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1. is one of the above names If you do not select anyone for a given particle the first one in each list is taken as default For details on the physics implemented in each of these physics models please read the Geant4 physics manual 10 5 2 GAMOS hadronic physics list The GAMOS hadronic physics list is based on the hadron therapy Geant4 advanced example It includes the previously defined electromagnetic physics list and adds several options for the physics models for protons and ions The following physics models are available plus all the models described in the previous section e photons photon nuclear include photo nuclear reactions not included by default e electrons electron nuclear include electro nuclear reactions for electrons not included by default e positrons positron nuclear include electro nuclear reactions for positrons not included by default e muons 5 2 GAMOS HADRONIC PHYSICS LIST 59 muon standard standard electromagnetic processes e protons proton precompound precompound evaporation model proton precompoundFermi precompound evaporation plus Fermi break up models proton precompoundG EM precompound GEM evaporation model proton precompoundGEMFermi precompound GEM evap oration plus Fermi break up models proton precompund binary binary cascade model with the default precompound e ions ion LowE low energy processes wi
2. GmGAPSCylinderSurfaceFlux Cylinder surface flux is a sur face based flux scorer and similar to the GmGAPSFlatSurfaceFlux The only difference is that the surface is defined at the inner sur face of a G4Tubs solid GmGAPSSphereSurfaceFlux Sphere surface flux is a surface based flux scorer and similar to the GmGAPSFlatSurfaceFlux The only difference is that the surface is defined at the inner sur face of a G4Sphere solid GmGAPSCellFlux Cell flux is a volume based flux scorer The cell flux is defined by a track length L of the particle inside a volume divided by the volume V of this cell The track length is calculated by a sum of the step lengths in the cell The expression for cell flux is given by the sum of W L V where W is a particle weight and is multiplied by the track length at each step GmGAPSPassageCellFlux Passage cell flux is a volume based scorer similar to GAPSCellFlux The only difference is that tracks which pass through a cell are taken into account It means that tracks generated or stopped inside the volume are excluded from the calculation e In Out behaviour For the following scorers GmG4PSCylinderSurfaceCurrent GmG4PSCylinderSurfaceFlux GmG4PSFlatSurfaceCurrent GmG4PSFlatSurfaceFlux GmGAPSSphereSurfaceCurrent GmG4PSSphereSurfaceF lux GmG4PSTrackCounter you can make the scoring only for tracks that are entering only for tracks that are exiting or both for tracks that are entering
3. rho rhoO rho3 1690 rho3 1690 rho3 1690 0 S quark sdO_diquark sdi_diquark sigma 1385 sigma 1385 sigma 1385 0 sigma 1660 sigma 1660 sigma 1660 0 sigma 1670 sigma 1670 sigma 1670 0 sigma 1750 sigma 1750 sigma 1750 0 sigma 1775 sigma 1775 sigma 1775 0 sigma 1915 sigma 1915 sigma 1915 0 sigma 1940 sigma 1940 sigma 1940 0 sigma 2030 sigma 2030 sigma 2030 0 sigmat sigma sigma0 sigma c sigma_ct sigma cO ssi_diquark suO diquark sui diquark t quark taut tau triton u quark udO diquark udi diquark uui diquark xi 1530 xi 1530 0 xi 1690 xi 1690 0 xi 1820 xi 1820 0 xi 1950 xi 1950 0 xi 2030 xi 2030 0 xi xiO xi c xi cO These are the names that should be used in the commands that need a particle name If you want to use hadrons GAMOS also provides the possibility of grouping them so that with a single name you can identify 14 8 USING PARTICLE NAMES 147 the whole group The groups defined are the following lightMeson Mesons that only contain up and down quarks pi piO eta eta prime kaon kaon kaonO kaonOL kaonOS 0 al 2 k 1 k2 star kO_star k2 star k3 star anti k anti_k0 anti ki anti k2 anti k star anti k2 star anti k3 star b1 f0 f1 209 f2 prime hi eta eta2 phi phi3 pi pi2 rho rho3
4. 1 2 Structure of GAMOS The acronym GAMOS stands for Geant4 based Architecture for Me dicine Oriented Simulations It is therefore a detector simulation soft ware and it is based on the Geant4 toolkit 1 The objective of GAMOS is to provide a software framework that serves the unexperienced user to sim ulate his her medical physics project without having to code in C and with a minimal knowledge of Geant4 and at the same time let an advanced user add new functionalities and easily integrate it with the rest of GAMOS functionality We have also tried to provide you with several tools that help you to understand in detail your simulation controlling the verbosity making his 1 2 CHAPTER 1 INTRODUCTION tograms about many variables scoring different quantities etc as well as other tools to help you in optimising your simulation GAMOS is composed of a core software that covers the main functionality of a Geant4 simulation and a set of example of medicine applications GAMOS source code is organized in the following subsystems each one subdivided in the following packages e GamosCore core software covering main Geant4 functionality GamosBase parameter manager analysis manager filters clas sifiers and other basic functionalities GamosFactories factories to convert the different simulation components geometry physics generator user actions in plug in s GamosGeometry geometry related uti
5. 137 14 2 Creating your plug in 138 14 3 Managing the input data files 140 14 4 Checking the usage of parameters 141 14 5 Using a parameter in your C code 141 1451 og tiles 2 54 dg eae a ee ed ee 142 14 6 Identifying touchables 0004 143 14 7 Using wildcards to get volume names 144 14 8 Using particle 144 Chapter 1 Introduction 11 About this document This manual refers to GAMOS version 2 0 1 It is written in IATEX and it is maintained at the following address http fismed ciemat es GAMOS doc gamos uguide 2 0 1 pdf We will use through this manual many terms common to the detector simulation terminology and specifically to the Geant4 1 terminology If you are new to it please read before for example the Geant4 documentation 2 We have tried though to make this manual self consistent and we hope that unless you need a deep knowledge of the Geant4 software you will not need to refer to any further documentation If you find that some of the instructions given here do not give the expected result please send a mail to pedro arceQciemat es detailing the problem the GAMOS version and providing as much information as possi ble We will also warmly welcome any kind of comment or suggestion you would like to send us about this guide or about the GAMOS functionalities or user interface
6. CUTS REGION NAME gamma CUT e CUT e _CUT where REGION_NAME is the name of a previously defined region gamma CUT e CUT e _CUT are the cuts for gamma electrons and positrons the cut for positron is optional if not set it will take the one for electrons Alternatively you can set the cuts in your user script through a user command gamos physics setCuts REGION NAME gamma_CUT e CUT e _CUT 5 5 2 Energy cuts to range cuts conversion If you want to know the traslation from an energy cut value to a range cut value for a given particle in a given material you can do with the following instructions First you have to instantiate the user action gamos userAction GmCutsEnergy2RangeUA and then you can use the command gamos physics ECuts2RangeCuts MATERIAL_NAME CUT_VALUE PARTICLE_NAME You may use in the material name an if you want to name several materials at the same time For the particle name only the following names have a meaning gamma e e e This will produce a table with the conversion for each material and particle similar to the following one 62 CHAPTER 5 PHYSICS GmCutsEnergy2RangeUA MATERIAL G4 AIR PART gamma ENERGY CUT 0 1 MeV RANGE CUT 286588 GmCutsEnergy2RangeUA MATERIAL G4 AIR PART e ENERGY CUT 0 1 MeV RANGE CUT 129 155 GmCutsEnergy2RangeUA MATERIAL G4_AIR PART e ENERGY CUT 0 1 MeV RANGE CUT 131 938 GmCutsEnergy2RangeUA MATERIAL G4_WATER PART gamma ENERGY CUT 0
7. Finally you may select the format of the scoring results by associating one of the available scorer printers for each scorer gamos scoring addPrinter2Scorer PRINTER NAME CLASS SCORER NAME PRINTER NAME CLASS is the name of a GmVPSPrinter class or the name you gave to a printer built from a printer class by using the command gamos printer see section on Scorer printers below and SCORER_NAME is one of the scorers defined above If no printer is attached to a scorer it will use the printer type GmGAPSPrinterDefault By default a different count is scored for each of the copies of the se lected volumes with different copy number This is managed by the scorer classifier GmScorerClassifierBylAncestor The user can attach differ ent classifiers to the different scorers so that the counts are done in different ways gamos scoring assignClassifier2Scorer CLASSIFIER_NAME CLASS SCORER_NAME CLASSIFIER_NAME CLASS is the name of a GmV Classifier class or the name you gave to a classifier built from a classifier class by using the com mand gamos classifier see section on Classifiers and SCORER_NAME is one of the scorers defined above The scoring is done by default taking into account the track weight ex cept for the scorers when it is explicitly mentioned see scorers description If you do not want to take weights into account you can switch them off with the command gamos scoring useTrackWeight SCORER_NAME FALSE SCORER_NAME is one of
8. NOTE If you are creating a plug in in a new directory that you have created you have to be sure to have the plugin option in the GNUmakefile as explained in the section Compiling your new code 14 3 Managing the input data files To run an example you will probably need some input data like for example the file describing the geometry the list of isotopes etc You can set the name of your file in your script but you do not need to tell the path where to look for it An environmental variable called GAMOS SEARCH PATH contains the list of directories where GAMOS will look for your file The directories are separated by a colon and their order in this variable reflects the order in which they will be searched This variable is set up when you configure GAMOS and takes a default value of MY GAMOS DIR data You may change this value at your will but remember not to reset the GAMOS configuration after that 14 4 CHECKING THE USAGE OF PARAMETERS 141 14 4 Checking the usage of parameters Many of the GAMOS classes or your own classes have a different be haviour depending on the value of some parameters You can see many examples of this throughout this guide You have to remember always to set a parameter before you invoke any code that may use it we recommend you to set all the parameters at the beginning of your command file The parameters are read usually in the class constructors therefore if you set a parameter after
9. e Position Y mm e Position Z mm e Number of original tracks One line per original track with track ID 7 85 HITS HISTOGRAMS 83 e Number of tracks One line per track with track ID The binary file contains the same information in the following format e Event ID float e Sensitive detector type 10 only first 10 characters are stored if type has less than 10 characters blank spaces will be added at the end e Detector unit ID unsigned long long e Energy MeV float e Minimum time ns unsigned long long e Maximum time ns unsigned long long e Position X mm e Position Y mm float e Position Z mm e Number of original tracks unsigned int One line per original track with track ID unsigned int e Number of tracks unsigned int One line per track with track ID unsigned int 7 8 Hits histograms There are two user actions that provide a number of hits statistics GmHit sHistosUA provides statistics about simulated hits while GmRecHit sHistosUA provides statistics about reconstructed hits 84 CHAPTER 7 SENSITIVE DETECTOR AND HITS Chapter 8 Scoring Geant4 provides several classes to score different quantities in the selected volumes GAMOS provides all the Geant4 functionality through user com mands and also some extra functionality that we describe in this section The first thing you should do to use GAMOS scoring is to create a multifunctional detector 15 and associate
10. COLOUR NDC chamber 0 2 0 4 0 1 By default the three colour proportions will be set to 1 32 CHAPTER 3 GEOMETRY Check overlaps Geant4 offers the possibility to check if a volume overlaps with other vol umes By default it is not set but you can activate it with the commands CHECK OVERLAPS 1 Volume name 2 ON or TRUE OFF or FALSE Example CHECKN OVERLAPS NDC chamber 0 2 0 4 0 1 By default the three colour proportions will be set to 1 Use of in names In the case of the VIS COLOUR and CHECK_OVERLAPS tags you may use to define the volume name This will be replaced by any name For example Crys means all the volume names starting by Crys means all volume names Use of parameters You can also define a parameter for later use in any tag P 1 parameter name 2 parameter value You can then use the parameter as parameter_name Example P InnerR 12 VOLU yoke TUBS Iron 3 InnerR 820 1270 Units Any value in a tag has a default unit that depends on the dimension of the value automatically known by the parser The default units are the following e length mm e angle degrees e density g cm3 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE 33 e atomic mass g mole The user can override the default value of a unit by indicating the unit of each value This can be done adding at the end of the value the unit name see CLHEP file Units SystemOfUnits h
11. Or MY GAMOS DIR config confgamos sh depending on your shell flavour Therefore before running you have to source this file source MY GAMOS DIR config confgamos csh Or source MY GAMOS DIR config confgamos sh Remember to type this command every time you start a new session to run GAMOS To run your application inside GAMOS you do not have to write a main program as GAMOS provides a unique main that serves to run any application When you run the GAMOS main it will load and call the components you want geometry physics generator hits building his tograms by simply defining them in the input command file Therefore to run your application simply type gamos MY INPUT FILE where MY INPUT FILE is a typical Geant4 macro file that includes Geant4 and GAMOS commands The minimum set of commands that you need are those to select a ge ometry a physics list and a generator to initialize Geant4 and to run N events In this case your input file may look like this one tracking verbose 1 gamos setParam GmGeometryFromText FileName geom txt gamos geometry GmGeometryFromText gamos physicsList GmEMPhysics gamos generator GmGenerator gamos generator addSingleParticleSource MY ELEC e 1 MeV run initialize run beamOn 10 This will create the geometry of a simple geometry described in the file geom txt lying in the current directory or in the MY_GAMOS_DIR data 2 3 COMPILING GAMOS 7 directory se
12. PROC_LIST e LowEnBrem PROC_LIST e LowEnergyloni PROC LIST e Transportation PROC LIST e msc e At the end of run how many times a process determined the step for each particle type PROC_COUNT e Transportation 31 PROC_COUNT e annihil 999 PROC_COUNT e eBrem 19 PROC_COUNT e eloni 1439 PROC_COUNT e msc 788 PROC_COUNT e LowEnBrem 46 PROC COUNT e LowEnergyloni 2362 PROC_COUNT e Transportation 18 PROC_COUNT e msc 1036 PROC COUNT gamma LowEnCompton 684 9 2 USER ACTION UTILITIES 97 PROC COUNT gamma LowEnPhotoElec 549 PROC COUNT gamma LowEnRayleigh 60 PROC COUNT gamma Transportation 5963 e At the end of run how many times a process was the creator of a particle for each particle type PROC CREATOR COUNT e Primary 1000 PROC CREATOR COUNT e LowEnCompton 541 PROC CREATOR COUNT e LowEnPhotoElec 549 PROC CREATOR COUNT e LowEnergyloni 140 PROC CREATOR COUNT e eloni 255 PROC CREATOR COUNT gamma LowEnBrem 33 PROC CREATOR COUNT gamma LowEnPhotoElec 235 PROC CREATOR COUNT gamma annihil 1998 PROC CREATOR COUNT gamma eBrem 19 e At the end of run how many particles of each type were created PART LIST e 1000 PART LIST e 1485 PART LIST gamma 2285 To activate this utility use the command gamos userAction GmCountProcessesUA 9 2 3 Counting the number of tracks in a volume This utility prin
13. charmMeson Mesons that contain a charm quark D D DO anit DO Ds Ds J psi bottomMeson Mesons that contain a bottom quark B B BO anti BO BsO anti BsO meson All mesons lightBaryon Baryons that only contain up and down quarks proton anti proton neutron anti neutron N anti N delta anti delta strangeBaryon Baryons that contain a strange quark lambda anti lambda sigma0O anti sigmaO sigmat anti sigmat sigma anti sigma xiO anto xiO xi anti xi omega anti omega lambda anti lambda sigma anti sigma xi anti xi omega omega3 charmBaryon Baryons that contain a charm quark lambda c anti lambda c sigma cO anti sigma cO sigma c anti sigma c sigma _ anti sigma ct xi c anti xi c _ 0 anti xi c0 omeca cO anti omega cO baryon All baryons ion ions GenericIon alpha He3 deuteron triton ALL All particles 148 CHAPTER 14 APPENDIX Bibliography 12 13 14 15 16 17 18 http www cern ch geant4 http geant4 web cern ch geant4 support userdocuments shtml http seal cern ch http proj clhep web cern ch proj clhep http root cern ch Penelope A Code System for Monte Carlo Simulation of Electron and Photon Transport Workshop Proceedings Issy les Moulineaux France 5 7 November 2001 AEN NEA http geant4 web cern ch geant4 UserDocumentation
14. one new generator position distribution and you want that a message is printed when somebody chooses it in the input file you can write a message like the following one in the constructor of your class G4cout lt lt GenerVerb infoVerb lt lt MyPositionGeneratorDistribution created lt lt G4endl This message will only be printed if the generator verbosity is set to info or a level above debug or test If you want for example that your distribution prints a message with the calculated position at each event you may do G4cout lt lt GenerVerb debugVerb lt lt MyPositionGeneratorDistribution position lt lt position lt lt G4endl This message will only be printed if the generator verbosity is set to debug or a level above test As you may have deduced the rules for using each of the GAMOS verbosity managers are that the name of the verbosity is the same as 11 3 CREATING YOUR OWN VERBOSITY MANAGER 113 the name of the verbosity manager simplified no Gm at the beginning and Verb instead of Verbosity e g from GmAnaVerbosity you use AnaVerb And the name of the level in C code is the same as the one in the input command file adding Verb e g for warning you use warningVerb 11 3 Creating your own verbosity manager You can create your own verbosity manager for the code you use taking as example one of the GAMOS verbosity managers for example the class GmGenerVerbostityMgr in the package
15. ostream amp out G4cout Dumps a physical volume with its attributes G4LogicalVolume GetTopLV Gets a pointer to the logical vol ume on top of the geometry hierarchy G4VPhysicalVolume GetTopPV Gets a pointer to the phys ical volume on top of the geometry hierarchy G4Material GetMaterial const G4String amp name bool ex ists Gets the material with the given name std vector lt G4LogicalVolume gt GetLogicalVolumes const G4String amp name bool exists Gets the list of logical volumes with the given name std vector lt G4VPhysicalVolume gt GetPhysicalVolumes const G4String amp name bool exists Gets the list of physical volumes with the given name std vector lt GmTouchable gt Get Touchables const G4String amp name bool exists Gets the list of touchables with the given name std setjG4String GetAlISDTypes Gets all distinct sensitive detector types 3 7 MAGNETIC FIELD 43 3 7 Magnetic field You can set a constant magnetic field with the command gamos magneticField setField FIELD X FIELD_Y FIELD Z where FIELD X FIELD Y FIELD Z are the field values along the three axes Remember than in Geant4 internal units 1 Tesla is equal to 0 001 therefore if you do not use any unit it will be understood as 1 that is 1000 Teslas 44 CHAPTER 3 GEOMETRY Chapter 4 Generator You can use the GAMOS generator selecting the time energy position and momentum distribution using the gen
16. other example you want to transform just substitute the line name exampleN02 with the name of your example indeed you can use any name you want it will be automatically detected by GAMOS Then you have to add a file that we called src module cc where all the plug in s are created The first line of this file after the correspond ing includes must be DEFINE SEAL MODULE For the detector construction it is only needed to add a line DEFINE GAMOS GEOMETRY ExN02DetectorConstruction For the physics in a similar way we add DEFINE GAMOS PHYSICS ExNO2PhysicsList The primary generator requires some more changes As you can see ExNO02PrimaryGeneratorAction constructor receives as argument the detector construction class so that it can then ask it for the dimen sions of the world This is not needed in GAMOS because all volumes are available in any class through the singleton class GmGeometry Utils Therefore we have deleted the detector construction argument in the constructor and then we have substituted the line G4double position 0 5 myDetector GetWorldFullLength with these 137 138 CHAPTER 14 APPENDIX G4Box worldBox G4Box GmGeometryUtils GetInstance gt GetLogicalVolumes World 0 gt GetSolid G4double position 0 5 worldBox gt GetXHalfLength After this in the src module cc a line has to be included DEFINE_GAMOS_GENERATOR ExN02PrimaryGeneratorAction For the user ac
17. you produce the hits with zero resolution and store them and in another run you can read applying a certain energy resolution this way you spare the time to recreate them what usually is several orders of magnitude slower than reading them To use this utility you just have to activate the user action gamos userAction GmHitsWriteUA The name of the file can be controlled with the parameter gamos setParam Output hits FileNameOut MY FILENAME If this parameter is not found the name will be hits out You can read back the hits by activating the user action gamos userAction GmHitsReadUA The name of the file can be controlled with the parameter gamos setParam Output hits FileNameln MY FILENAME If this parameter is not found the name will be hits out As commented above you can use all the other options in your script and just read the hits instead of generating them But probably you do not want that new hits are created when you are reading them from a file in this case you should also activate the user action gamos userAction GmKillAllUA 7 7 1 File format The file to be written can be a text file or a binary file The format depends on the value of the parameter gamos setParam SD GmHitsWriteUA BinFile TRUE FALSE The text file contains a line for each hit with the following information e Event ID e Sensitive detector type e Detector unit ID e Energy MeV e Minimum time ns e Maximum time ns e Position X mm
18. 000 000 Another utility of the GmVHistoBuilder class is that it provides a set of pa rameters to define the number of bins the minimum and the maximum limits of dif ferent histogram types position angle energy The default values of these pa rameters can be overriden in the command script by using the gamos setParam 9 2 USER ACTION UTILITIES 95 command with parameter names equal to the file name plus the type of parameter In the example above the commands to change the histogram definitions would be gamos setParam step GmSecondaryFilter GmClassifierByParticle hENbins NBINS gamos setParam step GmSecondaryFilter GmClassifierByParticle hEMin MIN gamos setParam step GmSecondaryFilter GmClassifierByParticle hEMax MAX The following parameters are defined in parenthesis their default value e Energy type histograms hENbins 100 hEMin 0 hEMax 10 MeV e Position type histograms hPosNbins 100 hPosMin 200 mm hPosMax 200 mm e Angle type histograms hAngleNbins 100 hAngleMin 0 hAngleMax 180 e Time type histograms hTimeNbins 100 hTimeMin 0 hTimeMax 1 ms e Number of steps type histograms hNStepNbins 100 hNStepMin 0 hNStepMax 100 e Number of secondary particles type histograms hNSecoNbins 100 hNSecoMin 0 hNSecoMax 100 9 2 User action utilities These are a set of utilities that can be
19. A TEXT FILE 19 2 Polar angle of the line joining the centres of the faces at pDz 3 Azimuthal angle of the line joining the centre of the face at pDz to the centre of the face at pDz 4 Half length along y of the face at pDz pDy1 5 Half length along x of the side at 1 of the face at pDz 6 Half length along x of the side at y pDy1 of the face at pDz 7 Angle with respect to the y axis from the centre of the side at y pDy1 to the centre at y pDyl of the face at pDz 8 Half length along y of the face at pDz pDy2 9 Half length along x of the side at y pDy2 of the face at pDz 10 Half length along x of the side at y pDy2 of the face at pDz 11 Angle with respect to the y axis from the centre of the side at y pDy2 to the centre at y pDy2 of the face at pDz or alternatively if your trapezoid is a simpler one you can use the parame ters 1 Length along z 2 Length along y 3 Length along x at the wider side 4 Length along x at the narrower side SPHERE sphere 1 Inner radius 2 Outer radius 3 Starting angle of the segment 4 Delta angle of the segment 5 Theta starting angle of the segment 6 Theta delta angle of the segment ORB full solid sphere 1 Outer radius 20 CHAPTER 3 GEOMETRY TORUS torus 5 Inside radius Outside radius Swept radius of torus Starting Phi angle fSPhi fDPhi lt 2PI fSPhi gt 2PI Delta angle of the segme
20. DIR X DIR Y DIR Z The position is randomly distributed in a 2D rectangle in the XY plane of widths WIDTH X in X and WID TH Y in Y at position 0 0 0 If you want it placed at a different position you have to add three optional extra parameters POS X POS Y POS Z By default the rectangle is not rotated If you want it rotated you have to add three optional extra parameters and always add the three positions 52 CHAPTER 4 GENERATOR even if they are 0 0 0 DIR X DIR Y DIR Z Those are the director cosines of the Z axis of the rectangle the axis perpendicular to the 2D surface Position in a disc gamos generator positionDist SOURCE NAME GmGenerDistPositionDisc RADIUS POS X POS Y POS_Z DIR X DIR Y Z The position is randomly distributed in a disc in the XY plane of radius RADIUS at position 0 0 0 If you want it placed at a different position you have to add three optional extra parameters POS X POS Y POS Z By default the cylinder is not rotated If you want it rotated you have to add three optional extra parameters and always add the three positions even if they are 0 0 0 DIR X DIR Y DIR Z Those are the director cosines of the Z axis of the cylinder the axis perpendicular to the 2D surface Position in a disc with gaussian distribution gamos generator positionDist SOURCE NAME GmGenerDistPositionDiscGaussian SIGMA POS X POS Y POS Z DIR X DIR Y DIR Z The position is distribu
21. Example Instead of SOLID HALL BOX 5000 5000 20000 VOLU HALL HALL Air use VOLU HALL BOX 5000 5000 20000 Air Placement of a volume All the possible ways to place a volume in Geant4 are supported a single placement a parameterised one a division a replica and an assembly Single placement PLACE 1 Volume name 2 Copy number 3 Parent volume name 4 Name of rotation matrix 5 X position 6 Y position 7 Z position Example VOLU yoke TUBS Iron 3 620 820 1270 PLACE yoke 1 11 0 0 0 0 370 Parameterisation The parameterisations supported are the placement of several copies of a volume along a line in a circle and in a bidimensional grid other types of parameterisation may be added at user request PLACE_PARAM 1 Volume name 26 CHAPTER 3 GEOMETRY 2 Copy number 3 Parent volume name 4 Parameterisation type 5 Name of rotation matrix 6 Number of copies T Step separation between copies 8 Offset 9 Extra arguments optional depend on parameterisation type There are three types of linear parameterisation along the three axis X Y Z types LINEAR X LINEAR Y LINEAR 2 and a general one type LINEAR for which you have to add as extra arguments the axis direction DIR X DIR Y DIR Z The offset for linear parameterisations represents the distance from the centre of the first copy to the point 0 0 0 along the line In the case of circle parameterisati
22. GamosCore GamosGenerator First create a class inheriting from GmVerbosityMgr and fill it as follows e In the include file i e the one with suffix hh of this class define an object of type GmVerbosity as extern extern GmVerbosity MyVerb e In the method void SetFilterLevel int fl call the same method of your GmVerbosity object MyVerb SetFilterLevel fl e In the method void GetFilterLevel int fl call the same method of your GmVerbosity object MyVerb GetFilterLevel fl Finally you have to transform your class into a plug in DEFINE_GAMOS_VERBOSITY MyVerbosityMgr 11 4 Controlling the Geant4 verbosity by event and track If you want to print the detailed step information provided by Geant4 for a given interval of events or tracks but you do not want that it is printed for all you can use the user action gamos userAction GmTrackingVerboseUA You have to define the minimum and maximum events for which you want the verbosity on and you can also set it ON only each N events gamos setParam GmTrackingVerboseU A EventMin gamos setParam GmTracking VerboseU A Event Max gamos setParam GmTrackingVerboseU A EventStep If these parameters are not set the verbosity will be ON for all events You can also define for which tracks interval in the selected events the verbosity will be ON and set it ON only each N tracks gamos setParam GmTrackingVerboseU A TrackMin gamos setParam Gm TrackingVerboseU A TrackMax 11
23. GmClassifierByParticle It assigns a different index to different particle types e GmClassifierByPrimaryParticle It assigns a different index follow ing the particle type for the primary that originated the current particle or the primary particle itself e GmCompoundClassifier This classifier receives a list of classifiers and builds an index as Classifier 1 NShift Classifier_2 NShift NShift Where NShift is defined by the parameter gamos setParam Gm CompoundClassifier NShift NSHIFT that by default takes a value of 100 Be aware that the classifier index is stored as a 32 bit in teger so be careful that the index is not too big bigger than 2 Filters are plug in s so that a user can create her his own filter and select it with a user command To learn how to do this see the instruc tions in the section Creating your plug in using the GmClassifierFactory 10 2 1 Passing parameter values to a classifier Some of the classifiers need a parameter like the GmClassifierByKinet icEnergy that needs the minimum the maximum and the interval width of energies To pass parameter values to a classifier so that it can later be used in a scorer or a user action you have to use the command gamos classifier CLASSIFIER NAME CLASSIFIER CLASS PARAMETER 1 PARAMETER 2 where CLASSIFIER NAME is the new name you want to give to the classifier with the list of parameters so that you can use this name to assign your classifi
24. The following histograms are produced in parenthesis their name without pre fix and the parameter type e Energy Energy E e Energy lost E lost E e Energy deposited E deposited E 9 2 USER ACTION UTILITIES 99 e Step length Step length Pos e Number of secondary tracks created N secondaries NSeco e Energy of secondary tracks created E secondaries E e X coordinate of postion Position X Pos e Y coordinate of position Position Y Pos e Z coordinate of position Position Z Pos e 2D radius coordinate of position Position R2 Pos e 3D radius coordinate of position Position R Pos e phi coordinate of position Position phi Angle e theta coordinate of position Position theta Angle e Change in position Position difference Pos e Change in angle Angle difference Angle e Change in time Time difference Time 9 2 7 Histograms of secondary track information This is a set of histograms produced for each secondary track created at each track step They are created by writing the command gamos userAction GmTrackSecondaryHistosUA This class inherits from Gm V HistoBuilder and invokes SetHistoNames method with parameters secondary and GmTrackSecondaryHistosUA The following histograms are produced in parenthesis their name without pre fix and the par
25. There are another set of filters that receive as argument one or several filters and act on them The list of composed filters in the current GAMOS version is the following GmORFilter returns true if one of the filters returns true GmXORFilter returns true if one and only of the filters re turns true GmANDFilter returns true if every filter returns true GmHistoryFilter returns true if all the filters in one of the previ ous step or the beginning of track have returned true i e it does not check again the current step if it was accepted in a previous one or begin of track 106 CHAPTER 10 FILTERS AND CLASSIFIERS GmHistoryAllFilter returns true if all the filters in all previous steps and the beginning of track have returned true i e it does not check again the current step if it was rejected in a previous one or begin of track GmHistoryAncestorsFilter behaves similarly as the GmHistory Filter but also returns true if the condition is fulfilled by any step or track of the ancestors of the current track GmHistoryAncestorsAllFilter behaves similarly as the GmHisto ryAllFilter but also returns true if the condition is fulfilled by any step or track of the ancestors of the current track GmOnSecondaryFilter makes the list of filters act of the secondary tracks created in the step returns true if one of the secondary tracks created accepts all the filters It does not implement the AcceptTrack method GmOnSe
26. UsersGuides ForApplicationDeveloper html ch02s02 html http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplicationDeveloper html ch04 htmlZ sect Geom Navig http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplicationDeveloper html ch02s06 html http geant4 web cern ch geant4 UserDocumentation UsersGuides PhysicsReferenceManual html ch02s05 html http geant4 web cern ch geant4 UserDocumentation UsersGuides PhysicsReferenceManual html PhysicsReferenceManual html http www slac stanford edu comp physics geant4 slac physics lists G4 Physics Lists html http geant4 web cern ch geant4 physics lists http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplicationDeveloper html apas08 html sect G4MatrDb NISTCmp http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplicationDeveloper html Detector geomSolids html http geant4 web cern ch geant4 UserDocumentation UsersGuides ForApplicationDeveloper html ch04s04 htmlZ sect Hits G4Multi http www irs inms nrc ca BEAM beamhome html http www nds iaea org phsp phsp htmlx Kawrakow I Rogers D W O Walters B R B Large efficiency improvements in BEAMnrc using directional bremsstrahlung split ting Medical physics 2004 31 10 2883 98 149
27. a certain plane in Z and the later starting of the next simulation from this set of particles 13 1 1 Writing phase spaces The writing of phase space can be done automatically in GAMOS by selecting the user action gamos userAction RTPhaseSpaceUA When a particle crosses any of the planes defined by the parameter gamos setParam RTPhaseSpaceUA ZStops Z12 223 its information is stored in a file whose name is given by the parameter gamos setParam RTPhaseSpaceUA FileName MY FILENAME plus a suffix AEAphsp The default value of this parameter is test If there are several Z planes the Z value of each plane will be added to the name with a _ in front so that each phase space will go to a different file If there is only one Z defined the Z value may be written in the file name if the parameter gamos setParam RTPhaseSpaceU A ZStopInFileName TRUE FALSE is set to TRUE If the plane crossed is the one with maximum Z the particle may be stopped if the parameter gamos setParam RTPhaseSpaceU A KillAfterLastZStop TRUE FALSE is set to TRUE The format of the phase space file is the one defined by the IAEA 17 generated using the official C files from IAEA First there is a header file that will have the same name but with the suffix AEAheader It 123 124 CHAPTER 13 RADIOTHERAPY APPLICATION is generated by the IAEA code and you can find the description of it at 17 The variables stored for each particle are the fol
28. automatically be Geant4 in the case of replicas the volume name used must be the name of a previously defined volume This solid is not really used for navigation but should have the correct type and dimensions for visualisation Assembly volumes Assembly volumes are sets of logical volumes that are combined together so that they act as if there were in a real mother but without creation of the mother To define assembly volumes you have to define the relative rotations and positions of all the logical volumes VOLU_ASSEMBLY 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE Volume name Number of logical volumes Axis of division Number of divisions Division width Offset not mandatory One line per logical volume with 4 5 Logical volume name Rotation matrix name position X position Y position Z Then to place the assembly volume you can use PLACE ASSEMBLY 1 2 6 7 Volume name Copy number Parent volume name Name of rotation matrix X position Y position Z position Example SOLID Crystal BOX 10 10 10 SOLID Crystal2 5 5 5 VOLU ASSEMBLY CrystalSet 3 Crystal RMO O O O Crystal RM1 0 O 20 Crystal2 RMO O 20 10 PLACE ASSEMBLY CrystalSet 1 expHall 100 29 30 CHAPTER 3 GEOMETRY Rotation matrix A rotation matrix is interpreted as the rotation that should be applied to the object in the reference system of its mother I
29. energy is deposited locally and it has enough energy to reach the next phantom voxel or enough energy to create a particle that reaches the next phantom voxel this happens mainly for electrons creating gammas which have a much higher range To calculate automatically the best production cut that is the one that gives the smallest CPU while biasing the dose computation a mini mal amount GAMOS uses an inverse reasoning For a given set of cuts for electron and gamma it does not apply them but tags the particles that would have been killed by them It also tags the voxel in which the parti cle is produced and then it computes all the dose deposited by the tagged particle or any of its children in a voxel that is not the same as the tagged voxel To use this utility in GAMOS you just have to associate to your dose scorer a filter of type GmProdCutOutsideVoxelFilter passing to it as argu ments the gamma cut and the electron cut like in the following example gamos scoring addFilter2Scorer ProdCutFilter GmProdCutOut sideVoxelFilter PDDscorerPC10 1 10 mm 1 mm 5 7 AUTOMATIC OPTIMISATION OF CUTS 67 You should add another scorer without filter to get the total dose After running your job with as many scorer filter combinations as you like you can look at the total dose deposited by each scorer and compare it with the total dose It may happen that the dose lost with certain cuts despite being a small proportion of the total dose is dis
30. extra parameters POS X POS Y POS Z 54 CHAPTER 4 GENERATOR By default the volume is not rotated If you want it rotated you have to add three optional extra parameters and always add the three positions even if they are 0 0 0 ANG_X ANG Y ANG_Z Those angles are interpreted as rotating the volume first around the X axis then around the Y axis and finally around the Z axis The direction is taken as the line that goes from the position to the point 0 0 0 As this distribution is of position and direction types at the same time you have to use the two commands gamos generator positionDist gamos generator directionDist You can see editing the file GamosCore GamosGenerator src GmGener Dist PositionDirectionIn VolumeSurface cc that internally the method GenerateDirection knows the position by inter rogating the source Creating your own distribution If you want to use a time energy position or direction distribution that is not foreseen in GAMOS you can easily create your own one Let s see as example the creation of a time distribution randomly distributed between two values You have to create your class inheriting from the class Gm V Gener Dist Time see for example the class GmGenerDistTimeConstant You have then to implement the method virtual G4double GenerateTime const GmParticleSource source that will return the time value for each event If you want the user to be able to input some paramete
31. file can be set by setting the parameter before the user action gamos setParam GmGeomTextDumperAction OutputName FILE NAME 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE 35 3 1 3 Adding new tags to your input text file You may want to add new tags to your text file and give them any meaning you like For example you may use your text file to define your G4Region s and assigning different production cuts to each region as it will be illustrated in the following lines The first step is to define a class inheriting from G4tgrLineProcessor see for example GamosCore GamosGeometry include GmGeom TextLineProcessor hh You should then define a method virtual G4bool GmGeomTextLineProcessor ProcessLine const std vector lt G4String gt amp wl This is the method that will be invoked each time a line in your file is read passing to it the line as a vector of strings In this method you should first call the default line processor to process the standard tags defined through this chapter G4bool iret G4tgrLineProcessor ProcessLine wl iret will be set to 1 if the tag is found else you should process the tag yourself For example if tiret ee cid parameter number if w10 REGION 1 GmRegionCutsMgr GetInstance gt AddRegionData wl iret 1 The second step is to define a class inheriting from G4tgbDetectorBuilder see GamosCore GamosGeometry include GmGeomTextDetectorBuilder
32. from the gamma entering SD to the point where a photoelectric interaction happened Diff dir when Pho toElec mm e Difference in kinetic energy from the gamma entering SD to the point where a photoelectric interaction happened Diff energy when PhotoElec mm e Energy lost in the Compton interactions Energy lost Compton keV e Angle variation in the Compton interactions Angle variation Compton mrad e Energy lost in the Rayleigh interactions Energy lost Rayleigh eV e Angle variation in the Rayleigh interactions Angle variation Rayleigh mrad All these histograms are repeated for the different types of events a prefix in the name marks the event type the histogram refers to e ALL every event e No PE events where no photoelectric interaction occurred e Only PE events where only photoelectric interaction occurred e PE 1 Compt events where one photoelectric interaction plus only one Compton interaction occurred e PE 1 Compt events where one photoelectric interaction plus more than one Compton interaction occurred 122 CHAPTER 12 PET APPLICATION Chapter 13 Radiotherapy application The Radiotherapy example contains some utilities for the simulation of a teletherapy linear accelerator and dose calculations in the patient 13 1 Using phase spaces A very common utility in teletherapy simulation is the writing of a phase space i e the set of particles that reach
33. geometries for common medical devices for example the ones you find in the PET directory and the one to build simple voxelised phantoms They have been designed to be used for describing dif ferent devices by simply changing the configuration data For more details please see the corresponding sections of this manual 3 3 Building your geometry with C code You can build your geometry by writing your C class inheriting from G4VUserDetectorConstruction see example in 7 After that you have to transform it into GAMOS plug in To learn how to do this see the instruc tions in the section Creating your plug in using the GmGeometry Factory 3 4 Reading DICOM files GAMOS is able to read the patient data resulting from a CT PET SPECT NMR etc in DICOM format To convert the DICOM format to a format readable by GAMOS adding the material and density information you may use the Geant4 example examples extended medical DICOM In this example you can also find the description of the DICOM format readable by Geant4 and GAMOS To use this utility you should define as your geometry the class gamos geometry GmReadPhantomG4Geometry You should have then a file where your phantom is described whose name is set with the parameter 3 4 READING DICOM FILES 39 gamos setParam GmReadPhantomGeometry Phantom FileName MY FILENAME and another file where you describe the rest of your geometry at least the world volume where the phantom is pla
34. hh You should then define a method virtual const G4tgrVolume GmGeomTextDetectorBuilder ReadDetector to set as line processor the one you have created and to trigger the reading of the file Da E E EE A EE CE ACE construct g4 geometry GmGeomTextLineProcessor tlproc new GmGeomTextLineProcessor G4tgrFileReader tfr G4tgrFileReader GetInstance tfr SetLineProcessor tlproc 36 CHAPTER 3 GEOMETRY tfr ReadFiles find top G4tgrVolume G4tgrVolumeMgr tgrVolmgr G4tgrVolumeMgr GetInstance const G4tgrVolume tgrVoltop tgrVolmgr gt GetTopVolume return tgrVoltop You should also define another method virtual G4VPhysicalVolume GmGeomTextDetectorBuilder ConstructDetector const G4tgrVolume tgrVoltop You should first call the default detector builder to build the Geant4 geometry using the standard tags defined through this chapter G4VPhysicalVolume topPV G4tgbDetectorBuilder ConstructDetector tgrVoltop After that you can add your code that will process your new tags Create regions GmnRegionCutsMgr GetInstance BuildRegions Finally in your detector construction class inheriting from GA4VUserDetectorConstruction you have to set up your detector builder Construct your detector builder GmGeomTextDetectorBuilder gtb new GmGeomTextDetectorBuilder Inform G4tgbVolumeMgr to use your detector builder instead of the default one G4tgbVo
35. in a volume surface of a volume defined by the user The user must provide the definition of the volume as extra parameters SOLID TYPE can be Box Orb Sphere Tubs Cons SOLID DIMENSIONS are the solid dimensions For the order and meaning of the solid dimensions please look at the corresponding Geant4 solid By default the volume is placed at position 0 0 0 If you want it placed at a different position you have to add three optional extra parameters POS X POS Y POS Z By default the volume is not rotated If you want it rotated you have to add three optional extra parameters and always add the three positions even if they are 0 0 0 ANG_X ANG Y ANG_Z Those angles are interpreted rotating the volume first around the X axis then around the Y axis and finally around the Z axis e Adding an extra volume If you have defined a distribution of type GmGenerDistPosition InG4Volumes GmGenerDistPositionInUser Volumes GmGen erDistPositionInG4Surfaces or GmGener Dist PositionIn User Surfaces you can add more volumes with the following user command For understanding the notation to identify touchables in GAMOS see Identifying touchables section Other volume types may be added at user request 41 USING GAMOS GENERATOR 51 gamos generator GmPositionVolumesA ndSurfaces add VolumeOrSurface SOURCE NAME LV NAME1 LV NAME2 for the Geant4 volumes or gamos generator GmPositionVolumesA ndSurfaces add VolumeOrSurface SOURC
36. ing them to his her will in a simple way GAMOS is based on the plug in concept This means that the main program runs without predefined components and the user tells it which components are being loaded at run time without needing to recompile by simply listing them in a text input file This mechanism also lets the user define a new component that was 4 CHAPTER 1 INTRODUCTION not foreseen by GAMOS and easily tell GAMOS to use it together with any other of his her own components or GAMOS components For each of the simulation component types we will describe in the cor responding section which is the command to select it and how to transform a new user component into a GAMOS plug in For the implementation of plug in s GAMOS has chosen the CERN li brary SEAL 3 A common example to better understand the plug in concept is the plug in s that are installed on your computer when you open some Internet page with your web browser Your web browser can use these plug in s to get an extra functionality viewing videos animated figures without your having to recompile it and even if the web browser designers had never before heard of the new plug in Chapter 2 Getting started This chapter explains the practical details to obtain the GAMOS code com pile and run it 2 1 Getting the code and installing it GAMOS has been tested in several Linux distributions Scientific Linux Fedora Core and Ubuntu as well as Mac O
37. instantiated through user commands As for any user action filters can be assigned to them to select for which type of tracks they will be activated 96 CHAPTER 9 ANALYSIS EXTRACTING INFORMATION 9 2 1 Counting the number of tracks and events This utility prints a line every N events with the event number the number of tracks in this event and the accumulated number of tracks in all events 44 EVENT O NTRACKS 4 TOTAL NTRACKS 4 44 EVENT 1000 NTRACKS 6 TOTAL NTRACKS 4663 44 EVENT 2000 NTRACKS 4 TOTAL NTRACKS 9440 Its main use is to inform the user of the progress of the job in interactive running To activate this utility use the command gamos userAction GmCountTracksUA The user can control the interval of events as well as the first event to start printing with the parameters gamos setParam GmCountTracksUA EachNEvent NEV 10 gamos setParam GmCountTracksUA FirstEvent NEV 0 This utility distinguishes for the ionisation and bremsstrahlung processes those cases when a secondary particle is emitted and those when the step is limited to assure a correct energy loss and multiple scattering but no secondary particle is emitted it adds _NoSeco at the end of the process name 9 2 2 Counting the processes This utility prints four tables e At the beginning of run all the active processes for each particle type PROC_LIST e Transportation PROC_LIST e annihil PROC_LIST e eBrem PROC_LIST e eloni PROC_LIST e msc
38. it with a list of logical volumes with the user command gamos scoring createMFDetector MFD LOGICAL VOLUME NAME s where MFD_NAME is the detector name that will be used later and LOGICAL_VOLUME_NAME s is a list of logical volumes that you associate to this detector Then you should add to the detector one of the GAMOS scorers or your own ones with the user command gamos scoring addScorer2MFD SCORER SCORER CLASS MFD NAME SCORER PARAMETERS SCORER NAME is a name you give to the scorer to be used later SCORER_CLASS is one of the available scorer classes MFD_NAME is one of the multifunctional detectors created above and SCORER PARAMETERS the extra parameters a scorer may need see below for the description of the scorers You may repeat this command to associate several scorers to the same detector To each of the defined scorers you can add a filter to select for which track conditions the scoring will be done gamos scoring addFilter2Scorer FILTER NAME CLASS SCORER NAME FILTER NAME CLASS is the name of a GmVFilter class or the name you gave to a filter built from a filter class by using the command gamos filter see section on Filters and SCORER NAME is one of the scorers defined above You may repeat this command to associate several filters to the same scorer See section on Filters for a description of the available filters and 85 86 CHAPTER 8 SCORING how to create your own one
39. logical volume You can also use the materials and volumes of the ASCII geometry in your C geometry retrieving them by name To retrieve the pointer of a material GmGeometryUtils geomUtils GmGeometryUtils GetInstance G4Material mate geomUtils GetMaterial Air exists true To retrieve a logical volume GmGeometryUtils geomUtils GmGeometryUtils GetInstance one volume G4LogicalVolume world logic geomUtils GetLogicalVolumes world true 0 several volumes with same name std vector lt G4LogicalVolume gt crystal logic geomUtils GetLogicalVolumes crystal exists true To retrieve the physical volumes GmGeometryUtils geomUtils GmGeometryUtils GetInstance std vector lt G4VPhysicalVolume gt crystal phys geomUtils GetPhysicalVolumes crystal exists true 3 1 2 Dumping your Geant4 geometry in text file format If you have already a Geant4 geometry written with C code or any other method you can get a geometry text file by simply adding a line in your code G4tgbGeometryDumper GetInstance DumpGeometry theFileName This line should be executed once your geometry has been built for example in a BeginOfRunAction method or at the end of the Construct method in your detector constructor class You can do this in GAMOS by simply adding in your command file the user action named GmGeomTextDumperUA gamos userAction GmGeomTextDumperUA The name of the output
40. of bits is not bigger than the available quantity 327ZNUM EXTRA LONG The order of declaration of the extra information user actions sets the order of bits occupancy At the end of the job each of these extra information user actions fills a file explainning the information contained in each bit By default this file is called RTExtraInfoProvider summ but the user may change the name of it with the parameter gamos setParam RTExtralnfoProviderLong FileName FILE NAME An example of a file is the following one 128 CHAPTER 13 RADIOTHERAPY APPLICATION RTExtraInfoProvider rigin INDEX REGION O DefaultRegionForTheWorld RTExtraInfoProvider rigin INDEX REGION 1 targetReg RTExtraInfoProvider rigin INDEX REGION 2 collimatorReg RTExtraInfoProvider rigin INDEX REGION 3 filterReg RTExtraInfoProvider rigin INDEX REGION 4 monitorReg RTExtraInfoProviderOrigin INDEX REGION 5 shieldingReg RTExtraInfoProvider rigin INDEX REGION 6 jawsReg The float extra information providers fill one of the two available words in the order they have been defined The user can add more float words by changing the the following line at source RadioTherapy include iaeaRecord hh define NUM EXTRA FLOAT 2 To store some information as float the user has to instantiate one of the following user actions e RTExtralnfoProviderZOrigin stores the Z position of the origin of the track e RTExtralnfoProviderZLast stores the Z position of the last inter action
41. of their composition in the Geant4 file source materials src G4NistMaterialBuilder cc The full list is the following G4 A 150 TISSUE G4 ACETONE G4 ACETYLENE G4 ADENINE G4 ADIPOSE TISSUE ICRP G4 AIR G4 ALANINE G4 ALUMINUM OXIDE G4 AMBER G4 AMMONIA G4 ANILINE G4 ANTHRACENE G4 B 100 BONE G4 BAKELITE G4 BARIUM FLUORIDE G4 BARIUM SULFATE 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE 15 G4 BENZENE G4 BERYLLIUM OXIDE G4 BGO G4 BLOOD ICRP G4 BONE COMPACT ICRU G4 BONE CORTICAL G4 BORON CARBIDE G4 BORON OXIDE G4 BRAIN ICRP G4 BUTANE G4 N BUTYL ALCOHOL G4 C 552 G4 CADMIUM TELLURIDE G4 CADMIUM TUNGSTATE G4 CALCIUM CARBONATE G4 CALCIUM FLUORIDE G4 CALCIUM OXIDE G4 CALCIUM SULFATE G4 CALCIUM TUNGSTATE G4 CARBON DIOXIDE G4 CARBON TETRACHLORIDE G4 CELLULOSE CELLOPHANE G4 CELLULOSE BUTYRATE G4 CELLULOSE NITRATE G4 CERIC SULFATE G4 CESIUM FLUORIDE G4 CESIUM IODIDE G4 CHLOROBENZENE G4 CHLOROFORM G4 CONCRETE G4 CYCLOHEXANE G41 2 DICHLOROBENZENE G4 DICHLORODIETHYL ETHER G4 1 2 DICHLOROETHANE G4 DIETHYL ETHER G4 N N DIMETHYL FORMAMIDE G4 DIMETHYL SULFOXIDE G4 ETHANE G4 ETHYL ALCOHOL G4 ETHYL CELLULOSE G4 ETHYLENE G4 EYE LENS ICRP G4 FERRIC OXIDE G4_FERROBORIDE G4 FERROUS OXIDE G4 FERROUS SULFATE G4 FREON 12 G4 FREON 12B2 G4 FREON 13 G4 FREON 13B1 G4 FREON 13II G4 GADOLINIUM OXYS
42. or exiting default behaviour To select among these three options you can add an extra parameter when defining the scorer that can be In Out or InOut e Other scorers GmGAPSMinKinEAtGeneration This scorer records the min imum kinetic energy of secondary particles at their production point in the volume in an event This primitive scorer does not integrate the quantity but records the minimum quantity GmGAPSNofSecondary This class scores the number of sec ondary particles generated in the volume A particle weight is not applied by default The user can choose if the scoring is done for all types of particles default or only for a set of particles by naming them as extra parameters GmG4PSNofStep This class scores the number of steps in the cell A particle weight is not applied by default If an extra 90 CHAPTER 8 SCORING parameter is set to T RUE those steps with step length zero will not be taken into account GmGAPSCellCharge This class scores the total charge of par ticles which have stopped or have been created in the volume i e the tracks that enter count as 1 and the tracks that exit count as 1 GmG4PSTrackCounter This class scores the number of tracks in a cell e for Event Biasing Scoring for event biasing is a very specific use case whereby particle weights and fluxes through importance cells are required The goals of the scoring technique are to appraise particle quantitie
43. pDz Half x length at the surface positioned at pDz Half y length at the surface positioned at pDz Half y length at the surface positioned at pDz Half z length pDz Twisted angle 24 CHAPTER 3 GEOMETRY TWISTED TUBS tube section twisted along its axis 1 Twisted angle 2 Inner radius at end cap 3 Outer radius at end cap 4 Half z length 5 Phi angle of a segment Boolean solids The three types of Geant4 boolean solids are supported union subtrac tion and intersection The same tag should be used as for normal solids but putting as solid type the type of boolean operation The parameters are 1 Solid name 2 Solid boolean operation UNION SUBTRACTION INTERSECTION 3 First component solid name 4 Second component solid name 5 Name of relative rotation matrix 6 Relative X position 7 Relative Y position 8 Relative Z position Example SOLID myunion UNION solidi solid2 RM30 11 8 12 5 O Volume There are two ways to define a volume You can build if from a previously declared solid associating a material to it VOLU 1 Volume name 2 Solid name 3 Material name Example 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE 25 VOLU HALL HALL Air or you can skip the definition of the solid and in one unique line define the solid and the material valid also for boolean solids You should then use the same format as for the SOLID tag but adding as last word the material name
44. preceded by a character e g 3 mm 1 4 rad Arithmetic Expressions For any value you want to define in a tag you can use the most common mathematical expressions instead of directly writing the figures e g 3 sin 8 2 3 5 3 4 7 log 3 You can also use parameters in the expressions e g 7 2 RADIUS X_LENGTH 1 5 If you use a regular expression remember that there can only be a unit in the whole expression and it must be at the end The regular expressions used include their meaning is evident sin cos asin acos atan atan2 sinh cosh tanh sqrt exp log log10 pow Including other files You can next several files by using the include directive any where in your geometry files Example include mygeom2 txt Combining C ASCII files If you want to define part of your geometry with C and another part with ASCII files you should follow the following instructions Write a C class inheriting from G4VuserDetectorConstruction and in the Construct method build the geometry from a set of ASCII files G4tgbVolumeMgr volmgr G4tgbVolumeMgr GetInstance volmgr AddTextFile mifilel txt volmgr AddTextFile mifile2 txt G4VPhysicalVolume physiSubWorld volmgr gt ReadAndConstructDetector 34 CHAPTER 3 GEOMETRY You can then use the returned G4V PhysicalVolume as the world vol ume or get its logical volume and place it inside any other
45. printer RTPSPDoseHistos gamos scoring addPrinter2Scorer PSPrinterHistos RTPSPDoseHistos DoseScorer By default the number of bins in the histograms will be equal to the number of voxels in the phantom nVoxel and the histogram limits are nVoxel 2 to nVoxel 2 The user can redefine the number of bins as well as the minimum and maximum values of the histograms independently for each of the three dimensions with the following parameters gamos setParam RTPSPDoseHistos X min gamos setParam RTPSPDoseHistos X max gamos setParam RTPSPDoseHistos XNbins gamos setParam RTPSPDoseHistos Y min gamos setParam RTPSPDoseHistos Y max gamos setParam RTPSPDoseHistos YNbins gamos setParam RTPSPDoseHistos Zmin gamos setParam RTPSPDoseHistos Zmax gamos setParam RTPSPDoseHistos ZNbins The histograms limits also define the limits of the voxels that will be used to fill the histograms before filling the histograms with the dose of a given voxel it is checked that the centre of the voxel is inside the limits The names of all these histograms start with RTPSPDoseHistos and they are all dumped into the file dose root csv The following histograms are produced e Dose in X direction Dose in X e Dose in Y direction Dose in Y e Dose in Z direction Dose in Z e Dose in XY direction Dose in XY e Dose in XZ direction Dose in XZ e Dose in YZ direction Dose in YZ e Dose of each voxel Dose e Integrated dose of
46. the number of tracks that would be killed by the range rejection and would not reach the target the tracks themselves 5 7 AUTOMATIC OPTIMISATION OF CUTS 69 or any of their children As for the production cuts they are printed by region by particle and by creator process type To get a closer inside on this technique several plots are produced one per each region each particle and each creator process representing the logarithm of the difference safety range vs the logarithm of the range To distinguish the cases where the range is bigger than the safety no range rejection those cases are plotted in the bins 15 to 5 while the cases where the range is smaller than the safety occupy the bins 5 to 5 if there is a case not likely for a radiotherapy simulation where the log10 fabs safety range is smaller than 5 of course before the 10 substraction it is set to 5 and if is bigger than 5 it is set to 5 TO CHAPTER 5 PHYSICS Chapter 6 User Actions Geant4 user actions are the way the user can interact with a job at the beginning end of each run beginning end of each event beginning end of each track or at each step The user can write a class inheriting from one of the Geant4 user action abstract classes and Geant4 will take care of calling the user code The GAMOS user actions classes provide all the functionality of the Geant4 classes and also allow the user to define several user actions of the same type in th
47. the scorers defined above The quantities scored are given per event by default If you want the score without dividing by the number of events use the command gamos scoring printByEvent PRINTER_NAME FALSE PRINTER is one of the printers defined above The error in the scored quantity per voxel is also calculated by default using the following formula SumW 2 nEvents SumW SumW nEvents 1 nEvents where nEvents is the total number of events in the run SumW is the sum of the scored quantity value times its weight i e the scored quantity itself SumW 2 is the sum of squares of scored quantity value x weight When the scoring is done per event this sum of squares is done summing first all the values x weight belonging to all the particles of the same event and then 8 1 SCORER CLASSES 87 squaring this quantity In this way the correlations between particles of the same event is properly taken into account If the scoring is not by event the error calculation uses the same formula but the sum of squares is not done summing the contribution of the particles of the same event but squaring each contribution individually Calculating the errors makes it necessary to store the square of the weights increasing substantially the memory usage and CPU time If you want to deactivate this option for a scorer use the command gamos scoring scoreErrors SCORER_NAME FALSE SCORER_NAME is one of the scorers defi
48. types described above If you want to set only one user limit type you can use one of the following commands 5 7 AUTOMATIC OPTIMISATION OF CUTS 63 e gamos physics userLimits setMaxStep USER LIMITS NAME LOGICAL VOLUME NAME PARTICLE NAME MAX STEP e gamos physics userLimits setMaxTrkLen USER LIMITS NAME LOGICAL VOLUME NAME PARTICLE NAME MAX TRK LENGTH e gamos physics userLimits set Max TOF USER LIMITS NAME LOGICAL VOLUME NAME PARTICLE NAME MAX TOF e gamos physics userLimits setMinEKin USER LIMITS NAME LOGICAL VOLUME NAME PARTICLE NAME MIN KIN e gamos physics userLimits setMinRange USER LIMITS NAME LOGICAL VOLUME NAME PARTICLE NAME MIN RANGE There is another command in GAMOS that serves to set the minimum range user limit using a distance value but internally it is applied as a minimum kinetic energy limit This permits to use range values but avoids the lengthy process of converting the kinetic energy at each step into range For this you can use the command e gamos physics userLimits setMinEKinByRange USER LIMITS NAME LOGICAL VOLUME NAME PARTICLE NAME MIN RANGE Once a user limit is set you may apply it to a new pair of logical volume and particle type with the following command e gamos physics userLimits addLVAndParticle USER LIMITS NAME LOGICAL VOLUME NAME PARTICLE NAME for the list of particle names in GAMOS see section Particle names 5 7 Automatic optimisation of cuts T
49. written e Classification index of event PET classification This index is the one described in the precedent section e Number of 511 keV reconstructed hits before cleaning if there are more than two and searching for Compton hits i e hits produced merging two crystals see above N 511 recHits initial e The energy of the 511 keV reconstructed hits PETEvtClass Ex tra PET RecHit energy keV e The energy of the 511 keV reconstructed hits that are rejected be cause there are more than two PETEvtClass Extra PET RecHit energy keV 118 CHAPTER 12 PET APPLICATION e Distance of closest approach between vertex and the line joining the two 511 keV reconstructed hits DCA PET dist line vertex mm There are also a histogram of the DCA and the reconstructed hit energies for each of the sixteen subclassification types combinations of the 4 subindices and also for the all the events that are far from vertex all the events where there were more than two hits all the events with random coincidences and all the scttered events 12 2 3 PET output for reconstruction If the event is classified as a PET one it is dumped in a binary file given by the name gamos setParam Output pet FileNameOut MY FILENAME that takes the name pet out by default The variables written are given by the structure struct PetOutput char 8 float xVtx yVtx zVtx x1 y1 21 x2 y2 22 where name is PET x y zVt
50. 0 After that you have to transform it into a plug in To learn how to do this see the instructions in the section Creating your plug in using the GmPhysicsFactory 5 4 Other physics lists You can use easily in GAMOS any of the Geant4 physics lists 12 All you have to do to use a Geant4 physics list is to add in the src module cc file in any of the ones in GAMOS code or create your own one two lines like include QGSP hh DEF INE_GAMOS_PHYSICS QGSP Compile it and then you can use it in your command file with the line gamos physicsList QGSP There is also in GAMOS a GmDummyPhysicsList that defines all the particles but only the process G4Transportation 5 5 Production cuts Several physics processes namely bremsstrahlung ionization and e e pair production from muons have very high cross sections at low energies It is therefore necessary to implement a production cut so that all particles below it are not generated but their energy is accounted as energy deposited Geant4 uses production cuts in range instead of in energy as used previously by and most Monte Carlo codes A cut of for example 1 mm for photons means that no photon will be produced if the expected range in the current material is less than 1 mm If you use the GAMOS electromagnetic physics list the default produc tion cut value is 0 1 mm for all processes in all materials The Geant4 com mand run particle setCut value unit set th
51. 0 0 delta 1920 delta 1920 delta 1920 delta 1920 0 delta 1930 delta 1930 delta 1930 delta 1930 0 146 CHAPTER 14 APPENDIX delta 1950 delta 1950 delta 1950 delta 1950 0 1 1 delta deltaO deuteron e e eta eta 1295 eta 1405 eta 1475 eta2 1645 eta2 1870 eta prime f0 1370 0 1500 f0 1710 0 600 0 980 1 1285 1 1420 2 1270 2 1810 2 2010 f2 prime 1525 gamma geantino gluon hi 1170 h1 1380 k 1460 k 1460 k 1460 0 kO_star 1430 kO_star 1430 kO_star 1430 0 k1 1270 k1 1270 k1 1270 0 k1 1400 k1 1400 k1 1400 0 k2 1770 k2 1770 k2 1770 0 k2_star 1430 k2 star 1430 k2 star 1430 0 k2 star 1980 k2 star 1980 k2 star 1980 0 k3_star 1780 k3 star 1780 k3 star 1780 0 k_star 1410 k star 1410 k star 1410 0 k_star 1680 k star 1680 k star 1680 0 start k star k starO kaon kaon kaonO kaonOL kaonOS lambda lambda 1405 lambda 1520 lambda 1600 lambda 1670 lambda 1690 lambda 1800 lambda 1810 lambda 1820 lambda 1830 lambda 1890 lambda 2100 lambda 2110 lambda c mu mu neutron nu e nu mu nu tau omega omega 1420 omega 1650 omega omega3 1670 omega cO opticalphoton phi phi 1680 phi3 1850 pi 1300 pi 1300 pi 1300 0 pi pi piO pi2 1670 pi2 1670 pi2 1670 0 proton rho 1450 rho 1450 rho 1450 0 rho 1700 rho 1700 rho 1700 0
52. 1 MeV RANGE CUT 334 152 GmCutsEnergy2RangeUA MATERIAL G4_WATER PART e ENERGY CUT 0 1 MeV RANGE CUT 0 134781 GmCutsEnergy2RangeUA MATERIAL G4_WATER PART e ENERGY CUT 0 1 MeV RANGE CUT 0 137686 5 6 User limits User limits are the way Geant4 gives the user to limit the tracking of a particle There are five types of user limits e Limit the step size e Limit the track length e Limit the time of flight e Stop the particle when the kinetic energy is below a limit and deposit its energy locally e Stop the particle when the expected range is below a limit and deposit its energy locally Different user limits can be applied in Geant4 for different logical vol umes although there is the limitation that all particles must have the same user limits in the same logical volume In GAMOS a user can set the user limits through simple user commands and user limits can be set independently for different particle types in the same or different logical volumes The set of commands to set user limits is e gamos physics userLimits setUserLimits USER LIMITS NAME LOGICAL VOLUME NAME PARTICLE NAME MAX STEP MAX TRK LENGTH MAX TOF MIN_KIN_E MIN RANGE where USER_LIMITS_NAME is the name of the user limits every user limits must have a name so that new logical volumes and particles can be added with user commands later MAX STEP MAX TRK LENGTH MAX_TOF MIN KIN E and MIN RANGE are the values of the five user limit
53. 1 4 Adding extra information to a phase space The IAEA format allows the storing of two long integers and two floats in the phase space file as extra information In GAMOS we have ex tended this functionality by putting the 324 32 bits of the two inte gers in a continuous stream that the user can divide in groups of bits of the desired length to store several informations The user can even add more sets of 32 bits by changing the the following line at source RadioTherapy include iaeaRecord hh define NUM EXTRA LONG 2 and recompiling cd MY_GAMOS_DIR source RadioTherapy make To store some information in this format the user has to instantiate one of the following user actions e RTExtralnfoProviderCrossings fills a bit if the track has crossed the corresponding region before reaching the phase space e RTExtralnfoProviderInteractions fills a bit if the track has inter acted in the corresponding region before reaching the phase space e RTExtralnfoProviderOrigin fills a bit if the track has been created in the corresponding region before reaching the phase space The user may select how many bits each information must occupy by using the GAMOS parameter gamos setParam EXTRA INFO NAME NBits NBITS where EXTRA INFO NAME is the name of the extra information class see above GAMOS will check that the index to be filled by a class is not bigger than the number of bits reserved for it And it will also check that the total number
54. 26 Gy 0 013747866 Gy 91 where MFD NAME is the name of multifunctional detector and SCORER NAME is the name of the scorer copy no have the following meaning The columns after Index scorer value scorer error relative i e error value unit name Other scorer printers are provided for specific applications See corre sponding sections in this guide 8 4 Classifier classes See section on Filters and classifiers 92 CHAPTER 8 SCORING Chapter 9 Analysis extracting information 9 1 Using histograms GAMOS supports several data analysis formats The format is selected at run time by the user so that the same C code can be used to write any format In this GAMOS version there are two formats implemented ROOT and CSV Comma Separated Value For the ROOT format we refer you to the ROOT documentation 5 The CSV format is explained below You can choose which format to use with the command gamos analysis fileFormat FORMAT where FORMAT can be ROOT root CSV csv 9 1 1 Histogram files common name If you are running a job and you want to identify all your histogram files with a characteristic suffix you may do it by defining the parameter gamos setParam GmaAnalysisMgr FileNameSuffix SUFFIX The name SUFFIX will be added at the end of all histogram names before the file type root or csv 9 1 2 Histograms in CSV format The CSV Comma Separated Value format is a simple text file where the valu
55. 4 CHAPTER 11 MANAGING THE VERBOSITY gamos setParam Gm TrackingVerboseU A TrackStep If these parameters are not set the verbosity will be ON for all tracks Finally you may select the Geant4 verbosity level by default 1 with the parameter gamos setParam GmTracking VerboseU A VerboseLevel Chapter 12 PET application The PET example contains two directories The first one PetGeometry contains an utility to build a simple PET ring detector by just defining a few parameters The second one contains the PET event classifier and a couple of histogram classes 12 1 PET geometry The directory PET PETGeometry contains an utility to build a simple PET ring detector by just defining the following parameters e block Number of crystals per block e Nblocks Number of blocks of crystals per ring e Nrings Number of rings of blocks e c transaxial Crystal size trans axial e c axial Crystal size axial e c radial Crystal size radial e diameter Detector ring diameter There are several examples of simplified commercial PET detectors in the files with suffix dat in that directory To use this utility you just have to choose as your geometry the PETGeometry one gamos geometry PETGeometry By default it reads the filename PETGeometry dat If you want to change it you can do it with the parameter gamos setParam PET Geometry FileName MY FILENAME There are two types of sources available 1994 and DOLL You can select th
56. 4_PROPANE G4_IPROPANE G4_N PROPYL_ALCOHOL G4_PYRIDINE G4_RUBBER_BUTYL G4 RUBBER NATURAL G4 RUBBER NEOPRENE G4_SILICON_DIOXIDE G4_SILVER_BROMIDE G4 SILVER CHLORIDE G4 SILVER HALIDES G4_SILVER_IODIDE G4 SKIN ICRP G4 SODIUM CARBONATE G4 SODIUM IODIDE G4 SODIUM MONOXIDE G4 SODIUM NITRATE G4_STILBENE G4 SUCROSE G4_TERPHENYL G4_TESTES_ICRP G4 TETRACHLOROETHYLENE G4_THALLIUM_CHLORIDE G4 TISSUE SOFT ICRP G4 TISSUE SOFT ICRU 4 G4 TISSUE METHANE G4 TISSUE PROPANE G4 TITANIUM DIOXIDE G4_TOLUENE G4 TRICHLOROETHYLENE G4_TRIETHYL_PHOSPHATE G4_TUNGSTEN_HEX AFLUORIDE G4_URANIUM_DICARBIDE G4 URANIUM MONOCARBIDE G4_URANIUM_OXIDE G4_UREA G4_VALINE G4_VITON G4 WATER G4_WATER_VAPOR G4 XYLENE G4 GRAPHITE G4 1H2 G4 IN2 G4 102 G4 lAr G4 IKr G4 1Xe G4 PbWOA G4 Galactic 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE 17 Solid SOLID 1 solid name 2 solid type name 3 List of solid parameters The meaning and order of the solid parameters is the same as in the corresponding Geant4 solid constructor All the Geant4 CSG and specific solids are implemented The list of solid types and the corresponding pa rameters is the following for better understanding of the solid parameters meaning we refer to the Geant4 user s manual 7 BOX box 1 X Half length 2 Y Half length 3 Z Half length TUBE tube 1 Inner radius 2 Outer radius 3 Half length i
57. 900 0 32 ELLIPTICAL TUBE elliptical tube CHAPTER 3 1 Half length X 2 Half length Y 3 Half length Z ELLIPSOID ellipsoid 1 Semiaxis in X 2 Semiaxis in Y 3 Semiaxis in Z 4 Lower cut plane level z 5 Upper cut plane level z ELLIPTICAL CONE elliptical cone 1 Semiaxis in X 2 Semiaxis in Y 3 Height of elliptical cone 4 Upper cut plane level HYPE hyperbolic profile 1 Inner radius 2 Outer radius 3 Inner stereo angle 4 Outer stereo angle 5 Half length in Z TET tetrahedron 1 Anchor point 2 Point 2 3 Point 3 4 Point 4 5 Flag indicating degeneracy of points GEOMETRY 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE 23 TWISTED BOX box twisted along one axis 1 2 3 4 Twist angle Half x length Half y length Half z length TWISTED TRAP trapezoid twisted along one axis 1 10 11 12 13 Twisted angle Half x length at y pDy Half x length at y pDy Half y length pDy1 Half z length pDz Polar angle of the line joining the centres of the faces at pDz Half y length at pDz pDy2 Half x length at pDz 1 Half x length at pDz y pDyl Half y length at pDz Half x length at pDz y pDy2 Half x length at pDz y pDy2 Angle with respect to the y axis from the centre of the side TWISTED TRD twisted trapezoid with the x and y dimensions vary ing along z 1 2 Half x length at the surface positioned at
58. AMOS the output that appear on your screen as stan dard output is also written to a log file called gamos log while the stan dard error messages are written to another log filegamos_error log You may select another name for the standard output log file by using the Geant4 command gamos log setCoutFile FILE NAME and you can also change the name of the standard error log file by using the Geant4 command gamos log setCerrFile FILE NAME You may choose to give the tow log files the same name if you want them to appear together in the same order they appear on your screen It is also possible to suppress the writing of any log file by using the Geant4 file gamos log writeFiles 0 Take into account that the above commands start to take effect when they are read this means that you may have part of the output written in a file the one that appeared before the command and the rest in another file the one that appeared after the command or in a similar way write part of the output only using the third command in the middle of your input file 14 6 IDENTIFYING TOUCHABLES 143 14 6 Identifying touchables As explained in several points through this guide you can use the con cept of touchable available in GAMOS We will explain first in a few lines the concept of touchable in Geant4 and GAMOS In Geant4 there are several geometrical objects 7 e G4AVSolid A solid is a geometrical object that has a shape and specific values f
59. ASESPACE FILE NAME you will get on the screen this information in an output similar to this READING ps iaea 20000 IAEAheader ORIGINAL HISTORIES 5000000 13 4 ANALYSIS UTILITIES 135 PARTICLES PER EVENT 0 0450874 9 70776e 05 GAMMAS PER EVENT 0 0450136 9 69947e 05 ELECTRONS PER EVENT 7 28e 05 3 8159e 06 POSITRONS PER EVENT 1e 06 4 47214e 07 If you want to compare two files you just have to add a second file name analysePS PHASESPACE FILE NAME 1 PHASESPACE FILE NAME 2 and you will get the contents of the first file the contents of the second file and the ratio of particles per event of the first file divided by the second one with the statistical errors included READING ps iaea 20000 1AEAheader ORIGINAL HISTORIES 5000000 PARTICLES PER EVENT 0 0450874 9 70776e 05 GAMMAS PER EVENT 0 0450136 9 69947e 05 ELECTRONS PER EVENT 7 28e 05 3 8159e 06 POSITRONS PER EVENT 1e 06 4 47214e 07 READING ps iaea 20001 1AEAheader EVENTS 5000000 PARTICLES PER EVENT 0 044927 9 68973e 05 GAMMAS PER EVENT 0 0448562 9 68176e 05 ELECTRONS PER EVENT 6 92e 05 3 72034e 06 POSITRONS PER EVENT 1 6e 06 5 65686e 07 RATIO PARTICLES PER EVENT 1 00357 0 00305842 RATIO GAMMAS PER EVENT 1 00351 0 00306059 RATIO ELECTRONS PER EVENT 1 05202 0 0789916 RATIO POSITRONS PER EVENT 0 625 0 356305 13 4 3 Making histograms out of a phase space file You can make histograms out of the particles contained in a
60. Compton interaction in SD per centage relates to n PE e n COMP number of original gammas with Compton interactions in SD e 1 COMP number of original gammas with only one Compton interaction in SD percentage relates to n COMP e gt 1 COMP number of original gammas with more than one Compton interactions in SD percentage relates to n COMP e nCOMP event number of Compton interactions in SD per orig inal gamma This class also makes several histograms all of them have the words Gamma At SD included in their names And all are written to the file gammaSD root csv The following histograms are defined e Event Type 100 i e no Rayleigh counting Event Type e Number of photoelectric interactions per original gamma N PhotoElec e Number of Compton interactions per original gamma N Comp ton e Number of Rayleigh interactions per origina gamma N Rayleigh e Number of photoelectric interactions vs Number of Compton Rayleigh interactions per origina gamma PhotoElec vs Compton Rayleigh 12 2 PET ANALYSIS 121 e Energy of gamma upon entering SD Energy at entering SD keV e Energy lost in the photoelectric interactions Energy lost Photo Elec keV e Difference in position from the gamma entering SD to the point where a photoelectric interaction happened Diff pos when Pho toElec mm e Difference in direction
61. Division There are several ways to define a division in Geant4 by giving e the number of divisions so that the width of each division will be automatically calculated e the division width so that the number of divisions will be automati cally calculated to fill as much of the mother as possible e both the number of divisions and the division width this is especially designed for the case where the copies do not fully fill the mother To each of these types correspond a different tag DIV_WIDTH 1 Volume name 2 Parent volume name 3 Material name 4 Axis of division 5 Division width 6 Offset not mandatory DIV_NDIV 1 Volume name 2 Parent volume name 3 Material name 4 Axis of division 5 Number of divisions 6 Offset not mandatory DIV_NDIV_WIDTH 1 Volume name 28 CHAPTER 3 GEOMETRY 2 Parent volume name Material name Axis of division Number of divisions 6 Division width 7 Offset not mandatory Example DIV WIDTH mybox mother AIR Z 10 DIV NDIV WIDTH mytube mother copper PHI 12 10 deg Replica To define a replica the following tag must be used REPL 1 Volume name 2 Parent volume name Axis of division A Number of divisions Division width 6 Offset not mandatory Example REPL crystal Block X 10 5 cm Remember that different to the divisions where the solid type and di mensions are calculated
62. E NAME POS X POS Y POS_Z ANG_X ANG Y ANG Z SOLID TYPE SOLID DIMENSIONS for the user defined volumes The primary particles will be distributed equally in the volumes proportionally to their volume or surface e Position in steps along a line gamos generator positionDist SOURCE NAME GmGenerDistPositionLineSteps POS X POS Y POS Z DIR X DIR Y DIR Z STEP The position is distributed uniformly along a line starting at position POS X POS Y POS Z and with direction given by the three di rector cosines DIR X DIR Y DIR Z Each event is generated in a different point along the line starting at the initial position and in steps given by STEP e Position in a square gamos generator positionDist SOURCE NAME GmGenerDistPositionSquare WIDTH POS X POS Y POS Z DIR X DIR Y DIR Z The position is randomly distributed in a 2D square in the XY plane of width WIDTH at position 0 0 0 If you want it placed at a different position you have to add three optional extra parameters POS X POS Y POS Z By default the square is not rotated If you want it rotated you have to add three optional extra parameters and always add the three positions even if they are 0 0 0 DIR X DIR_Y DIR Z Those are the director cosines of the Z axis of the square the axis perpendicular to the 2D surface e Position in a rectangle gamos generator positionDist SOURCE NAME GmGenerDistPositionRectanglee WIDTH X WIDTH Y POS X POS Y POS Z
63. Geant4 based Architecture for Medicine Oriented Simulations GAMOS Version 2 0 1 User s Guide Pedro Arce August 28 2009 Contents 1 Introduction 1 1 Aboutthisdocument ern 12 Structure of GAMOS 2er 13 The plug in concept css Getting started 2 1 Getting the code and installing it 2 2 Running an example 2 3 Compiling 58 2 3 1 Compiling your new code Geometry 3 1 Building your geometry with a text 3 1 1 Description of geometry text file format 3 1 2 Dumping your Geant4 geometry in text file format 31 3 Adding new tags to your input text file 3 14 Parallel 3 2 Building simple geometries 3 3 Building your geometry with C code 3 4 Reading DICOM files 3 4 1 Simple phantom geometries 3 5 Movements 24 04 RR eR RA 3 6 Geometry utilities 22e 3 7 Magneticfield 22e Generator 4 1 Using GAMOS generator 4 1 4 Introduction 4 1 2 Single particlesource llle 4 1 3 Isotope source leere 4 2 Building your generator with C 43 Reading your generator particles from a text file 44 Reading your generator particles from a binary fi
64. N 1710 0 anti N 1720 anti N 1720 0 anti N 1900 anti N 1900 0 anti N 1990 anti N 1990 0 anti N 2090 anti N 2090 0 anti N 2190 anti N 2190 0 anti N 2220 anti N 2220 0 anti N 2250 anti N 2250 0 anti b quark anti c quark anti d quark anti ddi diquark anti delta 1600 anti_delta 1600 anti delta 1600 anti delta 1600 0 anti delta 1620 anti_delta 1620 anti delta 1620 anti delta 1620 0 anti delta 1700 anti_delta 1700 anti delta 1700 anti delta 1700 0 anti delta 1900 anti_delta 1900 anti delta 1900 anti delta 1900 0 anti delta 1905 anti delta 1905 anti delta 1905 anti delta 1905 0 anti delta 1910 anti delta 1910 anti delta 1910 anti delta 1910 0 anti delta 1920 anti_delta 1920 anti delta 1920 anti delta 1920 0 anti delta 1930 anti_delta 1930 anti delta 1930 anti delta 1930 0 anti delta 1950 anti_delta 1950 anti delta 1950 anti delta 1950 0 anti delta anti delta anti delta anti deltaO anti k 1460 0 anti kO star 1430 0 anti k1 1270 0 anti k1 1400 0 anti k2 1770 0 anti k2 star 1430 0 anti k2 star 1980 0 anti k3 star 1780 0 anti k star 1410 0 anti k star 1680 0 anti star0 anti kaonO anti lambda anti lambda 1405 anti lambda 1520 anti lambda 1600 anti lambda 1670 anti lambda 1690 anti lambda 1800 anti lambda 1810 anti lambda 1820 anti lambda 1830 anti lambda 1890 anti lambda 2100 anti lambda 2110 a
65. OptimA xis kUndefined GAMOS is also able to read the DOSXYZnrc format for DICOM files that is commonly used in EGSnrc Simply use gamos geometry GmReadPhantomEGSGeometry and the rest of parameters are the same as for the Geant4 DICOM files By default the phantom is placed in the world volume If you want to place it into another physical volume you can set the parameter gamos setParam GmReadPhantomGeometry MotherName PHYSVOL_NAME 40 CHAPTER 3 GEOMETRY 3 4 1 Simple phantom geometries The user may build simple regular phantom geometries without the need of writing a DICOM file by using gamos geometry GmSimplePhantomGeometry The number of voxels is defined with the parameter gamos setParam GmSimplePhantomGeometry N Voxels NVOXEL X NVOXEL Y NVOXEL Z The minimum and maximum extensions in the three axes are defined with the parameter gamos setParam GmSimplePhantomGeometry PhantomDims MIN X MAX X MIN Y MAX Y MIN Z Z Then you can divide the phantom in different regions along the Z axis with the parameter gamos setParam GmSimplePhantomGeometry MaterialZVoxels NZ_1 NZ_2 where NZ_i is the number of voxels along Z of the i region Then you can assign the material and material densities of each Z region with the parameters gamos setParam GmSimplePhantomGeometry MaterialNames MATERIAL 1 MATERIAL 2 gamos setParam GmSimplePhantomGeometry MaterialDensities DENSITY 1 DENSITY 2 3 5 Movements Thanks t
66. PARAMETER 2 are the values of the parameters that the classifier needs Those classifiers that do not need any parameter can be assigned directly to a user action or a scorer without giving them a new name the name will be the one of the classifier class To attach one classifier to a user action you put its name after the user action name in the command line that selects it gamos userAction USER_ACTION CLASSIFIER_NAME CLASS or you can use a classifier to act on a scorer with the command gamos scoring assignClassifier28corer CLASSIFIER_NAME CLASS SCORER NAME If you want to use more than one classifier for a user action or a scorer you have to use the classifer GmCompoundClassifier see below Each classifier has a method GetIndexName G4int index that re turns a different name for each index value If a classifier does not im plement this method the one in the base class returns the index number converted to a string This method is used by user actions and scorers to add the index number to the name of the histograms tables or scores Classifiers are plug in s so that a user an create her his own classi fier and select it with a user command To learn how to do this see the instructions in the section Creating your plug in using the GmClassifier Factory or the Histograms and scorers tutorial The following classifiers are currently implemented in GAMOS e GmPSClassifierBylAncestor It assigns a different index to differ e
67. S 8 10 You can download GAMOS from http fismed ciemat es GAMOS GAMOS depends on Geant4 and on a number of other libraries CLHEP 4 and optionally ROOT 5 To download and install everything you can follow the instruction in the Code download area As explained there you need to get first the installation scripts and uncompress them in the scripts directory you may do it automatically by downloading the scripts installation utility from the web page After that you just need to type the command sh installGamos csh MY_INSTALLATION_DIR where MY_INSTALLATION_DIR is the directory where you want to install GAMOS This command will download the GAMOS code as well as CLHEP Geant4 and ROOT packages and it will compile them all It will first make sure that you have a C compiler Then it will check if you have the X11 and the OpenGL libraries installed and if not it will install GAMOS without OGLIX visualisation After that follow the instructions below on how to run an example ldo not use the test version Ubuntu 8 10 as it has been publicly reported to have problems with plu in s 6 CHAPTER 2 GETTING STARTED 2 2 Running an example If you have done a standard installation you will have your code compiled and ready to run Before running any example you have to set some configuration variables mainly where you have installed GAMOS and the depending libraries This is all done in the file MY GAMOS DIR config confgamos csh
68. TRACKS ALL 109 COUNT_NSTEPS gamma 399 COUNT_NSTEPS e 29 9 2 USER ACTION UTILITIES 101 4 432 COUNT NSTEPS e COUNT STEPS ALL 9 2 10 Detailed report of where CPU time is spent You may get a detailed report of where the CPU time is spent by instantiating the user action gamos userAction GmTimeStudyUA CLASSIFIER 1 CLASSIFIER 2 By selecting different classifiers you can get a report of the time spent by each particle in each logical volume in each energy bin etc see section on Classifiers The table will have a format similar to the following one hhhhh TIMING RESULTS for timer GmTimeStudyUA _GmClassifierByParticle_GmClassifierByKineticEnergy e 0 0001 0 001 User 0 Real 0 Sys 0 e 0 001 0 01 User 0 Real 0 Sys 0 e 0 01 0 1 User 0 Real 0 02 Sys 0 e 0 1 1 0 28 Real 0 26 Sys 0 01 e 1 10 User 0 18 Real 0 18 Sys 0 02 e 0 0001 0 001 User 0 94 Real 1 12 Sys 0 12 e 0 001 0 01 User 17 13 Real 19 2 Sys 1 85 e 0 01 0 1 User 31 67 Real 35 96 Sys 3 31 e 0 1 1 User 54 81 Real 58 4 Sys 4 61 e 1 10 User 209 36 Real 226 51 Sys 15 73 e 1e 05 0 0001 User 0 06 Real 0 09 Sys 0 e 1e 06 1e 05 User 0 03 Real 0 02 Sys 0 e 1e 07 1e 06 User 0 1 0 Sys 0 e 1e 08 1e 07 User 0 Real 0 Sys 0 gamma 0 001 0 01 User 8 49 Real 9 29 Sys 0 79 gamma 0 01 0 1 User 14 55 Real 15 64 Sys 0 92 gamma 0 1 1 User 33 Real 35 47 Sys 2 15 gamma 1 10 User 8 99 Real 9 35 Sys 0 49 that ca
69. ULFIDE G4 GALLIUM ARSENIDE G4 GEL PHOTO EMULSION G4 Pyrex Glass G4 GLASS LEAD G4 GLASS PLATE G4 GLUCOSE G4 GLUTAMINE G4 GLYCEROL G4 GUANINE G4 GYPSUM G4 N HEPTANE G4 N HEXANE G4 KAPTON G4 LANTHANUM OXYBROMIDE G4 LANTHANUM OXYSULFIDE G4 LEAD OXIDE G4 LITHIUM AMIDE G4 LITHIUM CARBONATE G4_LITHIUM_FLUORIDE G4 LITHIUM HYDRIDE G4 LITHIUM IODIDE G4 LITHIUM OXIDE G4_LITHIUM_TETRABORATE G4 LUNG ICRP G4 G4 MAGNESIUM CARBONATE G4 MAGNESIUM FLUORIDE G4 MAGNESIUM OXIDE G4 MAGNESIUM TETRABORATE G4 MERCURIC IODIDE G4 METHANE G4 METHANOL G4 16 CHAPTER 3 GEOMETRY G4 MS20 TISSUE G4 MUSCLE SKELETAL ICRP G4 MUSCLE STRIATED ICRU G4 MUSCLE WITH SUCROSE G4 MUSCLE WITHOUT SUCROSE G4 NAPHTHALENE G4 NITROBENZENE G4 NITROUS OXIDE G4 NYLON 8062 GA NYLON 6 6 G4 NYLON 6 10 G4 NYLON 11 RILSAN G4 OCTANE G4_PARAFFIN G4 N PENTANE 4 EMULSION G4_PLASTIC_SC_VINYLTOLUENE G4 PLUTONIUM DIOXIDE G4 POLYACRYLONITRILE G4 POLYCARBONATE G4_POLYCHLOROSTYRENE G4 POLYETHYLENE G4 MYLAR G4 PLEXIGLASS G4_POLYOXYMETHYLENE G4 POLYPROPYLENE G4 POLYSTYRENE G4_TEFLON G4 POLYTRIFLUOROCHLOROETHYLENE G4 POLYVINYL ACETATE G4 POLYVINYL ALCOHOL G4 POLYVINYL BUTYRAL G4_POLYVINYL_CHLORIDE G4 POLYVINYLIDENE CHLORIDE G4_POLYVINYLIDENE_FLUORIDE G4 POLYVINYL PYRROLIDONE G4_POTASSIUM_IODIDE G4 POTASSIUM OXIDE G
70. ack with the smallest range If you want to set a different cut for each region and are worried for this double counting you may have a look at the histogram named trackInfos per Track in target that plots per each track reaching the target how many track informations are kept in the histograms Another useful histogram for this case may be the 2D histogram trackInfo Region vs trackInfo Region that plots all the region number of all the pairs of track informations that correspond to the same track reaching the target you can get a list of which region number corresponds to which region at the end of the standard output file Although as mentioned above the production cuts are only necessary for ionization and bremsstrahlung processes this method allows to extend the production cuts to other processes To do this we provide the above mentioned numbers and plots separately for each process so that the cuts can be automatically set in an easy way If you want to apply the same cuts to all processes you can use the GAMOS command gamos GMphysics applyCutsToAllProcesses that will instantiate an object of type G4EmProcessOptions and invoke the method SetApplyCuts true To use this utility in GAMOS it is only needed to add this command in your script gamos userAction GmProdCutsStudyUA PETCutsStudy Filter that will use as target condition that a track enters a sensitive detector gamos userAction GmProdCutsStudyUA RTCutsStudyFilter or th
71. ake a virtual segmentation when you have a big sensitive volume that you want to segment in different pieces although you have not segmented it in your geometry The classes currently implemented are e GmSDVirtSegmentedSphereThetaPhi It divides a sphere into cubes of equal size in R phi and R theta 75 76 CHAPTER 7 SENSITIVE DETECTOR AND HITS e GmSDVirtSegmentedSphereRThetaPhi It divides a sphere into cubes of equal size in R R phi and R theta To attach a GAMOS sensitive detector to a logical volume in your ge ometry you have to use the command gamos SD assocSD2LogVol SD_CLASS SD_TYPE LOGICAL_VOLUME_NAME The SD_CLASS has to be one of the sensitive detector types described above or any other that you create The SD_TYPE serves to differen tiate your different sensitive detectors so that you can later apply differ ent properties to them e g different energy resolutions The LOGI CAL_VOLUME_NAME is the name of the G4LogicalVolume in your geom etry that you want to make sensitive You may repeat this command with different logical volumes 7 2 Building your sensitive detector with C code To build a new sensitive detector you can do it the usual Geant4 way that is inheriting from G4VSensitiveDetector see example in 10 After that you have to transform it into a plug in To learn how to do this see the instructions in the section Creating your plug in using the GmSensDetFac tory You may also choose to inher
72. ameter type e Energy of secondary tracks created E secondary E e Energy of primary track at interaction E primary E e Fraction of energy taken by secondary tracks created E secondary E pri mary C E e Angle between primary track pre step direction and secondary track direction Angle primary_pre secondary Angle e Angle between primary track post step direction and secondary track direc tion Angle primary post secondary Angle e Change of angle of primary track when secondary track is created Angle change of primary Angle 100 CHAPTER 9 ANALYSIS EXTRACTING INFORMATION 9 2 8 Event classification by interaction types There is a utility in GAMOS that helps you in counting and classifying the tracks by the type of interactions they have suffered You just have to create at each step a new Gm TrajPoint and at the end of track pass this list to a GmVSimuEvent Classifier that will return the classification You can see an example at GamosCore GamosAnalysis src GmHistosGammaAtSD cc that we ex plain here in detail This class counts the type of interaction of the photons in the sensitive detectors of your geometry The first thing it does at the PreUserTrackingAction is checking if the current track is an original gamma To do this it gets the help of the GmCheckOrigi nalGamma class that classifies the gammas as e 0 not an original gamma e 1 it is a p
73. asses or different ones GmaAnalysisMgr myAnaMgr GmaAnalysisMgr GetInstance MY FILENAME There are four types of histograms currently supported by GAMOS 1 dimensional 2 dimensional profile 1 dimensional and profile 2 dimensional 1 To create your histogram and register it to GAMOS you have to create it with a line like my AnaMer gt CreateHistol1D HNAM NBINS MAXBIN MINBIN HIS NUMBER myAnaMgr CreateHisto2D HNAM NBINSX MAXBINX MINBINX NBINS MAXBINY MINBINY HIS NUMBER myAnaMgr CreateHistoProfilel D HNAM NBINS MAXBIN MINBIN HIS NUMBER myAnaMgr CreateHistoProfile2D HNAM NBINSX MAXBINX MINBINX NBINS MAXBINY MINBINY HIS_NUMBER The last argument is the histogram number that can be later used to retrieve this histogram from any method in any class If you don t set it GAMOS will assign it automatically starting from 1 Once a histogram is registered you can get a pointer to it by asking GmaAnalysisMgr for a histogram by its number or its name my AnaMer gt GetHistol HIS_NUMBER gt Fill value my AnaMer gt GetHisto2 HIS_NUMBER gt Fill value my AnaMegr gt GetHistoProfilel HIS_NUMBER gt Fill value my AnaMegr gt GetHistoProfile2 HIS_NUMBER gt Fill value or similarly if you want to retrieve by the histogram name 1A profile histogram sets the value of a bin as the average of all entries in that bin and the error as the RMS of these entries Chapter 10 Filters and classifiers 10 1 F
74. at control their behaviour To use these filters they have to be declared first with the following command gamos filter FILTER NAME FILTER CLASS PARAMETER 1 PA RAMETER 2 where FILTER NAME is the new name you want to give to a filter to attach it to a user action of a scorer FILTER CLASS is the name of the filter class and PARAMETER 1 PARAMETER 2 are the values of 103 104 CHAPTER 10 FILTERS AND CLASSIFIERS the parameters that the filter needs Those filters that do not need any parameter can be assigned directly to a user action or a scorer without giving them a new name the name will be the one of the filter class To attach one or more filters to a user action you put them after the user action name in the command line that selects it gamos userAction USER ACTION FILTER NAME CLASS or you can use filters to act on a scorer with the command gamos scoring addFilter28corer FILTER NAME CLASS SCORER NAME Filter are plug in s so that a user an create her his own filter and select it with a user command To learn how to do this see the instruc tions in the section Creating your plug in using the GmFilterFactory or the Histograms and scorers tutorial 10 1 1 Simple filters The list of available filters can be obtained by typing SealPluginDump on your terminal window and looking for the word Filter The list of simple filters in the current GAMOS version is the following e GmGammaFilter accepts a track if the part
75. at will use as target condition that a track reaches a plane perpen dicualr to the Z axis defined with the parameters gamos setParam RTCutsStudyFilter PlaneZ ZPOS gamos setParam RTCutsStudyFilter PlaneXDim XDIM gamos setParam RTCutsStudyFilter PlaneYDim YDIM These commands will produce at the end of run a table and a histogram 66 CHAPTER 5 PHYSICS file with the needed information The table will contain the minimum range that can be applied for each region particle process not to lose any track reaching the target and it will look like this hhhhh PRODUCTION CUTS STUDY RESULTS GmProdCutsStudyUA REGION DefaultRegionForTheWorld PARTICLE gamma PROCESS ALL MIN RANGE 353161 38 GmProdCutsStudyUA REGION DefaultRegionForTheWorld PARTICLE gamma PROCESS eBrem MIN RANGE 353161 38 To get the cuts values for not losing a given percentage of particles in the target plane you can execute the ROOT script that can be found at GamosCore GamosPhysics GamosCuts getProdCutsEffect C root b p q x getProdCutsEffect C prodcuts root percentage and look at the last lines of output those that contain the word FINAL like the following ones PARTICLE e FINAL 17 19 PARTICLE e FINAL 72 34185 PARTICLE gamma FINAL 72 34184 5 7 2 Automatic determination of production cuts for a dose in a phantom simulation The use of production cuts in a dose computation may introduce a bias when a particle is killed and then its
76. before reaching the phase space At the end of the job each of these extra information user actions fills a file explaining the information contained in each bit By default this file is called RTExtraInfoProvider summ but the user may change the name of it with the parameter gamos setParam RTExtralnfoProviderFloat FileName FILENAME 13 1 5 Reusing a particle at a phase space without filling the phase space file It is common in radiotherapy treatment simulations that in a first job a phase space file is created and in a second job the particles therein are read and reused several times to calculate the dose in the patient GAMOS provides the possibility of reusing particles in a phase space file without having to divide the jobs in two To use this utility the user has to instantiate the user action gamos userAction RTReuseAtZPlaneUA and then use the command gamos RT ReuseAtZPlane and before that define the z value of the plane where particles will be replicated with the parameter gamos setParam RTReuseAtZPlane ZReusePlane Z POS and the number of times particles will be reused gamos setParam RTReuseAtZPlane NReuse NREUSE The user may independently create the phase space file or not at the same Z position or at others 13 2 OPTIMISATION OF A LINAC SIMULATION 129 13 2 Optimisation of a linac simulation To optimise your simulation in GEANT4 you may tune the physics pa rameters production cuts special cuts multiple scatteri
77. ber of tracks that reach the surface The user must choose a direction of the particle to be scored as extra argument in gamos scoring addScorer2MFD The choices are IN OUT or INOUT Here IN scores incoming particles to the cell while OUT scores only outgoing particles from the cell INOUT scores both directions The current is normalized for a unit area if an extra second parameter is set to TRUE GmG4PSCylinderSurfaceCurrent Cylinder surface current is asurface based scorer and similar to the GmG4PSFlatSurfaceCurrent The only difference is that the surface is defined at the inner sur face of a G4Tubs solid GmGAPSSphereSurfaceCurrent Sphere surface current is a surface based scorer and similar to GmG4PSFlatSurfaceCurrent The only difference is that the surface is defined at the inner sur face of a G4Sphere solid GmG4PSPassageCellCurrent Passage current is a volume based scorer The current is defined by the number of tracks that pass through the volume GmG4PSFlatSurfaceFlux Flat surface flux is a surface based flux scorer The surface flux is defined by the number of tracks that reach the surface The expression of surface flux is given by the sum of W cos t A where W t and A represent parti cle weight injection angle of particle with respect to the surface 8 1 SCORER CLASSES 89 normal and area of the surface The user must enter one of the particle directions as in GmG4PSFlatSurfaceCurrent
78. c physics list The GAMOS electromagnetic physics list is based on the hadron therapy Geant4 advanced example Only photons electrons positrons and opti cal photons are defined This physics list lets the user choose among the standard low energy or Penelope models The following physics models are available e photons photon standard standard electromagnetic processes no low energy photon epdl low energy Evaluated Particle Data Library photon penelope processes a la Penelope 6 e electrons electron standard standard electromagnetic processes no low energy electron eedl low energy Evaluated Particle Data Library electron penelope processes a la Penelope 6 e positrons positron standard standard electromagnetic processes no low energy 57 98 CHAPTER 5 PHYSICS positron penelope processes a la Penelope 6 e optical photons opticalphoton the scintillation process is activated for all the particles and the G4OpAbsorption G4OpRayleigh and G4OpBoundaryProcess processes are activated for optical pho tons To tell your job to use one of the possible combinations of physics models just described you have first to select the GAMOS electromagnetic physics list using the command gamos physicsList GmEMPhysics and then you can select one of the physics models for each particle with the command gamos GmPhysics addPhysics PHYSICS MODEL NAME where PHYSICS MODEL
79. ced The name of this file is set with the parameter gamos setParam GmReadPhantomGeometry FileName MY FILENAME In a phantom file the voxels of the same material may have a different density GAMOS allows you to group densities in intervals You have to set true the parameter gamos setParam GmReadPhantomGeometry RecalculateMaterialDensities 1 and choose the interval width with the parameter gamos setParam GmReadPhantomGeometry Phantom DensityStep DENSITY_INTERVAL so that that the voxels of each material will be grouped in density intervals of DENSITY_INTERVAL and a new material will be created for each group of voxels The navigation in the voxels is done using the Geant4 algorithm G4Regular Navigation that is the optimal one for regular geometries see 8 The user may select if when a track navigates through contiguous voxels with the same material the frontier between will be skipped or not with the parameter gamos setParam GmReadPhantomGeometry Phantom SkipEqualMaterials VALUE that by default takes a value of 1 For testing purposes other navigation algorithms may be selected namely voxel navigation with 1 dimensional optimization that occupies similar mem ory as RegularNavigation but is very slow gamos setParam GmReadPhantomGeometry Phantom RegularStructureID 0 or 3 dimensional optimization that occupies a lot of memory and it is almost as fast as G4Regular Navigation gamos set Param GmReadPhantomGeometry Phantom
80. common interface for its use These classes should invoke the method SetHistoNames passing to it a histogram name and a file name The histogram name will be the prefix that all histograms will have on their name The file name will be the prefix of the histogram file name As the histogramming files in GAMOS are user actions they can be used to gether with filters and classifiers see section on Filters and classifiers The names of the filtes used will be added to the histogram name prefix separated by a and to the file name prefix separated by a _ In a similar way the name of the classifier will be added to the file name and the name of each classifier index will be added to the histogram name prefix For example the class GmStepHisto sUA invokes the method SetHistoNames passing to it as arguments step and GmStepHistsoU A therefore the command gamos userAction GmStepHistosUA GmSecondaryFilter GmClas sifierByParticle will produce a file named step_GmSecondaryFilter_GmClassifierByParticle root and the histograms will have as prefix GmStepHistosU A GmSecondaryFilter gamma GmStepHistosU A GmSecondaryFilter e The GmVHistoBuilder class takes also care of building a base histogram number multiple of 1 000 000 guaranteeing that it is not repeated if several his togram classes are used The histogram classes may define their histograms by using the number as a base provided that they add histogram numbers smaller than 1
81. condaryAllFilter makes the list of filters act of the sec ondary tracks created in the step returns true if all secondary tracks created accept all the filters It does not implement the AcceptTrack method GmInverseFilter returns the opposite that the filter it receives as only argument 10 1 3 Volume filters These are a set of filters that accept tracks under one of the following conditions In particle is in a volume Enter particle is entering a volume Accept Track method returns always false Exit particle is exiting a volume AcceptTrack method returns always false except in the case where one of the selected volumes is the world and track is exiting it Traverse particle traverses a volume it does neither enter nor exits it Start particle is starting in a volume AcceptTrack method may only return true if it is the first step End particle is ending in a volume AcceptTrack method may only return true if the track is ending The volume names are given as extra arguments to the filter The types of volume are the following ones LogicalVolume a G4LogicalVolume object PhysicalVolume a G4VPhysicalVolume object The volume name and copy number are set separated with a character e g volA 1 see section on Identifying touchables 10 2 CLASSIFIERS 107 e Touchable a G4VTouchable object The volume name and copy number are set separated with a character the ancestors are separated by a charact
82. ctory where the GAMOS code is the rest are the external libraries used by GAMOS and the configuration utilities Before compiling you have to define a few variables mainly the location of the different external packages All this is done by sourcing the file source MY GAMOS DIR config confgamos csh To compile any directory of GAMOS and all the directories below you just have to go to that directory and type make This will compile the cc files found in the src directory build the library and the plug in s and in the case of the directory GamosCore GamosApplication it will also create the gamos executable You may need to type the Linux command rehash to refresh your environmental variables in case there was no executable file before starting the compilation 2 3 1 Compiling your new code If you have created a new directory with your code you have to compile it following the Geant4 way The implementation files should have the suffix cc and should be in a subdirectory called src For the declaration files 8 CHAPTER 2 GETTING STARTED you have a greater freedom the Geant4 way is that they have the suffix hh and lie in a subdirectory called include but you can do it your own way and after that you have to be consistent in the GNUmakefile as explained below You then have to build GNUmakefile that will steer the compilation and library building when you type the command make For building it you may follow the examples in t
83. d below Each type of particle source has default distributions of time energy position and direction that you may change with the commands described below 45 46 CHAPTER 4 GENERATOR An important point not to forget is that when you define a particle source you have to give it a name This name serves to distinguish it when you want later to change its time energy position or direction distribution 4 1 2 Single particle source To add a single particle source you have to use the command gamos generator addSingleParticleSource SOURCE NAME PARTICLE NAME ENERGY SOURCE_NAME is the name of this source that you have to use if you want later to change its time energy position or direction distribution PARTICLE NAME can be any of the Geant4 particles ENERGY is the initial energy of the particle If you don t change any property the particle will be generated at time 0 position 0 0 0 and random direction 4 1 3 Isotope source GAMOS implements an isotope generator that simulates the activity of dif ferent isotopes that decay in one or several photons electrons or positrons First a file is read with the description of the isotope decays in a format as the one that can be found at MY_GAMOS_DIR src GamosCore GamosGenerator test isotopes dat part of which we reproduce here ISOTOPE Na22 215 5 0 905 et 1275 0 0 9995 gamma 150 F18 249 8 0 967 gamma For each isotope there must be a first line starting b
84. d by the parameter gamos setParam PETCountScatteringU A ProcessNames PROCESS 1 PROCESS 2 and it has lost in the volumes more energy than the parameter gamos setParam PETCountScatteringU A EnergyMin ENER MIN e d Check PET line distance a line joining the position of the two reconstructed hits is built and the distance of closest approach DCA to the origin of the positron is calculated the events are classified as near of far if the DCA is smaller or bigger than the parameter gamos setParam PET EvtClass LineDist ToVtx DISTANCE where DISTANCE has a default value of 4 mm The Classify PET method returns an integer with several digits con taining the event classification e 0 if it is not PET 1 if it is PET and PET line is close to the event vertex 2 if it is PET and PET line is far from event vertex e 10 1 if the search for 511 keV reconstructed hits found more than 2 e 100 1 if the event is a random coincidence event e 1000 1 if the event is a scattered event At the end of the run a table is printed with the number of events in each of the combinations of the sub classification types 12 2 2 PET histograms event classification These histograms are related to the event classification explained above They are produced if the event classification user action is selected The name of all these histograms starts with PETEvtClass and all are written in the file pet root csv The following histograms are
85. d by the variable GAMOS SEARCH PATH For details see section on Managing the input data files 11 12 CHAPTER 3 GEOMETRY and lower case letters Each tag has a fixed number of arguments known by the parser therefore you may write all arguments in a line or in several lines at your will Isotope ISOT 1 Name 2 Z 3 N 4 Example ISOT C135 17 18 35 Element made of one unique isotope ELEM 1 Name 2 Symbol 3 Z 4 Example ELEM Hydrogen H 1 1 Element composed of several isotopes ELEM FROM ISOT 1 Name 2 Symbol 3 Number of components One line per isotope with 1 isotope name 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE 13 2 fraction of number of atoms per volume Example ELEM FROM ISOT Chlorine Cl 2 C135 0 4 C136 0 6 Material made of one element MATE 1 Name 2 Z 3 A 4 Density Example MATE Iron 26 55 85 7 87 Material made of a mixture of elements or materials 1 2 Density 3 Number of components One line per material or element with 1 material name 2 proportion of material in the mixture The components can be either all elements or all materials but both types cannot appear in the same mixture There are three mixture tags depending of the way the proportions are defined e Proportions by weight fractions MIXT BY WEIGHT This tag is equivalent to the MIXT tag 14 CHAPTER 3 GEOMETRY e Propo
86. ds virtual std vector lt GmDigit gt DigitizeHits const std vector lt GmHit gt amp 0 virtual void ClearDigits These two methods will be called automatically The first one at the end of each event to convert the hits in digits and the second one at the beginning of each event to clear the digits of the previous event You can then convert your digitizer into a GAMOS plug in To learn how to do this see the instructions in the section Creating your plug in using the GmDigitizerFactory After this you select it with the command gamos digitizer MY_DIGITIZER 7 5 2 Hits and digits reconstruction The digital signals are usually treated so that they become reconstructed hits which contain sensible variables like energy time This conversion is also very dependent on the detector and therefore GAMOS just provides a general class GmVRecHitBuilderFromDigits There is also another class GmVRecHitBuilderFromHits which serves in case the user wants to transform the hits into reconstructed hits directly The user may inherit her his own reconstructed hit builder from it and implement the two methods virtual std vector lt GmRecHit gt ReconstructDigits const std vector lt GmDigit gt amp 0 virtual void ClearDigits in the case of GmVRecHitBuilderFromDigits or 80 CHAPTER 7 SENSITIVE DETECTOR AND HITS virtual std vector lt GmRecHit gt ReconstructHits const std vector lt GmHit gt am
87. duction splitting zPlaneDir This bremsstrahlung splitting technique is more efficient than the uniform bremsstrahlung splitting because only a few gammas that are not aimed to the region of interest are tracked but it has the inconve nient that tracks with different weights 1 N and 1 reach the patient spoiling the efficiency gain To take profit of the definition of a region of interest while keeping the same weight for all the particles that reach the phantom a third splitting technique has been developed that is described below Equal weight directional bremsstrahlumg splitting The main ideas of this splitting technique are first that gammas are split at each interaction and Russian roulette is played with those that are not directed towards a square perpendicular to Z as in the technique above But this technique makes that all gammas that reach the user defined square have the same weight 1 N To achieve this gammas are split at each interaction not only if it is bremsstrahlung if their weight is 1 and they are not split if the weight is 1 N This technique is based on the Directional Bremsstrahlung Splitting 18 To apply this technique the following command should be used gamos physics varianceReduction splitting equal Weight Several paramters control the different options The same parame ters as for the other techniques are used to set the splitting number and the definition of the square of interest The implementation o
88. e 75 7 2 Building your sensitive detector with C code 76 Tid SHAGS uu out td ee m ee iets REI an eS 77 7 4 Detector effects eeri xe es esate ee de ed Be des 77 7 4 1 Energy and time resolutions 77 7 4 2 Detector measuring time 78 7 4 3 Detector dead time 0 0004 78 7 5 Hits digitization and reconstruction 79 7 5 1 Hits digitization 2 79 7 5 2 Hits and digits reconstruction 79 7 5 3 Examples of reconstructed hit builders 80 7 6 Identifying each sensitive detector copy 81 7 7 Storing and retrieving 81 Tod File formati 1 3 Suu ES 82 8 Hits histoerams d n seeded plies Re a ee a 83 CONTENTS 8 Scoring 8 1 Scorer classes 8 9 Filter classes nm fsa cc Ses aa AL ee RA 8 3 Scorer printers Rr o eee 8 4 Classifier classes 9 Analysis extracting information 9 1 Using 9 1 1 Histogram files common name 9 1 2 Histograms in CSV format 9 1 3 Using a common histogram class 9 2 User action utilities 2222s 9 2 1 Counting the number of tracks and events 9 2 2 Counting the 9 2 3 Counting the number of tracks in a volume 9 20 Will
89. e CutOutsideVoxelFilter PDDscorerPC10 1 10 mm 1 mm After running your job with as many scorer filter combinations as de sired you can look at the total dose deposited and compare it with the dose with very small cuts It may happen that the dose with certain cuts despite being a small number is distributed in a different manner than with very small cuts introducing some bias that you consider not acceptable To check in detail the dose produced with a certain filter you can add a scorer printer of type RTPSPDoseHistos that will produce several histograms of the dose PDD X amp Y profiles dose dose volume gamos scoring addPrinter2Scorer PDDhistoPC10 1 RTPSP DoseHistos PDDscorerPC10 1 The name of the printer will be passed to the name of the file containing the histograms 5 7 5 Range rejection The range rejection technique consists on killing a particle at creation and depositing all its energy locally if it is not going to leave the current volume To do this in practical terms the particle is killed if the range is smaller than the distance to the volume boundary although it would have a chance to exit the volume this chance is considered negligible 5 7 6 Automatic determination for an accelerator simulation You can analyze which would be the effect of applying this technique by using the same user action as for the production cuts gamos userAction GmProdCutsStudyUA RTCutsStudyFilter It will produce a table with
90. e classes for user action management Scoring controls the verbosity of the scoring classes Analysis controls the verbosity of the analysis classes 111 112 CHAPTER 11 MANAGING THE VERBOSITY e PET controls the verbosity of the classes in the PET package e RT controls the verbosity of the classes in the RadioTherapy pack age You can set the verbosity of each of the GAMOS verbosity types with a simple command on your command input file gamos verbosity GmGenerVerbosity VERB gamos verbosity GmPhysicsVerbosity VERB gamos verbosity GmSDVerbosity VERB gamos verbosity GmUAVerbosity VERB gamos verbosity GmAnaVerbosity VERB gamos verbosity GmScoringVerbosity VERB gamos verbosity PETVerbosity VERB gamos verbosity RTVerbosity VERB where VERB can be any of the six values described above in non capital letters Instead of the names you may use the numbers that appear besides them By default the values of all GAMOS verbosities are warning 11 2 Using a GAMOS verbosity manager in your code If you write some new code for example a new generator distribution you may use one of the GAMOS verbosity managers following the in structions below Each of the GAMOS verbosity managers instantiates an object of the type GmVerbosity If you want that your code is only printed when the corresponding verbosity level is set you have to write this verbosity with the value of the level in parenthesis For example if you write
91. e cuts for all process to the desired value But do not forget to use the command run initialize after setting the cuts if you want that your change is effective The Geant4 command run particle dumpCutValues dumps the list of materials and for each one the list of cuts for each particle 5 5 1 Production cuts by region A region in Geant4 is a set of GALogicalVolume s that share common proper ties You can define a region in the text file where you defined your geometry by using the tag 5 5 PRODUCTION CUTS 61 REGION REGION NAME LOGICAL VOLUME NAME s where REGION NAME is the name that identifies the region and LOGI CAL VOLUME NAME s is the list of G4LogicalVolume s that belong to the region For example REGION myRegion Crystal Wall Alternatively you can define a new region in your user script through a user command gamos geometry createRegion REGION NAME LOGICAL VOLUME NAME Do not forget that in Geant4 when a logical volume belongs to a region automatically all its daughters belong to the same region unless there is another region explicitly defined for some of the daughters Also do not forget that regions in Geant4 have to be set in a hierarchical way if you place a volume A in the world and inside it you place a volume B you cannot create a new region for B unless you have explicitly created a region for A Once you have defined a region you may set a cut for the particles that traverse that region with the tag
92. e same job and to define a class that inherits from several user action types at the same time Moreover as they are plug in s the user can activate them by means of a user command User actions can be associated to filters or classifiers as explained below Several functionalities are already implemented in GAMOS as user ac tions like the example histograms the event classifiers and you may use them as examples for creating your own one See the Geant4 user manual for a more detailed explanation of the user actions 6 1 Adding a filter One or several filters can be added to a user action by simply adding their names in the user command where an action is selected See section on Filters to get a list of the available filters in GAMOS and how to add pa rameters to a filter If the filter you are using is a step filter and your user action is a stepping user action the method SteppingAction will only be called if all the filters accept the step If the filter you are using is a track filter it affects the callings to the PreUserTrackingAction and Post UserTrackingAction for tracking actions and ClassifyNew Track for stacking actions For example gamos userAction GmTrackHistosUA GmGammaFilter 71 T2 CHAPTER 6 USER ACTIONS will only produce histograms for tracks whose particle is a gamma 6 2 Adding an indexer classifier One or several classifiers can be added to a user action by simply adding their names in the us
93. e the dose in the phantom with enough precision you may reuse the particles several times that is use the same particle in several consecutive events by setting the parameter gamos setParam RTGeneratorPhaseSpace MaxNReuse N to a value bigger than 1 In fact if this parameter is not explicitly set to 1 GAMOS calculates it automatically by dividing the number of events asked for by the number of events in the input phase space Alternatively you may recycle the full phase space several times i e when all particles in the phase space are read the file is closed and restarted again The number of times a phase space is recycled is con trolled by the parameter gamos setParam RTGeneratorPhaseSpace MaxNRecycle N which must take a value bigger than 1 If no reusing is explicitly set the number of reuses will be automatically calculated as mentioned above and the number of recyclings will be set to 1 so that no recycling is done Caution should be taken when recycling phase spaces as the error correlations due to the reusing of the same particles is not taken account Therefore you should first consider reusing instead of recycling If you think your phase space has X Y symmetry you may reduce the correlations due to reusing the same particle several times by mirroring your particles each time they are reused by setting the parameter gamos setParam RTGeneratorPhaseSpace Mirror WhenReuse OPT where OPT can be X or Y or XY If it is X it mean
94. each detector type with the parameter gamos setParam SD DeadTime SDTYPE that takes a default value of 100 ns The dead time affects by default all detectors in a block This means that if a detector is dead it considers that all detectors that are placed in the same mother are also dead the usual behaviour for example in a PET detector where all crystals in a block share the readout You can tell GAMOS to consider dead only the crystal itself by setting the parameter gamos setParam SD DeadTimeType SDTYPE byCrystal that by default takes the value byBlock You also have the option to define your detector as paralizable default or non paralizable by setting the parameter 3The time smeared is theTimeMin The event time is computed as the time of creation of the first particle in the event 7 5 HITS DIGITIZATION AND RECONSTRUCTION 79 gamos setParam SD DeadTimeParalizable SDTYPE TRUE FALSE In a non paralizable detector an event happening during the dead time since the previous event is simply lost while in a paralizable detector an event happening during the dead time since the previous one will not just be missed but will restart the dead time 7 5 Hits digitization and reconstruction 7 5 1 Hits digitization The conversion of the hits into digital signals is very dependent on the detector Therefore GAMOS just provides a general class GmV Digitizer The user may inherit her his own digitizer from it and implement the two metho
95. each voxel i e all the voxels that have dose equal to or greater that a given bin fill that bin Dose volume 13 4 Analysis utilities This is a set of utilities that may serve in the analysis of phase space and dose files for example to sum phase space or dose files from different jobs to get basic information of the file contents to fill histograms out of the file or to compare files from two jobs All these utilities are under the directory MY_GAMOS_DIR analysis They are compiled by default with the rest of GAMOS code and then 134 CHAPTER 13 RADIOTHERAPY APPLICATION they are available as executables as mentioned in the following subsec tions 13 4 1 Summing phase space files This utility serves to sum phase space files corresponding to different jobs with the same setup To use it you have to write a file containing the list of phase space header files one file per line for example ps iaea 20000 1AEAheader ps iaea 20001 1AEAheader ps iaea 20002 IAEAheader Then you just have to run the executable sumphsp INPUT FILE LIST NAME OUTPUT FILENAME where INPUT FILE LIST NAME is the name of the file containing the list of files to add and OUTPUT FILE NAME is the name of the output file that will contain the sum of all the files two files indeed as usual for IAEA phase space files OUTPUT FILE NAME IAEAheader and OUTPUT FILE NAME IAEAphsp When running you will see on the screen something similar to this Ope
96. efault Geant4 units are as sumed i e and rad you can change them in the usual way e g cm deg axis x axis y axis_z are the three coordinates of the axes time nevents interval is the interval after which the movements will hap pen offset 0 is an optional argument 0 if not set to change the value for the first movement and number of intervals infinite is an optional argument infinite by default to set the number of times the movement will happen If you want several movements in your run you can use these commands as many times as you want Then after each event GAMOS will check which of the movements must be done If you want for example to move the same volume with different types of movements one after the other you can use the number of intervals and offset arguments to do it The movements are managed in GAMOS by a user event action called GmMovementEventAction that checks at the beginning of event if the movement must be done Therefore you cannot forget to activate this action with the GAMOS command gamos userAction GmMovementEvent Action If you forget it the above commands will not exist and you will get a Geant4 exception There is an example of GAMOS movements that you can run in the directory MY GAMOS DIR examples test Just run gamos testMovement in and you will see an OpenGL view of a moving box 3 6 Geometry utilities There is a set of geometry utilities that are mean
97. elow it This is valid if you are only interested in counting how many particles you lose For other cases another approach should be used For example if you want to check how your dose distribution changes you can build a set of filters each one with a set of cut values These filters do not really cut the particles but only serve to tag a particle if it would have been killed by the set of cuts in the filter T herefore for each track that contributes to your results GAMOS can check if it or any of its ancestors would have been killed by each of these sets of cut values If you build your results N times each one using only those tracks that pass one filter you can compare each result to see how it changes with each set of cuts 5 7 1 Automatic determination of production cuts for an ac celerator simulation The method used in GAMOS to determine the best production cuts is based on what we can call an inverse reasoning We count each particle that reaches a given Z plane corresponding to the phantom surface and we calculate first the range of the particle in the region where it is created Then we can know that if we put a range cut in that region smaller than the calculated range that particle would not reach our target plane We also compute the range of the mother particle in the region where it was created and the same consecutively for all the ancestors We know then that if we set in any of the regions where each of the ance
98. em with the parameter gamos setParam PET Geometry Source MY SOURCE NOTE This module is just thought for simple PET geometries If you want to do more complicated geometries we recommend you to describe tehm with a text file see section Building your geometry with a text file 115 116 CHAPTER 12 PET APPLICATION 12 2 PET analysis 12 2 4 PET event classification The class PETEventClassifierUA in the directory PET PETAnalysis classifies the events as PET by looking at the reconstructed hits It is aGAMOS user action so you can activate it with the command gamos userAction PETEventClassifierUA First it counts how many reconstructed hits have 511 keV within a precision given by the two parameters gamos setParam PET EvtClass 511EPrecMin ENERGY MIN gamos setParam PET EvtClass 511EPrecMax ENERGY MAX where ENERGY MIN is the minimum energy that by default takes a value of 0 7 511 keV and ENERGY MAX is the maximum energy that by default takes a value of 1 3 511 keV Only hits whose relative time difference is less than the value given by the parameter gamos setParam PET EvtClass CoincidenceTime COINCIDENCE TIME will be taken into account to make a pair it is assumed that one of the two started the trigger and the other must be in the coincidence time open at that moment To recover hits when one of several Compton interactions have oc curred you may switch the merging of hits that are close into one You may set the dista
99. eposited energy is between the values given by the two extra parameters It does not implement the Accept Track method GmlnitialRangeFilter accepts a track if its range at creation is between the two values given as extra arguments GmRangeFilter accepts a track if the range is between the values given by the two extra parameters GmStepNumberFilter accepts a step if the step number is be tween the values given by the two extra parameters It does not implement the Accept Track method GmNumberOfSecondaries accepts a step if the number of secon daries created is between the values given by the two extra param eters It does not implement the Accept Track method GmProcessNameFilter accepts a step if the process name that defined it is in the list given as extra arguments It does not implement the Accept Track method GmParticleProcessFilter accepts a step if the particle and the pro cess that defined the step are in the list given as extra arguments The arguments must be provided as a list of pairs particle name process name It does not implement the Accept Track method GmCreatorProcessFilter accepts a step if the process that defined it is in the list given as extra arguments It does not implement the AcceptTrack method GmFilterFromClassifier accepts a step if the classifier given as first parameter returns a value equal to the second parameter It does not implement the Accept Track method 10 1 2 Filters of filters
100. er e g volB 3 volA 1 see section on Iden tifying touchables e Region a G4Region object e LogicalVolumeChildren a G4LogicalVolume object or any of the G4LogicalVolume children of it e PhysicalVolumeChildren a G4VPhysicalVolume object or any of the G4VPhysicalVolume children of it e RegionChildren a GAV Touchable object any of the G4V Touchable children of it e TouchableChildren a G4Region object or any of the G4Region children of it The name of these filters is constructed combining the geometry condition and the volume type e g GmInPhysicalVolumeFilter Gm TraverseTouchableFilter GmEndRegionFilter GmTraverseLogical Vol umeChildrenFilter GmExitRegionChildrenFilter There is a special case when parallel worlds are used the scorers see the parallel world volumes but the user actions do not please ask for this new feature if you need it This means that you cannot filter on a parallel world volume if you are using the filter for a user action while you can if you use it for a scorer And it also means that you cannot filter on a mass world whose position coincides with the one of a parallel world in the case of scorers because the scorer filter will see the parallel world volume instead of the mass one If you need to filter on mass volumes for a scorer a few volume filters are implemented namely GmInMass Logical VolumeFilter GmInMassPhysicalVolumeFilter and GmInMass RegionFilter 10 2 Classifiers A class
101. er command where an action is selected See section on Classifiers to get a list of the available classifiers in GAMOS and how to add parameters to a classifier It is up to the concrete user action to use the classifiers or not 6 3 Creating your GAMOS user action To create your class you have to inherit from one or several of the GAMOS user actions GmUserRunAction GmUserEventAction GmUser TrackingAction GmUserSteppingAction GmUserStackingAction Then you implement the same methods as for the Geant4 user actions e GmUserRunAction virtual void BeginOfRunAction const G4Run aRun virtual void EndOfRunAction const G4Run aRun e GmUserEvent Action virtual void BeginOfEventAction const G4Event anEvent virtual void EndOfEventAction const G4Event anEvent e GmUserTrackingAction virtual void PreUserTrackingAction const G4Track aTrack virtual void PostUserTrackingAction const G4Track aTrack e GmUserSteppingAction virtual void UserSteppingAction const G4Step aStep e GmUserStackingAction virtual G4ClassificationOfNewTrack Classify NewTrack const G4 Track aTrack G4ClassificationOfNew Track oldClassificationx 0 virtual void NewStage virtual void PrepareNewEvent 6 3 CREATING YOUR GAMOS USER ACTION 73 Finally you have to transform your class into a plug in To learn how to do this see the instructions in the section Creating your plug in using the G
102. er to a scorer or a user action CLASSIFIER CLASS is one of the above mentioned classifier classes or one that you create your own 110 CHAPTER 10 FILTERS AND CLASSIFIERS Chapter 11 Managing the verbosity 11 1 GAMOS verbosity managers While GAMOS is running you can control the amount of information you get on the screen with the GAMOS verbosity management There are six levels of verbosity each level includes the verbosity of the previous levels Silent 1 no output is printed only when there is an exception and the job stops you will get the details of why it happened Error 0 only error messages are printed Warning 1 only error and warning messages are printed Info 2 you get some detailed information of what is happening Mainly messages at each run and each event Debug 3 you get a quite detailed information of what is hap pening Mainly messages at each track and each step Test 4 this level is only meant for testing your code the first time you write it On top of this the verbosity in GAMOS is classified in different types so that you can set different verbosity options for different parts of the code Generation controls the verbosity of the GAMOS generator Physics controls the verbosity of the physics classes Sensitive detector controls the verbosity of the sensitive detectors hits digits and reconstructed hits User action controls the verbosity of the bas
103. erator that reads the primary particles from a text file or a binary file or in the standard Geant4 way by writing your C class inheriting from GAV UserPrimaryGenerator Action 4 1 Using GAMOS generator 4 1 1 Introduction The GAMOS generator provides several time energy position and direction distributions that the user may combine to his her will The user can select to generate as primary particles one or several single particles together with one or several isotopes and set any of the available time energy position or direction distributions for each one of the single particles or isotopes We describe below the commands to select the single particles the com mands to select the isotopes and then the commands for selecting the time energy position and direction distributions The first command you have to use is the one that tells GAMOS that you want to use the GAMOS generator gamos generator GmGenerator This command apart from instantiating the GAMOS generator man ager also instantiates the messenger Therefore if you forget to write this command first the other generator commands described below will not exist and Geant4 will throw an exception After this command you have to add one or several particle sources there is no default primary particle source therefore if you do not choose one GAMOS will throw an exception You may combine several particle sources in each event by repeatedly using the commands describe
104. es are separated by commas The utility of this format is that it can be easily read by any analysis package Excel Origin Matlab and converted to its own format The information written in GAMOS is the following e Histograms 1D The first word is HISTOID then the following info is dumped his name number of bins Xaxis minimum 93 94 CHAPTER 9 ANALYSIS EXTRACTING INFORMATION Xaxis_maximum bin_contents number_of_entries mean RMS The bin contents is the list of entries in each bin It has indeed num ber_of_binsX 2 numbers as the first one is the underflow entries be low axis minimum and the last one is the overflow entries above axis maximum e Histograms 2D The first word is HISTO2D then the following info is dumped his name number of binsX Xaxis minimum Xaxis maximum number of binsY Yaxis minimum Yaxis maximum bin contents number of entries mean RMS The bin contents is the bi dimensional list of entries in each bin It has indeed number of binsX 4 2 number of binsY numbers as the first row column is the underflow entries below axis minimum and the last row column is the overflow entries above axis maximum You can see an example of 1D histogram here 1D example 10 0 1000 0 3 3 1 3 5 6 12 15 16 2 66 0 460 2 353 81 9 1 3 Using common histogram class Several histogram classes inherit from a class named GmVHistoBuilder to fa cilitate the creation of histograms and to provide a
105. f this technique in this GAMOS version is a preliminary one Efficiency improvements of about 40 have been re ported but it is currently being improved and we expect to at least duplicate the efficiency gain 13 2 2 Killing particles at big X Y This utility serves to kill the particles that would probably not reach your detector because they have too big X and Y positions it is assumed that your detector is described along Z and that your initial particles move in this direction in the positive sense It makes a list of the volumes that are placed directly inside the world volume and computes the minimum and maximum extension in X and Y using the method G VSolid GetExtent This rectangular area extends from the minimum Z value of this volume until the minimum Z 13 3 SCORING DOSE IN PHANTOM 131 value of the next volume so that all tracks that are outside it will be killed This utility is activated by selecting the user action gamos userAction RTZRLimitsAutoUA You may argue that too many particles or too few are killed with this automatic definition of limits You may simply change the dimen sions of the volumes placed in the world adding container volumes made of air will not change your physics or you can define the limits yourself by selecting the user action gamos userAction RTZRLimitsUA Then you have to write a file named rtzrlimits lis with the list of values you want to use The format of that file should be the fol
106. have a resolution function that is not gaussian you may implement it by creating a new sensitive detector class inheriting from GmVSD GmSDSimple if you don t want to change the logic to define the detector unit IDs and overwrite the methods virtual G4double SmearEnergy G4double energy G4double enerResol virtual G4double SmearTimeMin G4double time G4double timeResol 7 4 2 Detector measuring time A detector has a finite time resolution so that it is not able to distinguish hits that come from different events when their time is close This effect is simulated in GAMOS with the help of the GmHitsEvent Mgr class This class accumulates the hits of several events and for each event builds up a list of good hits i e those that have a time after the event time minus the measuring time You can define the value of the measuring time for each detector type SDTYPE with the parameter gamos setParam SD MeasuringTime SDTYPE that takes a default value of 10 ns 7 4 3 Detector dead time A detector takes a finite time to transform an energy deposit into an elec tronic signal and during that time it is dead and cannot account for any other energy deposition This effect is simulated in GAMOS also with the help of the GmHitsEv entMgr class It holds a list of the dead sensitive detectors i e those that have produced a hit in a time prior than the current time minus the dead time You can define the value of the dead time for
107. he GamosCore GamosX XX directories We take as example the file GamosCore GamosGeometry GNUmakefile name GamosGeometry GATARGET name G4EXLIB true PHONY all all lib plugin include GAMOSINSTALL config binmake gmk include GAMOSINSTALL config general gmk EXTRALIBS 1G4geomtextread 1G4geomtextbuild lGamosBase lGamosUtils lGamosFactories lGamosUserActionMgr Let s go one by one through the lines In the first one you define the name of your library name GamosGeometry The following two lines are used internally by the GAMOS scripts and are mandatory GATARGET name G4EXLIB true Then you define what you want to do when you type make PHONY all all lib plugin There are several possibilities e lib Compile and build the library e plugin Build the plug in Use it if and only if you are creating a new plug in 2 3 COMPILING GAMOS 9 e plugin_check Check that you are linking with all the libraries that will be needed This check is not mandatory but if you do not do it and you are missing some library when you run you will get an error message e bin Build the executable You will probably never need this as GAMOS is based on dynamic loading and plug in s The following two lines are needed for configuration include GAMOSINSTALL config binmake gmk include GAMOSINSTALL config general gmk If you edit the file general gmk you will see that it is just inc
108. he directory list where GAMOS looks for this file please read the section Managing the input data files If you don t change any property the particle will be generated with a time distribution of type Decay see below energy distribution of type constant isotope decay see below position at 0 0 0 and random direc tion Time distributions e Constant time gamos generator timeDist SOURCE NAME GmGenerDistTimeConstant TIME All the primary particles will be generated at time 0 If you want to set it at a different time you can add the extra parameter TIME e Decay time gamos generator timeDist SOURCE NAME GmGenerDist TimeDecay ACTIVITY The primary particles will be generated with a time following a typical decay distribution with the activity of the particle source To be con crete the time is sampled with a Poisson distribution that is obtained as follows rnd poiss 1 0 activity second log RandFlat shoot the activity is given by the parameter ACTIVITY Energy distributions e Constant energy The available units in Geant4 are becquerel and curie 48 CHAPTER 4 GENERATOR gamos generator energyDist SOURCE NAME GmGenerDistEnergyConstant ENERGY All the primary particles will be generated with energy given by the parameter ENERGY e Constant decay energy gamos generator energyDist SOURCE NAME GmGenerDistEnergyConstantIsotopeDecay All the primary particles will be generated
109. he production cuts and user limits are powerful methods to tune your sim ulation so that you can save a lot of CPU time by not tracking the particles that are not going to contribute to your results Neverthelss the tuning of cuts is usually a long and difficult task We have developed in GAMOS a method to help the user to obtain the optimal value of the production cuts and user limits for her his application in a single job We describe here the basic idea of the method and then in the corresponding sections the details of its implementation for different cases To use this utility you have to define in a clear way which are the results you don t want to change when cuts change for example e Number of particles reaching a region 64 CHAPTER 5 PHYSICS e Dose distribution e Number Energy spatial distribution of hits e Shower shape in a volume For each track that contributes to your result GAMOS stores all its his tory for the track itself and each of its ancestors stores energy range region process and particle type In the case of production cuts this information is stored at particle creation In the case of user limits this information is stored at each step for parents only the steps before the creation of the interesting track At the end of run you can can get for each region process particle a list of all the ranges or energies of all the particles created Then you can easily know if you apply a cut how many particles are b
110. histograms of event generator particles that may serve to check that you have actually generated what you meant The names of all these histograms start with GmGenerHistosUA and they are all dumped into the file gener root csv The following histograms are produced e Kinetic energy of primary particles Primary Generator kinEnergy e X position Position X e Y position Position Y e Z position Position Z e Theta angle Angle theta e Phi angle Angle phi e Difference between consecutive event times taken as time of the first primary particle Time between source decays ns The user can control the minimum maximum and number of steps of these histograms with the following parameters gamos setParam gener hEMin gamos setParam gener hEMax gamos setParam gener hENbins gamos setParam gener hPosMin gamos setParam gener hPosMax gamos setParam gener hPosNbins gamos setParam gener hAngleMin gamos setParam gener hAngleMax gamos setParam gener hAngleNbins gamos setParam gener h TimeMin gamos setParam gener hTimeMax gamos setParam gener h TimeNbins To activate this user action use the command gamos userAction GmGenerHistosUA Chapter 5 Physics Yo can build your physics list using one of the Geant4 physics lists or following the standard Geant4 way by writing your C class inheriting from GAV UserPhysicsList or using anyone of Geant4 physics lists 5 1 GAMOS electromagneti
111. iables e long int theDet UnitID Identification of the touchable e G4int theEventID Event number e G4double theEnergy Total energy e G4double theTimeMin Minimum time of energy depositions e G4double theTimeMax Maximum time of energy depositions e G4ThreeVector thePosition Position it is defined in the Sensitive detector class it can be the centre of gravity of the energy depositions the centre of the volume e std set lt G4int gt theTrackIDs The list of track numbers e std set lt G4int gt theOriginalTrackIDs The list of original track numbers a track is called original if it is a gamma electron or positron and it is a primary particle or if it is a gamma created in an original positron annihilation std vector lt GmEDepo gt theEDepos The list of energy deposi tions GmEDepo contains the energy and position of each step G4String theSDType The type of sensitive detector 7 4 Detector effects 7 4 1 Energy and time resolutions If you use one of the GAMOS sensitive detectors or you inherit your own one from GmV SD you can smear automatically the energy and time of the hits for each detector type with a gaussian given by the value of the parameters gamos setParam SD EnergyResol SDTYPE This is the time considered when you call the method GetTime You may also invoke explicitly GetTimeMin or GetTimeMaz 78 CHAPTER 7 SENSITIVE DETECTOR AND HITS gamos setParam SD TimeResol SDTYPE If you
112. icle is a gamma e GmElectronFilter accepts a track if the particle is an electron e GmPositronFilter accepts a track if the particle is a positron e GmElectronOrPositronFilter accepts a track if the particle is an electron or positron e GmEMParticleFilter accepts a track if the particle is of electro magnetic type gamma electron or positron e GmParticleFilter accepts a track if the particle is in the list of particles given as extra arguments see the list of particle names in the section Using particle names e GmChargedFilter accepts a track if the particle is charged e GmNeutralFilter accepts a track if the particle is neutral e GmPrimaryFilter accepts a track if it is a primary it does not come from another track e GmSecondaryFilter accepts a track if it is a secondary it comes from another track e GmKineticEnergyFilter accepts a track if its kinetic energy is between the two values given as extra arguments For steps it considers the energy at the beginning that is the G4PreStepPoint energy e GmPostKineticEnergyFilter accepts a track if its kinetic energy is between the two values given as extra arguments For steps it considers the energy at the end that is the G4PostStepPoint energy 10 1 FILTERS 105 GmVertexKineticEnergyFilter accepts a track if its vertex kinetic energy the energy at creation is between the two values given as extra arguments GmDepositedEnergyFilter accepts a step if the d
113. ifier is a class that contains a method that receives a G4Step and returns a different index an integer depending on some given criteria In other words it classifies the step and returns the index of its classifica tion These classes are unique to GAMOS as Geant4 does not provide this functionality Classifiers can act on user actions or scorers If one or several classi fiers are set to act on a user action it is up to the concrete user action to determine which use it makes of them or to ignore them The most common use of classifiers by user actions is to produce a different his togram set or table for each classification index For details on classifiers acting on scorers see the section on Scorers The use of user actions and scorers together with classifiers is a powerful means to obtain very detailed information on the simulation through simple user commands See the tutorial in section Histograms and scorers for more details on this 108 CHAPTER 10 FILTERS AND CLASSIFIERS Several classifiers need some extra parameters see list of classifiers below that control their behaviour To use these classifiers they have to be declared first with the following command gamos classifier CLASSIFIER NAME CLASSIFIER CLASS PARAM ETER 1 PARAMETER 2 where CLASSIFIER NAME is the new name you want to give to a classifier to attach it to a user action or to a scorer CLASSIFIER CLASS is the name of the classifier class and PARAMETER 1
114. ilters A filter is a class that receives an G4Step or a G4Track and accepts it or not depending on some given criteria A GAMOS filter has therefore two main methods e AcceptStep const G4Step receives a G4Step pointer and de cides to return true or false e Accept rack const G4Track receives a G4Track pointer and decides to return true or false A filter may implement the two methods or only one of them If the AcceptStep method is not implemented by a filter the Accept Step method from the base class is invoked and it calls the Accept Track method passing to it the G4Track corresponding to the G4Step If the Accept Track method is not implemented by a filter the method from the base class returs true Filters can act on user actions or scorers If one or several filters are set to act on a user action the PreUserTrackingAction PostUser TrackingAction and ClassifyNew Track methods will only be invoked if the AccepTrack method of every filter returns true and UserSteppin gAction method will only be invoked if the AccepStep method of every filter returns true For details on filters acting on scorers see the section on Scorers The use of user actions and scorers together with filters is a powerful means to obtain very detailed information on the simulation through simple user commands See the tutorial on Histograms and scorers for more details on this Several filters need some extra parameters see list of filters below th
115. ing all tracks 52s RS 9 2 5 Histograms of track information 9 2 6 Histograms of step information 9 2 7 Histograms of secondary track information 9 2 8 Event classification by interaction types 9 2 9 Table of tracks and steps 9 2 10 Detailed report of where CPU time is spent 9 3 Creating your own histograms 004 10 Filters and classifiers Filters 20e Ra es xU ee Qe ln a nh 104 1 Simple filters qoo ca 22k em REY ee 10 1 2 Filters of f lters lll 10 L 3 Volume filters noo RR doy Be 10 2 C 8sSIHeES certi uu Soe rk x Re Bere eats SU E ETE 10 2 1 Passing parameter values to classifier 11 Managing the verbosity 11 1 GAMOS verbosity managers 11 2 Using GAMOS verbosity manager in your code 11 3 Creating your own verbosity manager 11 4 Controlling the Geant4 verbosity by event and track 12 PET application I2 L PET geomet ry a c d EET dr RT S 12 2 BET analysis a aaa boxe eee eA em a 12 2 1 PET event classification 12 2 2 PET histograms event classification 12 2 3 PET output for reconstruction iii 85 87 90 90 91 93 93 93 93 94 95 96 96 97 98 98 98 99 100 100 101 102 103 103 104 105 106 107 109 111 111 112 113 113 115 iv CONTENTS 12 2 4 PET histograms positro
116. it you have to write a file containing the list of sqdose files one file per line for example sqddose water 20000 out sqdose water 20001 out sqdose water 20002 out Then you just have to run the executable mergeSqdose INPUT_FILE_LIST_NAME OUTPUT_FILE_NAME where INPUT_FILE_LIST_NAME is the name of the file containing the list of files to merge and OUTPUT_FILE_NAME is the name of the output file that will contain the merging of all the files When merging files it will be checked that they correspond to the same phantom by checking the number of voxels and voxel limits 13 4 6 Making histograms out of a sqdose file You can make histograms out of dose information contained in a sqdose file by running analyseSqdose SQDOSE FILE NAME You will get a file named dose analyseSqdose root that contains the same histograms that you get when you run the job to write the dose file using the scorer printer RTPSPDoseHistos Chapter 14 Appendix 14 1 Converting a Geant4 example into a GAMOS example Converting a Geant4 example into a GAMOS examples usually requires only adding a few lines to transform the different simulation components into plug in s In examples NO02 you can see the official Geant4 example novice N02 transformed into a GAMOS example We will use it to illustrate the procedure to follow The first thing to do is substituting the Geant4 GNUmakefile with a GAMOS GNUmakefile You can use the file in this example for any
117. it your sensitive detector from the GAMOS class GmVSD so that you can profit easily from its extra functionality Namely it will take care of applying the energy and time resolutions by detector type accumulating the energy of different energy depositions if they happen in the same detector unit taking into account the measuring time and the dead time and invoking the digitization and reconstruction of hits at the end of the event There are at least two methods that you have to define in your class virtual long int GetDetUnitID G4Step aStep Serves to define the logic you want to apply to give a different number to each detector unit for example to each individual crystal virtual void CalculateAndSetPosition GmHit hit G4Step aStep 0 Serves to define the way you want to define the position of the hit lYou may see the PET application for an illustration of this 7 3 HITS 77 7 3 Hits If you have activated any of the GAMOS sensitive detectors each time a track deposits some energy in any copy of the selected logical volume you can indeed select several volumes by repeating the command a GmHit will be created If the energy deposition happens in the same volume copy a real one or a virtual one in case of a virtually segmented sensitive detector than a previous one in the same event a new hit is not created but the existing hit is updated adding to it the new energy deposition The GmHit stores the following var
118. king a copy of the parallel geometry in the mass geometry When a particle is going to enter the parallel geometry volume its position is shifted to the border of the copy of it in the mass geometry and when a particle exits the parallel volume copy its position is shifted back to the border of the parallel geometry To activate this utility you just have to use the command 38 CHAPTER 3 GEOMETRY gamos geometry copyParallelToMassGeom VOL NAME 1 VOL NAME 2 VOL DISP X DISP Y DISP Z where VOL NAME 1 VOL NAME 2 VOL NAME N is the list of volumes in a parallel geometry that will be copied and DISP X DISP Y DISP Z are the values of the displacement vector The user should check that the copy of the parallel geometry volumes in the mass geometry are inside the user defeind world volume and also that they do not overlap with any of the preexisting mass geometry vol umes GAMOS will check that these two conditions are satisfied but only a warning message will be sent We also recommend taht the copy is placed far from the rest of the mass geometry voules If this is not done it may happen taht some particles navigating in the mass geometry will enter the copy what is a non physical situation Alternatively the user can take care of killing the particles that approach the copy for example by using the user action GmKillAlIUA with the corresponding filters 3 2 Building simple geometries There are several examples of
119. ksUA EachNEvent TIMES USED TIMES 1 PARAMETER GmGeometryFromText FileName TIMES USED TIMES 1 14 5 Using a parameter in your code We describe in this section how to create and use a new parameter if you are creating a new C class GAMDOS provides an utility that allows you to change the value of a parameter in the input file together with the line commands and use 142 CHAPTER 14 APPENDIX it in any of your classes even in several of them There are four types of parameters numbers string list of numbers list of strings To change the value of a parameter of any of the four types in your input file you have to use the command gamos setParam MY PARAM NAME VALUE s Then you can use this parameter in your class with a line like this G4double value GmParameterMgr GetInstance gt GetNumericValue PARAM NAME DEFAULT VALUE if it is a number or G4String value GmParameterMgr GetInstance gt GetStringValue MY PARAM NAME DEFAULT VALUE if it is a string or std vector lt G4double gt vdefault std vector lt G4double gt values GmParameterMgr GetInstance gt Get VNumericValue MY_PARAM_NAME vdefault if it is a list of numbers or std vector lt G4String gt vdefault std vector lt G4String gt values GmParameterMgr GetInstance gt GetVStringValue MY_PARAM_NAME vdefault if it is a list of strings 14 5 1 Log files While running G
120. l par ticles each of weight 1 N To apply it the following command should be used gamos physics varianceReduction splitting uniform and before that the splitting number should be set with the parameter gamos setParam GmBremsSplittingProcess NSplit NSPLIT that by default takes a value of 10 Another parameter controls how many times a particle will be split gamos setParam GmBremsSplittingProcess SplitLevel SPLIT LEVEL that by default takes a value of 1 i e particles already split will not be split again Z plane directional bremsstrahlung splitting In this technique the user must define first a plane perpendicular to the Z axis at a given Z position and limit its dimensions in X and Y This can be done with the parameters gamos setParam GmBSZPlaneDirChecker ZPos ZPOS gamos setParam GmBSZPlaneDirChecker X Dim XDIM gamos setParam GmBSZPlaneDirChecker YDim YDIM 130 CHAPTER 13 RADIOTHERAPY APPLICATION When a bremmstrahlung interaction occurs it will be checked if the direction of each of the split gamma points towards the user defined square If it does the gamma is kept if it does not Russian roulette is played with a probability 1 N so that if the gamma survives its weight will be set back to 1 It is recommended that the square is placed close to the phantom s upper plane and has dimensions a few centimeteres wider than the phan tom To apply this technique the following command should be used gamos physics varianceRe
121. lWorldProcess_N where N is the number you gave to the parallel geometry that is acting The G4ParallelWorldScoringProcess process takes care of changing the touchable so that it points to the parallel geometry therefore if an scorer acts on a step the G4PreStepPoint and G4PostStetPoint will return a touchable corresponding to a volume of the parallel geometry in case the track navigates in it else a touchable of the mass geometry Nevertheless the G4VPhysicalVolume is not cahnged and it will always point to the mass geometry volumes In this way the user can access at the same time the volume of the parallel geometry and the volume of the mass geometry see an example in the Histograms and scorers tutorial The user must be aware that is the scorer mechanism that makes these changes therefore the user actions will not see the parallel geometry Please ask for this functionality in case you think you need it Simulating materials and interactions in parallel geometries In any case Geant4 can navigate in the parallle geometries but the materials are never taken into account This means that a track never interacts on a parallel geometry volume We have developed in GAMOS an utility that allows to have interactions in both geometries at the same time that is to have real overlapping geometries This maybe useful for example to simulate the real geometry of brachytherapy seeds or ionisation chambers inside a phantom This utility is based on ma
122. le 11 11 11 34 35 36 38 38 38 40 40 Al 43 CONTENTS 4 4 1 Event generator histograms 56 5 Physics 57 5 1 GAMOS electromagnetic physics list 57 5 2 GAMOS hadronic physics list 58 5 3 Building your physics list with C code 60 5 4 Other physics lists 60 5 5 Production cuts E A 60 5 5 1 Production cuts 60 5 5 2 Energy cuts to range cuts 61 5 6 User limits 203i 3 e848 dedos ES a necis 62 5 7 Automatic optimisation of cuts 63 5 7 1 Automatic determination of production cuts for an accelerator simulation 64 5 7 2 Automatic determination of production cuts for a dose phantom simulation 66 5 7 3 Automatic determination if user limits for an acceler ator simulation go euo RE a 67 5 7 4 Automatic determination for a dose in phantom sim Pete tere ete tha ot a 68 5 7 5 Range rejection 0 00 eee ee eee 68 5 7 6 Automatic determination for an accelerator simulation 68 6 User Actions 71 6 L filter 443 Bbw bgp URS RS ae E 71 6 2 Adding an indexer classifier 72 6 3 Creating your GAMOS user action 72 7 Sensitive Detector and Hits 75 7 1 Attaching a sensitive detector to a volum
123. les that are accepted by them For example gamos userAction GmKillANUA GmPrimaryFilter will only kill the primary particles 9 2 5 Histograms of track information This is a set of histograms produced for each track They are created by writing the command gamos userAction GmTrackHistosUA This class inherits from Gm V HistoBuilder and invokes the SetHistoNames method with parameters track and Gm TrackHistosUA The following histograms are produced in parenthesis their name without pre fix and the parameter type e Energy of tracks at creation E initial E e Total energy lost E lost E e Total energy deposited E deposited E e Number of steps N steps NStep e Track length Track length Pos e Deviation in position i e distance from the track end point to the line formed by the original position and the original momentum direction Deviation position Pos e Deviation in angle i e angle between the original momentum direction and the final momentum direction Deviation angle Angle e Number of secondary tracks created N secondaries NSeco 9 2 6 Histograms of step information This is a set of histograms produced for each track step They are created by writing the command gamos userAction GmStepHistosUA This class inherits from Gm V HistoBuilder and invokes the SetHistoNames method with parameters step and GmStepHistosUA
124. lities GamosApplication GAMOS run manager and the main program e text read text build packages to read geometry from text files to be moved to Geant4 official release e PET example of PET simulation PETGeometry example to simulate the most common PET devices by defining its properties in an input text file PETAnalysis PET event classifier and PET histograms e RadioTherapy example of RadioTherapy simulation including writ ing and reading phase space files Each package has the following subdirectories e src the source code e include the header files You do not need to follow this file distribution if you want to create a new package but we recommend you to do so There are also several directories containing examples of the different GAMOS functionalities as well of how to extend them Please refer to the examples chapter in this guide or the README files in each example for a detailed explanation In the directory tutorials you can find three step by step tutorials PET Radiotherapy and plug in s They include several exercises with in creasing difficulty and the exercise outputs as well as the exercise solutions are provided We recommend you to follow one or several of these tutorials to become acquainted with GAMOS 1 3 The plug in concept To provide the user with a big flexibility in choosing different simulation components geometry physics user actions histograms and combin
125. lities and support for text detector description GamosMovement support for displacements and rotations of volumes during a job GamosSD classes for sensitive detectors hits and digitization GamosGenerator utilities to support single particle and iso tope generators as well as different initial particle distributions GamosPhysics example of common physics list for medicine applications GamosPhysicsList example of electromagnetic physics list supporting standard low energy and Penelope classes and example of hadronic physics list meant for hadrontherapy GamosOtherPhysicsLists other examples of electromag netic and hadronic physics lists GamosCuts management of production cuts and user lim its including tools to automatically optimise them GamosVarianceReduction implementation of several bremsstrahlung splitting techniques GamosUserActionMgr user action manager to allow several user actions of the same type selectable by user commands GamosScoring scoring manager and messenger and examples of scoring plug in classes scorers filters and printers GamosAnalysis utilities that can help the advanced user to analyse results GamosReadDICOM code to read in DICOM files containing patient data 1 3 THE PLUG IN CONCEPT 3 GamosUtilsUA user action utilities tracking verbosity con trol track counting process counting time study GamosUtils general C uti
126. lowing e X coordinate cm e Y coordinate cm X direction cosine e Y direction cosine e Kinetic energy MeV e Particle statistical weight e Type of the particle 1 gamma 2 electron 3 positron 4 neutron 5 proton e Z direction cosine particle charge e Is new history 0 e Extra integer 0 e Extra float 0 The Z value may optionally be stored if the parameter gamos setParam RTPhaseSpaceUA StoreZ TRUE FALSE is set to TRUE The header file may be written each N events so that if the job ends abnormally the first N events may be recovered in the phase space The number of events is controlled with the parameter gamos setParam RTPhaseSpaceU A NEventsToSave N EVENTS By default this parameter takes a value of 1 and no header is saved until the end of the run As the Z plane is probably not a physical plane in the geometry particle steps will start before the plane and end after the plane There fore the position and energy are rescaled as if the particle would have stopped at the Z plane by a simple linear interpolation 13 1 2 Phase space histograms When a phase space is generated a set of histograms is produced to give you some information about the particles in the phase space The names of all these histograms start with PhaseSpace and they are all dumped into the file rt root csv For each of the following particle types a different set of histograms are produced containing the
127. lowing a set of lines with three numbers representing the Z value of the plane and then the X and Y limits The planes will be extended in Z until the previously defined Z for the minimum Z defined the world negative Z limit will be used If you want to change the name of the limits file you can do it with the command remember to define a parameter always before selecting the user action gamos setParam RTZRLimitsUA FileName MY_FILENAME 13 3 Scoring dose in phantom To use a phantom geometry you can use the GAMOS utilities to read phantom geometries in EGS or GEANT4 formats or build simple phan toms with a few user commands The scoring of the dose in the phantom volumes can be done using the scorer GmG4PSDoseDeposit and select ing as detector the voxels that are named patient For example you can use the following commands gamos scoring createMFDetector DoseDet patient gamos scoring addScorer2MFD DoseScorer GmG4PSDoseDeposit DoseDet This is all you need to get on the standard output the dose by event deposited in each voxel As explained in the section on Reading phase spaces remember that if phase space are used the number of events is the original number of events that were used to generate the phase space In fact GAMOS gets the ratio of particles written in the phase space per original event transported through the accelerator and multiplies this ratio by the number of phase space particles used This allows to get the bes
128. luding a different file for each package Therefore instead of using it you may include all or only a subset of them if you do not need them all Finally you define the GAMOS libraries that will be linked to yours i e the libraries of each of the files that you have included in your code EXTRALIBS lG4geomtextread 1G4geomtextbuild lGamosBase lGamosUtils lGamosFactories lGamosUserActionMgr If you have doubts about which GAMOS libraries to include you may in clude them all as in GamosCore GamosApplication GNU makefile If you have built several levels of directories you may want to have the possibility of typing make at the top most directory to trigger the com pilation of all the directories To do this you just have to add a GNU makefile at the top level directory similar to the one at GAMOSIN STALL source GamosCore GNUmakefile that we reproduce here include GAMOSINSTALL config architecture gmk SUBDIRS GamosUtils GamosFactories GamosBase GamosUserActionMgr GamosAnalysis GamosGeometry GamosMovement GamosPhysics GamosGenerator GamosSD GamosUtilsUA GamosReadDICOM GamosScoring GamosApplication include GAMOSINSTALL config globlib gmk You only have to change the line starting by SUBDIRS to list the name of your subdirectories For the external packages the set of libraries is fixed and defined in the configuration files 10 CHAPTER 2 GETTING STARTED Chapter 3 Geometry You can describe
129. lumeMgr volmgr G4tgbVolumeMgr GetInstance volmgr SetDetectorBuilder gtb Trigger the detector construction GAVPhysicalVolume physiWorld volmgr gt ReadAndConstructDetector return physiWorld 3 1 4 Parallel geometries You can define a parallel geometry by including a second file for GmGe ometryFromText with the command gamos setParam GmGeometryFromText FileNameParallel FILE NAME FILE NUMB ER 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE 37 where FILENAME is the name of a file similar to the one that describe your mass geometry you can indeed interchange them FILE NUMBER is the number you associate to the parallel geometry as you may have several parallel geometries at the same time The only difference between a parallle geometry file and a mass geometry file is that in the case of parallel geometry the volume at the top of the hierarchy world volume should not appear in the file as Geant4 creates it automatically copying the mass world volume This means that you should place your geometry in the same world as the volumes of the mass geometry The parallel geometry will not be seen by Geant4 unless a process is in statntiated to take care of it To do it you can create a G4ParallelWorldScoringProcess with the following command gamos physics useParallelScoringProcess When it is a parallel geometry volume boundary the one that limits the step the process that defined the step is called paralle
130. mSDSimple Calor CRYSTAL 1 will associate a sensitive detector to the two volumes CRYSTAL BGO 1 and CRYSTAL LUYAP 1 14 8 Using particle names Each particle type in Geant4 is identified by a unique name No particle is created by Geant4 unless the user does it explicitly At any time in your command file you can ask for a list of created particles with the command run particle dumpList If you do this after instantiating the GAMOS electromagnetic physics list you will get the following list anti nu e chargedgeantino e e gamma geantino nu e opticalphoton If you use the GAMOS hadronic physics list you will get the following list B B BO BsO D D DO Ds Ds Genericlon He3 J psi N 1440 N 1440 0 N 1520 N 1520 0 N 1535 N 1535 0 N 1650 N 1650 0 N 1675 N 1675 0 N 1680 1680 0 N 1700 N 1700 0 N 1710 N 1710 0 N 1720 N 1720 0 N 1900 1900 0 N 1990 N 1990 0 N 2090 2090 0 N 2190 N 2190 0 N 2220 N 2220 0 N 2250 N 2250 0 a0 1450 a0 1450 a0 1450 0 a0 980 a0 980 a0 980 0 1 1260 a1 1260 1 1260 0 a2 1320 a2 1320 a2 1320 0 alpha anti_BO anti_BsO anti DO anti_N 1440 anti_N 1440 0 anti_N 1520 anti_N 1520 0 anti_N 1535 anti_N 1535 0 14 8 USING PARTICLE NAMES 145 anti N 1650 anti N 1650 0 anti N 1675 anti N 1675 0 anti N 1680 anti N 1680 0 anti N 1700 anti N 1700 0 anti N 1710 anti
131. mUserActionFactory If you define twice the same user action in your command file you will get a warning message but it will be executed twice 74 CHAPTER 6 USER ACTIONS Chapter 7 Sensitive Detector and Hits 7 1 Attaching a sensitive detector to a volume The sensitive detector class in Geant4 has the task of creating hits de posits of energy each time a track traverses a sensitive volume and loses some energy You can write your own sensitive detector class inheriting from G4VSensitiveDetector that produces your own hits and attach it to any volume in your geometry However GAMOS provides some utilities to make this easier and without the need of C programming or a detailed knowledge of how the sensitive detector and hits work in Geant4 GAMOS provides several predefined sensitive detectors that you can find in GamosCore GamosSD e GmSDSimple It is a general purpose class that produces hits with the position at the centre of the detector The identification of each detector unit is done as explained in the sub chapter Identifying each sensitive detector copy e GmSDSimpleExactPos It is similar to GmSDSimple but the hits position is the centroid of the energy depositions of the different tracks that produced it weighted by their energy e GmSDOpticalPhoton This class inherits from GmSDSimple but only produces hits if the process that defined the step is OpAbsorp tion There are other classes that serve to m
132. n a mere warning when a track reaches the target we accumulate one track information of the last step in each region for each of the ancestor tracks Therefore it is very likely that there are more than one track information per track reaching the target and therefore there will be overcounting of the number of tracks killed by a cut As for the production cuts you should keep an eye on this and in any case use only the statistics To use this utility in GAMOS it is only needed to add the command in your script gamos userAction GmMinRangeLimitsStudyUA RTCutsStudy Filter what will produce at the end of run a table and a histogram file with the needed information root b p q x getMinRangeCutsEffect Ct prodcuts root percentage amp tee out 68 CHAPTER 5 PHYSICS and look at the last lines of output those that contain the word FINAL like the following ones PARTICLE e FINAL 17 19 PARTICLE e FINAL 72 34185 PARTICLE gamma FINAL 72 34184 5 7 4 Automatic determination for a dose in phantom simu lation The method used in GAMOS to determine the minimum range user limits is similar to the one used to determine the best production cut To use this utility in GAMOS you just have to associate to your dose scorer a filter of type GmProdCutOutsideVoxelFilter passing to it as argu ments the gamma cut and the electron cut like in the following example gamos scoring addFilter2Scorer ProdCutFilter GmMinRang
133. n be obtained with the command gamos userAction GmTimeStudyUA GmClassifierByParticle Gm ClassifierByK ineticEnergy The time in each category is the time counted at each step Ex actly it is the counting from the beginning to the end of the method G4SteppingManager Stepping To do this without modifying the Geant4 class the class GmTimeStudyMgr inherits from G4VStepping Verbose and it is set as the stepping verbose class substituting the class G4Stepping Verbose class that is the one that controls the verbosity of the command track ing verbose This means that this command will have no effect and if you want to use it you should do with the parameter gamos setParam GmTimeStudyUA G4VerboseLevel VERB You may observe that the time summmed over all the categories is smaller than the run time given by the command run verbose 1 This is because the time is only the time spent at the method mentioned above 102 CHAPTER 9 ANALYSIS EXTRACTING INFORMATION which does not take into account the initialisation and termination times of each track event and run 9 3 Creating your own histograms When you write your histogram you just have to take care of creating and filling it The class GmAnalysisMgr will take care of automatically writing it in the file format you chose To use GmAnalysisMgr you have to instantiate it in your histogram class passing to it the name of your file you may use the same name for several of your histogram cl
134. n z TUBS tube section 1 Inner radius 2 Outer radius 3 Half length in z 4 Starting phi angle 5 Delta angle of the segment CONE cone 1 Inner radius at fDz 2 Inner radius at fDz 3 Outer radius at fDz 18 4 5 CHAPTER 3 GEOMETRY Outer radius at fDz Half length in z fDz CONS cone section 1 Inner radius at fDz Inner radius at fDz Outer radius at fDz Outer radius at fDz Half length in z fDz Starting angle of the segment Delta angle of the segment TRD trapezoid 1 2 3 4 5 Half length along x at the surface positioned at dz Half length along x at the surface positioned at dz Half length along y at the surface positioned at dz Half length along y at the surface positioned at dz Half length along z axis PARA paralellepiped 1 2 Half length along x at the surface positioned at dz Half length along x at the surface positioned at dz Half length along y at the surface positioned at dz Angle formed by the y axis and by the plane joining the centre of the faces G4Parallel to the z x plane at dy and dy Polar angle of the line joining the centres of the faces at dz and dz in z Azimuthal angle of the line joining the centres of the faces at dz and dz in z Half length along y at the surface positioned at dz TRAP generic trapezoid 1 Half length along the z axis pDz 3 1 BUILDING YOUR GEOMETRY WITH
135. n z values e Array of dose relative error values n x n y n z values The second available file is a binary file where the dose and dose squared in each voxel are written The binary format allows for a faster writing and reading and the fact of writing the dose squared instead of the error serves to calculate in a proper way the error correlations when the doses from several jobs are added To obtain it you just have to add the scorer printer GmPSPrinterSqdose to your scorer for example gamos scoring addPrinter2Scorer PSPrinterSqdose GmPSPrinter Sqdose DoseScorer The output file is named by default sqdose out You may change it with the parameter gamos setParam Output sqdose FileNameOut MY_FILENAME All variables are of type float and the format is the following e Number of events original number of events used to generate a phase space file if phase space file is used as primary generator e Number of voxels in the X Y and Z directions e g n x n_y n z e Array of voxel boundaries cm in the X direction n x 1 values e Array of voxel boundaries cm in the Y direction n y 1 values e Array of voxel boundaries cm in the Z direction n_z 1 values e Array of dose values Gy cm n x n y n z values e Array of dose squared values Gy cm n x n y nz values 13 4 ANALYSIS UTILITIES 133 13 3 2 Saving scores in histograms If you want to store the scores in the phantom in a histogram file you can use the scorer
136. nManager ModuleDef nh DEFINE SEAL MODULE Then you have to include the relevant factory and define your plug in include GmCore GmFactories include GmXxxFactory hh DEFINE SEAL PLUGIN GmXxxFactory MY CLASS MY PLUGIN NAME Alternatively if you do not mind that the plug in name has the same name as your class you can use a short notation instead of DEFINE SEAL PLUGIN 140 CHAPTER 14 APPENDIX DEFINE XXX MY CLASS where XXX is the type of object you are defining the name of the factory without Factory e g from GmGenerDistEnergyFactory the Gm substituted by GAMOS and the separation of words with For example GAMOS GEOMETRY GAMOS USER ACTION GAMOS GENER DIST POSITION beware the capitals You can add these lines in your class or create a new file with these lines only see as example the files called module cc in almost all the GAMOS code directories Remember in any case that you cannot have two definitions of DEFINE SEAL MODULE in the same directory 3 Once this is done you can select your geometry with the command gamos xxx MY PLUGIN NAME For example if you have written DEFINE SEAL PLUGIN GmGeometryFactory MyGeometry MyGeom you can then use gamos geometry MyGeom to select your geometry Or if you have written DEFINE GAMOS GEOMETRY MyGeometry you can tell your job to select your geometry with the command gamos geometry MyGeometry
137. nce to merge hits with the parameter gamos setParam PET EvtClass ComptonRecHitDist DIST DIST takes by default a value of 0 that is no Compton hits merging will be done In this case you may select as position of the combined hits the one of the biggest energy or the second biggest or the n th biggest where the order is given by the parameter gamos setParam PET EvtClass SelectPosOrder ORDER ORDER takes by default a value of 1 that is the position is that of the hit with biggest energy If two 511 keV hits are finally found the event is classified as a good PET event Then the sub classification code enters in the game e a More than 2 511 keV hits If more than two hits are found the two that are closer to 511 keV will be taken and the event will receive a subclassification type of 3 gt 2 e b Random coincidence It is checked that each of the two 511 keV hits is built only from tracks from the same origina gamma and that the two hits come from the same event e c Scattered The event is classified as scattered if any of the 511 keV gammas has suffered a Compton interaction in the list of vol umes defined by the parameter gamos setParam PETCountScatteringU A VolumeNames VOLUME 1 VOLUME 2 Poriginal gammas are gammas that are primary particles or that are directly created by the annihilation of positron that is a primary particle 12 2 PET ANALYSIS 117 and this interaction is of one of the process types define
138. ned above You can substitute FALSE by TRUE if you want to activate back the error calculation As mentioned above the errors that are calculated taking into account the number of events You have to be careful then if you set to off the option of scoring by event and keep on the option of calculating the errors In the default GAMOS scorer printers the errors are printed are relative i e the error divided by the value so no caution is necessary but be careful if you define a printer yourself 8 1 Scorer classes All the available scorers in Geant4 are also available in GAMOS The classes have been slightly changed to provide the extra functionality The scorers can be classified in the following types e Track length scorers GmGAPS TrackLength The track length is defined by the sum of step lengths of the particles inside the cell i e the volume where the scoring happens A particle weight is not applied by default There are two extra parameters that are FALSE by de fault and can be set T RUE or FALSE to multiply by the kinetic energy and to divide by the velocity If the energy track flux is required then you should set them to TRUE FALSE Alterna tively to measure the flux per unit velocity then you should set them to FALSE TRUE Finally to measure the flux energy per unit velocity then you should set them to TRUE TRUE GmG4PSPassageTrackLength The passage track length is the same as the track length in GmG4PSTrackLeng
139. nergy vs e energy keV This is the energy deposited locally at annihilation 12 2 5 PET histograms distance between two gammas These histograms are related to the distance between the line joining two gammas originated at the positron annihilation and the vertex position at the moment of the gamma creation and when they hit the sensitive de tector Also other histograms about these two gammas are provided for further information They are produced if the user action PETHistos GammaDist is activated with the command gamos userAction PETHis tosGammaDist The name of all these histograms starts with PETGam maDist and all are written in the file pet root csv The histograms are the following e Angle between the direction of the two gammas when they are created angle between gammas at vertex deg e Angle between the direction of the two gammas when they en ter the sensitive detector angle between gammas at entering SD deg e Distance of closest approach between vertex and the line joining the vertices of the two gammas DCA orig from Gamma vertex mm e Distance of closest approach between vertex and the line joining the points where the gammas enter the sensitive detectors DCA orig from Gamma entering SD mm e Z position of vertex of gamma if it reaches the sensitive detector Orig Pos 2 if Gamma reaches SD mm e R position of vertex of gamma if it reaches the sensitive detector Orig Po
140. ng options as well as try some variance reduction techniques Please read the sections on automatic optimisation of production cuts and user limits for accelerator and dose calculation simulations See also the web page http fismed ciemat es GAMOS RToptim to get a list of the best electromagnetic physics parameters that can optimise your simulation See also sections on bremsstrahlung splitting 13 2 1 Bremsstrahlung splitting Bremsstrahlung splitting is a non biased variance reduction technique that may reduce the CPU time of your accelerator simulation by a big factor It basically consists on splitting the secondary particles in radio therapy mainly gammas generated by bremsstrahlung N times so that each time a bremsstrahlung gamma is created other N 1 gammas are created at the same position with weight 1 N re sampling the energy and or angle distribution As most of the particles that reach a patient in a radiotherapy accelerator are bremsstrahlung gammas by using this technique we can spare the time spent simulating the original electron usually even close to 50 of the total time can be saved and we can reduce the time spent tracking gammas that have small possibility of reaching the patient There are three splitting techniques implemented in GAMOS Uniform bremsstrahlung splitting This technique is the simplest one When a gamma suffers a bremsstrahlung interaction the resulting gamma is split N times producing N equa
141. ning phase space contained in ps iaea 20000 IAEAheader of type IAEA PARTICLES 225437 NPART TOT 225437 NPARTORIG TOT 5000000 RATIO 0 0450874 0 000101661 RATIO TOT 0 0450874 Opening phase space contained in scratch arce gamos prod ps iaea 20001 25 IAEAheader of type IAEA PARTICLES 224635 NPART TOT 450072 NPARTORIG TOT 10000000 RATIO 0 044927 0 000101455 RATIO TOT 0 0450072 Opening phase space contained in scratch arce gamos prod ps iaea 20002 25 IAEAheader of type IAEA PARTICLES 224813 NPART TOT 674885 NPARTORIG TOT 15000000 RATIO 0 0449626 0 000101501 RATIO TOT 0 0449923 N Particles 674885 N Photons 673804 N Electrons 1057 N Positrons 24 N Original Histories 1 5e 07 For each phase space file after the name of the file comes a line with the file statistics number of particles accumulated number of particles of all files accumulated number of original histories ratio of particles original histories ratio error accumulated ratio if particles original histories And at the end the statistics on the total number of particles photons electrons and positrons and the total number of original histories in all summed files 13 4 2 Comparing number of particles per event in two phase space files You can obtain information about the particle content of a phase space file and compare if it is statistically equal to the one from another phase space file If you type analysePS PH
142. ns 118 12 2 5 PET histograms distance between two gammas 119 12 2 6 Histograms of gammas at sensitive detectors 119 13 Radiotherapy application 123 13 1 Using phase spaces 123 13 1 1 Writing 123 13 1 2 Phase space histograms 124 13 1 3 Reading phase spaces 125 13 1 4 Adding extra information to a phase space 127 13 1 5 Reusing a particle at a phase space without filling the phase space files tonene s ea a 128 13 2 Optimisation of a linac simulation 129 13 2 1 Bremsstrahlung splitting 129 13 2 2 Killing particles at big X Y non eva th a di eee 130 13 3 Scoring dose in 131 13 3 1 Saving scores file 131 13 3 2 Saving scores in histograms 133 13 4 Analysis utilities 00200000000 133 13 4 4 Summing phase space files 134 13 4 2 Comparing number of particles per event in two phase space hlesc 2 4 xou hum ceiobom e bed 134 13 4 8 Making histograms out of a phase space file 135 13 4 4 Merging 3ddose files ls 135 13 4 5 Merging sqdose 136 13 4 6 Making histograms out of a sqdose 136 14 Appendix 137 14 1 Converting a Geant4 example into GAMOS example
143. nt POLYCONE polycone 1 2 3 Initial phi starting angle Total phi angle Number of z planes or Number of rz points For each z plane 1 2 3 Position of z plane Tangent distance to outer surface Half length along the z axis For each rz corner 1 2 R coordinate of these corners Z coordinate of these corners The software will know which if the numbers refer to plane or rz points by looking at the number of parameters provided and comparing it with the number expected Example SOLID polyc POLYCONE O 360 6 w 2 52 22 5b 0 75 75 1 75 2 or equivalently 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE 21 SOLID polyc POLYCONE O 360 4 23 3 5 0 75 3 3 5 1 3 5 3 7 2 3 3 7 POLYHEDRA polyhedra 1 Initial phi starting angle N Total phi angle 3 Number of sides 4 Number of z planes or Number of rz points For each z plane 1 Position of z plane 2 Tangent distance to outer surface 3 Half length along the z axis For each rz corner 1 R coordinate of these corners 2 Z coordinate of these corners The software will know which if the numbers refer to plane or rz points by looking at the number of parameters provided and comparing it with the number expected Example SOLID polyh POLYHEDRA 20 180 3 4 1900 32 1800 30 1800 0 1900 O or equivalently SOLID polyh POLYHEDRA 20 180 32 1800 0 30 1
144. nt copy numbers of a volume It has an extra argument that sets the level of the ancestor if it is N 0 it will use the copy numbers of the volume itself if it is N gt 0 it will look for the copy numbers of the N th ancestor e GmPSClassifierByAncestors It assigns a different index to differ ent copy numbers of the sensitive volume It has two extra argu ments that set the number of ancestor levels NAncestor and the maximum number of copies in a level NShift The index is built as N Ancestor 1 5 NShift copyNumber of Nancestor N 0 e GmClassifierByLogicalVolume It assigns a different index to dif ferent logical volumes e GmClassifierByPhysicalVolume It assigns a different index to dif ferent physical volumes 10 2 CLASSIFIERS 109 e GmClassifierByRegion It assigns a different index to different re gions e GmClassifierByKineticEnergy The user must define a minimum a maximum and a width of the energy intervals It creates kinetic energy intervals with these values and assigns a different index to different intervals e GmClassifierByProcessNames It assigns a different index to dif ferent process names that define the G4Step e GmClassifierByParticleProcess It assigns a different index to dif ferent particle process name pairs that define the G4Step This means that the ionisation for electrons and positrons will produce a different index despite the process being called the same for both particles e
145. nt is given the point is 0 0 0 Position in a Geant4 volume gamos generator positionDist SOURCE_NAME GmGenerDistPositionInG4Volumes LV_NAME1 LV NAME2 The position is distributed randomly inside one or several volumes of the Geant4 geometry The user must add as extra parameters the list of volume names The volumes can be physical volumes or touchables This distribution can only be used if the volumes are G4Box G4Orb G4Sphere G4Ellipsoid G4Tubs or G4Cons If you want to use it for any other volume shape you have to use the distribution gamos generator positionDist SOURCE NAME GmGenerDistPositionInG4VolumesGeneral LV NAME1 LV 2 This distributions works with any solid shape including boolean solids but it is in general quite slower than the previous one it creates a random position in the whole world volume and then looks if it is in one of the selected volumes which can be quite slow if the volume dimensions are small Position in a user defined volume gamos generator positionDist SOURCE NAME GmGener Dist PositionInUser Volumes POS X POS Y POS_Z ANG_X ANG Y ANG Z SOLID TYPE SOLID DIMENSIONS The particles are randomly distributed inside a volume defined by the user it does not need to be a real volume in the geometry The user must provide the definition of the volume as extra parame ters SOLID TYPE can be Orb Sphere Ellipsoid Tubs Box SOLID DIMENSIONS are the solid dimensions For the
146. nti lambda c anti neutron anti nu e anti nu mu anti nu tau anti omega anti omega cO anti proton anti s quark anti sdO diquark anti sdi diquark anti sigma 1385 anti sigma 1385 anti sigma 1385 0 anti sigma 1660 4 anti sigma 1660 anti sigma 1660 0 anti sigma 1670 anti sigma 1670 anti sigma 1670 0 anti sigma 1750 anti sigma 1750 anti sigma 1750 0 anti sigma 1775 anti sigma 1775 anti sigma 1775 0 anti sigma 1915 anti sigma 1915 anti sigma 1915 0 anti sigma 1940 anti sigma 1940 anti sigma 1940 0 anti sigma 2030 anti sigma 2030 anti sigma 2030 0 anti sigmat anti sigma anti sigmaO anti sigma c anti sigma ct anti sigma cO anti ssi diquark anti suO diquark anti sui diquark anti t quark anti u quark anti ud0 diquark anti udi diquark anti uui diquark anti xi 1530 anti xi 1530 0 anti xi 1690 anti xi 1690 0 anti xi 1820 anti xi 1820 0 anti xi 1950 anti xi 1950 0 anti xi 2030 anti xi 2030 0 anti xi anti xiO anti xi c anti xi cO b1 1235 b1 1235 b1 1235 0 b quark c_quark chargedgeantino d quark ddi diquark delta 1600 delta 1600 delta 1600 delta 1600 0 delta 1620 delta 1620 delta 1620 delta 1620 0 delta 1700 delta 1700 delta 1700 delta 1700 0 delta 1900 delta 1900 delta 1900 delta 1900 0 delta 1905 delta 1905 delta 1905 delta 1905 0 delta 1910 delta 1910 delta 1910 delta 191
147. o the functionality of Geant4 it is possible to displace or rotate a volume during a run To do this in GAMOS you have first to select the volume you want to move and if you want to move it after a certain number of events or after a certain time is elapsed the time will be checked after each event therefore the time interval will only be approximated You also have to choose how much you want to move it and the axis the axis of displacement or the axis around which happens the rotation You have then to set the interval of events or time between movements After you can define an offset so that the first interval does not start at 0 Finally you can choose that your movement is done forever i e until the number of events in the run are exhausted or it is only done n times The commands to tell GAMOS to make a movement are gamos movement moveEachTime if you want that the movement happens after a certain interval of time and gamos movement moveEachN Events if you want that the movement happens after a certain number of events In both cases the command has to be followed by these arguments 3 6 GEOMETRY UTILITIES A1 displace rotate volume name value axis x axis y axis z time interval nevents interval offset 0 number of intervals infinite where the first word has to be either displace or rotate volume name must be one of the Geant4 volumes of your geometry value is the amount by which you want to displace or rotate d
148. of the classes described above 7 6 Identifying each sensitive detector copy To identify each detector unit individually you have to give a different de tector unit ID to each copy of your sensitive detectors each G4Touchable in Geant4 terminology GAMOS does this automatically for you If you use the GmSDSimple class it will give each SD copy a detector unit ID that will be the copy number of physical volume 100 copy number of parent physical volume 4 100 100 copy number of grandparent physical volume You can change the number of ancestor particles to build the detector unit ID with the parameter gamos setParam SD DetUnitID N Ancestors that takes a default value of 3 You can also change the value of the shift that multiplies each ancestor copy number using the parameter gamos setParam SD DetUnitID NShift that takes a default value of 100 7 7 Storing and retrieving hits GAMOS provides yuo with the option of storing in a file the hits produced during a run and reading them back in another run Creating hits from track in the sensitive detector or reading them from a file will produce the same in memory representation therefore you can apply any of the above described effects and produce any histogram in the same way independently on how the hits are produced 82 CHAPTER 7 SENSITIVE DETECTOR AND HITS This can serve you for example for doing a study on how much your results change with different energy resolutions
149. on the circle is around the Z axis by default If you want a circle around another axis you can provide as extra arguments the axis and optionally the position of the first copy There are three types of square parameterisation in the planes XY XZ YZ types SQUARE XY SQUARE XZ SQUARE YZ and a general one type SQUARE For this bidimensional parameterisations you have to provide two copy numbers two steps and optionally two offsets For the general case SQUARE the offset is not needed but you have to add as extra arguments the two axis that do not have to be orthogonal and optionally the position of the first copy In the case of this paramerisation type you have to provide two number of copies one for each axis Example PLACE PARAM mytube 1 subworld2 LINEAR X RMO 5 20 O _ mytube 1 subworldi LINEAR 5 20 O 1 1 1 50 O O PLACE PARAM mybox mother CIRCLE RMO 30 0 209 1 150 _ mybox 1 subworld2 SQUARE XZ 5 5 20 20 PLACE PARAM mybox 1 subworldi SQUARE 5 8 20 10 0 1 1 0 1 O 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE 27 Be aware that putting offset 0 means that the first copy is placed at 0 0 0 This may be not what you want if for example you are filling a box with an square of small boxes using an square parameterisation offset 0 will mean that all the copies are placed in the positive positive quarter of the mother box
150. or each of that shape dimension e G4LogicalVolume A logical volume contains the volume s full prop erties It includes the geometrical properties of the solid and adds physical characteristics the material of the volume whether it contains any sensitive detector elements the magnetic field etc e G4VPhysicalVolume A physical volume is a volume placed already in another volume e G4VTouchable A touchable is each copy of a volume To under stand the difference with a physical volume we put an example If you place a volume A in 5 places inside volume B and place volume B in 12 places you will have 5 12 physical volumes each one with a distinct position and rotation matrix But you will have 5X12 60 individual copies that is 60 touchables To save memory usage the GA4V Touchable are instantiated in Geant4 when a track traverses the corresponding volume in space and they are immediately deleted when the track leaves In GAMOS you have the possibility of accessing any individual touchable whenever you like When you need it you can ask GAMOS to create a GmTouchable which will have the same characteristics as the corresponding G4V Touchable that would be created when a track reaches it To identify the touchable you want to use you have to use the fol lowing notation For example the name CRYSTAL identifies all individual crystals of your detector that have name CRYSTAL while BLOCK 7Z 2 CRYSTALZ71 refers only to the c
151. order and meaning of the solid dimensions please look at the corresponding Geant4 solid By default the volume is placed at position 0 0 0 If you want it placed at a different position you have to add three optional extra parameters POS X POS Y POS Z By default the volume is not rotated If you want it rotated you have to add three optional extra parameters and always add the three For understanding the notation to identify touchables in GAMOS see Identifying touchables section gt Other volume types may be added at user request 50 CHAPTER 4 GENERATOR positions even if they are 0 0 0 ANG_X ANG_Y ANG_Z Those angles are interpreted rotating the volume first around the X axis then around the Y axis and finally around the Z axis e Position in a Geant4 volume surface gamos generator positionDist SOURCE_NAME GmGenerDistPositionInG4Surfaces LV_NAME1 LV_NAME2 The position is distributed randomly in the surface of one or several volumes of the Geant4 geometry The user must add a number of extra parameters with the list of volume names The volumes can be physical volumes or touchables This distribution can only be used if the volumes are G4Box G4Orb G4Sphere G4Tubs or G4Cons e Position in a user defined volume surface gamos generator positionDist SOURCE NAME GmGenerDistPositionInUserSurfaces POS X POS Y POS Z ANG_X ANG Y ANG Z SOLID TYPE SOLID DIMENSIONS The particles are randomly distributed
152. os generator directionDist SOURCE NAME GmGener Dist DirectionCone The primary particles will be generated in a random distribution around a cone given by the extra parameters DIR_X DIR Y DIR_Z OPEN ING_ANGLE so that each solid angle receives the same number of particles Position and direction distributions It is also possible to create distributions where several of the four variables time energy position and direction are generated at the same time so that they are related You have nevertheless to keep in mind that the order of calling will be time position energy and direction distributions In case you need a different order for example if the position is deter mined by the value of the direction you can calculate both the direction and the position in the GeneratePosition method return only the position and keep the direction in a class data so that it can be returned in the GenerateDirection method e Position in volume surface pointing towards centre GmGenerDistPositionDirectionInVolumeSurface SOLID TYPE SOLID DIMENSIONS POS X POS Y POSZ ANG_X ANG_Y ANG Z The position is distributed in the surface of a volume defined by the user T he user must provide the definition of the volume as extra pa rameters SOLID TYPE can be of type Box SOLID_DIMENSIONS are the solid dimensions By default the volume is placed at position 0 0 0 If you want it placed at a different position you have to add three optional
153. p 0 virtual void ClearDigits in the case of GmVRecHit BuilderFromHits These two methods will be called automatically The first one at the end of each event to convert the digits or hits into reconstructed hits and the second one at the beginning of each event to clear the reconstructed hits of the previous event You can then convert your reconstructed hit builder into a GAMOS plug in To learn how to do this see the instructions in the section Creating your plug in using the GmRecHitBuilderFactory After this you select it with the command gamos recHitBuilder MY_RECHITBUILDER 7 5 3 Examples of reconstructed hit builders There are a few simple reconstructed hit builders implemented in GAMOS that serve to merge hits that are close to each other The energy of the reconstructed hit is the sum of the hit energies while the position is the weighted sum of the hit positions weighted by the energy of each hit This can be useful for example for recovering the total energy of a photon when it has suffered a Compton scattering near the photoelectric interaction the user has always the freedom to choose how near the other hits are or for clustering together all the energy depositions of the particle shower produced by the electron following a photoelectric interaction The merging of this is always started by the hit that has bigger energy in each detector type only hits in the same detector type are merged Then the hits a
154. particle type in the histogram name gamma e e plus a set of histograms for all particles named ALL Also histograms for neutron proton will be produce if the parameter gamos setParam RTPhaseSpaceHistos Hadrons TRUE FALSE is set to TRUE A full set of histograms is produced for each Z plane with the Z value on their names The following histograms are produced 13 1 USING PHASE SPACES 125 e Position X cm X at Zstop e Position Y cm Y at Zstop e Position X vs Y cm XY at Zstop e Radial position in the XY plane cm R at Zstop e Theta angle of direction degrees Direction Theta at Zstop e Phi angle of direction degrees Direction Phi at Zstop e Energy MeV Energy at Zstop e X direction cosine Vx at Zstop e Y direction cosine Vy at Zstop e Z direction cosine Vz at Zstop e Radial position in the XY plane cm vs theta angle of direction degrees R vs Direction Theta at Zstop e Radial position in the XY plane cm vs energy MeV R vs Energy at Zstop e Theta angle of direction degrees vs energy MeV Direction Theta vs Energy at Zstop The user can choose not to produce any of these histograms by setting the parameter gamos setParam RTPhaseSpaceUA Histos TRUE FALSE The name of the histogram file can be controlled with the parameter gamos setParam RTPhaseSpaceHistos FileName MY FILENAME that by default is phaseSpace Seve
155. phase space file by running gamos with the input script that you can find in Radio Therapy analysis phaseSpace analysePS rt analysePS in If you edit it and change the name of the input phase space file at gamos setParam RTGeneratorPhaseSpace FileName and run gamos rt analysePS in You will get a file named phaseSpace root that contains the same his tograms that you get when you run the job to write the phase space file see section on Phase space histograms 13 4 4 Merging 3ddose files This utility serves to merge dose files in the 3ddose format corresponding to different jobs with the same setup and averages the dose in them To use it you have to write a file containing the list of 3ddose files one file per line for example 136 CHAPTER 13 RADIOTHERAPY APPLICATION 3ddose water 20000 out 3ddose water 20001 out 3ddose water 20002 out Then you just have to run the executable merge3ddose INPUT_FILE_LIST_NAME OUTPUT_FILE_NAME where INPUT_FILE_LIST_NAME is the name of the file containing the list of files to merge and OUTPUT_FILE_NAME is the name of the output file that will contain the merging of all the files When merging files it will be checked that they correspond to the same phantom by checking the number of voxels and voxel limits 13 4 5 Merging sqdose files This utility serves to merge dose files in the sqdose format corresponding to different jobs with the same setup and averages the in them To use
156. ral parameters serve to control the number of histogram bins gamos setParam RTPhaseSpaceHistos Nbins NBINS that takes by default a value of 100 and the maximum absolute value for histograms of position gamos setParam RTPhaseSpaceHistos HisRMax MAX that takes by default a value of 100 histograms of angle gamos setParam RTPhaseSpaceHistos HisAngMax MAX that takes by default a value of 180 and histograms of energy gamos setParam RTPhaseSpaceHistos HisEMax MAX that takes by default a value of 10 MeV 13 1 3 Reading phase spaces To use the generated phase space you have to define as your primary generator gamos generator RTGeneratorPhaseS pace You can change the filename by default test with the parameter gamos setParam RTGeneratorPhaseSpace FileName MY_FILENAME The particles in the phase space can be translated or rotated by using the parameters 126 CHAPTER 13 RADIOTHERAPY APPLICATION gamos setParam RTGeneratorPhaseSpace InitialDisplacement POS X POS Y POS Z gamos setParam RTGeneratorPhaseSpace InitialRot Angles ANG_X ANG Y ANG_Z the position of the particles is first changed by the initial displacement then the momentum vector is rotated around the X axis by ANG_X around the Y axis by ANG Y and around the Z axis by ANG_Z and finally the position vector is rotated around the X axis by ANG_X around the Y axis by ANG Y and around the Z axis by Z If the number of phase space particles is not enough to calculat
157. re looked one by one to check if they are close Each time a hit is added the centre is recalculated The reconstructed hit builders implemented are e GmRecHitBuilderByDistance Two hits are merged if they are separated by a distance closer than the parameter gamos setParam SD GmRecHitBuilderByDistance HitsDistInRecHit that by default takes a value of 10 mm e GmRecHitBuilderByBlock Two hits are merged if they are in sensitive detectors that belong to the same block i e a volume whose parent volume is the same To check if two hits belong to the same block the detector unit ID ie the identification of the touchable where the hits is located is used Usually the detector unit ID is 7 6 IDENTIFYING EACH SENSITIVE DETECTOR COPY 81 built from the volume copy numbers of the volume ancestors e g vol ume copy number 100 parent volume copy number 100 100 grand parent volume copy number and therefore two detector unit IDs are considered to belong to the same block if their division by a number given by the parameter gamos setParam SD GmRecHitBuilderByBlock NShift gives the same results This parameter takes a default value of 100 e GmRecHitBuilderltol Two hits are never merged so that a re constructed hit is built for each hit If you want any of these reconstructed hit builders to be active you can select one of them with the command gamos recHitBuilder RHITBUILDER_NAME where RHITBUILDER is one
158. rimary particle created at the beginning of the event e 2 is is created at the annihilation of the positron it is assumed that the positron is a primary particle At each step the UserSteppingAction method checks that it is inside a volume declared as sensitive detector In this case it adds new Gm TrajPoint for this track with all the information of the track at this moment plus it adds at the beginning another point with the vertex information At the end of track if it is an original gamma it asks the class GmClassi fierByInteraction to classify it based on the type and number of interactions The method Classify of this class returns an integer with the meaning 100 100 Number of LowEnPhotoElec interactions 100 Number of LowEnCompton in teractions Number of LowEnRayleigh interactions See PET section for more details on the concrete class GmHistosGammaAtSD 9 2 9 Table of tracks and steps You may get a table of the number of tracks and steps by instantiating the user action gamos userAction GmCountTracksAndStepsUA It will produce a table with the number of tracks and steps in the whole run You may get more details by using it with filters and classifiers For example the command gamos userAction GmCountTracksAndStepsUA GmClassifierByPar ticle will produce a table similar to this one COUNT_TRACKS_AND_STEPS GmClassifierByParticle COUNT_TRACKS gamma 100 COUNT_TRACKS e 8 COUNT_TRACKS e 1 COUNT_
159. rimary particles in the event After this each line corresponds to a particle with a first word P followed by the following variables particle ID PDG encoding position X y Z in mm momentum x y z in MeV time in ns To select this generator you have to use the command gamos generator GmGeneratorFromFileText By default the file to be read is called generator txt you can see an example at MY_GAMOS_DIR data generator txt You can change its name with the command gamos setParam GmGeneratorFromFileText FileName FILENAME To change the search path please read the section Managing the input data files 4 4 Reading your generator particles from a bi nary file You can also define your event primary particles with a binary file The format of the input file is the following The first word is an integer containing the number of particles Then follows a record for each particle of the type GenerFileData struct GenerFileData int partID float posx posy posz momx momy momz time F3 To select this generator you have to use the command gamos generator GmGeneratorFromFileBin 56 CHAPTER 4 GENERATOR By default the file to be read is called generator bin You can change its name with the command gamos setParam GmGeneratorFromFileBin FileName MY_FILENAME To change the search path please read the section Managing the input data files 4 4 1 Event generator histograms These are
160. rs of your class from the command line like the minimum and maximum time you have to implement the method virtual void SetParams const std vector lt G4String gt amp params This method will be called automatically passing the extra parameters in the command line selecting your distribution Last you have to transform your distribution into a plug in To learn how to do this see the instructions in the section Creating your plug in using the GmGenerDistTimeFactory Then you can choose that any of the particle sources use your new dis tribution in any GAMOS job by adding the command line gamos generator directionDist SOURCE_NAME MyTimeDist where MyTimeDist is the name you chose when defining your plug in which can be different from the name of the class itself 42 BUILDING YOUR GENERATOR WITH C 55 4 2 Building your generator with C You can build your generator by writing your C class inheriting from G4VUserPrimaryGeneratorAction see example in 9 After that you have to transform it into GAMOS plug in To learn how to do this see the instructions in the section Creating your plug in using the GmGenerator Factory 4 3 Reading your generator particles from a text file You can also define your event primary particles with a text file The format of the input file is the following The first line of each primary event should start with a line that contains as first word EVENT and as second word the number of p
161. rtions by number of atoms MIXT_BY_NATOMS e Proportions by volume _ VOLUME The first two tags can be used to build material mixtures out of elements or materials but the last tag can only be applied with material components elements do not have density Example MIXT Fiber Lead 9 29 2 Lead 0 9778 Polystyrene 0 0222 Geant4 internal database of materials and elements Geant4 provides a list of predefined materials whose compositions corre spond to the NIST definition 13 Among them you can find all single elementary materials from Z 1 Hydrogen to Z 98 Californium You can use those materials when building a volume without the need to redefine them on your ASCII file It is just enough that the material name you assign to a volume corresponds to the name of one of these predefined materials they all start with G4_ The Geant4 materials have the mean excitation energy set explicitly instead of allowing an automatic calculation from its components You may override those materials if you want by redefining them in your ASCII file Also Geant4 provides the definition of all elements from Z 1 Hy drogen to Z 107 Bohrium Their names are the usual symbol in the periodic table of elements no G4_ These elements take into account the isotope composition Apart from the elementary materials many other are available usually related to medical physics applications you may find the details
162. rystal s with copy number 1 in block s with copy number 2 RING 3 BLOCK CRYSTAL 1 refers to all the crystal s with copy number 1 in all the block s whatever copy number they have in the ring s that have copy number 3 If you are writing a new plug in you can have easy access to the list of touchables with a given name with the line GmGeometryUtils GetInstance gt GetTouchables touch name itExists If the touchables do not exist in your geometry you will get a warning in case itExists is false and an exception if itExists is true There is a limitation on the use of touchables they cannot be used for assembly volumes as Geant4 creates internally the physical volumes 144 CHAPTER 14 APPENDIX 14 7 Using wildcards to get volume names In many commands described in this guide you give the name of a log ical volume physical volume or touchable so that GAMOS finds the corresponding Geant4 object In case you want to apply your command to several volumes with similar names you can use an asterisk that would mean any character For example if you have the volumes named CRYSTAL_BGO_1 CRYSTAL BGO 2 CRYSTAL_LUYAP_1 and CRYS TAL LUYAP 2 gamos SD assoc8SD2LogVol GmSDSimple Calor CRYSTAL will associate a sensitive detector to the four volumes while gamos SD assoc8D2LogVol GmSDSimple Calor CRYSTAL BGO will associate a sensitive detector to the two volumes CRYSTAL BGO 1 and CRYSTAL BGO 2 and gamos SD assoc8SD2LogVol G
163. s R if Gamma reaches SD mm 12 2 6 Histograms of gammas at sensitive detectors We describe here the GmHistosGammaAtSD an utility that prints in formation about the interaction of original gammas in the sensitive detector It is a user action and therefore it can be activated with the command gamos userAction GmHistosGammaAtSD At the end of run a table like the following one is printed Classification of Gamma Interactions in SD GC nEvents 1000000 GC n gamma in SD 516170 25 8085 7 120 CHAPTER 12 PET APPLICATION GC n PE 321588 62 30273 GC PE 0 COMP 157614 49 011157 GC PE 1 COMP 111304 34 610744 GC PE 1 COMP 52670 16 378099 GC n COMP 222590 43 12339 GC 1 COMP 159193 71 518487 GC 1 COMP 63397 28 481513 GC nGamma COMP event 0 585931 e nEvents total number of events e n gamma in SD number of original gammas reaching one sensi tive detector e n PE number of original gammas with photoelectric interaction in SD e PE 0 COMP number of original gammas with photoelectric in teraction and no Compton interactions in SD percentage relates to PE e PE 1 COMP number of original gammas with photoelectric in teraction and one Compton interaction in SD percentage relates to PE e PE gt 1 COMP number of original gammas with photoelectric interaction and more than one
164. s related to special regions or surfaces be applicable to all cells physical volumes or replicas of a given geometry be customizable A number of scorers have been created for this specific application GmGAPSNofCollision This scorer records the number of col lisions that occur within a scored volume cell GmG4PSPopulation This scores the number of tracks within in a given cell per event A particle weight is not applied by default GmG4PSTermination This scores the number of tracks that are terminated in a given cell per event A particle weight is not applied by default 8 2 Filter classes See section on Filters and classifiers 8 3 Scorer printers A scorer printers serves to select the format of the output of a scorer These classes are unique to GAMOS as Geant4 does not provide this functionality As mentioned above several printers can be associated to the same scorer The general use printer scorers currently in GAMOS are the following e GmPSPrinterDefault Prints in the standard output the summary of scoring in the following format 8 4 CLASSIFIER CLASSES MultiFunctionalDet MFD NAME PrimitiveScorer SCORER NAME Number of entries 5 copy no copy no copy no copy no copy no 0 1 2 6 7 2 6625344e 18 8 6617421e 17 2 1034987e 17 5 9651155e 17 8 2850179e 17 REL REL REL REL REL 0 031622777 Gy 0 011622713 Gy 0 021166675 Gy 0 014183
165. s that when a particle is used for n th time with even n the X original value of position and momentum will be changed sign while when it is for an n th time with n odd it will not be changed If it is Y the same but mirroring in Y And if it XY the second time a particle is used the X values will be changed sign the third time the Y values will be changed sign the fourth time both X and Y values will be changed sign the fifth time there will be no change and the cycle restarts When reading a phase space file you may skip the first N events by using the parameter gamos setParam RTGeneratorPhaseSpace NEventsSkip N You can produce the same histograms that were produced when writ ing the phase space file by setting the parameter gamos setParam RTGeneratorPhaseSpace Histos TRUE FALSE to TRUE 13 1 USING PHASE SPACES 127 When you use a phase space as input you may use as number of events the real number of events run in your job which would equal be to the number of particles in the phase space multiplied by the number of times each particle is reused or you may alternatively use as number of events the original number of events that were used to generate the phase space see section on Scoring dose in phantom To use the first the first one you can invoke the standard Geant4 method G4RunManager GetRunManager GetNumberOfEvent to use the second one you may invoke the GAMOS method GmNumberOfEvent Get NumberOfEvent 13
166. stor particles are created a cut smaller than the corresponding range we would stop the chain of particles and therefore we would have no particle in the target plane After running a big number of tracks we can know for each particle type and for each region which is the biggest range we can put if we do not want to lose any particle Indeed we may allow to lose a small amount of particles if this speeds up 5 7 AUTOMATIC OPTIMISATION OF CUTS 65 our simulation To know easily which is the biggest cut you can use to lose less than a given percentage of particles GAMOS provides a set of plots one per each particle type and per each region and a simple script to get automatically the cut values One warning is due here as mentioned above when a track reaches the target its range fills a histogram but also the range of all the ancestors of this track It may happen then that when you set a certain cut and the abovementioned script gives you how many tracks would be killed more than one killed track correspond to the same track reaching the target i e with a cut you kill the track that reaches the target and the parent track Therefore you might have an overcounting of the number of tracks killed by a cut To avoid this the total number of tracks the last lines of output is not computed as the sum of tracks in the region This number uses a histogram that contains only one entry per track reaching the target the one corresponding to the tr
167. t approximation to the correct number of events when the phase space is not used fully or when particles are reused it is indeed not the exact number if for example you use only the 10 first particles in the phase space the number of events that generated those 10 particles may be bigger or smaller than the number of events that generated the following 10 particles due to statistical fluctuations 13 3 1 Saving scores in file You can also store the dose in each voxel in a file which allows you to calculate the average dose from several jobs see dose analysis section 132 CHAPTER 13 RADIOTHERAPY APPLICATION The first file is a text file where the dose and dose error in each voxel are written To obtain it you just have to add the scorer printer GmPSPrinter3ddose to your scorer for example gamos scoring addPrinter2Scorer PSPrinter3ddose GmPSPrinter3ddose DoseScorer The output file is named by default 3ddose out You may change it with the parameter gamos setParam Output 3ddose FileNameOut MY FILENAME The format is the same as the 3ddose format used in DOSXYZnrc except that the first line contains the number of events e Number of voxels in the X Y and Z directions e g n x n_y n z e Array of voxel boundaries cm in the X direction n x 1 values e Array of voxel boundaries cm in the Y direction n y 1 values e Array of voxel boundaries cm in the Z direction n_z 1 values e Array of dose values Gy cm n x n y
168. t can be defined in three ways a By giving the three rotation angles around the X Y and Z axis in this order of rotations b By giving the polar and azimuthal angles of the X Y and Z axis after the rotation is applied c By giving the nine matrix elements of the rotation matrix XX XY XZ YX YY YZ ZX ZY ZZ The tag for the three cases is the same The parser will know which case is meant by the number of parameters a ROTM 1 Name 2 Angle of rotation around global X axis 3 Angle of rotation around global X axis 4 Angle of rotation around global X axis Example ROTM ROO O O b ROTM 1 Name 2 Polar angle for axis X 3 Azimuthal angle for axis X 4 Polar angle for axis Y 5 Azimuthal angle for axis Y 6 Polar angle for axis Z 7 Azimuthal angle for axis Z Example ROTM RO 90 0 90 90 3 1 BUILDING YOUR GEOMETRY WITH A TEXT FILE 31 c ROTM 1 Name 2 9 parameters defining the rotation matrix Example ROTM RO 1 0 0 0 1 0 0 0 1 Visibility VIS 1 Volume name 2 ON or TRUE OFF or FALSE Example VIS yoke OFF By default the visibility of all volumes is set to ON Colour and transparency To define the colour of a volume COLOUR COLOR 1 Volume name 2 Red colour proportion 3 Green colour proportion 4 Blue colour proportion 5 Transparency The four parameters can take a value between 0 and 1 The transparency parameter is not mandatory Example
169. t the physics as the standard electromagnetic Geant4 physics and run 10 events with an electron of 1 MeV as primary particle You can then add any of the command described in this document or any Geant4 command or any command you created yourself Beware that Geant4 is a state machine and the list of available com mands depends on the current state The main state change is triggered by the run initialize command which changes the state from G4State_PreInit to G4State_Idle You may get a full list of the available commands at any moment with the command control manual To run your first example you can use the one at the directory exam ples test Simply type the commands cd MY_GAMOS_DIR examples test gamos test in 2 3 Compiling GAMOS If you installed GAMOS as explained in the previous section the compilation will be done automatically Then you may run your application in GAMOS by writing your user commands without any need of compiling ever more Only if you want to extend the GAMOS functionality by providing new code you will have to follow the instructions in this section GAMOS uses the GNU make tool to manage the compilation and gener ation of executables It uses a set of configuration files based on the Geant4 ones Therefore if you are familiar to Geant4 you will find no difficulty in compiling GAMOS After untarring the installation file you will have a directory called MY_INSTALLATION_DIR GAMOS 2 0 1 This is the dire
170. t to help the user that is writing some C code to for example debug the geometry get a touchable or a volume by name etc They are all in the GmGeometry Utils class which is a singleton To use them in your C code you can do it like in the following example GmGeometryUtils GetInstance gt DumpG4LVList We list here the available methods with an explanation of their func tionality e void DumpSummary std ostream amp out G4cout Dumps a summary of the geometry number of solids logical volumes physical volumes touchables and materials 42 CHAPTER 3 GEOMETRY void DumpGALVList std ostream amp out G4cout Dumps list of logical volumes void DumpGALV Tree std ostream amp out G4cout Dumps the hierarchy of logical volumes void DumpGAP VLV Tree std ostream amp out G4cout Dumps in the following order 1 a logical volume with details 2 list of physical volumes that are daughters of this logical volume with details 3 list of logical volumes daughters of this logical volume and for each go to 1 void DumpMaterialList std ostream amp out G4cout Dumps list of materials void DumpSolid G4VSolid sol size_t leafDepth std ostream amp out G4cout Dumps a solid with its attributes void DumpLV G4LogicalVolume lv size_t leafDepth std ostream amp out G4cout Dumps a logical volume with its attributes void DumpP V GAVPhysicalVolume pv size_t leafDepth std
171. ted in a disc in the XY plane with the radius in a gaussian distribution of sigma SIGMA and random in phi at posi tion 0 0 0 If you want it placed at a different position you have to add three optional extra parameters POS X POS Y POS Z By de fault the cylinder is not rotated If you want it rotated you have to add three optional extra parameters and always add the three positions even if they are 0 0 0 DIR X DIR Y DIR Z Those are the director cosines of the Z axis of the cylinder the axis perpendicular to the 2D surface Position in the voxels of a phantom gamos generator positionDist SOURCE NAME GmGenerDistPosition VoxelPhantomMaterials MATERIAL1 MATERIAL2 The position is randomly distributed in the voxels of a phantom with material equal to one of the materials in the list of parameters There must be at least one volume defined by parameterisation of type G4PhantomParameterisation Direction distributions e Random distribution 4 1 USING GAMOS GENERATOR 53 gamos generator directionDist SOURCE NAME GmGener Dist DirectionRand The primary particles will be generated in a random distribution so that each solid angle receives the same number of particles Constant distribution gamos generator directionDist SOURCE NAME GmGener Dist DirectionConst The primary particles will be generated all in the same direction given by the extra parameters DIR X DIR Y DIR_Z Cone distribution gam
172. th except that only tracks which pass through the volume are taken into account This means that newly generated or stopped tracks in side the cell are excluded from the calculation A particle weight is not applied by default e Deposited energy scorers CHAPTER 8 SCORING GmG4PSEnergyDeposit This scorer stores a sum of particles energy deposits at each step in the cell GmG4PSDoseDeposit In some cases dose is a more conve nient way to evaluate the effect of energy deposit in a cell than simple deposited energy The dose deposit is defined by the sum of energy deposits at each step in a cell divided by the mass of the cell The mass is calculated from the density and volume of the cell taken from the methods of G4VSolid and G4LogicalVolume e Current and flux scorers There are two different definitions of a particle s flow for a given geometry One is a current and the other is a flux In our scorers the current is simply defined as the number of particles with the particle s weight passing through a certain surface or volume while the flux takes the particle s injection angle to the geome try into account The current and flux are usually defined at a surface but volume current and volume flux are also provided GmG4PSFlatSurfaceCurrent Flat surface current is a surface based scorer The present implementation is limited to scoring only at the Z surface of a G4Box solid The quantity is defined by the num
173. th ICRU49 as stopping power parameterisation ion standard standard electromagnetic processes ion LowE ziegler1977 low energy processes with Ziegler 1977 as stopping parameterisation ion LowE ziegler1985 low energy processes with Ziegler 1985 as stopping parameterisation ion LowE ziegler2000 low energy processes with SRIM2000 as stopping parameterisation jon inelastic binary cascade ion binary cascade model To tell your job to use one of the possible combinations of physics models just described you have first to select the GAMOS electromagnetic physics list using the command gamos physicsList GmHadronicPhysics and then you can select one of the physics models for each particle If you do not select anyone for a given particle the first one in each list is taken as default and then you can select one of the physics models for each particle with the command gamos GmPhysics addPhysics PHYSICS MODEL NAME where PHYSICS MODEL NAME is one of the above names or the names of the GAMOS electromagnetic physics list If you do not select anyone the first one in each list is taken as default For details on the physics implemented in each of these physics models please read the Geant4 physics manual 10 60 CHAPTER 5 PHYSICS 5 3 Building your physics list with C code To build your physics list first write it in the usual Geant4 way that is in heriting from G4VUserPhysicsList see example in 1
174. the class has been constructed it will take no effect and the default value will be used To guarantee that you have done it this way you will get at the end of a GAMOS job the information on the usage of parameters You will always get a list of the parameters that have not been used in the code This is probably an indication that you have mistyped a parameter name This list appears at the end of your output and looks similar to this one 4 PARAMETERS NOT USED DEFINED IN SCRIPT BUT NOT USED BY C CODE Ahh MAYBE YOU HAVE MISSPELLED THEM PARAMETER GmGeometryText FileNam Other lists are available at user request to get a more detailed infor mation You may get them anywhere in your simulation by using the command gamos printParametersUsage LEVEL If LEVEL takes a value gt 0 you will get the same list as above If LEVEL takes a value gt 1 you will get a list of parameters that are using the default value you may then check if this list contains one of the parameters whose values you thought you have changed This list looks similar to this one hhhhh PARAMETERS USING DEFAULT VALUE DEFINED IN C CODE BUT VALUE NOT DEFINED IN SCRIPT PARAMETER Generator Isotope FileName PARAMETER GmCountTracksUA FirstEvent If LEVEL takes a value gt 2 you will get a list of how many times each parameter has been used This list looks similar to this one hhhhh NUMBER OF TIMES EACH PARAMETER IS USED IN C CODE PARAMETER GmCountTrac
175. tions we have first to transform them into GAMOS user actions which requires simply to edit the hh classes and make them inherit from GmUserX XX Action instead of G4UserX XX Action Then we have to add the following lines in module cc DEFINE_GAMOS_USER_ACTION ExN02RunAction DEFINE_GAMOS_USER_ACTION ExN02Event Action DEFINE_GAMOS_USER_ACTION ExN02SteppingAction It is not needed to convert the sensitive detector into a plug in that could be called in the user command file because it is explicitly called in the detector construction class Indeed if you want to do it you should delete the lines that instantiate it there and then you can write DEFINE GAMOS SENS DET ExNO2TrackerSD The main class exampleN02 cc is not needed anymore We use the GAMOS main and a macro file that we may call exampleN02 mac with the user commands that select the example components like the following one gamos geometry ExNO2DetectorConstruction gamos physicsList ExNO2PhysicsList gamos generator ExNO2PrimaryGeneratorAction gamos userAction ExNO2RunAction gamos userAction ExNO2EventAction gamos userAction ExNO2SteppingAction run initialize run beamOn 10 You can then run gamos ezampleN02 mac and you will get the same results as if you run the original Geant4 example 14 2 Creating your plug in There are several factories in GAMOS that take care of the different plug in types To transform your class into a plug in you have
176. to follow the instructions in this section using the relevant factory and class as indicated in the relevant section of this guide e g GmPhysicsFactory and G4VUserPhysicsList for a geometry plug in GmVerbosityFactory and GmVerbosityMgr for a verbosity plug in To write a new plug in of any type follow these steps 14 2 CREATING YOUR PLUG IN 139 1 Create your class or use one of the existing Geant4 classes This class should inherit from the corresponding Geant4 or GAMOS class e G4VUserDetectorConstruction geometry e G4VUserPhysicsList physics list e G4VUserPrimaryGeneratorAction primary generator e GmVGenerDistPosition primary particles position distribu tion e GmVGenerDistDirection primary particles direction distri bution e GmVGenerDistEnergy primary particles energy distribution e GmVGenerDistTime primary particles time distribution e GmVUserAction user action e G4AVSensitiveDetector sensitive detector e GmVDigitizer hits digitizer e GmVRecHitBuilder reconstructed hits builder e GmVPrimitiveScorer scorer e GmVPSPrinter scorer printer e GmVFilter filter e GmVClassifier classifier e GmV VerbosityMgr verbosity If you are creating a new class you can use as example one of the classes in the directory examples PlugInTemplates that are nearly empty classes that contain the necessary methods that you have to implement for each plug in type 2 Include the SEAL module definition include Plugi
177. tributed in a different manner than the total dose introducing some bias in some region that you consider not acceptable To check in detail the dose produced with a certain filter you can add a scorer printer of type RTPSPDoseHistos that will produce several histograms of the dose PDD X amp Y profiles dose dose volume gamos scoring addPrinter2Scorer PDDhistoPC10 1 RTPSP DoseHistos PDDscorerPC10 1 The name of the printer will be passed to the name of the file containing the histograms 5 7 3 Automatic determination if user limits for an acceler ator simulation The method used in GAMOS to determine the minimum range user limits is similar to the one used to determine the best production cuts The main difference is that when a track reaches the target we do not have to look at the range it had when created but at the range it had in every step This is because even if we want the minimum step the track may have crossed several regions and the smallest range may not correspond to the last step What we do nevertheless is only consider the last step when there are a set of contiguous steps in the same region Also for the ancestor tracks we have to store the information of each step starting of course with the one when the track that reached the target or its n th ancestor if we are looking at the n 1 th ancestor was created The same warning as for the production cuts should be mentioned here but in this case it is more tha
178. ts a table with the number of tracks and steps in each of the geometry logical volumes COUNT PARTICLES arm steps 178 tracks 4 COUNT PARTICLES block steps 0 tracks 0 COUNT_PARTICLES body steps 248 tracks 4 COUNT_PARTICLES crystal steps 253 tracks 5 COUNT_PARTICLES head steps 58 tracks 3 COUNT_PARTICLES leg steps 289 tracks 2 COUNT_PARTICLES mother steps 406 tracks 12 COUNT_PARTICLES ring steps 38 tracks 1 Also a histogram file count Tracks root csv is created with the plots of kinetic energy of the tracks in each volume The minimum and maximum of the histogram X axis are defined by the parameters gamos setParam GmCountTracksInVolumeUA Emin ENER gamos setParam GmCountTracksInVolumeUA Emax ENER the default value of Emin is 1 E 12 MeV and of Emax is 1 E2 MeV You ca also choose the number of steps with the parameter gamos setParam GmCountTracksInVolumeUA NSteps NSTEPS 100 and also whether the axis of energies is logarithmic gamos setParam GmCountTracksInVolumeU A OptLogE LOG 1 To activate this utility use the command gamos userAction GmCountTracksInVolumeUA 98 CHAPTER 9 ANALYSIS EXTRACTING INFORMATION 9 2 4 Killing all tracks The action gamos userAction GmKillANUA This action serves to kill all particles at the stacking action G4ClassificationOfNew Track method i e before they start being tracked You may use it in combination with one or several filters to kill only the partic
179. with energy given by the energy of the isotope decay selected by the isotope source as read from the file isotopes dat e Random flat energy gamos generator energyDist SOURCE NAME GmGenerDistEnergyRandomFlat MIN ENERGY MAX ENERGY The primary particles will be generated with an energy given by a random distribution between the minimum and maximum energy Beta decay energy gamos generator energyDist SOURCE NAME GmGenerDist Energy BetaDecay The energy will be sampled following the energy distribution of the decay of the isotope The energy distribution will be read from a file called Energy Dist source_particle_name dat The data is taken from the LBNL LUND Table of Radioactive Isotopes http ie lbl gov toi html goto LBNL LUND Table of Ra dioactive Isotopes then Nuclide search and save the table Beta Spectrum There are several examples at MY GAMOS DIR src data EnergyDist X XX dat e Gaussian gamos generator energyDist SOURCE NAME GmGenerDistGaussian MEAN SIGMA Primary particles will be generated with an energy given by the gaus sian distribution of mean MEAN and sigma SIGMA Position distributions e Position at a point gamos generator positionDist SOURCE NAME GmGenerDistPositionPoint POS X POS Y POS Z 3This distribution can not be used for single particle sources 4 1 USING GAMOS GENERATOR 49 All primary particles are generated at the same position If no extra argume
180. x are the coordinates of the event vertex 21 are the coordinates of the first reconstructed hit x y z2 are the coordinates of the second vertex The same data that is written to the file can be written in the stan dard output if the parameter gamos setParam Output pet DumpToCout is set to true The positions in the standard output not in the file will be written in cylindrical coordinates by default If you want them in cartesian coordinates you should set to true the parameter gamos setParam Output pet DumpCartesian 12 2 4 PET histograms positrons These histograms are related to the original positron and the two sec ondary gammas created at its annihilation They are produced if the user action PETHistosPositron is activated with the command gamos userAction PETHistosPositron The name of all these histograms starts with PET Positron and all are written in the file pet root csv The histograms are the following e Positron energy at creation e initial energy keV e Positron range e range mm e Positron energy at annihilation e energy at annihilation keV e Positron energy at creation vs range e initial energy keV vs range mm 12 2 PET ANALYSIS 119 e Positron energy at annihilation vs secondary gammas energy e e gammas vs e energy keV e Positron energy at annihilation vs sum of secondary gammas en ergy 1 022 MeV positron energy at annihilation total gamma e
181. y ISOTOPE and followed by the isotope name Then there is a line for each of the possible isotope decays with three columns describing the decay particle energy the probability of the decay and the particle type This file contains the most common isotopes in medical physics If you want to use another isotope you can add it following the format described above If you selected this generator each event will be generated with one of several primary particles in the decay list of each of the selected isotopes The presence of each decay particle will occur following its corresponding probability lFor a list of the names of the available particles use the Geant4 command run particle dumpList or see Appendix 41 USING GAMOS GENERATOR 4T To choose an isotope as particle source you have to use the command gamos generator addIsotopeSource SOURCE NAME 5 NAME ACTIVITY SOURCE_NAME is the name of this source that you have to use if you want later to change its time energy position or direction distribution ISOTOPE_NAME is one of the isotopes read from the input file ACTIVITY is the activity you want to set for that isotope You may choose several isotopes by repeatedly writing this command This command triggers the reading of the file named isotopes dat if it has not been read yet You may change the name of this file with the command gamos setParam Generator Isotope FileName MY FILENAME To learn how to change t
182. your detector in three different ways by defining your setup in a text file by using one of the geometry examples provided or in the standard Geant4 way by writing your C class inheriting from G4VUserDetectorConstruction 3 1 Building your geometry with a text file You can define your geometry in a simple text file as described in the fol lowing subsection You can also use as example the one at MY_GAMOS_DIR data g4geom txt Once your file is ready you have to tell GAMOS to use your geometry definition first telling the name of your file with the command gamos setParam GmGeometryFromText FileName MY FILENAME and then telling GAMOS to use the constructor of geometry from text file gamos geometry GmGeometryFrom Text 3 1 1 Description of geometry text file format The description of the geometry is based on tags A tag is a word that appears at the first one in a line and sets what the line means There are no constraints on the order of the tags in the file except some logical restrictions e g a volume cannot be positioned or given at tributes if it has not been defined e g no PLACE VIS COLOUR CHECK OVERLAPS tags before VOLU tag We will explain in this section the tags used to describe the geometry also explaining the meaning of each of the words that follow the tag and an example of each tag Tags can be given with any combination of upper case lThe default path to look for this file is define

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