jLM.Solvers#

Generic RDME solvers

Functions

makeSolver(rdmeSolver, customSolver)

Create custom solver

Classes

ConstBoundaryConc(lmFile[, exact])

Solver with fixed concentration boundary conditions
class jLM.Solvers.ConstBoundaryConc(lmFile, exact=False)[source]#

Bases: object

Solver with fixed concentration boundary conditions

The simulation hook runs a cythonized function which destructively sets the specified boundaries to a prescribed concentration.

hookSimulation(t, lattice)[source]#

Replaces all particles on boundary according to B.C.s

setBoundary(species, concs, boundary)[source]#

Specify boundary conditions

Specify a boundary condition using a species (or list of species), a concentration (or list of concentrations; in mol/L), and a specification of the boundary in terms of a binary lattice. Subsequent calls will add new boundary conditions. When the boundary region given by a subsequent call overlaps with a previously described region, the later call will override the earlier conditions.

Parameters:

  • species (Species) – Species at boundary

  • concs (float) – Concentrations

  • boundary (ndarray) – Binary lattice describing the boundary

jLM.Solvers.makeSolver(rdmeSolver, customSolver)[source]#

Create custom solver

Note

The user defined class should define a hookSimulation(self, t, lattice) method where t is the current simulation time and lattice is the current state of the lm.CudaByteLattice.

Warning

If __init__ is overridden, super().__init__ must be called first.

Parameters:

  • rdmeSolver (lm.RDMESolver) – Base solver class

  • customSolver (class) – User defined solver class

Returns:

Composed class

Return type:

class