This is a program for calculating position-dependent diffusivity functions from trajectory data. It was written by Jeff Comer . The approach is described in:
Comer, Chipot and Gonzalez-Nilo (2013) J. Chem. Theory Comput., 9(2) 876-882, DOI: 10.1021/ct300867e
See the following for information on two-dimensional calculations and using reflecting boundary conditions, which are useful for an orientation angle:
Comer J, Schulten K, Chipot C (2014) Diffusive models of membrane permeation with explicit orientational freedom. J Chem Theory Comput 10(7):2710–2718. doi: 10.1021/ct500209j
See the following for information on use of the Smoluchowski and fractional Smoluchowski solver:
Chipot C, Comer J (2016) Subdiffusion in membrane permeation of small molecules. Sci. Rep. 6:35913. doi: 10.1038/srep35913
You need the Gnu Scientific Library development package installed (for random numbers). Here is the Ubuntu package, which may or may not help you:
sudo apt-get install gsl-bin libgsl0-dev
You may also have to install OpenMP support for g++ (multithreading). Here is the Ubuntu package, which may or may not help you:
sudo apt-get install libgomp
On a Mac, this might work better:
Just running diffusion fusion with no parameters will give you the usage information.
See the Examples/ directory for more information.