Software Links

I use a Mac. Much of the software below is Mac-only.

Calculation

• Mathematica
  Unequalled platform for symbolic and numerical mathematics. A theorist's best software friend.
  www.wolfram.com/
• COMSOL
  Powerful, easy-to-use platform for finite-element solution of PDEs. GUI for drawing problem geometry; automatic mesh generation; menu-driven specification of equations, boundary conditions, and parameters; versatile visualization of results.
  www.comsol.com/

Simulation

• GROMACS
  Fast, free atomistic MD simulation platform. Well-documented set of command line simulation and analysis tools that work seamlessly together.
  www.gromacs.org/
• NAMD
  Widely used atomistic MD platform. NAMD - Scalable Molecular Dynamics
  www.ks.uiuc.edu/Research/namd/
• Avogadro
  Well-designed free point-and-click molecule builder and visualizer.
  http://avogadro.openmolecules.net/wiki/Main_Page
• iBabel
  Converts molecular structure files between the many formats used by various simulation and calculation packages.
  http://openbabel.org/wiki/IBabel

Programming

• C++ reference pages
  Excellent online reference for C/C++ language and standard libraries, particularly including the C++ STL (Standard Template Library) containers and methods. C++ Reference
  www.cplusplus.com/reference/
• Numerical Recipes in C online
  Free online version of older edition of Numerical Recipes book. Numerical Recipes in C
  www.nrbook.com/a/bookcpdf.php
• Python
  Powerful, well designed, widely used scripting language. Dive Into Python http://diveintopython.org/toc/index.html The Python Tutorial — Python v2.6.5 documentation
  http://docs.python.org/tutorial/
• SmartSVN
  GUI for subversion, version control software for collaborative development of programs and documents.
  www.syntevo.com/smartsvn/index.html

Writing

• LaTeX
  Tutorial and reference websites for using LaTeX, by far the best choice for technical word processing. WYGIBTWYT ("wiggibtawitt") -- What You Get Is Better Than What You Type.
• Cambridge University Engineering Department - Text Processing using LaTeX
  www-h.eng.cam.ac.uk/help/tpl/textprocessing/LaTeX_intro.html
• Getting to Grips with LaTeX - LaTeX Tutorials by Andrew Roberts @ School of Computing, University of Leeds
  www.andy-roberts.net/misc/latex/
• LaTeX - Wikibooks, collection of open-content textbooks
  http://en.wikibooks.org/wiki/LaTeX
• TeXLive
  Open source installation of TeX, LaTeX, TeXShop, BibDesk, LaTeXit. TeX Live - TeX Users Group
  http://www.tug.org/texlive/
• BibDesk
  GUI for editing and managing .bib files.
  http://bibdesk.sourceforge.net/
• LatexIt
  GUI for using LaTeX to typeset equations to paste into Keynote, Pages, (Powerpoint, Word,...)
  http://chachatelier.fr/programmation/latexit_en.php

Shareware

• Macupdate
  Widely used repository of shareware, freeware, demo software. MacUpdate: Download Apple Mac Software & iPhone Software
  http://macupdate.com/

Graphics

• GraphicConverter
  Converts graphics among many formats, as well as performing many editing functions.
  www.lemkesoft.com/
• GraphClick
  Indispensable for grabbing data point values from images of graphs.
  www.arizona-software.ch/graphclick/
• OmniGraffle
  Excellent vector drawing program.
  www.omnigroup.com/products/omnigraffle/
• Plot
  Very nice open source 2D plotting program, for publication quality plots.
  http://plot.micw.eu/
• iPhoto Library Manager
  Allows you to have multiple iPhoto libraries, easily switching between them.
  www.fatcatsoftware.com/iplm/

Organization

• OmniFocus
  Excellent task management software, compatible with the GTD (Getting Things Done) methodology.
  www.omnigroup.com/products/omnifocus/

Communication

• Cyberduck
  Well-designed, convenient, free FTP client.
  http://cyberduck.ch/