diff --git a/FullSimLight/README.md b/FullSimLight/README.md
index 77b135f083b3b7a97a13500d1b6612a99ffa66ce..e892452981921f3da5d67e7514221b281fe3dcc7 100644
--- a/FullSimLight/README.md
+++ b/FullSimLight/README.md
@@ -11,586 +11,4 @@ FullSimLight project consists of different tools based on [Geant4](https://geant
The supported geometry formats are SQLite (.db), GDML (.gdml) and dual-use plugins (.dylib/.so) as the ones described in the [GeoModelPlugins repo](https://gitlab.cern.ch/atlas/GeoModelPlugins). The ATLAS detector geometry description can be imported via a SQLite or a GDML file. If the ATLAS magnetic field map is available to the user, it can be used in fullSimLight.
-# Installation
-
-## Dependencies:
-
-FullSimLight repository has been recently merged in a big monorepository under the main [GeoModel repository](https://gitlab.cern.ch/GeoModelDev/GeoModel).
-FullSimLight project depends on [GeoModelCore](https://gitlab.cern.ch/GeoModelDev/GeoModel/GeoModelCore), [GeoModelIO](https://gitlab.cern.ch/GeoModelDev/GeoModel/GeoModelIO),
-[Geant4](https://geant4.web.cern.ch),
-[GeoModelG4](https://gitlab.cern.ch/GeoModelDev/GeoModel/GeoModelG4) and
-[nlohmann_json](https://github.com/nlohmann/json.git)
-
-GeoModelCore, GeoModelIO and GeoModelG4 will be built as part of the monorepository, and also nhlomann_json can be built within the monorepository. Before installing them you need to have Geant4 installed on you machine.
-Following are the installation instructions.
-
-
-## Geant4:
-
-Before installing Geant4, check at the Geant4 website the pre-requisites needed:
-http://geant4-userdoc.web.cern.ch/geant4-userdoc/UsersGuides/InstallationGuide/html/gettingstarted.html
-An installation of Geant4 including the GDML extension (which requires the XercesC version >=3 package installed in the system) is required, i.e. the Geant4 toolkit must be built with the -DGEANT4_USE_GDML=ON CMake option.
-
-### Xerces-c installation
-```bash
-- wget https://archive.apache.org/dist/xerces/c/3/sources/xerces-c-3.2.2.tar.gz
-- tar -xf xerces-c-3.2.2.tar.gz
-- cd xerces-c-3.2.2 ; mkdir build ; cd build
-- cmake -DCMAKE_INSTALL_PREFIX=../../install ../
-- make -j8 ; make install
-```
-
-
-Now that you have installed xerces-c, clone the repository at [Geant4 repo](https://gitlab.cern.ch/geant4/geant4.git), then:
-
-```bash
-git clone https://gitlab.cern.ch/geant4/geant4.git
-cd geant4
-git tag
-```
-Choose the release you want to use, i.e. Geant4-10.6.0, and checkout the corresponding tag:
-
-```bash
-git checkout tags/v10.6.0
-mkdir build ; cd build
-cmake -DCMAKE_INSTALL_PREFIX=../../install -DCMAKE_BUILD_TYPE=Release ../ -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_GDML=ON -DGEANT4_BUILD_MULTITHREADED=ON
-make -j8 ; make install
-```
-Before running ./fullSimLight and ./gmgeantino make sure to source the *geant4.sh* file to set correctly all the Geant4 environment variables.
-```bash
-source <path_to_geant4_install_dir>/bin/geant4.sh
-```
-Alternatively, you can modifiy the .bash_profile file in the following way:
-```bash
-#GEANT4
-export G4INSTALL=<full_path_to_Geant4_install_dir>
-export G4NEUTRONHPDATA=$G4INSTALL/data/G4NDL4.6
-export G4LEDATA=$G4INSTALL/data/G4EMLOW7.9.1
-export G4LEVELGAMMADATA=$G4INSTALL/data/PhotonEvaporation5.5
-export G4RADIOACTIVEDATA=$G4INSTALL/data/RadioactiveDecay5.4
-export G4PARTICLEXSDATA=$G4INSTALL/data/G4PARTICLEXS2.1
-export G4PIIDATA=$G4INSTALL/data/G4PII1.3
-export G4REALSURFACEDATA=$G4INSTALL/data/RealSurface2.1.1
-export G4SAIDXSDATA=$G4INSTALL/data/G4SAIDDATA2.0
-export G4ABLADATA=$G4INSTALL/data/G4ABLA3.1
-export G4INCLDATA=$G4INSTALL/data/G4INCL1.0
-export G4ENSDFSTATEDATA=$G4INSTALL/data/G4ENSDFSTATE2.2
-```
-
-## nlohmann_json:
-You can build nlohmann_json internally to the GeoModel build. Alternatively, clone the repository at [nlohmann_json repo](https://github.com/nlohmann/json.git), then:
-```bash
-git clone https://github.com/nlohmann/json.git
-cd json
-mkdir build ; cd build
-cmake -DCMAKE_INSTALL_PREFIX=../../install -DCMAKE_BUILD_TYPE=Release -DJSON_BuildTests=False ../
-make -j8 ; make install
-```
-
-## FullSimLight:
-
-Clone the new GeoModel monorepository at [GeoModel repo](https://gitlab.cern.ch/GeoModelDev/GeoModel), then:
-
-```bash
-git clone https://gitlab.cern.ch/GeoModelDev/GeoModel.git
-cd GeoModel
-mkdir build ; cd build
-cmake -DCMAKE_INSTALL_PREFIX=../../install -DCMAKE_BUILD_TYPE=Release ../ -DGEOMODEL_BUILD_FULLSIMLIGHT=1 ../
-make -j8 ; make install
-```
-
-If you want to build nlohman_json as part of GeoModel build, add the following cmake option:
-```bash
--DGEOMODEL_USE_BUILTIN_JSON=TRUE
-```
-
-**NOTE:** If you experience issues with CMake not finding Geant4 properly, try to pass the Geant4 lib installation dir to CMake, to let it correctly find the Geant4Config.cmake file:
-
-```bash
-cmake -DGeant4_DIR=<path_to_geant4_install_dir>/lib/Geant4-10.6.0/ -DCMAKE_INSTALL_PREFIX=../../install -DCMAKE_BUILD_TYPE=Release ../
-```
-
-Alternatively, you can source the Geant4 setup, before running cmake:
-
-```bash
-source <path_to_geant4_install_dir>/bin/geant4.sh
-cmake -DCMAKE_INSTALL_PREFIX=../../install -DCMAKE_BUILD_TYPE=Release ../
-```
-
-### How to use a custom version of Xerces-C
-
-The Geant4 GDML format depends on the Xerces-C library. Therefore, different Geant4 releases can use different versions of the Xerces-C library. If you want to build FullSimLight with a custom, locally installed Xerces-C library, you can pass the XercesC_INCLUDE_DIR and XercesC_LIBRARY variable to CMake while configuring the build of FullSimLight:
-
-```bash
-cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DXercesC_INCLUDE_DIR=<path-to-local-XercesC-installation>/include -DXercesC_LIBRARY=<path-to-local-XercesC-installation>/lib/libxerces-c.dylib ../../install
-```
-# Detector Construction
-
-
-## Geometry:
-
-The detector can be built starting from a SQLite .db file, from a GDML file or from a dual-use plugin like the ones in the [GeoModelPlugins repo](https://gitlab.cern.ch/atlas/GeoModelPlugins). Use the -g flag to specify the name of the input geometry file. Alternatively, a GDML file can be set through the macro file by using the:
-
-```bash
-/FSLdet/setGdmlFile <gdml-file-name.gdml>
-```
-
-## ATLAS Geometry Files:
-
-The .gdml and .SQLite files of ATLAS geometry tags ATLAS-R2-2016-01-00-01 are available at:
-```bash
-wget https://gitlab.cern.ch/GeoModelATLAS/geometry-data/raw/master/geometry/geometry-ATLAS-R2-2016-01-00-01.gdml
-wget https://gitlab.cern.ch/GeoModelATLAS/geometry-data/raw/master/geometry/geometry-ATLAS-R2-2016-01-00-01_wSPECIALSHAPE.db
-```
-The new ATLAS geometry SQLite files where the EMEC is built using 3 new different variants (Wheel, Cone, Slices) are available at:
-
-```bash
-wget https://gitlab.cern.ch/GeoModelATLAS/geometry-data/raw/master/geometry/geometry-ATLAS-R2-2016-01-00-01_with_EMEC_Wheel.db
-wget https://gitlab.cern.ch/GeoModelATLAS/geometry-data/raw/master/geometry/geometry-ATLAS-R2-2016-01-00-01_with_EMEC_Cone.db
-wget https://gitlab.cern.ch/GeoModelATLAS/geometry-data/raw/master/geometry/geometry-ATLAS-R2-2016-01-00-01_with_EMEC_Slices.db
-```
-
-# FullSimLight: Build, run and options
-
-The application can be built and used both with sequential and multithreaded
-Geant4 builds. In case of multithreaded Geant4 toolkit, the applications will
-run in proper multithreaded mode. You can find the executables under the build/bin directory and/or under the install/bin dir.
-
-NB: Before running fullSimLight make sure to source the *geant4.sh* file to set correctly all the Geant4 environment variables.
-```bash
-source <path_to_geant4_install_dir>/bin/geant4.sh
-```
-Alternatively, you can modifiy the .bash_profile file in the following way:
-```bash
-#GEANT4
-export G4INSTALL=<full_path_to_Geant4_install_dir>
-export G4NEUTRONHPDATA=$G4INSTALL/data/G4NDL4.6
-export G4LEDATA=$G4INSTALL/data/G4EMLOW7.9.1
-export G4LEVELGAMMADATA=$G4INSTALL/data/PhotonEvaporation5.5
-export G4RADIOACTIVEDATA=$G4INSTALL/data/RadioactiveDecay5.4
-export G4PARTICLEXSDATA=$G4INSTALL/data/G4PARTICLEXS2.1
-export G4PIIDATA=$G4INSTALL/data/G4PII1.3
-export G4REALSURFACEDATA=$G4INSTALL/data/RealSurface2.1.1
-export G4SAIDXSDATA=$G4INSTALL/data/G4SAIDDATA2.0
-export G4ABLADATA=$G4INSTALL/data/G4ABLA3.1
-export G4INCLDATA=$G4INSTALL/data/G4INCL1.0
-export G4ENSDFSTATEDATA=$G4INSTALL/data/G4ENSDFSTATE2.2
-```
-
-Run the executable with the --help option to see the available options:
-
-``` bash
--m : REQUIRED : the standard Geant4 macro file name
--g : REQUIRED : the Geometry file name
--o : flag ==> run the geometry overlap check (default: FALSE)
--f : physics list name (default: FTFP_BERT)
--P : generate events with Pythia [config. available: ttbar/higgs/minbias or use ascii input file]
--p : flag ==> run the application in performance mode i.e. no user actions
- : - ==> run the application in NON performance mode i.e. with user actions (default)
-```
-FullSimLight uses by default the Geant4 particle gun as primary generator, but it supports also
-input events from the Pythia generator (see the Primary generator section for more details)
-A minimal set of "observable" is collected during the simulation: the mean energy
-deposit, mean charged and neutral track lengths, mean number of steps made by charged
-and neutral particles, mean number of secondary e-, e+ and gamma particles.
-These are reported at the end of the simulation together with the run time and
-total number of events transported.
-
-The simulation can be executed in "performance" mode by providing the -p
-input flag. No any user actions are created in this case beyond the
-only one RunAction (only for the Master-thread in case of MT) that will
-start and stop a timer at the beginning and the end of the simulation
-(initialization time won't be included). Therefore, there is no any scoring
-in this case.
-
-## Examples
-
-During the installation a default macro file <macro.g4> will be installed in your `share/FullSimLight` directory.
-To execute the application using the <macro.g4> macro file, with the FTFP_BERT_ATL
-Physics List, in performance mode and building the detector from the geometry-ATLAS-R2-2016-01-00-01_wSPECIALSHAPE.db file :
-
-``` bash
-./fullSimLight -m ../share/FullSimLight/macro.g4 -f FTFP_BERT_ATL -p -g geometry-ATLAS-R2-2016-01-00-01_wSPECIALSHAPE.db
-```
-To execute the application using the <macro.g4> macro file, with the FTFP_BERT_ATL
-Physics List, not in performance mode and building the detector from my geometry gdml file:
-``` bash
-./fullSimLight -m ../share/FullSimLight/macro.g4 -f FTFP_BERT_ATL -g mygeometry.gdml
-```
-To execute the application using the <macro.g4> macro file and building the detector with a geometry described in one of the [GeoModelPlugins repo](https://gitlab.cern.ch/atlas/GeoModelPlugins), i.e. *HGTDPlugin* :
-``` bash
-./fullSimLight -m ../share/FullSimLight/macro.g4 -g libHGTDPlugin.1.0.0.dylib
-```
-
-## Parameters settings via geant4 macro
-
-Fullsimlight and in general Geant4 based simulations, need a Geant4 macro to read some input parameters when executed in batch mode. The default macro used by `fullSimLight` is called 'macro.g4' and it should be found under the `<install-path>/share/FullSimLight` directory. The macro can be edited to change some parameters, i.e the verbosity, the number of threads, or to tune the simulation. The most relevant macro commands are explained in what follows.
-
-## Magnetic field
-
- A constant magnetic field can be set through the macro command:
-
-``` bash
- /FSLdet/setField <field-value> <unit>
-```
-The default value is a uniform magnetic field of 4 Tesla.
-
-## ATLAS Magnetic Field
-
-The ATLAS magnetic field is integrated in FullSimLight and can be used from it. The Magnetic field map file used and supported are:
-- full_bfieldmap_7730_20400_14m_version5.root
-- solenoid_bfieldmap_7730_0_14m_version5.root
-- toroid_bfieldmap_0_20400_14m_version5.root
-- bmagatlas_09_fullAsym20400.data
-
-If the magnetic field maps are not available, a constant magnetic field can be set through the macro file. The test application "testMagneticField" can be used to test the different magnetic field maps and produce Maps in 2D histograms that are saved in a ROOT file (i.e 'ATLAS_BField_default.root') .
-However there is no dependency on ROOT, because the histograms are created, filled and saved using the G4AnalysisManager.
-
-### testMagneticField examples:
-Run the application with the --help flag to see the options:
-``` bash
-./testMagneticField --help
-
--f : OPTIONAL: magnetic field filename [.data/.root] (default : use ATLAS magnetic field maps)
--r : FLAG: use root field map (default : false, use .data file)
--s : FLAG: set Solenoid Off
--t : FLAG: set Toroids Off
-```
-By default the file tested is the bmagatlas_09_fullAsym20400.data. Use the -r option to test the ROOT file maps, add the -s flag to set the solenoid off and use the toroid_bfieldmap_0_20400_14m_version5.root:
-
-``` bash
-./testMagneticField -r -s
-```
-
-Use the -t to set the Toroids off, and test the solenoid_bfieldmap_7730_0_14m_version5.root file.
-
-``` bash
-./testMagneticField -r -t
-```
-
-
-## Primary Generator
-
-The primary generator used by default is the Geant4 particle gun, but FullSimLight also supports the [Pythia generator](http://home.thep.lu.se/Pythia/)
-
- ## Particle gun
- The particle gun used by default will generate primary particles
- at the (0,0,0) position with the following options:
-
-### Number of primaries per event:
-The number of primary particles per event can be set through the macro
-command:
-
-``` bash
-/FSLgun/primaryPerEvt <number>
-```
-
-By default, i.e. if it is not specified by the above command, the number of primary particles will be randomly selected for each individual event from the [1, 10] interval uniformly.
-
-### Primary particle energy:
-The primary particle energy can be set through the macro command:
-
-``` bash
- /FSLgun/energy <energy-value> <unit>
-```
-By default, i.e. if it is not specified by the above command, the kinetic energy will be randomly selected for each individual primary particle from the [1 GeV, 100 GeV] uniformly.
-
-### Primary particle direction:
-The primary particle momentum direction can be set through the macro command:
-
-``` bash
- /FSLgun/direction <xdir-value> <ydir-value> <zdir-value>
-```
-By default, i.e. if it is not specified by the above command, the momentum direction will be randomly selected for each individual primary particle from isotropic distribution.
-
-### Primary particle type:
-The primary particle type can be set through the macro command:
-
-``` bash
- /FSLgun/particle <particle-name>
-```
-By default, i.e. if it is not specified by the above command, the type will be randomly selected from a pre-defined list for each individual primary particle uniformly. The current list of particles includes e-, e+ and gamma particles. It can be extended by adding more particles to the list in the FSLPrimaryGeneratorAction class.
-
- ## Pythia generator
-
- FullSimLight supports Pythia as primary particles generator. In order to use Pythia, the user should have it installed in their system and if Pythia is found FullSImLight will be compiled with the support on. There are three different default options available when using the -P or --pythia flag (i.e. ttbar, higgs and minbias):
- ``` bash
- -P : generate events with Pythia [config. available: ttbar/higgs/minbias or use ascii input file]
- ```
- Alternatively the user can plug their own Pythia configuration file to simulate the desired events.
- For example, in order to simulate the default *ttbar* events, the command to be run is the following:
-
- ``` bash
-./fullSimLight -m ../share/FullSimLight/pythia.g4 -P ttbar -g geometry-ATLAS-R2-2016-01-00-01_wSPECIALSHAPE.db
- ```
- The number of events that the user wants to simulate must be specified in the g4 macro file. A specific *pythia.g4* macro file can be found in the *share* directory, that should be used when simulating Pythia events and can be edited according to the user needs.
-
-## Physics List
-
- The Physics List can be specified as an input argument with the `-f` flag
- (e.g. `-f FTFP_BERT`). Notice that the name of the Geant4 built in Physics List
- must be in upper case, exactly as the corresponding header file. By default,
- i.e. if the Physics List name is not provided as an input argument, the `FTFP_BERT`
- Physics List will be used. FullSimLight has also the possibility to use a
- special custom Physics List `FTFP_BERT_ATL_WDCK`: a Geant4 Physics
- List that corresponds to the `FTFP_BERT_ATL` reference physics list with the differences:
- - the standard EM physics constructor is replaced by the local `StandardEmWithWoodcock` that can utilise *Woodcock*-tracking of gamma photons in a specified detector region
- - the EM extra physics constructor is replaced with a local version that is identical to the one delivered by Geant4 with the only difference that its `G4GammaGeneralProcess` parts are replaced with the local `GammaGeneralProcess`
- - the neutron tracking cut module is replaced by one that sets a 150 [ns] tracking cut
- This latter is applied now in all cases of dedicated ATLAS physics lists (i.e. those with the `ATL` sub-string in their name) in order to use a similar setting that is in Athena.
-
-# GeoModelClash: run and options
-
-GeoModelClash (gmclash) allows to run geometry overlap checks on a geometry file specified as input with the -g flag. It supports SQLite and GDML formats. The geometry can also be described with a dual-plugin (.dylib or .so) as the ones available at the [GeoModelPlugins repo](https://gitlab.cern.ch/atlas/GeoModelPlugins). The clashes report is given in an output json file (default: gmclash_report.json).
-
-Run the executable with the --help option to see the available options:
-
-``` bash
--g : MANDATORY: the Geometry file name [.db/.gdml/.dylib/.so]
--r : OPTIONAL : root volume name (default: the Geometry top volume)
--o : OPTIONAL : clashes report file name (default: gmclash_report.json)
--t : OPTIONAL : tolerance threshold value in mm (default: 0)
--n : OPTIONAL : number of random points (default: 1000)
--v : OPTIONAL : verbose output (default: off)
-```
-
-The output json file format is the following:
-
-``` bash
-"distance[mm]": 51.21328179620343,
-"typeOfClash": 1,
-"volume1CopyNo": 16969,
-"volume1EntityType": "G4Tubs",
-"volume1Name": "LAr::Barrel::Cryostat::Cylinder::#13Phys",
-"volume2CopyNo": 16969,
-"volume2EntityType": "G4UnionSolid",
-"volume2Name": "LAr::DM::SectorEnvelopes2r",
-"x": -1.736718203796568,
-"y": -1263.348806272393,
-"z": -166.75403155804725
-```
-where:
-* *distance* is the minimum estimated distance of the overlap
-* *typeOfClash* can be 0 for *withMother*, 1 for *withSister*, 2 for *fullyEncapsSister*, 3 for *invalidSolid*
-* *x,y,z* are the global coordinates of the point of impact in cm
-
-## Examples
-
-To run GeoModelClash one has to specify with the -g flag the geometry file (this is mandatory). By default gmclash writes out the clashes report in the *gmclash_report.json* file
-``` bash
-./gmclash -g geometry-ATLAS-R2-2016-01-00-01_wSPECIALSHAPE.db
-```
-To execute a clash detection on a geometry described with the SQLite file *LArBarrel.db* and write out the clashes report in the *cr_LArBarrel.json* file :
-``` bash
-./gmclash -g LArBarrel.db -o cr_LArBarrel.json
-```
-To execute a clash detection on a geometry described with one of the [GeoModelPlugins repo](https://gitlab.cern.ch/atlas/GeoModelPlugins), i.e. *HGTDPlugin* and write out the clashes report in the *cr_HGTD.json* file :
-``` bash
-./gmclash -g libHGTDPlugin.1.0.0.dylib -o cr_HGTD.json
-```
-
-# GeoModelGeantino: run and options
-
-GeoModelGeantino (gmgeantino) is a Geant4 based application that allows you to produce geantino maps for the geometry specified as input. It supports .db/.gdml/.dylib/.so geometry formats and it writes out the geantino maps in a ROOT file. However, it does not depend on ROOT, cause it uses the G4AnalysisManager to create/fill/write 1D and 2D Profiles.
-The 1D and 2D profiles are filled during the simulation, per Event or per Step. The creation of different profiles can be tuned with command line flags. In general X-Y, Z-R, eta-Phi RadiationLength/InteractionLength profiles can be created per DetectorVolume/Material/Element.
-
-gmgeantino uses a default geant4 macro, called *geantino.g4*, to take some input parameters. You should find this macro under your <install-path>/share/FullSimLight directory. You can edit this macro to change some parameters, like the verbosity, the n. of threads, the n. of primaries per event, the primary particle energy.. etc.
-
-By default the primary particles shot by 'gmgeantino' are geantinos (this parameter should not be changed). By default the number of simulated geantinos is set to 1000. To increase the resolution of the maps, the n. of simulated events can be increased, editing the macro and changing the value at the following line:
-
-```bash
-/run/beamOn <n. of events>
-```
-
-NB: Before running gmgeantino make sure to source the *geant4.sh* file to set correctly all the Geant4 environment variables.
-```bash
-source <path_to_geant4_install_dir>/bin/geant4.sh
-```
-Alternatively, you can modifiy the .bash_profile file in the following way:
-```bash
-#GEANT4
-export G4INSTALL=<full_path_to_Geant4_install_dir>
-export G4NEUTRONHPDATA=$G4INSTALL/data/G4NDL4.6
-export G4LEDATA=$G4INSTALL/data/G4EMLOW7.9.1
-export G4LEVELGAMMADATA=$G4INSTALL/data/PhotonEvaporation5.5
-export G4RADIOACTIVEDATA=$G4INSTALL/data/RadioactiveDecay5.4
-export G4PARTICLEXSDATA=$G4INSTALL/data/G4PARTICLEXS2.1
-export G4PIIDATA=$G4INSTALL/data/G4PII1.3
-export G4REALSURFACEDATA=$G4INSTALL/data/RealSurface2.1.1
-export G4SAIDXSDATA=$G4INSTALL/data/G4SAIDDATA2.0
-export G4ABLADATA=$G4INSTALL/data/G4ABLA3.1
-export G4INCLDATA=$G4INSTALL/data/G4INCL1.0
-export G4ENSDFSTATEDATA=$G4INSTALL/data/G4ENSDFSTATE2.2
-```
-
-Run the executable with the --help option to see the available options:
-
-``` bash
-./gmgeantino --help
-
--g : [REQUIRED] the Geometry file name (supported extensions: .db/.gdml/.dylib/.so)
--m : [OPTIONAL] the standard Geant4 macro file name (default: 'geantino.g4')
--r : [OPTIONAL] r limit for geantino maps in mm (default: '12500')
--z : [OPTIONAL] z limit for geantino maps in mm (default: '23000')
--x : [OPTIONAL] x limit for geantino maps in mm (default: '12500')
--y : [OPTIONAL] y limit for geantino maps in mm (default: '12500')
--o : [OPTIONAL] output ROOT file name (supported extention: .root - default: 'geantinoMaps.root')
--e : [FLAG] use this flag to create eta-phi radiation-interaction length 1D profile histograms (caveat: the process might run out of memory!)
--d : [FLAG] use this flag to create xy-rz radiation-interaction length 2D profile histograms for 'detectors' (caveat: the process might run out of memory!)
--a : [FLAG] use this flag to create xy-rz radiation-interaction length 2D profile histograms for 'materials' (caveat: the process might run out of memory!)
--l : [FLAG] use this flag to create xy-rz radiation-interaction length 2D profile histograms for 'elements' (caveat: the process might run out of memory!)
-```
-
-
-## Examples
-
-To run *gmgeantino* one has to specify with the -g flag the input geometry file (mandatory option). By default a 'geantinoMaps.root' file is created as output and it contains R-Z RadiationLenght and Interaction Lenght 2D profiles. To run gmgeantino on *LArBarrel.db* geometry, with the default *geantino.g4* macro file, and producing eta-phi maps and detector maps:
-
-``` bash
-./gmgeantino -m ../share/FullSimLight/geantino.g4 -g LArBarrel.db -e -d
-```
-
-To produce geantino maps of a geometry described by one of the [GeoModelPlugins repo](https://gitlab.cern.ch/atlas/GeoModelPlugins), i.e. *HGTDPlugin*, using a custom macro file *mymacro.g4*, activate detectors/materials and elements maps, and write out the geantino maps in the *geantinoMaps_HGTD.root* file :
-``` bash
-./gmgeantino -m mymacro.g4 -g libHGTDPlugin.1.0.0.dylib -d -a -l -o geantinoMaps_HGTD.root
-```
-
-# GeoModelMassCalculator: run and options
-
-# GeoModelMassCalculator
-
-GeoModelMassCalculator (gmmasscalc) is a command line tool that calculates the inclusive and exclusive mass of a geometry specified as input with the -g flag. The mass report is given in an output json file (default: *gmmasscalc_report.json*).
-
-Run the executable with the --help option to see the available options:
-
-``` bash
--g : [MANDATORY] the Geometry file name [.db/.gdml/.dylib/.so]
--p : [OPTIONAL] prefix of the Logical Volumes of interest (i.e. Pixel::)
--m : [OPTIONAL] material of interest (i.e. Aluminium)
--o : [OPTIONAL] mass report json file name (default: gmmasscalc_report.json)
--v : [OPTIONAL] verbose mode: 1 - print all the Logical Volume names and materials, 2 - print materials composition (default: off)
-```
-By default (if the optional flag are not used) *gmmasscalc*, takes the main *World Volume*, and calculates the inclusive and exclusive masses of the respective daughters, saving the calculated quantities in the output json file. At the end of the report, the total masses are reported for the whole *World Volume*. The output json file format is the following:
-
-``` bash
-"exclusiveMass[kg]": 1.3358800280858636,
-"inclusiveMass[kg]": 133.81273262584054,
-"logicalVolumeName": "SCT_ForwardC",
-"material": "Air",
-"physicalVolumeName": "SCT",
-"volumeCopyNo": 16969,
-"volumeEntityType": "G4Tubs"
-```
-where:
-- *exclusiveMass* is the mass of the considered volume only (from which the volumes occupied by the daughters volumes have been subtracted)
-- *inclusiveMass* is the mass of the considered volume, comprehensive of the masses of the respective daughters (propagated in an iterative way to their daughter volumes).
-
-At the end of the report, additional information about the whole geometry is reported. The last item of the json file will look like the following:
-
-``` bash
-"apparentWeightInAir[kg]": 2405.2018407511378,
-"densityThreshold[g/cm3]": 0.02,
-"excludedFilteredMass[kg]": 14.649883998898723,
-"exclusiveMass[kg]": 1.3704943478464804,
-"inclusiveFilteredMass[kg]": 2406.500411630485,
-"inclusiveMass[kg]": 2421.156760687377,
-"logicalVolumeName": "newWorldLog",
-"material": "Air",
-"volumeEntityType": "World Volume"
-```
-where:
-- *apparent weight in Air* by definition, the weight of a body as affected by the buoyancy of a fluid (such as air) in which it is immersed. It is calculated only on the total geometry, assuming that the World Volume is made of Air
-- *exclusiveFilteredMass* is the sum of the exclusive masses of all the volumes with density>densityThreshold (0.02 g/cm3)
--*excludedFilteredMass* is the sum of the exclusive masses of all the volumes with density<densityThreshold (0.02 g/cm3)
-
-In addition to the default behaviour, *gmmasscalc* offers the possibility to apply 2 filters to the geometry, described in what follows.
-
-The -p (--prefix) option allows to indicate the prefix of the volumes of interest. In this case *gmmasscalc* will loop over the geometry tree and calculate the mass of every Logical Volume that has the specified prefix in its name. For every Logical volume found, a different entry will be filled in the output report file.
-
-The -m (--material) option allows to specify to which material the user is interested. In this case *gmmasscalc* will loop over the geometry tree and calculate the mass of those volumes that are made of the material of interest.
-
-If both the -p and -m flags are used, *gmmasscalc* will combine the 2 filters and retrieve in the output file only the masses of the volumes containing the specified prefix and made of the desired material.
-
-At the end of the report, the total exclusive mass for the requested geometry is reported for all the volumes that satisfy the user request. The last item in the report will look like the following:
-
-```bash
-{
-"exclusiveMass[kg]": 14.676774220119631,
-"inclusiveMass[kg]": -999.0,
-"logicalVolumeName": "",
-"material": "CO2",
-"physicalVolumeName": "",
-"volumeCopyNo": 0,
-"volumeEntityType": "Total for filtered Geometry"
-}
-
-```
-where:
-- *logicalVolumeName* and *material* are respectively the prefix used as filter for the Logical Volume names in the geometry tree navigation, and the material used as a second filter in the search.
-
-The -v flag is a verbosity flag. Two different levels of verbosity can be set: level 1 prints all the logical volume names and respective materials, level 2 adds also the material composition for each material in the geometry.
-
-## Examples
-
-To run GeoModelMassCalculator one has to specify with the -g flag the geometry file (this is mandatory). By default *gmmasscalc* writes out the masses report in the *gmmasscalc_report.json* file:
-``` bash
-./gmmasscalc -g geometry-ATLAS-R2-2016-01-00-01_wSPECIALSHAPE.db
-```
-To calculate the mass of a geometry described with the SQLite file *LArBarrel.db* and write out the masses report in the *mass_LArBarrel.json* file :
-``` bash
-./gmmasscalc -g LArBarrel.db -o mass_LArBarrel.json
-```
-To calculate the mass of a geometry described with the SQLite file *SCT.db*, only for the logical volumes that have *BRLSensor* in their names, and only for those volumes that are made of *Silicon* and write out the masses report in the *mass_SCT.json* file:
-
-``` bash
-./gmmasscalc -g SCT.db -p BRLSensor -m Silicon -o mass_SCT.json
-```
-To calculate the mass of a geometry described with one of the [GeoModelPlugins repo](https://gitlab.cern.ch/atlas/GeoModelPlugins), i.e. *HGTDPlugin*, looking for volumes made of *Aluminium* and write out the masses report in the *mass_HGTD.json* file :
-``` bash
-./gmmasscalc -g libHGTDPlugin.1.0.0.dylib -m Aluminium -o mass_HGTD.json
-```
-
-# GeoModel2GDML: run and options
-
-GeoModel2GDML (gm2gdml) is a command line tool based on Geant4, to convert geometries and dump them in gdml.
-The geometry is first built in GeoModel, converted in Geant4 and dumped in gdml format.
-The supported input geometries are : sqlite (.db), plugin (.so/dylib) and gdml.
-Before the dump operation the geometry is revised and the unidentified volumes are pulled out from the geometry.
-Run the executable with the --help option to see the available options:
-
-``` bash
-./gm2gdml --help
-
- **** Parameters:
--g : [MANDATORY] input geometry file name [.db/.gdml/.dylib/.so]
--o : [OPTIONAL] output GDML geometry file name (default: geometry.gdml)
-
-```
-
-
-## Examples
-
-To run GeoModel2GDML one has to specify with the -g flag the geometry file (this is mandatory). By default a 'geometry.gdml' output file is created, but the name of the file can be changed using the -o option.
-To run gm2gdml on *LArBarrel.db* geometry, and dump the output gdml file in the *LArBarrel.gdml* file:
-``` bash
-./gm2gdml -g LArBarrel.db -o LArBarrel.gdml
-```
-
-To dump your geometry described with a plugin, i.e. *HGTDPlugin*, and write out the geometry file in the *HGTDPlugin.gdml* file :
-``` bash
-./gm2gdml -g libHGTDPlugin.1.0.0.dylib -o HGTDPlugin.gdml
-```
-
-
-# Final Remark
-
- To get the most performant Geant4 build, one needs to build the Geant4 toolkit
- with the following CMake options (in addition to -DGEANT4_USE_GDML=ON):
-
-``` bash
- -DGEANT4_BUILD_MULTITHREADED=ON
- -DGEANT4_BUILD_VERBOSE_CODE=OFF
- -DGEANT4_BUILD_STORE_TRAJECTORY=OFF
-```
- Then set the number of threads in the macro.g4 macro to the maximum available
-and execute the fullSimLight application with the -p flag.
+For updated documentation on how to install and run fullsimlight please refer to the main GeoModel documentation [webpage](https://geomodel.web.cern.ch/home/fullsimlight/fullsimlight/)
diff --git a/documentation/docs/about/contacts.md b/documentation/docs/about/contacts.md
index c987b40b4ce5288c99a7600cc2c17655a76a510f..7fcefa7ed0542e2c19c3f23770ea792cfdbef010 100644
--- a/documentation/docs/about/contacts.md
+++ b/documentation/docs/about/contacts.md
@@ -1,5 +1,7 @@
# GeoModel Contacts
In case of questions, you can contact the GeoModel Core Team at:
+[geomodel-core-team@cern.ch](mailto:geomodel-core-team@cern.ch)
+We also have an active community of developers that can be contacted at:
[geomodel-developers@cern.ch](mailto:geomodel-developers@cern.ch)
diff --git a/documentation/docs/dev/build_fullsimlight.md b/documentation/docs/dev/build_fullsimlight.md
index 18d1e7e464f5c9d0c553827da8f123e97e5bae72..7d64c71599abc2887ba18e05d2ec78e80f579733 100644
--- a/documentation/docs/dev/build_fullsimlight.md
+++ b/documentation/docs/dev/build_fullsimlight.md
@@ -1,13 +1,21 @@
-# How to build FullSimLight and FSL
+# FullSimLight and FSL installation from source
+
+FullSimLight and its graphical user interface FSL, are experiment agnostic detector simulation tools that have been implemented and are mantained by the [ATLAS](https://atlas.cern) collaboration. In what follows you will find instructions on how to build and install FullSimLight and FSL from the source code. If you are interested in testing FullSimLight and FSL with the ATLAS experiment configuration please refer to the ATLAS Extensions section below.
# Prerequisites
-FullSimLight depends on Geant4, Xerces-C and HDF5. Additionally, the user might want to install [Pythia8] (http://home.thep.lu.se/Pythia/) and [HepMC3](https://gitlab.cern.ch/hepmc/HepMC3) as optional dependencies.
-## Geant4
-There is no specific requirement for the version of Geant4 to use with FullSimLight. Our team try to keep FullSimLight compatible with the most recent Geant4 versions. If you have any issues with a specific Geant4 version please open a ticket at the following [link](https://gitlab.cern.ch/GeoModelDev/GeoModel/-/issues).
+Before proceeding with this section please make sure that you visited the GeoModel installation instructions page to check the prerequisites list and install all the dependencies of GeoModel.
+
+FullSimLight and its tools depend on Geant4, Xerces-C and HDF5. Additionally, the user might want to install [Pythia8](http://home.thep.lu.se/Pythia/) and [HepMC3](https://gitlab.cern.ch/hepmc/HepMC3) as optional dependencies.
+
+## Geant4 installation
+There is no specific requirement for the version of Geant4 to use with FullSimLight. Our team tries to keep FullSimLight compatible with the most recent Geant4 versions. If you have any issues with a specific Geant4 version please open a ticket at the following [link](https://gitlab.cern.ch/GeoModelDev/GeoModel/-/issues).
-Before installing Geant4, check at the Geant4 website the pre-requisites needed [here](http://geant4-userdoc.web.cern.ch/geant4-userdoc/UsersGuides/InstallationGuide/html/gettingstarted.html)
-An installation of Geant4 including the GDML extension (which requires the XercesC version >=3 package installed in the system) is required, i.e. the Geant4 toolkit must be built with the -DGEANT4_USE_GDML=ON CMake option.
+Before installing Geant4, check at the [Geant4 website](http://geant4-userdoc.web.cern.ch/geant4-userdoc/UsersGuides/InstallationGuide/html/gettingstarted.html) the pre-requisites needed and install them.
+
+!!! note
+
+ Please note that an installation of Geant4 including the GDML extension (which requires the XercesC version >=3 package installed in the system) is required, i.e. the Geant4 toolkit must be built with the `-DGEANT4_USE_GDML=ON` CMake option.
###Xerces-C installation
Please choose the Xerces-C installation that is required by the Geant4 version that you are installing. As an example here we show how to install xerces-c 3.2.2.
@@ -20,38 +28,65 @@ cmake -DCMAKE_INSTALL_PREFIX=../../install ../
make -j8 ; make install
```
-Now that you have installed xerces-c, clone the [Geant4 repository](https://gitlab.cern.ch/geant4/geant4.git), then:
+Now that you have installed xerces-c, you are ready to install Geant4. Clone the [Geant4 repository](https://gitlab.cern.ch/geant4/geant4.git), then:
```bash
git clone https://gitlab.cern.ch/geant4/geant4.git
cd geant4
git tag
```
-Choose the release you want to use, i.e. Geant4-11.2.1, and checkout the corresponding tag:
+
+Choose the release you want to use amongst the listed ones (i.e. Geant4-11.2.1), and checkout the corresponding tag:
+
```bash
git checkout tags/v11.2.1
+```
+We recommend to build Geant4 with the multithreading support on, so that you can take advantage of it and run your simulation in multithreaded mode.
+
+!!! note
+
+ To get the most performant Geant4 build, one needs to build the Geant4 toolkit
+ with the following CMake options (in addition to -DGEANT4_USE_GDML=ON):
+
+ ``` bash
+ -DGEANT4_BUILD_MULTITHREADED=ON
+ -DGEANT4_BUILD_VERBOSE_CODE=OFF
+ -DGEANT4_BUILD_STORE_TRAJECTORY=OFF
+ ```
+
+```bash
mkdir build ; cd build
cmake -DCMAKE_INSTALL_PREFIX=../../install -DCMAKE_BUILD_TYPE=Release ../ -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_GDML=ON -DGEANT4_BUILD_MULTITHREADED=ON
make -j8 ; make install
```
-We suggest to build Geant4 with the multithreading support on, so that you can take advantage it and run your simulation in multithreaded mode.
-Before running ./fullSimLight and all the tools that depend on Geant4 make sure to source the geant4.sh file to set correctly all the Geant4 environment variables.
+
+Before running FullSimLight and all the tools that depend on Geant4 please make sure to source the geant4.sh file to set correctly all the Geant4 environment variables.
+
##Pythia installation
+
If you wish to run FullSimLight with Pythia events you will need to install Pythia in your system. Follow the instructions at the [official website](http://home.thep.lu.se/Pythia/) for that.
In order to build FullSimLight and FSL with Pythia you should then use the following flag: `-DGEOMODEL_USE_PYTHIA=ON` (see the following section for more details).
##HepMC3 installation
+
If you wish to run FullSimLight with HepMC3 events you will need to install HepMC3 in your system. Follow the instructions at the [official repository](https://gitlab.cern.ch/hepmc/HepMC3) for that.
In order to build FullSimLight and FSL with HepMC3 you should then use the following flag: `-DGEOMODEL_USE_HEPCM3=ON`(see the following section for more details).
-# Standard build
+# How to build FullSimLight and FSL
+
+FullSimLight and FSL can be built as part of the GeoModel build, by enabling the related configuration flags `GEOMODEL_BUILD_FULLSIMLIGHT` and `GEOMODEL_BUILD_FSL`.
-FullSimLight can be built as part of the GeoModel build, by enabling the related configuration flag `GEOMODEL_BUILD_FULLSIMLIGHT`.
+## Standard installation
+
+If you want to install FullSimLight in the standard installation path you can follow the instructions below:
```bash
+git clone https://gitlab.cern.ch/GeoModelDev/GeoModel.git
+cd GeoModel
+mkdir build ; cd build
cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 ../GeoModel
make -j
make install
@@ -61,39 +96,54 @@ That will compile the base GeoModel packages (*i.e.*, `GeoModelCore`, `GeoModelI
This will install all the base libraries and the `fullSimLight` executable in the standard installation path (*e.g.*, `/usr/local` on macOS). If you want to have a local installation, see below.
+!!! note
+
+ If you are interested in running FullSimLight with the full ATLAS detector geometry and the real ATLAS magnetic field map, please refer to the ATLAS Extensions section below.
-# Local installation
+
+## Local installation
You can install FullSimLight in a local folder as well. This let you remove everything by simply deleting the local folder, and lets you have multiple versions of the packages installed.
-You can install FullSimLight locally by using the `CMAKE_INSTALL_PREFIX` option. In the example below, we instruct CMake to install everything inside a local folder named `install` besides the `build` folder where we are launching CMake from:
+You can install FullSimLight locally by using the `CMAKE_INSTALL_PREFIX` option. In the example below, we instruct CMake to install everything inside a local folder named `install` besides the `GeoModel` folder:
```bash
-cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DCMAKE_INSTALL_PREFIX=../install ../GeoModel
+git clone https://gitlab.cern.ch/GeoModelDev/GeoModel.git
+cd GeoModel
+mkdir build ; cd build
+cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DCMAKE_INSTALL_PREFIX=../../install ../GeoModel
make -j
make install
```
-At the end, you will find all the libraries and executables installed in:
+At the end, you will find all the libraries and executables installed under:
```bash
-ls ../install
+ls ../../install
```
-# Build FSL
+## Build FSL
FSL is the graphical user interface to FullSimLight. It allows you to configure your simulation and run it by using a json configuration file. Similarly to what said above, if you want to build FSL, you will have to enable the related configuration flag `GEOMODEL_BUILD_FSL`. If you enable the build of FSL automatically also FullSimLight will be built.
```bash
-cmake -DGEOMODEL_BUILD_FSL=1 ../GeoModel
+git clone https://gitlab.cern.ch/GeoModelDev/GeoModel.git
+cd GeoModel
+mkdir build ; cd build
+cmake -DGEOMODEL_BUILD_FSL=1 -DCMAKE_INSTALL_PREFIX=../../install ../GeoModel
make -j
make install
```
## How to build FullSimLight and FSL with Pythia
-In order to build FullSimLight and FSL with Pythia you will need to activate the appropriate flag:
+
+In order to build FullSimLight and FSL with Pythia you will need to activate the appropriate flag `GEOMODEL_USE_PYTHIA`:
+
```bash
-cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DGEOMODEL_USE_PYTHIA=ON -DCMAKE_INSTALL_PREFIX=../install ../GeoModel
+git clone https://gitlab.cern.ch/GeoModelDev/GeoModel.git
+cd GeoModel
+mkdir build ; cd build
+cmake -DGEOMODEL_BUILD_FSL=1 -DGEOMODEL_USE_PYTHIA=ON -DCMAKE_INSTALL_PREFIX=../../install ../GeoModel
make -j
make install
```
@@ -101,15 +151,22 @@ make install
If you installed Pythia in a local folder, CMake might not be able to find it. In this case you should specify manually the path to the include directory and to the library.
```bash
-cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DGEOMODEL_USE_PYTHIA=ON - DPythia_INCLUDE_DIR=<path_to_your_Pythia_install_dir>/include -DPythia_LIBRARY=<path_to_your_Pythia_install_dir>/lib/<library name, i.e. libPythia.so/dylib> -DCMAKE_INSTALL_PREFIX=../install ../GeoModel
+git clone https://gitlab.cern.ch/GeoModelDev/GeoModel.git
+cd GeoModel
+mkdir build ; cd build
+cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DGEOMODEL_USE_PYTHIA=ON - DPythia_INCLUDE_DIR=<path_to_your_Pythia_install_dir>/include -DPythia_LIBRARY=<path_to_your_Pythia_install_dir>/lib/<library name, i.e. libPythia.so/dylib> -DCMAKE_INSTALL_PREFIX=../../install ../GeoModel
make -j
make install
```
## How to build FullSimLight and FSL with HepMC3
+
In order to build FullSimLight and FSL with HepMC3 you will need to activate the appropriate flag:
```bash
-cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DGEOMODEL_USE_HEPMC3 =ON -DCMAKE_INSTALL_PREFIX=../install ../GeoModel
+git clone https://gitlab.cern.ch/GeoModelDev/GeoModel.git
+cd GeoModel
+mkdir build ; cd build
+cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DGEOMODEL_USE_HEPMC3=ON -DCMAKE_INSTALL_PREFIX=../../install ../GeoModel
make -j
make install
```
@@ -117,6 +174,9 @@ make install
If you installed HepMC3 in a local folder, CMake might not be able to find it. In this case you should specify manually the path to the include directory and to the library.
```bash
+git clone https://gitlab.cern.ch/GeoModelDev/GeoModel.git
+cd GeoModel
+mkdir build ; cd build
cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DGEOMODEL_USE_HEPMC3=ON -DHEPMC3_LIB=<path_to_your_HepMC3_install_dir>/lib/<library name, i.e. libHepMC3.so/dylib> -DCMAKE_INSTALL_PREFIX=../install ../GeoModel
make -j
make install
@@ -129,6 +189,9 @@ The Geant4 GDML format depends on the Xerces-C library. Therefore, different Gea
If you want to build FullSimLight with a custom, locally installed Xerces-C library, you can pass the `XercesC_INCLUDE_DIR` and `XercesC_LIBRARY` variable to CMake while configuring the build of FullSimLight:
```bash
+git clone https://gitlab.cern.ch/GeoModelDev/GeoModel.git
+cd GeoModel
+mkdir build ; cd build
cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DXercesC_INCLUDE_DIR=<path-to-local-XercesC-installation>/include -DXercesC_LIBRARY=<path-to-local-XercesC-installation>/lib/libxerces-c.dylib ../GeoModel/
```
@@ -151,14 +214,48 @@ cmake -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DXercesC_INCLUDE_DIR=<path-to-local-Xerc
Normally, those warnings do not harm the build. But please judge by yourself if the difference isn the Xerces-C library can affect the project you are working on.
-
-
## Combining different configuration/build options
You can also combine different configuration options. For example, here below we build FullsimLight by using the built-in `nlohmann-json` library together with the custom Xerces-C library, and we install the outcome in a local `../install` folder:
```bash
+git clone https://gitlab.cern.ch/GeoModelDev/GeoModel.git
+cd GeoModel
+mkdir build ; cd build
cmake -DCMAKE_INSTALL_PREFIX=../install -DGEOMODEL_USE_BUILTIN_JSON=1 -DGEOMODEL_BUILD_FULLSIMLIGHT=1 -DXercesC_INCLUDE_DIR=<path-to-local-XercesC-installation>/include -DXercesC_LIBRARY=<path-to-local-XercesC-installation>/lib/libxerces-c.dylib ../GeoModel/
```
+# How to build the ATLAS Extensions submodule
+
+FullSimLight is an experiment agnostic detector simulation tool that has been implemented and is mantained by the [ATLAS](https://atlas.cern) collaboration. Its initial goal was to make it possible to simulate the full ATLAS detector with the real magnetic field map in full standalone mode. All the ATLAS specific customizations are available at the [ATLAS Extensions](https://gitlab.cern.ch/atlas/geomodelatlas/ATLASExtensions) repository that is linked to the GeoModel repository as a git submodule. In order to have the corresponding code cloned inside the GeoModel repository the user would need to clone recursively the main repository.
+
+If you didn't clone the GeoModel repository, you can clone it recursively:
+
+```c++
+git clone --recursive https://gitlab.cern.ch/GeoModelDev/GeoModel.git
+```
+
+Alternatively, if you already cloned the GeoModel repository, it will be sufficient to type the following commands from the main `GeoModel` repository folder:
+
+```c++
+cd GeoModel
+git submodule init
+git submodule update
+```
+
+A flag **GEOMODEL_BUILD_ATLASEXTENSIONS** is available to build the ATLAS extentions (by default OFF) and it should be turned ON in order to build all the extensions. If you want to build the ATLAS Extensions and FullSimLight you should then:
+
+```c++
+cd GeoModel
+mkdir build ; cd build
+cmake ../ -DGEOMODEL_BUILD_ATLASEXTENSIONS=ON -DGEOMODEL_BUILD_FULLSIMLIGHT=ON
+make -j
+make install
+```
+
+A configuration file **atlas-conf.json** with all the ATLAS specific customizations is provided with the ATLASExtensions and will be installed under **<install>/share/FullSimLight/ATLAS**. In order to run a Geant4 simulation with the ATLAS configuration please visit the [ATLAS Extensions page](https://geomodel.web.cern.ch/home/fullsimlight/atlas-extensions/).
+
+
+
+
diff --git a/documentation/docs/fullsimlight/atlas-extensions/index.md b/documentation/docs/fullsimlight/atlas-extensions/index.md
index b5a703378841a787e3a8acf1ed496398b308dcac..5beb7f8c1b6736344ba859789d612e8fd9e4f56a 100644
--- a/documentation/docs/fullsimlight/atlas-extensions/index.md
+++ b/documentation/docs/fullsimlight/atlas-extensions/index.md
@@ -1,6 +1,6 @@
# ATLAS Extensions
-FullSimLight is an experiment agnostic detector simulation tool that has been implemented and is mantained by the ATLAS collaboration. All the ATLAS specific customizations are available at the [ATLAS Extensions](https://gitlab.cern.ch/atlas/geomodelatlas/ATLASExtensions) repository that is linked to the GeoModel repository as a git submodule. In order to have the corresponding code cloned inside the GeoModel repository the user would need to clone recursively the main repository. So either:
+FullSimLight is an experiment agnostic detector simulation tool that has been implemented and is mantained by the [ATLAS](https://atlas.cern) collaboration. All the ATLAS specific customizations are available at the [ATLAS Extensions](https://gitlab.cern.ch/atlas/geomodelatlas/ATLASExtensions) repository that is linked to the GeoModel repository as a git submodule. In order to have the corresponding code cloned inside the GeoModel repository the user would need to clone recursively the main repository.
If you still didn't clone the repository you can clone it recursively:
@@ -18,17 +18,22 @@ git submodule update
A flag is available to build the ATLAS extentions (by default OFF) and it should be turned ON in order to build all the extensions:
```c++
-cmake ../ -DGEOMODEL_BUILD_ATLASEXTENSIONS=ON
+cmake ../ -DGEOMODEL_BUILD_ATLASEXTENSIONS=ON -DGEOMODEL_BUILD_FULLSIMLIGHT=ON
```
-A configuration file **atlas-conf.json** with all the ATLAS specific customizations is provided with the ATLASExtensions and will be installed under **<install>/share/FullSimLight/ATLAS**. In order to run a Geant4 ATLAS with your favourite geometry tag you only have to run the following:
+A configuration file **atlas-conf.json** with all the ATLAS specific customizations is provided with the ATLASExtensions and will be installed under **<install>/share/FullSimLight/ATLAS**.
+
+To run FullSimLight with the ATLAS experiment settings you need a geometry file describing the full ATLAS detector and the ATLAS magnetic field map. These files can be downloaded as explained in the following sections. However please note that they are available only under CERN SSO. If you experience problems with downloading those files please contact the [geomodel-core-team](mailto:geomodel-core-team@cern.ch)
+
+## ATLAS Geometry File
+<!---->
+Some ATLAS geometry SQLite and .gdml files are available at the following [link](https://geomodel.web.cern.ch/atlas-geometry-data/), only working under CERN SSO.
+They describe the whole geometry tree of different tags used during the different LHC runs. You can select your favourite one and use it with fullSimLight! For example:
+
```c++
-./fullSimLight -g geometry.db -c atlas-conf.json
+wget https://geomodel.web.cern.ch/atlas-geometry-data/geometry-ATLAS-R3S-2021-03-02-00.db
```
-## ATLAS Geometry File
-Some ATLAS geometry SQLite files are available at the following [link](https://geomodel.web.cern.ch/atlas-geometry-data/), only worrking under CERN SSO.
-They describe the whole geometry tree of different tags used during the different LHC runs. You can select your favourite one and use it with fullsimlight!
## ATLAS Magnetic Field Map and plugin
<!---->
@@ -40,3 +45,11 @@ wget https://geomodel.web.cern.ch/atlas-magnetic-field/bmagatlas_09_fullAsym2040
<!---->
This folder contains the LArCustomSolid Extension that describes the ATLAS LAr EMEC custom shape. The LAr EMEC custom shape extension is build starting from a copy of the corresponding code in the Athena repository.
To keep the code of the LArCustomSolid Extention synchronized with the latest available version in the Athena repository, just run the autonomous-lar.sh script.
+
+## Run ATLAS Simulation!
+
+Now you're ready to simulate the ATLAS detector in Geant4 with its real magnetic field map. You only have to run the following:
+
+```c++
+./fullSimLight -g geometry-ATLAS-R3S-2021-03-02-00.db -c atlas-conf.json
+```
diff --git a/documentation/docs/fullsimlight/fullsimlight/index.md b/documentation/docs/fullsimlight/fullsimlight/index.md
index 013fa86fb12ba9b8fc8219e286f29e119a0ad5a3..10b3a15edeaf06d493307adbd52249bc2ba9d56d 100644
--- a/documentation/docs/fullsimlight/fullsimlight/index.md
+++ b/documentation/docs/fullsimlight/fullsimlight/index.md
@@ -19,15 +19,7 @@ Use the -g flag to specify the name of the input geometry file.
### ATLAS Geometry Files:
-At installation time an ATLAS geometry file and the ATLAS Magnetic field map file will be automatically downloaded and installed under *< path-to-install >/share/FullSimLight/ATLAS* if the user will activate the `GEOMODEL_INSTALL_FSLDATA` flag at compile time.
-
-Additional .gdml and .SQLite files of ATLAS geometry tag ATLAS-R2-2016-01-00-01 are available at:
-s
-```bash
-wget https://gitlab.cern.ch/GeoModelATLAS/geometry-data/raw/master/geometry/geometry-ATLAS-R2-2016-01-00-01.gdml
-wget https://geomodel.web.cern.ch/atlas-geometry-data/geometry-ATLAS-R2-2016-01-00-01.db
-```
-For instructions on how to produce your own SQLite dump of your preferred ATLAS geometry tag, please refet to the [ATLAS Extensions](https://geomodel.web.cern.ch/home/fullsimlight/atlas-extensions/) page.
+If you are interested in running with the ATLAS geometry files, please refer to the [ATLAS Extensions](https://geomodel.web.cern.ch/home/fullsimlight/atlas-extensions/) page.
## FullSimLight: run and options
@@ -40,24 +32,6 @@ NB: Before running fullSimLight make sure to source the *geant4.sh* file to set
source <path_to_geant4_install_dir>/bin/geant4.sh
```
-Alternatively, you can modifiy the .bash_profile file in the following way:
-
-```bash
-#GEANT4
-export G4INSTALL=<full_path_to_Geant4_install_dir>
-export G4NEUTRONHPDATA=$G4INSTALL/data/G4NDL4.6
-export G4LEDATA=$G4INSTALL/data/G4EMLOW7.9.1
-export G4LEVELGAMMADATA=$G4INSTALL/data/PhotonEvaporation5.5
-export G4RADIOACTIVEDATA=$G4INSTALL/data/RadioactiveDecay5.4
-export G4PARTICLEXSDATA=$G4INSTALL/data/G4PARTICLEXS2.1
-export G4PIIDATA=$G4INSTALL/data/G4PII1.3
-export G4REALSURFACEDATA=$G4INSTALL/data/RealSurface2.1.1
-export G4SAIDXSDATA=$G4INSTALL/data/G4SAIDDATA2.0
-export G4ABLADATA=$G4INSTALL/data/G4ABLA3.1
-export G4INCLDATA=$G4INSTALL/data/G4INCL1.0
-export G4ENSDFSTATEDATA=$G4INSTALL/data/G4ENSDFSTATE2.2
-```
-
To run FullSimLight you can specify a json configuration file (generated with fsl) with the -c flag or use the following command line parameters. Run the executable with the --help option to see the available options:
``` bash
@@ -72,12 +46,13 @@ To run FullSimLight you can specify a json configuration file (generated with fs
```
FullSimLight uses by default the Geant4 particle gun as primary generator, but it supports also
-input events from the Pythia generator (see the Primary generator section for more details), HepMC3 formats or custom generators plugins.
-A minimal set of "observable" is collected during the simulation per-primary
+input events from the Pythia generator (see the Primary generator section below for more details), HepMC3 formats or custom generators plugins.
+
+A minimal set of "observables" is collected during the simulation per-primary
particle type: mean energy deposit, mean charged and neutral step lengths,
mean number of steps made by charged and neutral particles, mean number of
secondary e-, e+ and gamma particles. The result is reported at the end of
-each event for each primary particle that were transported in the given event.
+each event for each primary particle that was transported in the given event.
At the end of the simulation a final report is printed showing the run time,
the primary generator and magnetic field settings used during the run, the
total number of events and primary particles transported and the per-primary
@@ -92,19 +67,16 @@ in this case.
## Examples
-FullSimLight can be very easily configured and run via fsl, both from within the GUI or from the command-line, passing the configuration file with the -c flag. Alternatively FullSimLight can be executed via command line using the basic available flags. The only mandatory parameter necessary for starting a simulation is the geometry file (can be specified inside the config file or with the -g flag). Following are some examples that illustrates the different possibilities.
+`FullSimLight` can be very easily configured and run via `fsl`, both from within the GUI or from the command-line, passing the configuration file with the -c flag. Alternatively, `FullSimLight` can be executed via command line using the basic available flags. The only mandatory parameter necessary for starting a simulation is the geometry file (can be specified inside the config file or with the -g flag). Following are some examples that illustrates the different possibilities.
If you have created your custom configuration file <myconfig.json> with fsl, you can simply run fullSimLight as follows:
``` bash
./fullSimLight -c myconfig.json
```
+This is the best and more complete way of configuring FullSimLight because it allows you to customize also the use of plugins and to use all the different primary particles generation methods.
-To run fullSimLight with the ATLAS configuration file you only need to run fullSimLight using the custom **atlas-config.json** file and passing the desired geometry file via command line, as follows:
-
-``` bash
-./fullSimLight -c atlas-config.json -g geometry-ATLAS-R2-2016-01-00-01.db
-```
+As an alternative to using the json configuration file, one can use the available command line options and a classical geant4 macro to configure fullsimlight.
During the installation a default macro file *<macro.g4>* will be installed in your *< install-path >/share/FullSimLight* directory. So the macro file doesn't need to be specified if you intend to use the default one.
@@ -115,10 +87,10 @@ Physics List, not in performance mode and building the detector from < mygeometr
./fullSimLight -g mygeometry.db
```
-To execute the application using the default < macro.g4 > macro file and building the detector with a geometry described in one of the [GeoModelPlugins repo](https://gitlab.cern.ch/atlas/GeoModelPlugins), i.e. *HGTDPlugin* :
+To execute the application using the default < macro.g4 > macro file and building the detector with a geometry described in one of the [GeoModelPlugins repo](https://gitlab.cern.ch/atlas/geomodelatlas/GeoModelATLAS/-/tree/master/GeoModelPlugins?ref_type=heads), i.e. *PixelPlugin* :
``` bash
-./fullSimLight -g libHGTDPlugin.1.0.0.dylib
+./fullSimLight -g libPixePlugin.1.0.0.dylib/.so
```
To execute the application using a custom <mymacro.g4> macro file, with the ATLAS FTFP_BERT_ATL Physics List, in performance mode and building the detector from the geometry-ATLAS-R2-2016-01-00-01.db file :
@@ -127,7 +99,7 @@ To execute the application using a custom <mymacro.g4> macro file, with the ATLA
./fullSimLight -m mymacro.g4 -f FTFP_BERT_ATL -p -g geometry-ATLAS-R2-2016-01-00-01.db
```
-Please note that the last option is deprecated, as it doesn't allow full flexibility, and we suggest to configure your simulation via fsl.
+Please note that the last option is deprecated, as it doesn't allow full flexibility, and we suggest to configure your simulation via `fsl`.
## Parameters configuration via fsl (suggested)
@@ -185,7 +157,7 @@ Use the -t to set the Toroids off, and test the *solenoid_bfieldmap_7730_0_14m_v
## Primary Generators
-The primary generator used by default is the Geant4 particle gun, but FullSimLight also supports the [Pythia generator](http://home.thep.lu.se/Pythia/)
+The primary generator used by default is the Geant4 particle gun, but FullSimLight also supports the [Pythia generator](http://home.thep.lu.se/Pythia/) and HepMC3 format.
## Particle gun
@@ -243,6 +215,10 @@ By default, i.e. if it is not specified by the above command, the type will be r
```
The number of events that the user wants to simulate must be specified in the Geant4 macro file. A specific *pythia.g4* macro file can be found in the *< path-to-install >/share/FullSimLight* directory, that should be used when simulating Pythia events and can be edited according to the user needs.
+
+## HepMC3 events input
+
+FullSimLight supports reading events in HepMC3 format both the standard Asciiv3 format (introduced in HepMC3) as well as the old Ascii format (used in HepMC and HepMC2). This option is only available when configuring fullSimLight with FSL and the json configuration file. Please refer to the [FSL section](https://geomodel.web.cern.ch/home/fullsimlight/fsl/) for more info.
## Physics List
diff --git a/documentation/docs/start/install.md b/documentation/docs/start/install.md
index b30c47468c612a5554019b2952967d0bd67cf4e2..d732d634bed00fa7b2492032561cfde2399adeda 100644
--- a/documentation/docs/start/install.md
+++ b/documentation/docs/start/install.md
@@ -1,13 +1,13 @@
# Install the GeoModel Applications and Development kits
-In this section, you will find instructions on how to **install** the latest **stable** version of GeoModel applications and development kits on different platforms.
+In this section, you will find instructions on how to **install** the latest **stable** version of GeoModel applications and development kits on different platforms. If you are a developer and would like to install the GeoModel toolkit from source, please refer to the [Developers installation instructions](../dev/index.md).
The GeoModel applications include:
* **gmex**, the geometry explorer, an interactive 3d geometry visualizer
* **gmstatistics**, tool to monitor the memory consumption
* **fullsimlight**, a command-line tool to run Geant4 simulation, and its graphical user interface, *fsl*.
-* **gmclash**, a Geant4 based command-line tool too perform clash detection
+* **gmclash**, a Geant4 based command-line tool to perform clash detection
* **gmgeantino**, a Geant4 based command-line tool to generate geantino maps
* **gmmasscalc**, a Geant4 based command-line tool to compute the mass of a given piece of detector geometry
* **gm2gdml** and **gdml2gm**, command line tools to convert GeoModel to and from GDML
@@ -16,8 +16,9 @@ The GeoModel applications include:
The development kits include header files and precompiled libraries for the development of detector description code. On some platforms (macOS) the development environment is installed together with the prebuild applications and libraries.
-## Ubuntu 20.0.4 (focal, LTS) or 21.0.10 (impish) or 22.0.4 (jammy, LTS)
+## How to install GeoModel on Ubuntu
+The following instructions have been tested for Ubuntu 20.0.4 (focal, LTS) or 21.0.10 (impish) or 22.0.4 (jammy, LTS).
Add the geomodel repository to your source list:
```
@@ -49,7 +50,7 @@ If you have outdated packages, these commands will replace those packages with t
We strongly suggest to use the alternative X11 window manager when running GEMX (or all other SoQt/Coin3D-based applications) on Ubuntu, for the time being.
-## macOS
+## How to install GeoModel on macOS
On macOS, we use the [Homebrew package manager](http://brew.sh) to handle and install the GeoModel packages. If you don't have Homebrew installed on your machine, you should first install it by following the instructions on the Homebrew website: <http://brew.sh>. Please be attentive to any instructions printed after the installation procedure; there might be environment variables to set.
@@ -172,7 +173,7 @@ On any other platform (such as Centos or Fedora), you can build GeoModel from so
## Visualize geometry data
-After installinmg the tools, you can test your installation on an example ATLAS geometry file.
+After installing the tools, you can test your installation on an example ATLAS geometry file. Please note that in order to run GeoModel on the full ATLAS geometry you will need to install the **geomodel-extensions-atlas** package.
First, download the geometry data file: