Tim Brooks

Glen Cowan

My Links

• My web space at RHUL
• My research
• Slides for talks
• Datasets I'm using
• My Event Generation
• My Service Work Log
• Papers I'm reading/have read
• My Public Physics Bookmarks
• My jobs in the panda framework

ATLAS Links

• ATLAS Home
• AFS console
• ATLAS data summary - Daily plots of collected data.
• GridView - Nice visualisation of what the grid is doing
• ATLAS Operations - Online detector information.
• OP Vistars - Online LHC Status updates.
• AMI 7TeV Datasets
• CERN AIS management page - CERN users can manage their lxplus preferences and search the CERN directory here.
• Vidyo Linux Client Download
• ATLAS Luminosity Calculation (as of 25-06-2010)
• ATLAS 'Physics Containers' information
• Current ATLAS software releases
• OTP shift booking
• ATLAS data periods
• ATLAS SUSY Meetings

My Research

See my research page in the ATLAS web. Currently working on top-quark background estimation in supersymmetry selections. Investigating boosted decision trees for characterization of top events. ATLAS SUSY points:

• SU4 = { m_{0} = 200, m_{1/2} = 160, A_{0} = -400, tan \beta = 10, sign \mu = + }

Programming Tips

Command line-fu

dataset="user.brooks.mc11_7TeV.555555.Dataset.NTUP_SUSY/"
dq2-ls -f $dataset | cut -f 2 | grep root | tr "\\n" "," | xargs -i dq2-get -f {} $dataset

Of course, all that's kind of long to type, so you might want a script for that anyway.

Bash Basics

It's handy to have a /bin folder in your home area. This can be added to your path in your bash start script: export PATH=~/bin:$PATH
Placing scripts here can make mindless tasks much easier.
e.g. To rename a bunch of files that are called xxxthisxxx to xxxthatxxx, I have a bash script called mvls that is run like: mvls this that and changes every file in the pwd that contains 'this' in the name to have 'that' instead.
Here's the script

#!/bin/bash
for file in *;do
newfile=$(echo $file | sed s/$1/$2/g)
test "$file" != "$newfile" && mv "$file" $newfile
done

JaxoDraw needs to be run in it's home directory for axoDraw.sty else it can't export to .eps
A quick script switches the wd, and returns it to how it was:

#!/bin/bash
export jaxodrawdir=/scratch0/brooks/tools/JaxoDraw-2.0-1/
export OWD=$PWD
cd $jaxodrawdir
java -jar ${jaxodrawdir}jaxodraw-2.0-1.jar
cd $OWD

PyROOT

Basic script

import user 
import ROOT
import PyCintex
import AthenaROOTAccess.transientTree

# a bit less ugly ROOT style...
ROOT.gROOT.SetStyle("Plain")

f = ROOT.TFile.Open('/scratch0/brooks/MC09/mc09_7TeV.105200.T1_McAtNlo_Jimmy.recon.AOD.e510_s765_s767_r1205_tid123042_00/AOD.123042._000001.pool.root.1')
tt = AthenaROOTAccess.transientTree.makeTree(f)

Save this as something like tutorial.py and run it using python -i tutorial.py

Batching plots

ROOT.gROOT.SetBatch(True)                  # Switch to batch mode
c1=ROOT.TCanvas( 'c1', 'Plot', 640, 480 )  # Make a canvas of size 640x480
c1.cd()                                    # Set the output canvas (lets us have several going at once)
tt.Draw("ElectronAODCollection.phi()")     # Draw the phi distribution of electrons in the AOD
c1.Print("plot.png")                       # Save the canvas as an image file (ROOT uses the extension given)

Some things to play around with

• from PyAnalysisUtils import PDG Lets you use PDG. instead of remembering pdgIds. Cool feature -> PDG.root_names[-PDG.nu_mu] returns a string with the ROOT syntax for an anti-muon-neutrino.
• import AthenaCommon.SystemOfUnits as Units Gives you a Units object with most units in the ATLAS base units. e.g. Units.TeV = 1000000.0
• ROOT.gROOT.SetBatch(True) Switches Root to batch mode.

Root

Installing Root

sudo apt-get install root-system

Installing Root from source

sudo apt-get install make g++ gcc binutils libx11-dev libxpm-dev libxft-dev libxext-dev

Setting up root

Setting the plot style to plain

Rint.Logon: ~/rootlogon.C

{
  gROOT->SetStyle("Plain");
  gStyle->SetCanvasBorderMode(0); // turn off canvas borders
  cout << "******************************" << endl; 
  cout << "* Welcome to ROOT v" << gROOT->GetVersion() << " *" << endl; 
  cout << "******************************" << endl; 
  cout << endl;
}

Adding Legends to Plots

leg = new TLegend(0.6,0.7,0.89,0.89);
leg->AddEntry(hist_A, "Sample A","f");
leg->AddEntry(hist_B, "Sample B","f");
leg->SetFillStyle(0)
leg->Draw("same") 

Setting up an Axis

h->GetXaxis()->SetNdivisions(105) -Sets tick number. Format is minor ticks per major one * 100 + major ticks in the axis, i.e. to divide into 13 major ticks with 5 minors each; use 500 + 13 = 513.

Getting reasonable colour palettes

Adding multiple files with hadd

hadd usage:

Usage: hadd [-f] [-T] targetfile source1 [source2 source3 ...]
This program will add histograms from a list of root files and write them
to a target root file. The target file is newly created and must not 
exist, or if -f ("force") is given, must not be one of the source files.
Supply at least two source files for this to make sense... ;-)
If the first argument is -T, Trees are not merged
When -the -f option is specified, one can also specify the compression
level of the target file. By default the compression level is 1, but
if "-f0" is specified, the target file will not be compressed.
if "-f6" is specified, the compression level 6 will be used.
if Target and source files have different compression levels
 a slower method is used

TMVA

In booking a tree the option Boost_AdaBoostBeta (Default=1) is "The ADA boost parameter that sets the effect of every boost step on the event weights"

Bugs

• In TMVA Manual,

ATLAS Software Links

• Neil's atlfast I tutorial
• Files in our network storage

PowHeg for ATLAS

Packages of note

• Generators/EvgenJobTranforms
• Generators/EvgenATLAS.JobOptions - Set of standard JobOptions for many processes of importance. Standardized such that samples can be merged with production sets.

Computing resources

The faraday cluster is controlled via linappserv0. Instructions for using the cluster are here: How to use the cluster. The cluster can be used for ATLAS production. See my event generation page.

• poster.pdf: RAL Summer School Poster