Index: trunk/examples/delphes_card_ATLAS_PileUp.tcl
===================================================================
--- trunk/examples/delphes_card_ATLAS_PileUp.tcl	(revision 1260)
+++ trunk/examples/delphes_card_ATLAS_PileUp.tcl	(revision 1260)
@@ -0,0 +1,617 @@
+#######################################
+# Order of execution of various modules
+#######################################
+
+set ExecutionPath {
+
+  PileUpMerger
+  ParticlePropagator
+
+  ChargedHadronTrackingEfficiency
+  ElectronTrackingEfficiency
+  MuonTrackingEfficiency
+
+  ChargedHadronMomentumSmearing
+  ElectronEnergySmearing
+  MuonMomentumSmearing
+
+  TrackMerger
+  Calorimeter
+  TrackPileUpSubtractor
+  EFlowMerger
+
+  GenJetFinder
+
+  Rho
+  FastJetFinder
+  JetPileUpSubtractor
+
+  JetEnergyScale
+
+  PhotonEfficiency
+  PhotonIsolation
+
+  ElectronEfficiency
+  ElectronIsolation
+
+  MuonEfficiency
+  MuonIsolation
+
+  MissingET
+
+  BTagging
+  TauTagging
+
+  UniqueObjectFinder
+
+  ScalarHT
+
+  TreeWriter
+}
+
+###############
+# PileUp Merger
+###############
+
+module PileUpMerger PileUpMerger {
+  set InputArray Delphes/stableParticles
+
+  set OutputArray stableParticles
+
+  # pre-generated minbias input file
+  set PileUpFile MinBias.pileup
+
+  # average expected pile up
+  set MeanPileUp 50
+  # spread in the beam direction in m (assumes gaussian)
+  set ZVertexSpread 0.07
+}
+
+#################################
+# Propagate particles in cylinder
+#################################
+
+module ParticlePropagator ParticlePropagator {
+  set InputArray PileUpMerger/stableParticles
+
+  set OutputArray stableParticles
+  set ChargedHadronOutputArray chargedHadrons
+  set ElectronOutputArray electrons
+  set MuonOutputArray muons
+
+  # radius of the magnetic field coverage, in m
+  set Radius 1.15
+  # half-length of the magnetic field coverage, in m
+  set HalfLength 3.51
+
+  # magnetic field
+  set Bz 2.0
+}
+
+####################################
+# Charged hadron tracking efficiency
+####################################
+
+module Efficiency ChargedHadronTrackingEfficiency {
+  set InputArray ParticlePropagator/chargedHadrons
+  set OutputArray chargedHadrons
+
+  # add EfficiencyFormula {efficiency formula as a function of eta and pt}
+
+  # tracking efficiency formula for charged hadrons
+  set EfficiencyFormula {                                                    (pt <= 0.1)   * (0.00) + \
+                                           (abs(eta) <= 1.5) * (pt > 0.1   && pt <= 1.0)   * (0.70) + \
+                                           (abs(eta) <= 1.5) * (pt > 1.0)                  * (0.95) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 0.1   && pt <= 1.0)   * (0.60) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 1.0)                  * (0.85) + \
+                         (abs(eta) > 2.5)                                                  * (0.00)}
+}
+
+##############################
+# Electron tracking efficiency
+##############################
+
+module Efficiency ElectronTrackingEfficiency {
+  set InputArray ParticlePropagator/electrons
+  set OutputArray electrons
+
+  # set EfficiencyFormula {efficiency formula as a function of eta and pt}
+
+  # tracking efficiency formula for electrons
+  set EfficiencyFormula {                                                    (pt <= 0.1)   * (0.00) + \
+                                           (abs(eta) <= 1.5) * (pt > 0.1   && pt <= 1.0)   * (0.73) + \
+                                           (abs(eta) <= 1.5) * (pt > 1.0   && pt <= 1.0e2) * (0.95) + \
+                                           (abs(eta) <= 1.5) * (pt > 1.0e2)                * (0.99) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 0.1   && pt <= 1.0)   * (0.50) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 1.0   && pt <= 1.0e2) * (0.83) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 1.0e2)                * (0.90) + \
+                         (abs(eta) > 2.5)                                                  * (0.00)}
+}
+
+##########################
+# Muon tracking efficiency
+##########################
+
+module Efficiency MuonTrackingEfficiency {
+  set InputArray ParticlePropagator/muons
+  set OutputArray muons
+
+  # set EfficiencyFormula {efficiency formula as a function of eta and pt}
+
+  # tracking efficiency formula for muons
+  set EfficiencyFormula {                                                    (pt <= 0.1)   * (0.00) + \
+                                           (abs(eta) <= 1.5) * (pt > 0.1   && pt <= 1.0)   * (0.75) + \
+                                           (abs(eta) <= 1.5) * (pt > 1.0)                  * (0.99) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 0.1   && pt <= 1.0)   * (0.70) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 1.0)                  * (0.98) + \
+                         (abs(eta) > 2.5)                                                  * (0.00)}
+}
+
+########################################
+# Momentum resolution for charged tracks
+########################################
+
+module MomentumSmearing ChargedHadronMomentumSmearing {
+  set InputArray ChargedHadronTrackingEfficiency/chargedHadrons
+  set OutputArray chargedHadrons
+
+  # set ResolutionFormula {resolution formula as a function of eta and pt}
+
+  # resolution formula for charged hadrons
+  set ResolutionFormula {                  (abs(eta) <= 1.5) * (pt > 0.1   && pt <= 1.0e1) * (0.20) + \
+                                           (abs(eta) <= 1.5) * (pt > 1.0e1 && pt <= 2.0e2) * (0.20) + \
+                                           (abs(eta) <= 1.5) * (pt > 2.0e2)                * (0.20) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 1.0   && pt <= 1.0e1) * (0.20) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 1.0e1 && pt <= 2.0e2) * (0.20) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 2.0e2)                * (0.20)}
+}
+
+#################################
+# Energy resolution for electrons
+#################################
+
+module EnergySmearing ElectronEnergySmearing {
+  set InputArray ElectronTrackingEfficiency/electrons
+  set OutputArray electrons
+
+  # set ResolutionFormula {resolution formula as a function of eta and energy}
+
+  set ResolutionFormula {                  (abs(eta) <= 2.5) * (energy > 0.1   && energy <= 2.5e1) * (energy*0.015) + \
+                                           (abs(eta) <= 2.5) * (energy > 2.5e1)                    * sqrt(energy^2*0.005^2 + energy*0.05^2 + 0.25^2) + \
+                         (abs(eta) > 2.5 && abs(eta) <= 3.0)                                       * sqrt(energy^2*0.005^2 + energy*0.05^2 + 0.25^2) + \
+                         (abs(eta) > 3.0 && abs(eta) <= 5.0)                                       * sqrt(energy^2*0.107^2 + energy*2.08^2)}
+
+}
+
+###############################
+# Momentum resolution for muons
+###############################
+
+module MomentumSmearing MuonMomentumSmearing {
+  set InputArray MuonTrackingEfficiency/muons
+  set OutputArray muons
+
+  # set ResolutionFormula {resolution formula as a function of eta and pt}
+
+  # resolution formula for muons
+  set ResolutionFormula {                  (abs(eta) <= 1.5) * (pt > 0.1   && pt <= 1.0)   * (0.03) + \
+                                           (abs(eta) <= 1.5) * (pt > 1.0   && pt <= 5.0e1) * (0.03) + \
+                                           (abs(eta) <= 1.5) * (pt > 5.0e1 && pt <= 1.0e2) * (0.04) + \
+                                           (abs(eta) <= 1.5) * (pt > 1.0e2)                * (0.07) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 0.1   && pt <= 1.0)   * (0.04) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 1.0   && pt <= 5.0e1) * (0.04) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 5.0e1 && pt <= 1.0e2) * (0.05) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 1.0e2)                * (0.10)}
+}
+
+##############
+# Track merger
+##############
+
+module Merger TrackMerger {
+# add InputArray InputArray
+  add InputArray ChargedHadronMomentumSmearing/chargedHadrons
+  add InputArray ElectronEnergySmearing/electrons
+  set OutputArray tracks
+}
+
+#############
+# Calorimeter
+#############
+
+module Calorimeter Calorimeter {
+  set ParticleInputArray ParticlePropagator/stableParticles
+  set TrackInputArray TrackMerger/tracks
+
+  set TowerOutputArray towers
+  set PhotonOutputArray photons
+
+  set EFlowTrackOutputArray eflowTracks
+  set EFlowTowerOutputArray eflowTowers
+
+  set pi [expr {acos(-1)}]
+
+  # lists of the edges of each tower in eta and phi
+  # each list starts with the lower edge of the first tower
+  # the list ends with the higher edged of the last tower
+
+  # 10 degrees towers
+  set PhiBins {}
+  for {set i -18} {$i <= 18} {incr i} {
+    add PhiBins [expr {$i * $pi/18.0}]
+  }
+  foreach eta {-3.2 -2.5 -2.4 -2.3 -2.2 -2.1 -2 -1.9 -1.8 -1.7 -1.6 -1.5 -1.4 -1.3 -1.2 -1.1 -1 -0.9 -0.8 -0.7 -0.6 -0.5 -0.4 -0.3 -0.2 -0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2 2.1 2.2 2.3 2.4 2.5 2.6 3.3} {
+    add EtaPhiBins $eta $PhiBins
+  }
+
+  # 20 degrees towers
+  set PhiBins {}
+  for {set i -9} {$i <= 9} {incr i} {
+    add PhiBins [expr {$i * $pi/9.0}]
+  }
+  foreach eta {-4.9 -4.7 -4.5 -4.3 -4.1 -3.9 -3.7 -3.5 -3.3 -3 -2.8 -2.6 2.8 3 3.2 3.5 3.7 3.9 4.1 4.3 4.5 4.7 4.9} {
+    add EtaPhiBins $eta $PhiBins
+  }
+
+  # default energy fractions {abs(PDG code)} {Fecal Fhcal}
+  add EnergyFraction {0} {0.0 1.0}
+  # energy fractions for e, gamma and pi0
+  add EnergyFraction {11} {1.0 0.0}
+  add EnergyFraction {22} {1.0 0.0}
+  add EnergyFraction {111} {1.0 0.0}
+  # energy fractions for muon, neutrinos and neutralinos
+  add EnergyFraction {12} {0.0 0.0}
+  add EnergyFraction {13} {0.0 0.0}
+  add EnergyFraction {14} {0.0 0.0}
+  add EnergyFraction {16} {0.0 0.0}
+  add EnergyFraction {1000022} {0.0 0.0}
+  add EnergyFraction {1000023} {0.0 0.0}
+  add EnergyFraction {1000025} {0.0 0.0}
+  add EnergyFraction {1000035} {0.0 0.0}
+  add EnergyFraction {1000045} {0.0 0.0}
+  # energy fractions for K0short and Lambda
+  add EnergyFraction {310} {0.3 0.7}
+  add EnergyFraction {3122} {0.3 0.7}
+
+  # set ECalResolutionFormula {resolution formula as a function of eta and energy}
+  # http://arxiv.org/pdf/physics/0608012v1 jinst8_08_s08003
+  # http://villaolmo.mib.infn.it/ICATPP9th_2005/Calorimetry/Schram.p.pdf
+  # http://www.physics.utoronto.ca/~krieger/procs/ComoProceedings.pdf
+  set ECalResolutionFormula {                  (abs(eta) <= 3.2) * sqrt(energy^2*0.0017^2 + energy*0.101^2) + \
+                             (abs(eta) > 3.2 && abs(eta) <= 4.9) * sqrt(energy^2*0.0350^2 + energy*0.285^2)}
+
+  # set HCalResolutionFormula {resolution formula as a function of eta and energy}
+  # http://arxiv.org/pdf/hep-ex/0004009v1
+  # http://villaolmo.mib.infn.it/ICATPP9th_2005/Calorimetry/Schram.p.pdf
+  set HCalResolutionFormula {                  (abs(eta) <= 1.7) * sqrt(energy^2*0.0302^2 + energy*0.5205^2 + 1.59^2) + \
+                             (abs(eta) > 1.7 && abs(eta) <= 3.2) * sqrt(energy^2*0.0500^2 + energy*0.706^2) + \
+                             (abs(eta) > 3.2 && abs(eta) <= 4.9) * sqrt(energy^2*0.9420^2 + energy*0.075^2)}
+}
+
+##########################
+# Track pile-up subtractor
+##########################
+
+module TrackPileUpSubtractor TrackPileUpSubtractor {
+# add InputArray InputArray OutputArray
+  add InputArray Calorimeter/eflowTracks eflowTracks
+  add InputArray ElectronEnergySmearing/electrons electrons
+  add InputArray MuonMomentumSmearing/muons muons
+
+  # assume perfect pile-up subtraction for tracks with |z| > fZVertexResolution
+  # Z vertex resolution in m
+  set ZVertexResolution 0.0001
+}
+
+####################
+# Energy flow merger
+####################
+
+module Merger EFlowMerger {
+# add InputArray InputArray
+  add InputArray TrackPileUpSubtractor/eflowTracks
+  add InputArray Calorimeter/eflowTowers
+  add InputArray MuonMomentumSmearing/muons
+  set OutputArray eflow
+}
+
+#############
+# Rho pile-up
+#############
+
+module FastJetFinder Rho {
+  set InputArray Calorimeter/towers
+
+  set ComputeRho true
+  set RhoOutputArray rho
+
+  # area algorithm: 0 Do not compute area, 1 Active area explicit ghosts, 2 One ghost passive area, 3 Passive area, 4 Voronoi, 5 Active area
+  set AreaAlgorithm 5
+
+  # jet algorithm: 1 CDFJetClu, 2 MidPoint, 3 SIScone, 4 kt, 5 Cambridge/Aachen, 6 antikt
+  set JetAlgorithm 4
+  set ParameterR 0.6
+  set GhostEtaMax 5.0
+  set RhoEtaMax 5.0
+
+  set JetPTMin 0.0
+}
+
+#####################
+# MC truth jet finder
+#####################
+
+module FastJetFinder GenJetFinder {
+  set InputArray Delphes/stableParticles
+
+  set OutputArray jets
+
+  # algorithm: 1 CDFJetClu, 2 MidPoint, 3 SIScone, 4 kt, 5 Cambridge/Aachen, 6 antikt
+  set JetAlgorithm 6
+  set ParameterR 0.6
+
+  set JetPTMin 20.0
+}
+
+############
+# Jet finder
+############
+
+module FastJetFinder FastJetFinder {
+  set InputArray Calorimeter/towers
+
+  set OutputArray jets
+
+  # area algorithm: 0 Do not compute area, 1 Active area explicit ghosts, 2 One ghost passive area, 3 Passive area, 4 Voronoi, 5 Active area
+  set AreaAlgorithm 5
+
+  # jet algorithm: 1 CDFJetClu, 2 MidPoint, 3 SIScone, 4 kt, 5 Cambridge/Aachen, 6 antikt
+  set JetAlgorithm 6
+  set ParameterR 0.6
+
+  set JetPTMin 20.0
+}
+
+###########################
+# Jet Pile-Up Subtraction
+###########################
+
+module JetPileUpSubtractor JetPileUpSubtractor {
+  set JetInputArray FastJetFinder/jets
+  set RhoInputArray Rho/rho
+
+  set OutputArray jets
+
+  set JetPTMin 20.0
+}
+
+##################
+# Jet Energy Scale
+##################
+
+module EnergyScale JetEnergyScale {
+  set InputArray JetPileUpSubtractor/jets
+  set OutputArray jets
+
+ # scale formula for jets
+  set ScaleFormula {1.0}
+}
+
+###################
+# Photon efficiency
+###################
+
+module Efficiency PhotonEfficiency {
+  set InputArray Calorimeter/photons
+  set OutputArray photons
+
+  # set EfficiencyFormula {efficiency formula as a function of eta and pt}
+
+  # efficiency formula for photons
+  set EfficiencyFormula {                                      (pt <= 10.0) * (0.00) + \
+                                           (abs(eta) <= 1.5) * (pt > 10.0)  * (0.95) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 10.0)  * (0.85) + \
+                         (abs(eta) > 2.5)                                   * (0.00)}
+}
+
+##################
+# Photon isolation
+##################
+
+module Isolation PhotonIsolation {
+  set CandidateInputArray PhotonEfficiency/photons
+  set IsolationInputArray EFlowMerger/eflow
+  set RhoInputArray Rho/rho
+
+  set OutputArray photons
+
+  set DeltaRMax 0.5
+
+  set PTMin 0.5
+
+  set PTRatioMax 0.1
+}
+
+#####################
+# Electron efficiency
+#####################
+
+module Efficiency ElectronEfficiency {
+  set InputArray TrackPileUpSubtractor/electrons
+  set OutputArray electrons
+
+  # set EfficiencyFormula {efficiency formula as a function of eta and pt}
+
+  # efficiency formula for electrons
+  set EfficiencyFormula {                                      (pt <= 10.0) * (0.00) + \
+                                           (abs(eta) <= 1.5) * (pt > 10.0)  * (0.95) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.5) * (pt > 10.0)  * (0.85) + \
+                         (abs(eta) > 2.5)                                   * (0.00)}
+}
+
+####################
+# Electron isolation
+####################
+
+module Isolation ElectronIsolation {
+  set CandidateInputArray ElectronEfficiency/electrons
+  set IsolationInputArray EFlowMerger/eflow
+  set RhoInputArray Rho/rho
+
+  set OutputArray electrons
+
+  set DeltaRMax 0.5
+
+  set PTMin 0.5
+
+  set PTRatioMax 0.1
+}
+
+#################
+# Muon efficiency
+#################
+
+module Efficiency MuonEfficiency {
+  set InputArray TrackPileUpSubtractor/muons
+  set OutputArray muons
+
+  # set EfficiencyFormula {efficiency as a function of eta and pt}
+
+  # efficiency formula for muons
+  set EfficiencyFormula {                                      (pt <= 10.0) * (0.00) + \
+                                           (abs(eta) <= 1.5) * (pt > 10.0)  * (0.95) + \
+                         (abs(eta) > 1.5 && abs(eta) <= 2.7) * (pt > 10.0)  * (0.85) + \
+                         (abs(eta) > 2.7)                                   * (0.00)}
+}
+
+################
+# Muon isolation
+################
+
+module Isolation MuonIsolation {
+  set CandidateInputArray MuonEfficiency/muons
+  set IsolationInputArray EFlowMerger/eflow
+  set RhoInputArray Rho/rho
+
+  set OutputArray muons
+
+  set DeltaRMax 0.5
+
+  set PTMin 0.5
+
+  set PTRatioMax 0.1
+}
+
+###################
+# Missing ET merger
+###################
+
+module Merger MissingET {
+# add InputArray InputArray
+  add InputArray EFlowMerger/eflow
+  set MomentumOutputArray momentum
+}
+
+##################
+# Scalar HT merger
+##################
+
+module Merger ScalarHT {
+# add InputArray InputArray
+  add InputArray UniqueObjectFinder/jets
+  add InputArray UniqueObjectFinder/electrons
+  add InputArray UniqueObjectFinder/photons
+  add InputArray UniqueObjectFinder/muons
+  set EnergyOutputArray energy
+}
+
+###########
+# b-tagging
+###########
+
+module BTagging BTagging {
+  set PartonInputArray Delphes/partons
+  set JetInputArray JetEnergyScale/jets
+
+  set BitNumber 0
+
+  set DeltaR 0.5
+
+  set PartonPTMin 1.0
+
+  set PartonEtaMax 2.5
+
+  # add EfficiencyFormula {abs(PDG code)} {efficiency formula as a function of eta and pt}
+  # PDG code = the highest PDG code of a quark or gluon inside DeltaR cone around jet axis
+  # gluon's PDG code has the lowest priority
+
+  # default efficiency formula (misidentification rate)
+  add EfficiencyFormula {0} {0.001}
+
+  # efficiency formula for c-jets (misidentification rate)
+  add EfficiencyFormula {4} {                                      (pt <= 15.0) * (0.000) + \
+                                                (abs(eta) <= 1.2) * (pt > 15.0) * (0.2*tanh(pt*0.03 - 0.4)) + \
+                              (abs(eta) > 1.2 && abs(eta) <= 2.5) * (pt > 15.0) * (0.1*tanh(pt*0.03 - 0.4)) + \
+                              (abs(eta) > 2.5)                                  * (0.000)}
+
+  # efficiency formula for b-jets
+  add EfficiencyFormula {5} {                                      (pt <= 15.0) * (0.000) + \
+                                                (abs(eta) <= 1.2) * (pt > 15.0) * (0.5*tanh(pt*0.03 - 0.4)) + \
+                              (abs(eta) > 1.2 && abs(eta) <= 2.5) * (pt > 15.0) * (0.4*tanh(pt*0.03 - 0.4)) + \
+                              (abs(eta) > 2.5)                                  * (0.000)}
+}
+
+module TauTagging TauTagging {
+  set ParticleInputArray Delphes/allParticles
+  set PartonInputArray Delphes/partons
+  set JetInputArray JetEnergyScale/jets
+
+  set DeltaR 0.5
+
+  set TauPTMin 1.0
+
+  set TauEtaMax 2.5
+
+  # add EfficiencyFormula {abs(PDG code)} {efficiency formula as a function of eta and pt}
+
+  # default efficiency formula (misidentification rate)
+  add EfficiencyFormula {0} {0.001}
+  # efficiency formula for tau-jets
+  add EfficiencyFormula {15} {0.4}
+}
+
+#####################################################
+# Find uniquely identified photons/electrons/tau/jets
+#####################################################
+
+module UniqueObjectFinder UniqueObjectFinder {
+# earlier arrays take precedence over later ones
+# add InputArray InputArray OutputArray
+  add InputArray PhotonIsolation/photons photons
+  add InputArray ElectronIsolation/electrons electrons
+  add InputArray MuonIsolation/muons muons
+  add InputArray JetEnergyScale/jets jets
+}
+
+##################
+# ROOT tree writer
+##################
+
+module TreeWriter TreeWriter {
+# add Branch InputArray BranchName BranchClass
+  add Branch Delphes/allParticles Particle GenParticle
+  add Branch TrackMerger/tracks Track Track
+  add Branch Calorimeter/towers Tower Tower
+#  add Branch Calorimeter/eflowTracks EFlowTrack Track
+#  add Branch Calorimeter/eflowTowers EFlowTower Tower
+#  add Branch MuonMomentumSmearing/muons EFlowMuon Muon
+  add Branch GenJetFinder/jets GenJet Jet
+  add Branch UniqueObjectFinder/jets Jet Jet
+  add Branch UniqueObjectFinder/electrons Electron Electron
+  add Branch UniqueObjectFinder/photons Photon Photon
+  add Branch UniqueObjectFinder/muons Muon Muon
+  add Branch MissingET/momentum MissingET MissingET
+  add Branch ScalarHT/energy ScalarHT ScalarHT
+  add Branch Rho/rho Rho Rho
+}
+
