bin keyword value(s) ...
diff value = D D = diffusion coefficient (cm^2/sec) gsize values = Lx Ly Lz Lx,Ly,Lz = geometry bin sizes in each dimension (microns) gcount values = Nx Ny Ny Nx,Ny,Nz = geometry bin count in each dimension react value = cutoff cutoff = max distance between a pair of reacting particles (microns) rsize values = Lx Ly Lz Lx,Ly,Lz = reaction bin sizes in each dimension (microns) rcount values = Nx Ny Ny Nx,Ny,Nz = reaction bin count per geometry bin in each dimension
bin diff 1.0e-8 bin react 0.02 diff 1.0e-7 bin gcount 30 35 40
Create two sets of bins that overlay the simulation domain. Geometry bins are used for storing the location of geometry elements (regions, surface triangles) so that particles can be efficiently moved. Reaction bins are used to quickly find pairs of nearby reacting particles. In general, simulations will run faster if these bin sizes are as small as possible, while still meeting the constraints described below. However, this is not always the case, so this command gives you the freedom to tune the performance of particular simulations.
Geometry bins must be large enough that particles with the largest diffusion coefficient will not move further than one bin length in a single timestep.
Reaction bins must be large enough that the largest distance at which a pair of particles react is not greater than one bin length. Additionally, reaction bins can be no larger than geometry bins and in each dimension an integer number of reaction bins must fit inside each geometry bin. Thus, in a dimension, reaction bins can be equal in size to geometry bins, or 1/2 size, or 1/3 size, etc.
The number and size of geometry bins is determined by using zero or more of 3 keywords: diff, gsize, and gcount. If multiple keywords are used, the geometry bin size is set to the maximum of the sizes induced by each keyword. If none of the 3 keywords are used, geometry bins are setup as if the diff keyword had been specified with a diffusion coefficient of 0.0, which as described below is the same as using the largest diffusion coefficient currently defined. Note that the global simulation domain must have an integer number of geometry bins in each dimension, so the bin size may be set slightly larger than the values inferred by these keywords.
The diff keyword sets the geometry bin size to the maximum distance a particle will move in one timestep, which depends on the specified diffusion coefficient, the timestep size, and move_style settings. If the specified diffusion coefficient is 0.0, then ChemCell will compute the maximum distance using the largest diffusion coefficient currently defined. Note that if these values are changed after using the bin command (e.g. you change the timestep or reset some particle's diffusion coefficient), you may end up with an invalid geometry bin size. Also note that you can run ChemCell once (e.g. for zero timesteps) to see the maximum diffusive distance printed out.
The gsize keyword sets the geometry bin size in each dimension to the specified values.
The gcount keyword sets the number of geometry bins in each dimension to the specified values.
The number and size of reaction bins is determined by using zero or more of 3 keywords: react, rsize, and rcount. If multiple keywords are used, the reaction bin size is set to the maximum of the sizes induced by each keyword. If none of the 3 keywords are used, reactions bins are set to the same size as the geometry bins.
The react keyword sets the reaction bin size in all 3 dimensions to the specified size, which is assumed to be the largest distance at which a binary reaction between 2 particles will occur. If the specified cutoff is 0.0, then the maximum reaction distance is computed, which depends on reaction rates, the probability settings, the timestep, and particle diffusion coefficients. Note that if these values are changed after using the bin command (e.g. you change the timestep or reset a reaction rate), you may end up with an invalid reaction bin size. Also note that you can run ChemCell once (e.g. for zero timesteps) to see the maximum reaction distance printed out.
The rsize keyword sets the reaction bin size in each dimension to the specified values.
The rcount keyword sets the number of reaction bins per geometry bin to the specified values in each dimension. E.g. a setting of rcount 1 1 1 will make reaction bins equal in size to the geometry bins. A setting of rcount 4 4 4 will put 64 reaction bins inside each geometry bin.
This command can only be used for spatial simulations.
The global command must be used before this command, to specify the size of the simulation box.
Related commands: none
Using the bin command with no arguments, sets geometry bins to the size inferred by the maximum diffusivity of any particle, and sets reaction bins to the same size as geometry bins.