cernlib CERNLIB is a suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the biological sciences.
paw PAW is an interactive program providing interactive graphical presentation and statistical and mathematical analysis tools. It is designed to work on objects familiar to physicists such as histograms, event files (Ntuples), vectors, etc.
geant321 Particle detector description and simulation tool.
CLHEP HEP foundation class library.
Feynmf set of LaTeX macros for creating Feynman diagrams
gerris Gerris is a system for the solution of the partial differential equations describing fluid flow.
gpiv gpivtools A collection of programs for images that are generated during a Particle Image Velocimetry (PIV) experiment. This is a technique to obtain the velocity field of a fluid flow quantitatively and is performed by tracking tracer particles that have been seeded to a fluid.
See also DebianScience/Engineering
Crystal Structure calculation
abinit A package for electronic structure calculations.
OpenMx Package for nano-scale material simulations.
See also DebianScience/Chemistry
http://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid_state_physics_software has a list of software - both free and commercial.
Electromagnetism and Optics
tessa simulation of 3D optical systems with the FDTD method
mpb The MIT Photonic-Bands package is a free program for computing the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures.
meep Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems.
gdis A GTK based program for the display and manipulation of isolated molecules and periodic systems.
v-sim V_Sim visualizes atomic structures such as crystals, grain boundaries and so on
Scanning probe microscopy
gwyddion Scanning Probe Microscopy visualization and analysis
XAS/ XAFS / EXAFS
horae (contrib) interactive graphical processing and analysis of EXAFS data.
ifeffit (contrib) An interactive program for XAFS analysis
sixpack (contrib) full-featured package for XAS analysis
objcryst-fox A program for the ab initio structure determination from powder diffraction.
pyMCA ITP: 514903 - Python toolkit and application for X-ray fluorescence analysis
fityk Fityk is a flexible and portable program for nonlinear fitting of analytical functions (especially peak-shaped) to data (usually experimental data). In other words, for nonlinear peak separation and analysis.
Numerical Computation (MATLAB/IDL like)
http://blends.alioth.debian.org/science/tasks/numericalcomputation lists Matlab/IDL like packages for calculations on arrays, data analysis and visualisation.
Computer Algebra Systems
See DebianScience/ComputerAlgebraSystems for a comparison of some of these.
maxima Maxima is a fully symbolic computation program.
sagemath Mathematics software written in Python
yacas Yacas is a small and highly flexible computer algebra language.The syntax is very close to Mathematica. The distribution contains a small library of mathematical functions, but its real strength is in the language in which you can easily write your own symbolic manipulation algorithms. It supports arbitrary precision arithmetic.
See http://blends.alioth.debian.org/science/tasks/imageanalysis.html for applications to extract quantitative data from images.
Physics tools that could be considered for inclusion in Debian
see jmol for display.
http://www.opennovation.org/ Opennovation.org is an open source engineering portal - an extensive list of free engineering/physics software.
http://en.wikipedia.org/wiki/Category:Physics_software lists physics software - some of it commercial.
Tools with unofficial .deb
cmpr peak fitting and x-ray diffraction data viewer already packaged by Carlo Segre
expgui GUI for GSAS (OK for Debian but GSAS isn't) already packaged by Carlo Segre
mcmaille x-ray structure solution already packaged by Carlo Segre
tpf x-ray profile refinement already packaged by Carlo Segre
xgen macromolecular crystallography already packaged by Carlo Segre
Gxsm Gnome X scanning microscopy package, tool for data acquisition of STM/SPM/AFM and visualization, available from http://gxsm.sf.net.