This page contains links to software libraries or applications that I have either authored myself or made a substantial contribution to.
Aboria
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- Aboria implements a C++ STL container of particles in 3D space. The library is header-only. The container supports random access of particles, as well as the normal STL algorithms. Neighbourhood searches are possible, using a bucket search method (uniform bucket spacing)
- Includes examples showing how to implement DEM and SPH algorithms (in 3D) using Aboria
Tyche
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- C++/Python library for multiscale lattice and off-lattice simulation of spatial stochastic reaction-diffusion networks
- off-lattice (particle-based) model based on the Smoluchowski model, including diffusion, zeroth-order, unimolecular and bimolecular reactions.
- on-lattice model based on the Next Subvolume Method. This models stochastic diffusion, and reactions of arbitrary order
- coupling between the off-lattice and on-lattice models (ATRM)
- Modular Design. Users can add new models or take models to use in own code
- C++ or Python interface. Integrates into normal Python environment (e.g. Matplotlib, tvtk)
Sph-Dem
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The SPH portion of this code was developed during my PhD, then the DEM functionality and coupling with SPH was added during my current postdoc at U. Twente.
- Written in C++
- Fully parallel implementation using MPI
- Modular structure separates the parallel data structure from the SPH/DEM equation. Uses C++ templates to efficiently apply arbitrary functions on particles and their neighbours
- Output files use VTK format
- SPH Functionality
- Weakly compressible formulation
- Lenard-Jones type boundary particles, periodic boundaries and ghost boundaries
- Variety of different viscosity terms and kernel options
- First order corrected kernel derivatives
- And more...
- SPH-DEM coupling based on Locally Averaged Navier-Stokes Eqns. Drag terms: De Felice, Ergun and Stokes.
Smoldyn
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- Smoldyn is a computer program for cell-scale biochemical simulations, developed by Dr Steve Andrews at the Fred Hutchinson Cancer Research Center
- I have contributed to the latest version of Smoldyn by including a lattice-based model that can be coupled to the standard off-lattice model
- See the main Smoldyn page for more details...
Inpainting Plugin
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- Gimp Plug-in developed in collaboration with Dr. Thomas März (Oxford)
- Inpainting refers to the process of removing or recovering image regions by "inpainting" the surrounding image features into the region to be recovered.
Kairos
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- C++/Python library for multiscale PDE and off-lattice simulation of spatial stochastic reaction-diffusion networks