SALSA simulation codes


This is a package for the simulation and analysis of stresses in colloidal hard sphere particles. It is used to extract and verify stresses in colloidal crystalline materials using the SALSA method (Stress Assessment from Local Structural Anisotropy). In brief the SALSA method uses extracted particle positions to estimate collision frequency and anistropy in order to translate particle positions into stress. At its base, SALSA currently assumes that colloids interact through a hard sphere potential (a very good assumption for many types of samples).

In order to calculate these stresses, first the particle positions and sizes are extracted from confocal microscope images using one of many standard featuring algorithms. Then, for each particle, the fabric tensor is calculated by determining the arrangment of colliding particles within a certain length tolerance. The stress for that individual particle is then determined by prefactors of kT and local volume as shown in the figure.

The code is mostly written in Python and C/CUDA with binding in SWIG between the two; its main interface is in Python. For example uses and codes, look in the scripts directory. To install, have CUDA installed and simply run

python install [--prefix=<DIRECTORY>]

The script will use whichever nvcc is on PATH at the time of installation.