Back to Jeremy's Homepage

1. General Information
1. Contact Information
2. NICADD
3. SLAC


2. NICADD Documents
1. Projects
2. Computing
3. Presentations and Papers
4. Notes


3. Particle Physics Software
1. General
2. Libraries
3. Geant4
4. Detector Simulation
5. Event Generation
6. Analysis
7. Graphics and Visualization


4. Computing
1. Manuals and Guides
2. Linux & Unix
3. Development Resources
4. Programming Languages
5. Software Download
6. Distributed Computing


5. Physics
1. Publications
2. Research Labs and Collaborations
3. Conferences
4. Experiments
5. Explication


6. Miscellaneous
1. Internet Search
2. Science and Math

• Jeremy I. McCormick
  SLAC, Mail Stop 71
  2575 Sand Hill Road
  Menlo Park, CA 94025
  office tele: 650-926-8794
  
  
• jeremy AT nicadd.niu.edu
  
• jeremym AT slac.stanford.edu
  
• SLAC Employee Record

• Homepage - Northern Illinois Center for Accelerator and Detector Development
• K2 Cluster System Administration
• LCD Computing
• NICADD elog - requires user/password
• Research
• Staff Directory
• Web Statistics
• NICADD CVS Web

• Homepage - Stanford Linear Accelerator Center
• Webmail

General

• International Linear Collider Resources
• LCD Simulation Resources

LCDG4

• LCDG4 Homepage
• Source Documentation

LCDD

• Source Documentation
• XML Schema Documentation

SLIC

• Source Documentation
• Getting Started Guide

Test Beam in Mokka

• Test Beam in Mokka User Guide - does not cover particulars of the latest driver (TB03)
• Requirements Document for Test Beam Simulator
• Requirements Document for Test Beam Analysis Framework

LCComponents (deprecated)

• Source Documentation - includes prose write-up on mainpage

Standalone Test Beam Simulator (deprecated)

• Test Beam Simulator Homepage
• Source Documentation

Condor

• Condor for High Throughput Computing - project proposal for Grid-enabled batch computing; includes instructions
• Condor View - NICADD Condor stats

CVS

• CVS Instructions
• CVSWeb

Development Server

• Instructions for Accessing via SCP/sftp
• LCD Computing Development Server
• Programming and Shell Scripting

Simulations

• NICADD Simulation Guidelines

My Presentations (ppt)

• LCD Computing Overview - NICADD
• NICADD Test Beam Simulator - Fermilab Geant4 Tutorial
• Test Stand and Test Beam Projects - NICADD
• NICADD LCD Computing - LC-CAL
• Test Beam - NICADD
• G4 Optical Processes and cellsim project - NICADD
• Test Beam Simulations - LC-CAL
• Test Beam in Mokka - NICADD
• MC Particle Handling in LCDG4 - SLAC Geant4 Tutorial
• Test Beam in Mokka - SLAC Geant4 Tutorial
• Test Beam Update - NICADD
• Mutual Certification of TB00 and TB02: A Preliminary Report - NICADD
• LC Geometry Overview - ANL LCSW
• Test Beam Simulations - ANL LCSW
• SLAC Simulations Update: LCDD and SLIC - DESY ILC Sim Workshop (virtual)
• ILC Simulations Update - NICADD
• ILC Simulations Architecture Proposal Diagrams

Web Papers

• Comparison of Mokka and LCDG4 Geometry Handling - presented at a SLAC LCD simulations conference
• LCD Simulation Design Document - D. Chakraborty

Archives

• NICADD CDS Agenda Server - current NICADD meetings
• NICADD DHcal presentations - password protected; to Nov '03
• American Working Group on LC: Bi-weekly Meetings
• Mirrored Documents - includes NICADD, ALCWG, CHEP and others

Articles

• A. Dyshkant, D. Beznosko, G. Blazey, D. Chakraborty, K. Frances, D. Kubik, J. McCormick et al,
  "Small Scintillating Cells as the Active Elements in a Digital Hadron Calorimeter for the e+e- Linear Collider Detector",
  FERMILAB-PUB-04/015, Feb 9, 04
• "Towards a Scintillator Based Digital Hadron Calorimeter for the Linear Collider Detector", co-author
• Fermilab Design Proposal for DESY/Calice LC Test Beam Tail Catcher Module, simulations programmer

Current

• LCD Simulation and Physics Notes - notes on simulations, event generation, physics, Pandora-Pythia, DHCal, etc.
• LCD Computing To Do List - annotated To Do list organized by topic; no longer maintained

Links

• Computer Books - Amazon links
• Detector Description and Geometry
• DocBook
• Silicon Detector (SiD) Study
• XML

Meetings & "One-time"

• LCD Computing 7-28-03 - notes for LCD Computing meeting
• New Server Configuration 9-27-03
• World Simulation Group Meeting 4-30-04 - shorthand text minutes by JM

Internship

• Fall/Summer Internship 2003: Weekly Journal - week-by-week accounting of work time; frozen "ToDo" list; no longer maintained
• Summer Internship 2003, Final Report - "What I did this summer..."

Software Listings

• CERN API links
• CERN Savannah
• CPC Program Library
• Fermitools
• LCG Software Process Infrastructure - top-level access to many links and packages
  • Distribution Area - large collection of packages in tar.gz
• LCG Code Documentation using Doxygen
• Physics Software Links
• SLAC Software Directory

Projects

• D0 Dist
• LCG Project - Applications Area

FreeHEP

• Freehep.org - AIDA, WIRED, JAS, etc.
• Current API
• hep.lcd
• Bug Database
• User Forum

CERNlib

• CERN Program Library - aka CERNlib

CLHEP

• CLHEP Homepage
• Reference Manual 1.8
  • HEPStrings Class Reference
• Reference Manual 1.7
  • HEP Random

Homepage, Download and Support

• Homepage
• Download Source
• HyperNews Forum - primary forum on Geant4 issues
  • Recent Posts

Core Docs

• User Docs - top-level index to Geant4 documentation
• User's Guide for Application Developers - core docs for programmers
• User's Guide for Toolkit Developers
• Physics Reference Manual
• Object-Oriented Analysis and Design
• Command Reference
• LXR Source Code Browser

Doxygen (NICADD)

• Geant4
• File List
• Class Hierarchy

Resources (some duplication)

• Collaborating Institutions
• CERN Training Materials
• DESY Tutorial
• Educated Guess Physics Lists
• INFN - papers, some command/class explication, projects, etc.
  • Advanced Examples
• Results, Reports & Publications
• SLAC Tutorials and Tips
  • Presentations from Feb '02 Tutorial at SLAC
    • Presentations Directory
  • Presentations from October '03 Tutorial at Fermilab
  • Presentations from March '04 Tutorial at SLAC
  • Tips on Tracking and Trajectories
  • Using Geant4 at SLAC
• Space Information System Collaboration
• Space User's Workshop
• Technical Forum
• Technology Transfer - applications in medical/astro
• TRIUMF - links @ Canada's national physics lab; includes Geant4 source code browser
  • Presentations from '03 Workshop at TRIUMF

Tools and Applications

• DAWN viewer
• FLUGG - FLUKA interface
• GDML - a geometric markup language for detector description
  • CVS Online
  • GDML Sourcecode Browser - Doxygen at NICADD
  • GDML 2.0 Schema Documentation
• Geant4-Python
• General Particle Source (GPS)
  • Examples
• Geant4 Geometry XML Convertor
• Gain and RGAG Technical Manual
• G4UIRoot
• GUI and Environments at Naruto - GAG, Gain and Momo (GGE + GPE)
  • Downloads Page
• JAS Plugin - SLAC CVS for most recent

Mokka

• Getting started with Mokka - user/pwd required
• Mokka main page - public
• Mokka CGA - Common Geometry Access; usr/pwd required
• Mokka MySQL DB - usr/pwd required
• Mokka Sourcecode

Gismo (legacy)

• Gismo - many dead links
• Altering Detector Geometries in JAS and Gismo
• Gismo on Linux: Installation and Running Tutorial
• Running Gismo
• Gismo Install
• North American LCD Simulations Talk - historical interest plus gives Gismo capabilities
• EGS

Lelaps

• Parameterized Shower Simulation in Lelaps: a Comparison with Geant4 (pdf)
• Fast Simulation using LELAPS (ppt)
• Matprop on the WWW

Miscellaneous Simulators

• FLUKA
• GEANT3
• LCDROOT

LCIO and SIO

• LCIO Homepage
  • Java API 1.0 (JavaDoc)
  • C++ API 1.0 (Doxygen)
  • User Guide 1.0
• SIO manual (pdf)

Listing

• Inventory of Event Generators for Linear Collider Physics - comprehensive

Pythia, Pandora-Pythia and related

• Pandora-Pythia - includes links to Pandora-Pythia README (setup/usage) and Pandora Documentation
  • Pandora-Pythia Manual (pdf)
• Pandora
  • Mike Peskin Pandora Presentation (pdf)
  • Pandora 2.3 Patches
• Pythia
  • Pythia Manual (html)
  • Pythia 6.2 (pdf)
  • Pythia Decay Listing
  • Pythia7 - C++ rewrite (alphaware)

Other Generators

• HERWIG
  • HERWIG++
• ISAJET

Java Interface

• Java-based Linear Collider Physics and Detector Studies - Java interfaces to Pandora, Pythia, et al
• Java Physics Generator and Analysis Modules

Frameworks and General Toolkits

• Atlas Event Generation - requires Athena
• CERNlib
• CMS Generators
• LCG Event Generator Review
• ThePEG - toolkit for HEP Event Gen

StdHep

• Monte Carlo Numbering Scheme
• StdHEP - output format for Monte Carlo events
• StdHEP C++ - the stdHEP C++ libraries (included in CLHEP)
• StdHEP 5 Manual (ps)

HepMC

• HepMC

• HEPEvt Standard - node from PYTHIA manual
• JNI Interface

Java Analysis Studio (JAS)

• HEP API Docs
• JAS homepage
• JAS Mailing List
• JAS 3
• JAS in Atlas - links to useful material
• OO Design and Implementation: Java and Java Analysis Studio - JAS2
• JAS-Geant4 Tutorial - driving Geant4 from JAS
• Full Reconstruction Example

AIDA and related

• AIDA Homepage
• AIDA-JNI
• API
  • IHistogramFactory
• Fitting in AIDA (pdf)
• JAIDA
  • JAIDA 3.2.1 Release Notes - important info on styles
• Open Scientist - AIDA compliant interface
• PAIDA
• Physicist Interface (PI) Project
• Adding AIDA to Geant4
• Using AIDA for Analysis with Geant4

ROOT

• ROOT Homepage
• ROOT User's Guide
• ROOT @ FNAL
• ftp archive
• PyROOT - Python binding
• Tutorials
• Virtual Monte Carlo

Analysis Packages and Libraries

• Anaphe - superceded by LCG Application area of LHC Computing Grid Project (includes Lizard)
• COLT Distribution - Java library
• HBook Manual
• HippoDraw
• HTL - Histogram Template Language
• PAW Homepage

HEP Geometry and Event Visualization

• GraXML
• IGUANA
• Persint
• Wired Event Display
  • Wired Tutorial

Framework

• AliROOT
• CMT - Configuration Management Tool; used by LHCb
  • A Project Under CMT
• COBRA
• EPICS - embedded control systems
• GAUDI
• SCRAM - Software, Configuration, Release and Management
• SEAL

Basic Graphing and Plotting, Software and Instructions

• Drawing Tools for Scientific Graphs
• Grace
• Graphiz toolkit - AT&T open source graphing toolkit; used for Doxygen dependency graphs
• GNU Plot
• Scientific Graphs with Microsoft Excel

These are not specifically for HEP, but this section fits best here rather than in General Computing.

Scientific Data Visualization

• Advanced Visual Systems
• GRI
• NAS SW Downloads
• Scientific Computing and Visualisation - BU dept.
  • Recent Visualizations
• Scientific Graphics Toolkit
• Scientific Visualization Sites - aka "visWeblets"
• Scientific Visualization Software
• Vis5d+

Graphic Software and Toolkits, Listings

• Coin3D - Inventor backend
• Graphics Hotlist
• Graphics Software - @ Lawrence Livermore
• OpenDX
• OpenGL

VTK (Visualization Toolkit) and Related

• MayaVi
• Paraview
• PV-Wave
• VTK

Feynman Diagrams

• FeynMF
• FeynDiagram
• ROOT example

Linux and Unix Guides

• Advanced Bash Scripting Guide
  • On Single Page
  • Tests
• Fultus eLibrary - extensive collection on RH, FreeBSD and Linux
• Linux Cookbook
• The Linux Documentation Project
• Linux System Administrator's Guide
• Red Hat Linux Manuals
• Rute User's Tutorial and Exposition - comprehensive guide to Linux system administration
  • Linux File System Standard
• SuperMan Pages
• Unix Power Tools

Software Manuals

• Apache Project
  • Authentication, Authorization and Access Control
• CVS Home
  • CVS HowTo
• Emacs Online Docs
• Emacs Wiki
• Maximum RPM
• MySQL manual
• Pine Homepage
• UPS4

Unix GUI

• Gnome 2.4
• GNU/Linux Desktop Survival Guide
• KDE
  • Desktop Userguide
  • Developer
  • KDE Docs
  • Trolltech Qt Docs

Kernel Sourcecode

• Kernel Source Browser
• Cross-Referencing Linux
• Public Linux Archive

Kernel Docs

• Index of Documentation for People Interested in Writing and/or Understanding the Linux Kernel
• Chris Gould's Linux Kernel Architecture and Other OS Links
• Kernel HOWTO
• Linux Kernel Archives

General

• Loads of Linux Links
• Fermi Linux

• Autobook - online book covering automake, autoconf and libtool
• autoconf Macro Archive
• GCC online docs
• GDB ToC
• GNU Manuals - essential documents for all Linux distributions
  • binutils
  • libtool
  • make

Documentation

• BoostBook
  • Doxygen to Boostbook to Docbook - see bottom section
• DocBook
  • Definitive Guide
  • DocBook Open Repository
  • FAQ
  • Wiki
• Doxygen - homepage
  • Doxygen Manual - @ nicadd
  • Short Doxygen HowTo
• LateX Math Symbols
• texinfo

Debugging

• Debugging Linux Apps
• Debugging Tools for Dynamic Storage Allocation and Memory Management
• Using GDB under GNU Emacs
• Etnus' TotalView - commerical debugger
• Valgrind - C++ memory debugger

• Computer Books - looks like all of them
• Bruce Eckel Downloads - Thinking in Java, C++, Patterns
• C++ Pro Handbook
• Dive into Python
• Industrial Strength C++
• How to Write Unmaintainable Code - a little humor
• Learning to Program - Python
• Programming in C: UNIX System Calls and Subroutines using C
• Structure and Interpretation of Computer Programs
• Thinking in C++: Volume 1, Volume 2
• Thinking in Java
• Numerical Recipes
• Linux Device Drivers, 2nd Edition
• Internet Application Workbook - interesting textbook by Philip Greenspun
• The Art of Unix Programming
• On Lisp
• How to Think Like a Computer Scientist
• On Search, the Series
• Teach Yourself C++ in 21 Days

C

• Beej's Guide to Network Programming in C
• C Standard Library and Iostream Reference
• C Standard Library Quick Reference
• Indian Hill C Style Guide

C++

• Association of C and C++ Users (ACCU) - book reviews, articles
• Artistic Style - auto-indenter (for other langs, too)
• Association of C & C++ Users
  • C/C++ Resources
• BOOST library
  • Boost.Python
• Available C++ Libraries
• Bjarne Stoustrup's C++ Programming Language
• C plus plus Resource Network
• C++ Annotations - written for C programmers
• C, C++ and STL Tutorial - 40 lessons
• C++ Glossary
• C++ Notes
• C++ Links - old but good
• Containers Cheat Sheet
• Cpp Reference - C, C++ and STL
• Defining Iterators
• FAQ Lite
• libstdc++ - docs on GNU impl. of C++ standard
• Mozilla's Portable C++ Guide
• C++ ISO Standard
• File I/O
• Function Pointers - includes C
• libstd++ Doxygen
• OpenTop
• SQLAPI++ - a fully-featured C++ SQL API
• STL Programmer's Guide
• STL Newbie Guide
• SWIG - interface generator for Python, Java, et al
• Taligent Docs
  • Taligent Guide to Designing Programs
  • Taligent Style Guide
• Type Reflection Support

Python

• Activestate Python
  • Python Cookbook
• Cheetah
• DB-API HowTo
• GUI Programming with PyQt
• IPython Homepage - interactive Python command shell
  • manual
• Modeling - Object-Relational Bridge (ORB)
• NumPy - numerical processing; rewrite of Numeric
• Psyco
• Python Homepage - ground zero
  • Current Python Docs - keep this under your pillow at night
• PyQt
• Python 2.4 Reference Card
• ReportLab
• SciPy
• Statistical Computing Using Python
• Text Processing in Python - complete book
• Twisted Python - application framework
• Vaults of Parnassus
• WxPython
  • Boa Constructor
• Zope - web application framework
  • Collective - Zope CMS projects
  • Plone - Zope-based CMS

Java

• API Specification 1.4.2
• Colt - scientific / math lib
• Learning the Java Language Tutorial
• Eclipse - uber-IDE
• Eclipse Tutorials
• IBiblio Java Links
• Integrating Java with C++
• Introductory Java Tutorial
• Enterprise Java for Linux HOWTO
• Java Glossary
• Hibernate - ORB
• java.sun.com
• JNI Trail
• Programming with JNI
• RMI
• Sun's Java Glossary
• The Server Side
• Tools and Utilities
• XDoclet - code generation

HTML and Web Dev

• HTML 4.01 Specification @ WWW3.org
• HTML Special Characters
• W3 Schools

• Freshmeat - package releases
• GNU Free Software Directory
• IBiblio, IBiblio Linux - free software and other materials
• Scientific Applications on Linux - includes Parallel Computing
• Sourceforge - open source repository
• Tucows - all platforms

Admin

• Top 75 Security Tools

RPMs

• RPM Seek
• RPM Search @ PBone
• Fresh RPMs
• Apt Fresh RPMs
• RPM Find

Linux Distributions

• Links
• Linux ISO

• Parallel Computing Sites
• Batch Computing Software Overview

Beowulf

• Beowulf Clusters
• How to Build a Beowulf: a Tutorial
• Beowulf Cluster Mini-HowTo

Parallel Computing Software

• TOP-C
• PVM
• MPI
• Open Mosix

Batch Processing

• Condor
  • User Manual 6.6
    • Command Reference
• FBSNG - Fermi Lab batch processing system
• Portable Batch System - used at Fermilab, clued0
• Distributed Queueing System
• Network Queueing System

Administration

• Cfengine - configuration engine

General Grid Projects

• Grid.org
• Teragrid
• Global Grid Forum
• Datagrid Project
• Globus Alliance
• Sun Grid Computing
  • GridEngine
• Platform
  • LSF
• CollabNet

Physics Grid

• Globally Interconnected Object Databases - CALTech/CERN/HP joint project
• LHC Computing Grid Project (LCG)
• Particle Physics Data Grid
• International Virtual Data Grid Laboratory
• Distributed Particle Accelerator Design
• Grid Physics Network
• US Physics Grid Projects (ppt)

• American Institute of Physics
• arXiv - preprints archive
• CERN Document Server
• FNAL Library
• HEPDATA
• KISS - KEK Information Service System
• Net Advance of Physics - links to papers by topic
• SPIRES
• SLAC Library
• Web Lectures Archive Project

Journals

• Particle Physics Review
• Physical Review Letters

Authors

• Vasiliy Morgunov - LC topics
• T. Torbjorn - PYTHIA maintainer
• Steven Wolfrom - particle physics papers

Books

• Perturbative QCD Handbook

• Brookhaven
• CERN
• DESY
• European Particle Physics Outreach Group
• Fermi Lab
• Institute of Physics
• KEK
• Los Alamos
• SLAC
• US DOE HEP Site

• SPIRES Conferences Database

Proceedings and Homepages

• CALOR 04
• CHEP 03
• CHEP 04
• SSI 2004

• High Energy Physics Information Center
• Current experiments in particle physics - comprehensive list of HEP experiments by laboratory

Detectors and Accelerators

• ALICE
• Atlas Experiment - A Toroidal LHC ApparatuS
  • Internal Portal
  • Offline Computing
• BABAR - "The BaBar detector was built at SLAC to study the millions of B mesons produced by the PEP-II storage ring."
• CMS - Compact Muon Solenoid @ CERN
• D0 Homepage
• Large Hadron Collider

• Contemporary Physics Education Project
• interactions.org
• PSIGate - Physical Sciences Information Gateway, physics section
• Physics Central
• PhysLink

Encyclopedias

• Hyperphysics - graphical explanations of physics concepts and equations; very good
• Annotated Physics Encyclopaedia
• Eric Weisstein's Physics World

Introductory Notes and Resources

• Particle Chart
• Particle Adventure
• Visual Quantum Mechanics
• Physics 2000
• IUN/FYDE Introductory Physics Notes

HEP

• Particle Detector BriefBook
• Passage of Particles Through Matter (pdf) - from PDG

Topical

• Arthur H. Compton Lectures
• Lecture Notes on General Relativity
• Standard Model
• Superstring Theory

• Google
• Groups
• Directory
• Images
• News
• Froogle
• Services and Tools - some really nifty stuff here

Encyclopedias and Dictionaries

• Dictionary.com
• Free On-line Dictionary of Computing
• Whatis
• Wikipedia
  • Physics

• Mathworld - comprehensive online math resource
• Scienceworld - another excellent Wolfram site
• Mathematical Symbols

Publications

• Scientific Literature Digital Library
• Computing Research Repository
• MIT Open Courseware
• The Directory of Computing Science Journals

Group Theory, Lie Algebra and Matrix Theory

• What is a Lie Group?
• Group Theory - online book

Chemistry

• Computational Chemistry
• Electron Orbitals
• Electron Shells
• Electron Configuration

Wavelets

• Bibliographies on Wavelets
• Wavelet Transform

Geometry & Topology

• Algebraic Topology
• Algebraic Topology Book
• Journal of Differential Geometry
• Hausdorff Space
• Tessellation
• Topology
• Tangent Bundles

Neural Nets

• Artificial Neural Networks in HEP
• Neural Net FAQ
• Neural Nets Book

Pattern Recognition

• The Pattern Recognition Files
• Pattern Recognition on the Web

Monte Carlo

• Monte Carlo Simulations for Statistical Physics