URDME v. 1.1: User's manual

Technical report / Department of Information Technology, Uppsala University,1404-3203 ;2011-003

The latest version of URDME can be obtained from www.urdme.org. For earlier versions of URDME consult Technical Report 2008-022.
We have developed URDME, a general software for simulation of stochastic reaction-diffusion processes on unstructured meshes. This allows for a more flexible handling of complicated geometries and curved boundaries compared to simulations on structured, cartesian meshes. The underlying algorithm is the next subvolume method (NSM), extended to unstructured meshes by obtaining jump coefficients from the finite element formulation of the corresponding macroscopic equation. This manual describes the changes in the software compared to the previous version, URDME 1.0. Notable changes include support for Comsol Multiphysics 3.5a and a stronger decoupling between core simulation routines and the Matlab interface by making core solvers stand-alone executables. This opens up for more flexible simulation workflows when many realizations of the stochastic process need to be generated.

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