
+#set the radius of the disks
+/det/setTargetRadius 2.0 cm
+#set the position of the disks
+/det/setDiskPosition1 -6.682 cm
+/det/setDiskPosition2 -5.052 cm
+/det/setDiskPosition3 -3.322 cm
+/det/setDiskPosition4 -1.592 cm
+/det/setDiskPosition5 +0.938 cm
+/det/setDiskPosition6 +3.568 cm
+/det/setDiskPosition7 +5.498 cm
+#set the thickness of the disks
+/det/setDiskThickness1 0.08 cm
+/det/setDiskThickness2 0.08 cm
+/det/setDiskThickness3 0.08 cm
+/det/setDiskThickness4 0.08 cm
+/det/setDiskThickness5 0.08 cm
+/det/setDiskThickness6 0.08 cm
+/det/setDiskThickness7 0.08 cm
+#initialise the geometry and the physics tables
+/run/initialize
+#set the beam parameters
+/gps/particle proton
+/gps/time 0.0 ns
+/gps/energy 40 MeV
+/gps/direction 0 0 1
+/gps/ang/type focused
+/gps/pos/type Point
+/gps/pos/centre 0. 0. -15. cm
+#run the code
+/run/beamOn 6242000000
+</code>
+==== Isotope Diffusion ====
+<code>
+#set the number of thread to be used in the calculation
+/run/numberOfThreads 1
+#set the random seeds
+/random/setSeeds 8904138 1546569
+#set the temperature of the disks
+/det/setTemperature 2000 kelvin
+#set the number of disks
+/det/setNumberOfDisks 7
+#set the disk material
+/det/setTargetMaterial UC4
+#set the density of the target material
+/det/setTargetDensity 4.0 g/cm3
+#set the init of the envelope
+/det/setBoxInit -10.702 cm
+#set the end of the envelope
+/det/setBoxEnd 9.448 cm
+#set the radius of the disks
+/det/setTargetRadius 2.0 cm
+#set the position of the disks
+/det/setDiskPosition1 -6.682 cm
+/det/setDiskPosition2 -5.052 cm
+/det/setDiskPosition3 -3.322 cm
+/det/setDiskPosition4 -1.592 cm
+/det/setDiskPosition5 +0.938 cm
+/det/setDiskPosition6 +3.568 cm
+/det/setDiskPosition7 +5.498 cm
+#set the thickness of the disks
+/det/setDiskThickness1 0.08 cm
+/det/setDiskThickness2 0.08 cm
+/det/setDiskThickness3 0.08 cm
+/det/setDiskThickness4 0.08 cm
+/det/setDiskThickness5 0.08 cm
+/det/setDiskThickness6 0.08 cm
+/det/setDiskThickness7 0.08 cm
+#initialise the geometry and the physics tables
+/run/initialize
+#set the beam parameters
+/gps/particle ion
+/gps/ion 36 80
+/gps/time 0.0 ns
+/gps/energy 0.24210389477849997 eV
+/gps/ang/type iso
+/gps/pos/type Volume
+/gps/pos/shape Cylinder
+#the ion starts from disk1
+/gps/pos/halfz 0.04 cm
+/gps/pos/radius 2.00 cm
+/gps/pos/centre 0. 0. -6.682 cm
+#run the code
+/run/beamOn 41
+</code>
+====== Output ======
+==== Primary Generation ====
+The output is a single file named ''isotope_table.dat''
+The file contains two columns separated by commas:
+  - The first column is a unique key identifying the atomic number (''ZZZ'') the atomic mass number (''AAA'') and the disk (''X''), in the form ''XAAAZZZ''.
+  - The second column is the number of isotopes generated.
+A typical output would be:
+<code>
+1148059 , 10
+1096040 , 17
+1082034 , 14
+1138054 , 25
+1092039 , 15
+1136053 , 23
+1098041 , 35
+</code>
+==== Isotope Diffusion ====
+The output is a series of files named ''output_nt_detector_tY.csv'', where ''Y'' is the thread number that spans from 0 to the maximum number of thread used minus one.
+The file contains three columns separated by commas:
+  - The first column is the release time in seconds.
+  - The second column is the atomic mass number.
+  - The third column is the atomic number.
+The symbol for comment is ''#''.
+A typical output would be:
+<code>
+#class tools::wcsv::ntuple
+#title Detector hits
+#separator 44
+#vector_separator 59
+#column double t
+#column double A
+#column double Z
+.0160635,94,37
+.99183,94,38
+.180522,94,37
+.87909,94,37
+</code>
+====== Log File ======
+After the initialisation of the physics lista and the detector geometry, each thread starts processing the particles assigned to it.
+When a thread starts the execution, the following line is printed
+<code>
+G4WT10 > ### Run 0 starts on worker thread 10.
+</code>
+where ''G4WT10'' stands for Geant4 Working Thread 10.
+When an event starts on a thread, the following line is printed:
+<code>
+G4WT37 > --> Event 0 starts with initial seeds (13049039,61775110).
+</code>
+where ''37'' is the number of thread, ''0'' is the event number and ''(13049039,61775110)'' are the random seeds.
+The line is printed every 100 events and the distribution of the events among the threads is not sequential, e.g.:
+<code>
+G4WT13 > --> Event 80600 starts with initial seeds (6519702,53088888).
+G4WT29 > --> Event 51300 starts with initial seeds (83578766,80435366).
+G4WT22 > --> Event 22000 starts with initial seeds (65123969,63355841).
+</code>