Expand description
Cellular Potts tissue simulation, with a serial CPU reference and a GPU sweep that has to agree with it.
Named after James Glazier, whose work with Graner and Hogeweg applied the Potts lattice to tissue.
The lattice, the energies and the serial sweep are glazier-core. The
device sweep is glazier-cuda, behind the cuda feature. This crate is
the facade over both, and the binary that runs a Blueprint from JSON.
Modules§
- blueprint
- The model description both engines read.
- cpu
- Serial Metropolis on the CPU. This is the correctness reference.
- lattice
- The site lattice and its periodic neighbourhood.
- model
- Model description: cell types, the contact matrix and the constraints.
- npy
- A writer for the one NumPy array shape this crate produces.
- rng
- xoshiro256++, one stream per site so the CPU and the GPU draw the same way.
Structs§
- Blueprint
- The whole description.
- Cell
Type - A cell type’s own parameters. Type 0 is the medium and takes no volume constraint.
- Lattice
- A periodic lattice of cell labels. Label 0 is the medium.
- Model
- The whole model: what a Blueprint would state, in one struct.
- Simulation
- A running simulation: the lattice, one volume and one type per cell, and the random stream.