(r23) IFAEAtlasAnalysis < Main

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----+Introduction

This page is created by IFAE Barcelona. It is supposed to collect or share useful information about ATLAS analysis.
In order to edit TWiki pages you have to [[https://uimon.cern.ch/twiki/bin/view/TWiki/TWikiRegistration][register with your AFS password]]

----+ Useful links
<!--Add the main topic here. i.e. create some new headings as follows:!-->
   *  *IFAE Cvs Repository* IFAECvsRepo
   *  *CSC data*
      *  [[http://gridui02.usatlas.bnl.gov:25880/server/pandamon/query?mode=jobquery][panda monitor]]
      *  [[http://jarguin.home.cern.ch/jarguin/dc3requests_sm.html][DC3 requests]]
   *  *Analysis tools*
      * Introduction into the [[http://indico.cern.ch/materialDisplay.py?contribId=4&amp;sessionId=2&amp;materialId=slides&amp;confId=a057209][Atlas analysis model]]
      * Introduction into SusyView 
         * Up-to-date information about Susy View: SusyViewInfo
         * Introduction injto the new Susy View configuration style: NewSusyView
      * Introduction into TopView
      * Introduction into EventView
         * Tutorial about configurables: EventViewBuilderTutorialConf
         * Our own collected information: IFAEAtlasAnalysisEV
   *  *MC production*
      * Introduction: see _Running Athena_ in the Atlas  WorkBook
   *  *General information*
      * [[https://hypernews.cern.ch/HyperNews/Atlas/top.pl][Hypernews forum]]
----+ Z+jets 
---++  Links
   *  Alpgen production of Z+jets:  ZplusJetsAlpgen
 
---++  *Object ID*
---++ Electron Reconstruction
   *  *Short description and Documentation*
      * As long as the CSC note is not finished, the best EMID documentation can be found in the EgammaATLASRecoPerformance page. Here you can find the [[http://documents.cern.ch/cgi-bin/setlink?base=atlnot&categ=Communication&id=com-phys-2004-074][link to the most recent performance note]].
      * Electron candidates are separated in reconstruction from Photon candidates by applying a loose track match. The default electron ID uses isolation in a hollow 0.45 cone and the  _IsEM_ flag which is composed of bits that correspond to various requirements on the shower shape in the calorimeter and the  track in the ID. The _IsEM_  flag is described in  ElectronGammaIsEM page. Alternative approaches using multivariate techniques (NN, Likelihood, HMatrix, ..) are in advanced stage of development.
      * A complete list of the AOD content can be accessed from the [[http://atlas-computing.web.cern.ch/atlas-computing/links/buildDirectory/AtlasOffline/latest/InstallArea/doc/ElectronPhotonIDEvent/html/classElectron.html][Class references in the AOD pages]]
      * There is no documentation of the meaning of these variables, but it can be inferred from the EgammaCBNT page using the similarities in the naming conventions
      * A good source of information are also various recent talks in the EMID group
         * [[http://indico.cern.ch/materialDisplay.py?contribId=2&amp;sessionId=9&amp;materialId=slides&amp;confId=a06105][Egamma Status]] by S. Rajagopalan  on the Stockholm ATLAS Overview Week
         * [[http://indico.cern.ch/materialDisplay.py?contribId=14&amp;materialId=slides&amp;confId=a058235][Comparative Electron ID studies]] by Jamie Boyd
         * A [[http://indico.cern.ch/materialDisplay.py?contribId=1&amp;materialId=slides&amp;confId=7402][status report ]] of Christophe Clement in the CAT meeting which contains documentations and distributions of the ID variables for electrons and fakes and the corresponding [[http://indico.cern.ch/materialDisplay.py?contribId=103&amp;sessionId=4&amp;materialId=slides&amp;confId=6824][presentation]] in the T and P week. 
         * A presentation of Gia Khoriauli about [[http://indico.cern.ch/materialDisplay.py?contribId=10&amp;materialId=slides&amp;confId=a058238][EM ID in 12.0.4]] 
         * [[http://indico.cern.ch/materialDisplay.py?contribId=8&amp;materialId=slides&amp;confId=a058238][EM calibration in 12.0.4]] by Claire Adam Bourdarios
   * *Overview: Electron ID*
      * Sliding Window Clusters in 5x5, 3x5 and 3x7 
      * Clusters corrected for position and energy modulations
      * Separation of Electron and Photon candidates by SimpleTrack Match: Matching criteria : DEta < 0.025 , DPhi < 0.05;  E/p < 4
      * Hadronic activitity < 20%
      *  IsEM calculated (no cut applied in AOD), using
         * Hadronic Leakage
         * Lateral shower shape in second sampling of EM Calorimeter
         * Lateral shower shape in strips
         * Track Quality Cuts (# of hits and impact parameter)
         * Track Calorimeter spatial matching
         * E/p
         * Fraction of high threshold TRT hits

---++ Muon Reconstruction
   * *Documentation*
      * [[http://indico.cern.ch/materialDisplay.py?contribId=4&amp;sessionId=9&amp;materialId=slides&amp;confId=a06105][Combined Muon Status]] by Peter Kluit at the Stockholm ATLAS Overview Week
---++ Jet Reconstruction
   * *Documentation*
      * [[http://indico.cern.ch/materialDisplay.py?contribId=3&amp;sessionId=9&amp;materialId=slides&amp;confId=a06105][Jet-Tau-ETmiss Status Report]] bt Donatella Cavalli at the Stockholm ATLAS Overview Week
---++  MC samples
   * *Pythia Z-> leplep inclusive*
      * Z->ee:       5144 =/castor/cern.ch/grid/atlas/datafiles/csc11/recon/csc11.005144.PythiaZee.recon.AOD.v11004201=
      * Z->mumu: 5145 =/castor/cern.ch/grid/atlas/datafiles/csc11/recon/csc11.005145.PythiaZmumu.recon.AOD.v11004205=
      * Z->tautau: 5146 =/castor/cern.ch/grid/atlas/datafiles/csc11/recon/csc11.005146.PythiaZtautau.recon.AOD.v11004205=
   * *Higgs group Z+jets _Loose_ samples:*  
      * generation conditions:
         * Parton CUT   Pt>20GeV eta < 6
         * Factorization Q^2=Mz^2+sum_Pt^2_of jet (but due to ALPGEN bug Factorization Q^2=Mz^2+ (Pt^2_of Z))
         * renormalization each PT
         * PT_lep>5GeV  eta < 3
         * Mll=40-200GeV
      * Event Filter:
         * ele or mu: N>=2(ee,mumu)>=1(tautau) with Pt>10GeV, |eta|<2.7
         * truth jet(Cone4TruthJets): N>=1 with Pt>20GeV, |eta|<5.0
      * Information:   ZplusJetsAlpgen
      * ID 8130 .... 8135 (0 jets .... >=5 jets) 
      * atlfast samples: =/castor/cern.ch/grid/atlas/users/jtanaka/HiggsWG/Z_samples/fast/CBNT/=
   * *Alpgen Susy background: Z->nunu*
      * Information:  ZplusJetsAlpgen
      * ID: 8124 ... 8129
      * atlfast samples (directory contains also other SUSY background ): =/castor/cern.ch/grid/atlas/datafiles/susy/atlfast/2006_b= 
---++  Zmumu+jets 
   * workplans:
      * [[%ATTACHURL%/workplan16Gener.pdf][workplan16Gener.pdf]]

----+ TTbar-> tau
---++  *MC samples*
   * Top MC samples are defined [[https://uimon.cern.ch/twiki/bin/view/Atlas/TopMC][here]].
          Any sample reconstructed with release 11 can found at [[http://gridui02.usatlas.bnl.gov:25880/server/pandamon/query?mode=jobquery][panda monitor]].
          Production with release 12 is on going, not much was produced until now (for Top analysis), however some few AODs were reconstructed by Elzbieta, and can be found at:
      * W->e nu: 5104 = /castor/cern.ch/grid/atlas/users/ashibata/cscpre12-5104
      * Z->tautau: 5188 = /castor/cern.ch/grid/atlas/users/ashibata/cscpre12-5200
      * ttbar: 5200 = /castor/cern.ch/grid/atlas/users/ashibata/cscpre12-5200
      * single top: 5501 = /castor/cern.ch/grid/atlas/users/ashibata/cscpre12-5200
   * And replicated at pic at:
      * /nfs/atlas-data03/cosuna/official_data/cscpre12/csc11.005200.T1_McAtNlo_Jimmy.digit.RDO.v11004205
   * As the statistics for rel12 is not enough, we reconstructed more events (running on rel11 digit files) and placed them under:
      * /nfs/atlas-data03/cosuna/official_data/cscpre12/csc11.005200.T1_McAtNlo_Jimmy.digit.RDO.v11004205_IFAE
   * Ntuples produced with the leptonic W's daughter-number fix are placed under:
      * /nfs/atlas-data03/fiorini/cspre12/ntuples    =TopViewAANtuple.new.root= has been obtained merging the 2 other files.
---++   *TopView ntuples*
   * [[DocuTopViewNtuple][Ongoing detailed documentation on ntuple variables.]]
   * For a full description of ntuple variables: [[http://www.pa.msu.edu/hep/atlas/index.php?p=msu_single_top/topview_variables_Truth0][Truth]], [[http://www.pa.msu.edu/hep/atlas/index.php?p=msu_single_top/topview_variables_EV0][Reco]].
     Another description (should be the "official") [[https://twiki.cern.ch/twiki/bin/view/Atlas/TopNtuple][here]].
   * release 11. Large TopView athena aware ntuples were produced with [[https://uimon.cern.ch/twiki/bin/view/Atlas/TopNtupleAvailability][release 11]].
   * release 12. Few files were produced for release 12 (and TopView-00-12-xx ) for validation. With this release two types of AAN are being generated, depending on the type of tau identification algorithm used (tauRec or tau1p3p):
      * /castor/cern.ch/grid/atlas/users/ashibata/cscpre12-TopView.

---++ *B-tagging*
     B tagging is done by default combining the results of 2 different algorithms: IP3D and SV1. 
   * IP3D calculates with tracks informations the 3-D impact parameter  (=d=) of a b vertex candidate and its significance: =s = d/sigma(d)=. 
   * SV1 reconstructs secondary vertices in the !BJet. SV1 algorithm uses a bottom-up approach: it fits vertices with all pairs of tracks, retaining the fit with the highest probability and fitting the remaining tracks of the jet to this vertex. All tracks below a certain fit probability will be rejected. A likelihood variable is calculated with the secondary vertex parameters (mass, fit probability, multiplicity and distance from the reconstructed primary vertex).
   * The two informations are summed in a bjet weight variable, that is variable used to discriminate bjets from other jets. The standard cut on the weight is at value of 3 (b-tagged jets having a weight greater than 3). The cut can be changed in TopView inside =python/TopViewInserters_module.py= .
     The default tagging algorithm has an efficiency of 60% and a Rejection factor for light jets of 240 in ttjjenu and ttH events. 
   * More details are available at [[BTagging][BTagging Homepage]] and the main !BTagging algorithm is in CVS under: =PhysicsAnalysis/JetTagging/JetTagAlgs/BTagging= 
   * ...
----+ EV groupArea at PIC.
   The PAT group is continuosly developing and applying patched to official atlas releases, even when the release is out. Therefore they make use the so called groupArea, where they install updates packages that will overload the default packages to be found in the release. In order to use the latest EV, SUSYView, TopView,... we need to install a given EVTag at PIC (exactly in the same way as they do in groupArea at CERN). There are several ways one can do that (consult [[https://uimon.cern.ch/twiki/bin/view/Atlas/InstructionsForEventViewin1105][here]]), but the easiest and faster is to use pacman. %BR%

I installed the latest EV version at: 
<verbatim>
/nfs/pic.es/user/c/cosuna/scratch/public/EVgroupArea/EventView-12.0.4.3
</verbatim>
In order to use this area, prepend this path to your CMTPATH before running athena:
<verbatim>
export CMTPATH=/nfs/pic.es/user/c/cosuna/scratch/public/EVgroupArea/EventView-12.0.4.3:$CMTPATH
</verbatim>
Future updates can be installed in the same EVgroupArea directory using pacman

   *   *Using Pacman at PIC*
Let say you want to install EventView-$Release at PIC. First configure pacman:
<verbatim>
      * cd /nfs/pic.es/user/c/cosuna/scratch/public/pacman/pacman-$VERSION
      * source setup.sh
</verbatim>
Then go to the EV groupArea directory and create a new directory for the desired version
<verbatim>
      * cd /nfs/pic.es/user/c/cosuna/scratch/public/EVgroupArea/
      * mkdir EventView-$RELEASE
      * cd EventView-$RELEASE
</verbatim>
and execute the pacman command:
<verbatim>
      * pacman -v all -get http://atlas-computing.web.cern.ch/atlas-computing/links/kitsDirectory/PAT/EventView/:EventView-$RELEASE.pacman
</verbatim>

----+ Bibliography
Under this section are stored some interesting documents, talks and lectures that you can find helpful to  consult during your analysis:
   * K. Ellis [[http://theory.fnal.gov/people/ellis/Talks/Fermi06/][Introduction to QCD at Colliders]]
<!-- MAJOR UPDATES
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-----
*Major updates*:%BR%
<!--Future editors should add their signatures beneath yours!-->
-- Main.UllaBlumenschein - 09 Jan 2007
-- Main.cosuna - 09 Jan 2007

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