PhysAnalysis < Main

Main Web>TWikiUsers>FrancescoSpano>PhysAnalysis (2011-01-12, FrancescoSpano) (raw view)
---+!!<nop> PhysAnalysis
%TOC% 

---+Machine properties and Status 
_How are we going to know how the machine is running and with what conditions?_

The LHC real time information is produced in the  [[http://op-webtools.web.cern.ch/op-webtools/vistar/vistars.php?usr=LHC1][LHC real time monitoring]].
Daily and weekly information about LHC status , performance  and are obtained from the [[http://lpc.web.cern.ch/lpc/][LHC Programme Coordination web pages]]. In particular the [[http://lhc-commissioning.web.cern.ch/lhc-commissioning/news-2010/LHC-latest-news.html][latest daily news report in ppt]], [[http://lpc-afs.web.cern.ch/lpc-afs/last_brief_news.txt][the daily operations report]], [[http://op-webtools.web.cern.ch/op-webtools/Vistar/vistars.php?usr=LHCCOORD][the weekly plan]]

The other essential page is the [[https://espace.cern.ch/be-dep-op-lhc-machine-operation/default.aspx][LHC machine operation]] where all the LHC online info pages are reported. In particular the [[http://op-webtools.web.cern.ch/op-webtools/vistar/vistars.php?usr=LHC2][status of the cryogenics system]] also seen visually in[[http://hcc.web.cern.ch/hcc/cryo_main/cryo_maintain.php][the hardware commission visual page]].

The [[https://atlasop.cern.ch/atlas-point1/LHC_Commissioning.html][LHC Page 1]] is reported also from the [[https://atlasop.cern.ch/atlas-point1/operation.php][ATLAS Operation web page]] with  [[http://lhcportal.com/Portal/Info/Page1.htm][its detailed meaning]].

Info about the meaning of the parameters  can be obtained by looking at the [[https://edms.cern.ch/file/445830/5/Vol_1_Chapter_2.pdf][LHC Beam parameters]] and the whole [[http://lhc.web.cern.ch/lhc/LHC-DesignReport.html][LHC design report]].
In addition the jargon about the definition of the different machine states (flat top, squeeze,...) is defined [[https://espace.cern.ch/be-dep-op-lhc-machine-operation/LHC%20Modes/Document%20Library/1/LHC-OP-ES-0005-10-00.pdf][here]].

The updated status of the machine is reported in the [[http://indico.cern.ch/categoryDisplay.py?categId=2687][LHC report presentation]].
The [[http://lhc-commissioning.web.cern.ch/lhc%2Dcommissioning/]["LHC commissioning  with beam" page ]] provides the evolution of plans.


---+ ATLAS properties and Status
The ATLAS updated status will be found at [[http://atlas.web.cern.ch/Atlas/GROUPS/DATAPREPARATION/DataSummary/][the ATLAS data summary pages]].
The [[http://op-webtools.web.cern.ch/op-webtools/vistar/vistars.php?usr=LHC3][general experiments's status ]] is also available.

---+ The Handshake

Machine adn expriments exchange data to ascertain the possibility of collisions by determining their present state: [[http://lhc-commissioning.web.cern.ch/lhc-commissioning/systems/data-exchange/data-exchange.htm][the data exchange]] is defined .
One can even subscribe to the mailing list lhc-exp-coms@cern.ch.
The definition  of Machine experiment Handkshake  is [[http://lhc-commissioning.web.cern.ch/lhc-commissioning/systems/data-exchange/handshakes.htm][here]]


---+ Groups whose activities are important 
   * [[http://lpcc.web.cern.ch/LPCC/][ The LHC Physics Centre at CERN]]
   * [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/TopWorkingGroup][TopGroup]]
   * [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/JetEtMiss][Jet ETMIss]]
   * SM QCD subgroup
   * [[AtlasProtected.StandardModelWZjetsSubgroup][SM W/Z+jets]] 



---+ Data Retrieval and Format

_What data sets do we use?_

We start from 
   * skimmed topdAODs  (when available)
   * or physics containers (when available)
   * or single run AODs 

We make D3PDs(ntuples)/get them thorugh the general proudction systrem

We store the D3PDs on xenia in


The [[http://cdsweb.cern.ch/record/1223952][Analysis Model for the first Year]]  foresees a limited number of data formats:

   * centrally produced ( atTier0 and then reprocessed and stored at Tier1s/Tier2s): ESDs,dESDs, AODs,
   * group produced (at Tier1s/Tier2s , then stored in group areas at Tier2s):  dAODs   

The user is expected to run on AODs or dAODs and produce D3PDs.
The plan is to use [[https://svnweb.cern.ch/trac/atlasoff/browser/PhysicsAnalysis/D3PDMaker/TopD3PDMaker][TopD3PDMaker]].
The Top dAODs are documented in [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/TopD2PD2010][TopD2PD2010]].

The data set are 

Retrieving data for the user means to produce a good run list
Operationally= Good Run list + Reprocessed data so as to get update calibrations + consistent release and bug fixes
Remeber to check the [[https://twiki.cern.ch/twiki/bin/view/Atlas/OutputStreamNamingConvention][OutPut Stream naming convention]].
This is important for DPD making.

At Nevis a tier3 is being set up with [[http://www.nevis.columbia.edu/twiki/bin/view/ATLAS/UsingNevisT3][these instructions]] that also need  [[https://atlaswww.hep.anl.gov/twiki/bin/view/UsAtlasTier3/Tier3gUsersGuide][Tier3 users' s guide]].

---++  Initial data sets
Check the list of interesting runs
[[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/InterestingRuns2010][InterestingRuns2010]]

---++ Data Set Content and browsing

The Top given format is the D2PD. We need to start from those and they are described in  [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/TopPhysD2PDEventFilters][the D2PD event filters]].

The location of reprocessed D2PD is given in th [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/TopD2PD2010][TopD2PD 2010 Twiki]].
The proper way to run on a large set of runs is to use the [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/PhysicsContainers][Physics Containers]].

These are the datasets that are produced for every run (by David Cote)

HIST: always produced with f235, and never with f236.

SD: always produced.

AOD: always produced.

TAG_COMM: always produced.

NTUP_MUONCALIB: always produced.

NTUP_TRIG: always produced.

NTUP_TRKVALID: produced for express, IDCosmic, RNDM, MinBias and debug streams.

 
DESD_SGLEL: produced for collision runs, for debug, MinBias and L1CaloEM streams.

DESD_PHOJET: produced for collision runs, for debug, MinBias and L1CaloEM streams.

DESD_SGLMU: produced for collision runs, for debug and MuonswBeam streams.

DESD_MBIAS: produced for collision runs, for debug and MinBias streams.

DESDM_TRACK: produced for collision runs, for debug and L1Calo streams.

DESDM_MUON: produced for collision runs, for debug and MuonswBeam streams.

DESDM_CALJET: produced for collision runs, for debug and L1Calo streams.

DESD_MET: produced for collision runs, for debug and L1Calo streams.

DESDM_EGAMMA: produced for collision runs, for debug, L1CaloEM and MinBias streams.
 
DESD_TILECOMM: produced for cosmics runs, for debug and CosmicMuons streams.

DESD_IDCOMM: produced for cosmics runs, for debug, IDCosmic and CosmicMuons streams.

DESD_CALOCOMM: produced for cosmics runs, for debug, L1Calo and L1CaloEM streams.

DESD_PIXELCOMM: produced for cosmics runs, for debug and IDCosmic streams.

DESD_MUONCOMM: produced for cosmics runs, for debug, CosmicMuons and MuonswBeam streams.

The tag being used for reconstruction for a given dataset  is available from Tier0 according to [[https://twiki.cern.ch/twiki/bin/view/Atlas/CosmicCommissioningReconstructionStatus#How_do_i_find_out_what_release_i][How do I find the release used at Tier0]]

The [[http://ami.in2p3.fr/AMI/servlet/net.hep.atlas.Database.Bookkeeping.AMI.Servlet.Command?linkId=501][AMI description]] (click “browse f tags”) provides the info about the datasets corresponding to a given reconstruction tag.

All of these data sets properties are defined by the [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/PrimaryDPDMaker][PrimaryDPDMaker]] and specifically  in the [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/PerformanceDPD][Performance DPD Twiki]].
For jets  the interest is on 
Notice that that the DESDM has calocells and basic track info.

Some datasets are also found on /castor/cern.ch/grid/atlas/tzero/prod1/perm.

---++ Monitoring Data replication

The links below will allow you to monitor the dataset replication across  T1's and T2's (by lexei Klimentov and the DDM team through  G Brooijmans)

The status can be monitored using links below

[[http://panda.cern.ch:25980/server/pandamon/query?mode=listReproDSReplications][ replication between Tier-1s - Pandareplication]]

[[http://atladcops.cern.ch:8000/drmon/repromon.html][ replication between Tier-1s - dcops]]


[[http://atladcops.cern.ch:8000/drmon/repromon_tier2s.html][ replication within clouds (to T2s)- dcops]]

[[http://panda.cern.ch:25980/server/pandamon/query?mode=listReproDSReplications&testType=T1toT2s][ replication within clouds (to T2s) - panda]]


Note that replication to Tier-2s is started only when parent T1 has a complete replicas.


[[http://atladcops.cern.ch:8000/drmon/crmon_TiersInfo.html][replicas distribution between tiers]] 


Information about data reprocessing is on the [[https://twiki.cern.ch/twiki/bin/viewauth/Atlas/DataPreparationReprocessing][Data Preparation Reprocessing page]].

---++ Time scales for data availability

Have a look at the general 
[[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/DataMCForAnalysis][Data /MC for Analysis page]]
also reachable from the [[https://twiki.cern.ch/twiki/bin/viewauth/Atlas/DataPreparationReprocessing][Data Preparation Reprocessing page]].

---++ Data Quality And DB releases
We need to have 
   * Time and range  and machine conditions
   * DQ
   * Trigger config

_What data format are we going to use to extract info at different steps ?_

_What formats are produced at Tier0 and how do we know them for a given run?_

Raw Data are located here
For Top a central production of  D2PDs is planned.
Data format already available from production are defined here.

For performing  the phys an we need good-run/LB list and data availability on the grid.

Grid space/production manager for Top Group is  Marcello Barisonzi
Data quality strategy si summarized in [[http://cdsweb.cern.ch/record/1168026/files/ATL-COM-GEN-2009-015.pdf][theDQ paper]] and the most updated meaning of the DQ flags is kept on the [[https://twiki.cern.ch/twiki/bin/view/Atlas/DQFlagInterpretation][the DQ Flag interpretation page]]. The definition of virtual flags is stored on the [[https://twiki.cern.ch/twiki/bin/view/Atlas/DQVirtualFlagProposal][DQ Flag proposal page]]. All info are found on the DQ page. 

_How are we going to access database info?_

Appropriate database information  for any GRID submission and any release is usually taken care of in the main JO.
The updated status of the database is found in [[https://twiki.cern.ch/twiki/bin/view/Atlas/AtlasDBRelease][AtlasDBRelease]]. In particular the connection between a given release and the database is found in [[https://twiki.cern.ch/twiki/bin/view/Atlas/AtlasDBRelease#S_W_release_vs_DB_Release][SW release vs DB Release]].
The inclusion of the database information in non-standard Job options (not using the standard RecExCommon for instance ) is included as mentioned in 
[[https://twiki.cern.ch/twiki/bin/view/Atlas/CoolIOVDbSvcConfigurable#Conditions_DB_in_standalone_cont][Conditions database in standalone job options]].
[[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/PhysicsAnalysisWorkBookAODAnalysisRel15#How_to_setup_a_special_dataBase][The instructions to set up a special Database]] should also be kept in mind. For specifying the correct database release when running on the grid, [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/PhysicsAnalysisWorkBookBatch2#Specifying_a_database_release][this]] is especially useful.
An essential troubleshooting page  is [[https://twiki.cern.ch/twiki/bin/view/Atlas/AtlasDBRelease?topic=CoolTroubles][the CoolTroubles twiki]].

Example errors being caused by the wrong  DB are

IOVDbSvc                                  ERROR Tag OFLCOND-DR-BS7T-ANom-04 cannot be resolved for folder /LAR/Align

_How do we know what geometry is being used?_

Have a look at [[https://twiki.cern.ch/twiki/bin/view/Atlas/AtlasGeomDBTags][tthe Geometry DaB tags]].


---++ Useful references 
---+++ Twikis
[[https://twiki.cern.ch/twiki/bin/viewauth/Atlas/GoodRunsLists][GoodRunList page]]

[[Atlas.GoodRunsListsTutorial][GoodRunListsTutorial]]

[[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/PerformanceDPD][Performance DPDS]] (in particular
[[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/PerformanceDPD#The_DESD_COLLCAND][Definition of old DESDCOLLCAND]])




---+++ Talks
[[http://torrence.web.cern.ch/torrence/Atlas/tutorial/torrence_overview.pdf][Eric's presentation for the software tutorial]]

[[http://indico.cern.ch/getFile.py/access?contribId=1&resId=0&materialId=0&confId=73639][MaxBaak's tutorial]]


---+ Data Selection,Trigger and Luminosity 
_How does your analysis treat luminosity? If your favorite trigger is prescaled because of rate, what is your backup plan?_

Luminosity  can be calculated only after final GRL and trigger info is specified.  

For calculating cross sections 
The efficiencies for calculating cross section are as follows
   * unprescaled trigger efficiency (prescales are included in LUmi calculation)
   * skimming efficiency in dAOD based analysis
   * TAG selection efficiency (in TAG based analysis)
   * event selection cut efficiencies:

---+++ Trigger


Consider the initial express stream being used at the HLT. Preferred triggers for muons and electrons 

A useful [[http://arxiv.org/pdf/0901.4118v1][paper]] on trigger combination.

---++ Luminosity
Need to understand Trigger prescales, L1 trigger deadtime (provided by Lumi group in its calculation)
The value of luminosity is determined by more than one detector.
The absolute measurement from the machine comes from the [[https://twiki.cern.ch/twiki/bin/view/LHCb/AbsoluteLuminosityMeasurementWithVanDerMeerMethod][Van Der Meer scan]] with a summary of the procedure at LHC [[http://indico.cern.ch/getFile.py/access?contribId=6&resId=1&materialId=slides&confId=92298][here].

---+++Useful references
[[Atlas.CoolLumiCalc][Coll Lumi Calc page]]
[[Atlas.CoolLumiCalcTutorial][Lumi Calculation tutorial]]


---+ Data Quality
_What input to the data quality group have you provided? How do you get the good run/lumi blok  list?_

Good runs lists are produced by the DQ group.
ForJet/ETmiss  the info about GRLs is on the [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/JetEtMiss][main page]] under recommendation for jet/etmiss data analysis
For Top the info about GRLs is in [[https://atlas-top-grls.web.cern.ch/atlas-top-grls/xmlGRL/][TopGRLs]]. The standard info  is in
[[http://atlasdqm.web.cern.ch/atlasdqm/grlgen/StandardGRL/top_allchannels_7TeV/][StandardTopGRLs]].
The overall 2010 Top GRL is in [[http://atlasdqm.web.cern.ch/atlasdqm/grlgen/StandardGRL/top_allchannels_7TeV/data10_7TeV.pro04.merged_LBSUMM_top_allchannels_7TeV.xml][2010TopGrl]]


The general GRL calculator is  [[http://atlasdqm.cern.ch:8080/grl/][here]]

---+ Selection
__Are there duplicate events in your ntuple?Are there missing runs? What are the values for selection? How do we handle overlap removal?__

---+ Event reconstruction And Visualization
_What level of  calibration and aligment do you need? How do we habvdle overlap removal? How do we recalculate missing ET? How do we recalibrate jets?_

The object definition for top analyses is obtained by the [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/TopReconstructionGroup][Top Reconstruction group]] in the [[AtlasProtected.TopCommonObjects][Top Common Objects page]].

Cut flows that are preliminary to top are important.
Onee needs to validate the code first using the Top MC/Data challenge for [[https://espace.cern.ch/topxsec/Lists/Comparisons/AllItems.aspx][semileptonic channel]] and [[https://espace.cern.ch/topxsec/Lists/Dilepton%20MC%20Challenge/AllItems.aspx][the di-lepton channel]].


The recommendation for making event displays are  described in the twiki on [[https://twiki.cern.ch/twiki/bin/view/Atlas/OfficialEventDisplayGuidelines][Official event display Guidelines]]. In order to get hold of single events in an ESD for event display one can use  the [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/SimpleGetEventsScript][ SimpleGetEventScript]].
 
---++ Leptons
   * Electrons are reconstructed according to  [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/ElectronReconstruction][here]].
   * A reminder on bitmask usage is in [[http://www.cprogramming.com/tutorial/bitwise_operators.html][here for bitwise operators]] and in [[http://www.somacon.com/p125.php][here]].  
      * So  in the expression
           const unsigned int HADLEAKETA_ELECTRON =      0x1 << ClusterEtaRange_Electron  |    0x1 << ClusterHadronicLeakage_Electron;
         << is a [[http://www.c-point.com/javascript_tutorial/jsoprlshift.htm][left shift operator]]  and "| " is the logical OR ; with 
       This line is taken from the [[http://alxr.usatlas.bnl.gov/lxr-stb4/source/atlas/Reconstruction/egamma/egammaEvent/egammaEvent/egammaPIDdefs.h?v=release_15_6_9][electronID definition]] 
      * For instance the electron cut definition  shown in [[http://alxr.usatlas.bnl.gov/lxr/source/atlas/Reconstruction/egamma/egammaPIDTools/src/egammaElectronCutIDTool.cxx][ElectronCutIDTool]] at lines 345 and 349 is calling calo=based and track based selection respectively that (see line 459) simply set certain bits based on the [[http://alxr.usatlas.bnl.gov/lxr-stb4/source/atlas/Reconstruction/egamma/egammaEvent/egammaEvent/egammaPIDdefs.h?v=release_15_6_9][electronID definition]]  (for instance flag |= ( 0x1 << egammaPID::ClusterHadronicLeakage_Electron)). At the end m_iflag is the variable that needs to be checked against the masks of the [[http://alxr.usatlas.bnl.gov/lxr-stb4/source/atlas/Reconstruction/egamma/egammaEvent/egammaEvent/egammaPIDdefs.h?v=release_15_6_9][electronID definition]] . The isem method is defined at line 580 of  the [[http://alxr.usatlas.bnl.gov/lxr/source/atlas/Reconstruction/egamma/egammaEvent/src/egamma.cxx][egamma event appropriate code]]. It uses the isEM fnction from the [[http://alxr.usatlas.bnl.gov/lxr/source/atlas/Reconstruction/egamma/egammaEvent/src/egPID.cxx#125][egammaPID cide]] (at line 125 ): it  compares the given mask with the  isEM flag . Notice that if a cut is NOT passed then a bit is set in the isEMflag. This is why the isEm method has to return zero when compared with the mask that identifies a given type of electron: if all bits related to that definitions are not set it means that the electron passes those cuts. 
   * Notice that the isEM E/p  bit is set according to the lines  of  the line 905 to 910 [[http://alxr.usatlas.bnl.gov/lxr-stb4/source/atlas/Reconstruction/egamma/egammaPIDTools/src/egammaElectronCutIDTool.cxx?v=release_15_6_9#910][egammaElectronCutIDTool]].  The values changes in bins of eta with the recipe defined at line 852 of [[http://alxr.usatlas.bnl.gov/lxr-stb4/source/atlas/Reconstruction/egamma/egammaPIDTools/src/egammaElectronCutIDTool.cxx?v=release_15_6_9#910][ElectronCutIDTool]].The  variables(m_CutminEp_electrons) and (m_CutmaxEp_electrons) that represent the cuts are defined in the[[http://alxr.usatlas.bnl.gov/lxr-stb4/source/atlas/Reconstruction/egamma/egammaPIDTools/src/egammaElectronCutIDTool.cxx?v=release_15_6_9#179][ElectronCutIDTool]] and the python JO that sets the values for each given special eta bin is the [[http://alxr.usatlas.bnl.gov/lxr-stb4/source/atlas/Reconstruction/egamma/egammaPIDTools/python/egammaElectronCutIDToolBase.py?v=release_15_6_9][egammaElectronCutIDToolBase.py]].


---++ Missing Energy

   * For early use consider Missing ET topo and Base
   * For later on missing et red final  should consider the new MissingETComposition map in which each object used in the MissingET calculation is stored   together with its weight. Some more details can be found in the talk by Silvia [[http://indico.cern.ch/conferenceDisplay.py?confId=71770][here]]
   * To be able to re-run MET consistently with the appropriate jet collection we have to look at [[https://twiki.cern.ch/twiki/bin/view/Main/MultiMetForJESCorr][Multi MET-JES correction]]
   * Check  [[https://svnweb.cern.ch/trac/atlasgrp/browser/Physics/Top/TTBar2010/Note3/note3_v1.pdf][op note III on MET]]
   * Notice that in TopPhysD2PDMAker the customization/steering is performed in [[https://svnweb.cern.ch/trac/atlasoff/browser/PhysicsAnalysis/TopPhys/TopPhysD2PDMaker/trunk/share/TopPhys_dAODMissingEt.py][TopPhys_dAODMissingEt.py]] and the implemntation takes place in [[https://svnweb.cern.ch/trac/atlasoff/browser/PhysicsAnalysis/TopPhys/TopPhysD2PDMaker/trunk/share/TopPhys_MissingEtMaking.py][TopPhys_MissingEtMaking.py]] which uses [[http://alxr.usatlas.bnl.gov/lxr/source/atlas/Reconstruction/MissingET/python/METRefGetter_new.py#046][MetRefGetter_new.py]]
   * It is important to remember that the [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/MissingETComposition][Missing ET COmposition tool]] is an important ingredient


---++ Jets

Various Jets calibrations can be obtained. 
The configuration of a calibration scheme goes through four steps

   *  configure individual calib tools. Setting up  an individual jet calibrator has a series of helper functions in [[http://alxr.usatlas.bnl.gov/lxr/source/atlas/Reconstruction/Jet/JetCalibTools/python/SetupJetCalibrators.py][SetupJetCalibrators.p]] .
   These are elements that go into the configuration o fthe JetAlgorithms
   *  configure sequences of calib tools. The list and dictionary of sequences is in [[http://alxr.usatlas.bnl.gov/lxr/source/atlas/Reconstruction/Jet/JetCalibTools/python/MakeCalibSequences.py][MakeCalibSequences.py ]]
   *  configure  JetAlgTools with the sequences (using  getJetCalibrationTool)
   *  add these JetAlgTools the global list of JetAlgTool inside a JetAlgorithm

The most updated recipes are obtaiend form the Jet/Et miss page on re-runninng jets.
The implementation for Top Note II and the latest TopPhys dAOD jo are the most useful places to look up as far as implementation.
The [[https://twiki.cern.ch/twiki/bin/view/Sandbox/TopPhysSetupForAnalysis][TopPhysStup studies ]] provde the devlopment info for multiple jet containers and multiple top inputs objects to be built.
The implementation is by now absorbed in Top

Pile-up issues are crucial for the 2010-2011 dataset so for jets  one has [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/JetQualityAndSelectionForPileup][etQualityAndSelectionForPileup]] and the older, but still interesting  [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/JetsWithPileup][JetsWithPileUp]].
Notice that as of June 2010, the cell-ralted quality variables (n90 and jet quality) are not filled when re-running the container on the fly from AODS.
A solution to this is under study.

---+++ Available Jets in AOD
The available collections  are documented in te AOD CLass summary[[https://twiki.cern.ch/twiki/bin/view/Atlas/AODClassSummary][https://twiki.cern.ch/twiki/bin/view/Atlas/AODClassSummary]]
For release 15 it is  [[https://twiki.cern.ch/twiki/bin/view/Atlas/AODClassSummary15#Jets][here]] and the software status evolution is documented in  [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/JetSoftwareStatu?topic=JetSoftwareStatus][the Jet Software status twiki]]

---++ Consistent Jet and missing Et implementation for top





---+ Measurements
__What are the first plots important things to see at 1pb? 10 pb^-1? 20 pb^-1?  50 pb ^{-1} ?  100pb^{-1}? How quickly are we supposed to get these values of lumi? What are the control samples?__

---++ The control samples 


---++ The pre-analysis validation plots
Criteria: they need to be important plots for the objcts we use in the final state and plots that tell us about every single cut we make they need to be important plots where there are still data-monte carlo discrepancies


---++ Measurement of jet multiplicity (  top, Z+jets, W+jets, ratios)
---++ dsigma/dmtt 

---+Systematics
_What is the strategy for data-driven background determination?How do you deal with fakes?_ 

---+Data Samples
_What will 900 GeV data tell you about your analysis?_



---+Monte Carlo Cross sections and Samples 
_Is the simulation adequate for your analysis? How will you handle the inevitable mismatch between our present simulation and real data?_



Use the information present in the [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/StandardModelCrossSectionTaskForce][Standard model Cross Section Task Force]].
THe production of Monte Carlo samples can be checked at the [[http://www-f9.ijs.si/atlpy/atlprod/][Atlas Production Team Pages]]
min bias @ 900 GeV

min bias @ 7 TeV

---+++7 TeV  Samples


---++++Pre-Top-Analysis


Minimum bias samples (check line 24)

[[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/JetEtMissMCSamples][Jet /ETmiss MC samples]] 




---++++Top Analysis
We need to check updates in [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/TopMC2009][TopMC09]]

*Most important datasets:*

ttbar:
   * mc09_7TeV.105200.T1_McAtNlo_Jimmy.merge.AOD.e510_s624_s633_r1064_r1051/
   * mc09_7TeV.105861.TTbar_PowHeg_Pythia.merge.AOD.e505_s624_s633_r1064_r1051/

Single Top:
   * mc09_7TeV.108340.st_tchan_enu_McAtNlo_Jimmy.merge.AOD.e508_s625_s633_r907_r879/ (check for tag r1064_r1051)
   * mc09_7TeV.108346.st_Wt_McAtNlo_Jimmy.merge.AOD.e508_s624_s633_r1064_r1051

W+jets:
   * Still waiting, see TopMC2009

Z+jets:
   * Still waiting, see TopMC2009

Diboson:



*Secondary:*

Single Top:
   * mc09_7TeV.108341.st_tchan_munu_McAtNlo_Jimmy.merge.AOD.e508_s624_s633_r1064_r1051
   * mc09_7TeV.108342.st_tchan_taunu_McAtNlo_Jimmy.merge.AOD.e508_s625_s633_r907_r879 (check for r1064_r1051)

W+jets:

Z+jets:

Diboson:

QCD:


   
---+Tools   And Computing
_Is enough effort going into validation? How will you handle time varying conditions? Does your analysis even run with Monte Carlo truth dropped? Does your code run on  cosmic rays data?_

Keep notice of this [[http://jetweb.cedar.ac.uk/][useful Jet  validation facility]]

---++ Simulation truth info
The findings of the [[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/MonteCarloTruthTaskForce][MC Truth task force\]] are important.

---++ The software to use

__We need to be able to 
   * run on the grid
   * read D2PDs
   * manipulating objects  info: cuts/overlap/recalibration (re-do TopInputs)
   * dump info into a D3PD__

---++ Working on the grid

It is important to be able to know what sites to submit to in case it is needed
We submit jobs mainly using pathena.

---++Full Analysis

The code we use is base don the Top Reconstruction code.
It is useful to keep an eye on[[https://svnweb.cern.ch/trac/atlasoff/browser/PhysicsAnalysis/StandardModelPhys/WZBenchmarks][The WZBenchmark analysis]]

---++ Ntuple Dumpers
The Top ntuples we use are based on the top PhysD3PD maker
[[AtlasProtected.JetEtMissD3PD][Jet D3PD maker]]



---++ Computing
Computers to be used: 
   * at CERN:  pcnevis1, pcnevis2, pcnevis3
   * at [[http://www.nevis.columbia.edu/computing.html][Nevis]]: we use the [[http://www.nevis.columbia.edu/twiki/bin/view/Nevis/LinuxCluster][Linux Cluster]]
   * at [[https://www.racf.bnl.gov/experiments/usatlas/welcome/?searchterm=None][BNL]]:just check the [[https://www.racf.bnl.gov/experiments/usatlas/getstarted/gettingstarted][how to get started]] , particularly for logging in  at BNL do not forget [[https://www.racf.bnl.gov/docs/howto/interactive/login][the login page]] and report problems [[https://www.racf.bnl.gov/docs/rt][here]]. An important starting point is also [[http://www.usatlas.bnl.gov/USATLAS_TEST/Physics.shtml][this one]].


---+ Reference Papers at Tevatron (CDF and D0)
---++ Top discovery

[[http://lutece.fnal.gov/Papers/PhysNews95.html][ very short summary]] 

[[http://prl.aps.org/abstract/PRL/v74/i14/p2626_1][Observation of Top Quark Production in p &#772;p Collisions]] by F. Abe et al. (CDF collaboration), Phys. Rev. Lett. 74, 2626–2631 (1995), also available as [[http://arxiv.org/pdf/hep-ex/9503002v2][hep-ex/9503002v2]]

[[http://prl.aps.org/abstract/PRL/v74/i14/p2632_1][Observation of the Top Quark]] by S. Abachi, et al.  (DØ collaboration), Phys. Rev. Lett.  74, 2632 (1995), also available as [[http://arxiv.org/abs/hep-ex/9503003][hep-ex/9503003]]


---++ Performance info
[[http://lcgapp.cern.ch/project/docs/noteStatusHadronic2010.pdf][Hadronic Status]]

---+++ Jets 
[[http://www.desy.de/~heralhc/][heratoLHC]]

[[http://arxiv.org/abs/hep-ex/0510047][Determination of the Jet Energy Scale at the Collider Detector at Fermilab]]

[[http://www-d0.fnal.gov/~daniel/jesgroup/jes_nim_accepted.ps.gz][D0 jet energy scale]] at the  [[http://www-d0.fnal.gov/~daniel/jesgroup/jesgroup.html][ JES group at D0]]

[[http://arxiv.org/pdf/1003.3146v1][Studying the Underlying Event in Drell-Yan and High Transverse Momentum Jet Production at the Tevatron]] the CDF collaboration 

[[http://projects.hepforge.org/jimmy/][Jimmy MPI generator]] 

---++ Integral cross sections


---++ Differential cross sections
[[http://arxiv.org/pdf/0903.2850][First Measurement of the tt Di&#64256;erential Cross Section d&#963;/dMtt in pp Collisions at sqrt(s)= 1.96 TeV]] by T. Aaltonen et al., the CDF Collaboration,  PRL 102 222003

[[http://www-cdf.fnal.gov/physics/new/top/2009/tprop/AllHadMtt/][Mtt resonance search in all jets (2.8 fb-1)]]



---+ Reference Papers in ATLAS 

---++ Performance papers

---++ Reconstruction for Top

---+++ Jets and Missing Energy



---++ Single Lepton Channel
[[http://cdsweb.cern.ch/record/1226764/files/ATL-COM-PHYS-2009-633.pdf][Study on reconstructed object definition and selection for top physics]] by Abbott, B; Allwood-Spiers, S; Astalos, R; de Bell, M; Benekos, N; BoisVert, V; Bordoni, S; Brooijmans, G; De Bruyn, K; Cerrito, L et al. - ATL-COM-PHYS-2009-633.- Geneva : CERN, 2009 - 146 p. 
http://cdsweb.cern.ch/record/1200287?ln=en

[[https://twiki.cern.ch/twiki/bin/view/Atlas/AtlPhysPub2009087][
[[http://cdsweb.cern.ch/record/1200436/files/ATL-PHYS-PUB-2009-087.pdf][Prospects for the Top Pair Production Cross-section at s  = 10 TeV in the Single Lepton Channel in ATLAS]], The ATLAS Collaboration -ATL-PHYS-PUB-2009-087 ; ATL-COM-PHYS-2009-404,Geneva : CERN,2009- 19 p.

[[http://cdsweb.cern.ch/record/1180281/files/ATL-COM-PHYS-2009-306.pdf][ Prospects for measuring the Top Quark Pair Production Cross-section in the Single Lepton Channel at ATLAS in 10 TeV p-p Collisions ]] by Acharya, B; Bartsch, D; Besana, I; Bentvelsen, S; Bosman, M; Brock, I C; Cobal, M; Cristinziani, M; De~Sanctis, U; Doxiadis, A et al. ATL-COM-PHYS-2009-306.- Geneva : CERN, 2009 - 60 p.

---++ Di-lepton Channel

[[http://cdsweb.cern.ch/record/1200287/files/ATL-PHYS-PUB-2009-086.pdf][Prospects for measuring top pair production in the dilepton channel with early ATLAS data at s = 10 TeV]], the ATLAS Collaboration, ATL-PHYS-PUB-2009-086 ; ATL-COM-PHYS-2009-402- Geneva : CERN, 2009 - 20 p.

[[http://cdsweb.cern.ch/record/1180282/files/ATL-COM-PHYS-2009-307.pdf][Sensitivity of the top dilepton cross-section measurement at sqrt{s} = 10 TeV ]] by  Cristinziani, M; Loginov, A; Adelman, J; Allwood-Spiers, S; Auerbach, B; Cranmer, K; Gellerstedt, K; Guo, B; Kaplan, B; Lockwitz, S et al.
ATL-COM-PHYS-2009-307.- Geneva : CERN, 2009 - 54 p. 

---++ QCD

[[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/MbPaperOverview900GeV][MInimum bias paper and Twiki]]

[[http://cdsweb.cern.ch/record/1208466/files/CERN-THESIS-2009-098.pdf][Study of fully hadronic ttbar decays and theirseparation from QCD multijet background events in the first year of the ATLAS experiment]] by Marion Lambacher - Ph.D. Thesis - LMU - Munich

---++ Detector basic performance 
[[http://cdsweb.cern.ch/record/1176570/files/ATL-COM-CAL-2009-004.pdf][Response and Shower Topology of 2 to 180 GeV Pions Measured with the ATLAS Barrel Calorimeter at the CERN Test–beam and Comparison to Monte Carlo Simulations]] by T. Carli et al, ATL-COM-CAL-2009-004.

[[http://cdsweb.cern.ch/record/1139228/files/ATL-TILECAL-PUB-2009-001.pdf][Calibration of ATLAS Tile Calorimeter at Electromagnetic Scale]], K. Anderson et al,  ATL-TILECAL-PUB-2009-001

[[http://cdsweb.cern.ch/record/942528/files/larg-pub-2006-003.pdf][2004 ATLAS Combined Testbeam: Computation and Validation of the Electronic Calibration Constants for the Electromagnetic Calorimeter]], ATLA-LARG-PUB-2006-003


[[http://cdsweb.cern.ch/record/1263862/files/ATL-CAL-INT-2010-001.pdf][Study of Energy Reconstruction Algorithms for Pions from 2 to 180 GeV Measured with the ATLAS Barrel Calorimeter at the CERN SPS Test-beam]]

[[http://arxiv.org/pdf/physics/0608012][Energy Linearity and Resolution of the ATLAS Electromagnetic Barrel Calorimeter in an Electron Test-Beam]]


---++ Jets  and Constituents

[[http://cdsweb.cern.ch/record/1099735/files/larg-pub-2008-002.pdf][Calorimeter Clustering Algorithms: Description and Performance]] by W . Lampl et al., ATL-LARG-PUB-2008-002


#AtlasComputingModel
---++ Atlas Analysis Model 

[[http://cdsweb.cern.ch/record/1223952][The AMFY document]]

[[http://tinyurl.com/DataChallengesInAtlasComputin][Data Challenges in ATLAS computing]]

[[http://cdsweb.cern.ch/record/1206256/files/ATL-COM-SOFT-2009-013.pdf][Short ATLAS Computing model summary]]


[[http://atlas-proj-computing-tdr.web.cern.ch/atlas-proj-computing-tdr/PDF/Computing-TDR-final-July04.pdf][Computing TDR]]


---++ Atlas Simulation

[[http://cdsweb.cern.ch/record/1239901/files/ATL-SOFT-INT-2010-002.pdf][The ATLAS Simulation project]] , ATLAS -SOFT-INT-2010-002
[[http://cdsweb.cern.ch/record/1095009/files/ATL-COM-LARG-2008-002.pdf][The simulation of the ATLASLiquid Argon Calorimetry]]

---++ Monte Carlo Truth info

[[https://twiki.cern.ch/twiki/bin/view/AtlasProtected/MonteCarloTruthTaskForce][Monte Carlo Truth Task force]]

---++ Basics of Setup

Atlas software works with separate projects that can have their own development time and independent releases.
This is properly described in [[https://twiki.cern.ch/twiki/bin/view/Atlas/WorkingWithProjectBuilds][Working with Project Builds]].
The general projects that incorporate all the others are AtlasProduction and AtlasOffline.
Now each project has its own release cycle according to the numbering
<verbatim> ProductionRelease.DevelopmentRelease.BugFixRelease </verbatim>

Info to setup at Nevis are [[http://www.nevis.columbia.edu/twiki/bin/view/ATLAS/UsingNevisT3][here]].





-- Main.FrancescoSpano - 30-Nov-2009
-- Main.FrancescoSpano - 11-Feb-2010
Topic revision: r89 - 2011-01-12 - FrancescoSpano
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