- Adding possibility to handle Jpsi (default is Upsilon) in efficiency

[u/mrichter/AliRoot.git] / MUON / README

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/* $Id$ */

==========================================================
Please add  to this README file all information concerning 
config files, simulation, digitalization, clusterization, 
reconstruction and macro analysis

==========================================================
 How to check that your aliroot is working well
==========================================================
There is a script file AlirootRun_MUONtest.sh which 
allows for simulating, reconstructing and making the
invariant analysis of the generated Upsilon (1S).
The used configuration file is Config.C in MUON 
directory.
You have to type :
source $ALICE_ROOT/MUON/AlirootRun_MUONtest.sh 
The results of this test are saved in test_out/ directory

==========================================================
 How to run a MUON generation
==========================================================
aliroot
root [0] gAlice->Run(10,"$ALICE_ROOT/MUON/Config.C");

1 single muon of 7 GeV/c in the MUON spectrometer 
acceptance will be simulated using geant3. 
Hit information will be store in the root file in the
execution directory.
If you want to change the option or to define a new directory
for hits, you have to do the following before:
root [0] gAlice->SetConfigFunction("Config( \"/home/martinez/aliroot/work_NewIO/test/\" , \"box\" );"); 

============================================================
 How to run MUONCheck macro
============================================================
To check the content of a root data file, the MUONCheck
provides a ascii output on screen.

To compile MUONCheck.C
.includepath $ALICE_ROOT/STEER
.includepath $ALICE_ROOT/MUON
.includepath $ALICE_ROOT/MUON/mapping
.L $ALICE_ROOT/MUON/MUONCheck.C++
To Load
gSystem->Load("$ALICE_ROOT/MUON/MUONCheck_C.so")

To print Kine : (default file is galice.root )
MUONkine() or MUONkine(##,"galice.root") for the event number ##

To print hits : (default file is galice.root if not MUONhits("toto.root""); )
MUONhits()  or MUONhits(##,"galice.root") for the event number ##

To print digits : (default file is galice.root)
MUONdigits()  or MUONdigits(##,"galice.root") for the event number ##

To print rawcluster : (default file is galice.root)
MUONrecpoints() or MUONrecpoints(##,"galice.root") for the event number ##

To print trigger : (default file is galice.root)
MUONrectrigger() or MUONrectrigger(##,"galice.root") for the event number ##

....

============================================================
 How to check the Geometry 
============================================================
gAlice->Init("$ALICE_ROOT/MUON/Config.C");
.L $ALICE/geant3/TGeant3/G3GUI.C
G3GUI()

============================================================
 How to check the Geometry with the new Geometrical modeler
 ftp://root.cern.ch/root/doc/chapter16.pdf
 http://agenda.cern.ch/fullAgenda.php?ida=a05212
============================================================
gAlice->Init("$ALICE_ROOT/MUON/Config.C");
gGeoManager->GetMasterVolume()->Draw();


============================================================
 How to check the overlap with the new Geometrical modeler
 ftp://root.cern.ch/root/doc/chapter16.pdf
 http://agenda.cern.ch/fullAgenda.php?ida=a05212
============================================================
gAlice->Init("$ALICE_ROOT/MUON/Config.C");
gGeoManager->CheckOverlaps();
gGeoManager->PrintOverlaps();

============================================================
 How to run MUONdisplay
============================================================
First you need to perform a full simulation: 
generation, digitalisation and clusterisation
To run MUONdisplay with Root 5.04/00 you need to get a fix in
the gpad/src/TPad.cxx from Root CVS:
 cvs update -r 1.200 gpad/src/TPad.cxx
and recompile root. 

.L $ALICE_ROOT/MUON/MUONdisplay.C
MUONdisplay(0,"galice.root")

============================================================
 Tracking parameters, cuts, energy loss and physics processes
============================================================
Tracking parameters in MUON are automatically defined by GEANT
MUON takes the default values of CUTs  and physics processes
defined by the Config files, except for the gas mixture medium 
of the tracking chambers. The CUT's and physics processes of
the gas mixture medium  is then defined in the galice.cuts file
in the data directory. In particular ILOSS parameter MUST be
equal unity (1) in order simulate a realistic energy loss
distribution (mean value and fluctuations) in the active gas.

============================================================
 Tracking of particle in the magnetic field
============================================================
GEANT has two ways for tracking charged particles in the 
magnetic field: HELIX et RKUTA.
HELIX is faster and works well if the gradient of magnetic 
field is small. 
For MUON, HELIX is a not a good approximation and we must 
use RKUTA to get the optimal mass resolution of the 
spectrometer. The choice of HELIX or RKUTA is done in the
config file when the magnetic field is defined:
  AliMagFMaps* field = new AliMagFMaps("Maps","Maps", TRACKING, FACTOR, MAXB, AliMagFMaps::k4kG);
  gAlice->SetField(field);
TRACKING must be 1 for RKUTA and 2 for HELIX (the default value for aliroot is 2 (HELIX))
FACTOR allows you to set the magnetic field to 0, just putting FACTOR=0. Default value is 1.
MAXB is the maximum magnetic field which is 10.T

===========================================================
 MUON cocktail for physics ..............
===========================================================
There is a MUON cocktail generator of the muon sources in the
EVGEN directory. This class derives from AliGenCocktail.
In the init of this class I have filled the cocktail with 
the muon sources: J/Psi, Upsilon, Open Charm, Open Beauty, 
Pion, Kaons. The code needs only the production cross section 
at 4pi (for the moment this values are in the code since I 
prefere them do not be modified), and the code calculates the  
rate of particles in the acceptance, making the scaling based 
on the number of collisions for the hard probes and on the  
number of participants for soft sources: Pions and Kaons.

In the Genereate of this class all entries in the cocktail 
are called and we define a "primordial trigger" with requires 
a minimum number of muons above a Pt cut in the required acceptance.
In order to normalized to the real number of simulated events, 
there are 2 data members in the class fNsuceeded adn fNGenerate 
which tell us what is the biais source.

Enclose an example to use this generator:   
AliGenMUONCocktail * gener = new AliGenMUONCocktail();
gener->SetPtRange(1.,100.);       // Transverse momentum range  
gener->SetPhiRange(0.,360.);    // Azimuthal angle range 
gener->SetYRange(-4.0,-2.4);
gener->SetMuonPtCut(1.);
gener->SetMuonThetaCut(171.,178.);
gener->SetMuonMultiplicity(2);
gener->SetImpactParameterRange(0.,5.); // 10% most centra PbPb collisions
gener->SetVertexSmear(kPerTrack);  
gener->SetOrigin(0,0,0);        // Vertex position
gener->SetSigma(0,0,0.0);       // Sigma in (X,Y,Z) (cm) on IP position
gener->Init();
 
================================================================
 csh Script for the full reconstruction with raw data generator
================================================================
The rawdata generation and analysis is working with the new segmentation.
So the config file must use the version "AliMUONFactoryV3"

Generation
The method AliSimulation::SetWriteRawData("MUON") enables on 
the muon rawdata generation
aliroot -b << EOF  
AliSimulation MuonSim("$ALICE_ROOT/MUON/Config.C")
MuonSim.SetWriteRawData("MUON")
MuonSim.Run(10)
.q
EOF

Reconstruction
aliroot -b << EOF 
AliReconstruction MuonRec("galice.root");
MuonRec.SetInput("$YOUR_WORKING_DIRECTORY/");  Do not forget the slash at the end!
MuonRec.SetRunVertexFinder(kFALSE);
MuonRec.SetRunLocalReconstruction("MUON");
MuonRec.SetRunTracking("");
MuonRec.SetFillESD("MUON");
MuonRec.SetOption("MUON", "VS"); // to use VS cluster finder
// MuonRec.SetOption("MUON", "VS Original"); // to run VS and original track finder
// MuonRec.SetOption("MUON", "Combi"); // to run combined cluster / track finder
MMuonRec.Run();
.q
EOF



============================================================
 How to run MUONRecoCheck macro
============================================================
To check the muon reconstruction by comparing the reconstructed tracks
with the reference tracks made of "AliTrackReference" for the hits and
kinematic informations (TParticle) for the vertex.
This macro can be used to check the track reconstruction e.g. efficiency,
momentum resolution ... but also to make physics analysis whenever
track identification is needed.   

To compile MUONRecoCheck.C
.includepath $ALICE_ROOT/STEER
.includepath $ALICE_ROOT/MUON
.L $ALICE_ROOT/MUON/MUONRecoCheck.C+

// To run MUONRecoCheck
MUONRecoCheck(nEvent,"galice.root"); // nEvent = nb of events


============================================================
 How to run MUONTracker macro
============================================================
To make the track reconstruction directly from AliTrackReference hits 
which are recorded in TrackRefs.root during the simulation.
It can be used to check the reconstruction without clusterization.	

To compile MUONTracker.C
.includepath $ALICE_ROOT/STEER
.includepath $ALICE_ROOT/MUON
.L $ALICE_ROOT/MUON/MUONTracker.C+

// To run MUONTracker
MUONTracker(iEventMin,iEventMax,"galice.root"); // iEventMin: first event

===========================================================
 Macro  MUONGenerateGeometryData.C
===========================================================
						
Macro for generating the geometry data files:
(transform.dat, svmap.dat).
- MUON/data/transform.dat file contains all the information 
about the transformation (traslation + rotation) needed for 
the positionning of each detection element of the MUON
spectrometer.
- MUON/data/svmap.dat file contains all the information to link 
each geant volume (it can be extended to other virtual MC) with
a detection element. The point here is that a given detection
element, i.e. a slat chamber consists of many geant volumes.
the correspondence is then defined in an input file.
Each time there is a change in the definition of MC geometry, these
input files must be re-generated via the macro  
MUONGenerateGeometryData.C

To be run from aliroot:
.x MUONGenerateGeometryData.C

The generated files do not replace the existing ones
but have different names (with extension ".out").
Replacement with new files has to be done manually.


==========================================================
 How to Merge events
==========================================================

You can merge 2 types of simulated events. For example, 
you can simulate Hijing events, and then simulate muons
merging both.

Merging is done at the sdigits level, so Kinematics files 
of the merged events will just correspond to the 
Config.C simulated file (not to Config_HIJING.C).

You must, first, do the Hijing simulation and store it 
in directory $HIJING_SIM. Note that for merging you 
won't need Kinematics files of the Hijing simulation...

Hijing simulation

aliroot -b << EOF
AliSimulation HijingSim("$HIJING_SIM/Config_HIJING.C")
HijingSim.Run(5)
.q
EOF


Then you can do muon simulation and reconstruction
merging both simulated events. In next example, we are
merging 20 times each Hijing event in order to simulate 
100 muons merged with 5 Hijing events.


aliroot -b << EOF
AliSimulation MuonSim("$ALICE_ROOT/MUON/Config.C")
MuonSim.MergeWith("$HIJING_SIM/galice.root",20) //parameters are the Hijing simulation file and the number of times we use each Hijing event
MuonSim.Run(100) // number of muon (Config.C) events
.q
EOF


aliroot -b << EOF
TPluginManager * pluginmanager = gROOT->GetPluginManager()
pluginmanager->AddHandler("AliReconstructor","MUON","AliMUONReconstructor","MUON","AliMUONReconstructor()")
AliReconstruction  MuonRec("galice.root")
MuonRec.SetRunTracking("")
MuonRec.SetRunVertexFinder(kFALSE)
MuonRec.SetRunLocalReconstruction("MUON")
MuonRec.SetFillESD("MUON")
MuonRec.Run()
.q
EOF

===========================================================
 Still working ..............
===========================================================