Core modules¶

The core modules of morphosolver.

morphosolver.core.tissuebase¶

class morphosolver.core.tissuebase.TissueBase(mesh0=<sphinx.ext.autodoc.importer._MockObject object>, params={})[source]¶

TissueBase defines the problem geometry and mechanics. It is a base class, where init() and update() functions should be overridden by the derived class.

Parameters:	mesh0 (`dolfin.Mesh`) – A mesh of the initial condition params (`dict`) – A dictionary of parameters

init()[source]¶: Virtual initialisation function. It ss only run once before the start of the simulation.

plotMesh()[source]¶: Virtual iupdate function. Is run at every time-step of the simulation before solving the growth mechanics by the call to the solve() function.

update(dt)[source]¶

Virtual iupdate function. Is run at every time-step of the simulation before solving the growth mechanics by the call to the solve() function.

Parameters:	dt (`float`) – A time-step, passed by the `Simulator` object.

morphosolver.core.simulator¶

class morphosolver.core.simulator.Simulator(tissue, outputDir='/home/docs/checkouts/readthedocs.org/user_builds/morphosolver/checkouts/latest/docs/source')[source]¶

Handles running the simulation of the problem defined by a morphosolver.core.tissuebase.TissueBase object

Parameters:	tissue (`morphosolver.core.tissuebase.TissueBase`) – tissue to simulate outputDir (`str`) – path to an output directotry, defaults to the current workind directory

run(dt, n, growthOn=True)[source]¶

Runs the simulation

Parameters:	dt (`float`) – A time-step n (`int`) – Number of time-steps growthOn (`bool`) – Enable growth. Defaults to True

morphosolver.core.chemical¶

class morphosolver.core.chemical.Chemical(tissue, name)[source]¶

Bases: morphosolver.core.util.SmartFunction

Chemical defines a concentration field which can be subject to diffusion and user-specified reaction.

Parameters:	tissue (`morphosolver.core.tissuebase.TissueBase`) – the host name (`str`) – Name of the chemical

setDiffusion(D)[source]¶

Set diffusion

Parameters:	D (`float`) – Diffusion rate

setReaction(R)[source]¶

Set reaction term

Parameters:	R (`dolfin.cpp.function.GenericFunction`) – Reaction term

update(dt)[source]¶

Update function by calculating reaction-diffusion step

Parameters:	dt (`float`) – Time-step

morphosolver.core.util¶

Collection of the utility functions.

class morphosolver.core.util.SmartFunction(name, functionSpace0=None, function=None, functionSpace=None)[source]¶

Smart function is a derivative of the dolfin.Function with an extended functionality. It allows to specify two function spaces (dolfin.FunctionSpace) for both an initial and current conditions. The state of the Smart functions are automatically saved at each simulation step to the outputDir

Parameters:	name (`str`) – Name of the function. The name is used for a filename, where the function state will be saved. functionSpace0 (`dolfin.FunctionSpace`) – Function space of the initial condition. functionSpace (`dolfin.FunctionSpace`) – Function space of the current condition. Either supplied at the initialisation or is derived from the supplied `function`.

class morphosolver.core.util.GenericDomain(func)[source]¶

A helper class to define a subdomain with a given function. Derivative of dolfin.SubDomain.

Parameters:	func (`lambda(x, onBoundary)`) – A lambda function, which returns true if the point x is inside the defined subdomain.