org.catacomb.numeric.difnet.calc

Class NetDiffuser

java.lang.Object

org.catacomb.numeric.difnet.calc.NetDiffuser

All Implemented Interfaces:

DiffusionCalculator

public class NetDiffuser
extends java.lang.Object
implements DiffusionCalculator

CcNetDiffuser computs diffusion or sparse or dense networks, with access via the NetDiffuser interface. It does not require any special structure in the network, but instead makes its own copy of the network geometry and rearranges that for an in-place sparse diffusion solution (aka Hines method) copying data in and out from the supplied DiffusiveNet via theresulting permutation. Its only state information is the network geometry, so one CcNetDiffuser can be used for networks derived from the same DiffusiveNetProperties object. Typical use is for the network builder to prodice a DiffusiveNetProperties object (such as CcDiffusiveNetProperties), Which makes a CcNetDiffuser of itself, and exports DiffusiveNet instances as required. When such an instance is required to update, it calls the properties object which runs diffuse from its NetDiffuser on the instance.

Field Summary

Fields

Modifier and Type	Field and Description
(package private) int	icall
(package private) static int	IERROR
(package private) static int	IOK
(package private) OrderedNetMap	orderedNetMap

Constructor Summary

Constructors

Constructor and Description
NetDiffuser(NetStructure dnetprop) creates and initialises a CcNetDiffuser for any diffusive nets sharing the same diffusiveNetProperties.

Method Summary

Methods

Modifier and Type	Method and Description
void	advance(NetState difnet, DiffusibleQuantity dq, Timestep tstep) Run the diffusion calculation for the supplied network, diffusible quantity and timestep.
private void	calculateFixedNodeCurrents(NetMapNode[] node)
private int	fullNetDiffuse(OrderedNetMap ordNM, double dt)
void	init(NetStructure dnetprop) initialise the internal mapping of the network geometry.
void	printNet()
void	printNet(NetState ns)
private int	sparseNetDiffuse(OrderedNetMap ordNM, double dt)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

icall

int icall

IOK

static final int IOK

See Also:

Constant Field Values

IERROR

static final int IERROR

See Also:

Constant Field Values

orderedNetMap

OrderedNetMap orderedNetMap

Constructor Detail

NetDiffuser

public NetDiffuser(NetStructure dnetprop)

creates and initialises a CcNetDiffuser for any diffusive nets sharing the same diffusiveNetProperties.

Parameters:

dnetprop - the shared properties for nets to be handled by this diffuser.

Method Detail

init

public void init(NetStructure dnetprop)

initialise the internal mapping of the network geometry. an OrderedNetMap is constructed specific to the given network structure. It is ordered such as to minimise the work in any subsequent diffusion calculation.

Specified by:

init in interface DiffusionCalculator

Parameters:

dnetprop - the shared properties for nets to be handled by this diffuser.

printNet

public void printNet()

printNet

public void printNet(NetState ns)

advance

public void advance(NetState difnet,
           DiffusibleQuantity dq,
           Timestep tstep)

Run the diffusion calculation for the supplied network, diffusible quantity and timestep. The values in the DiffusiveNet are read with getValue(DiffusibleQuantity) and set after the calculation with setValue(DiffusibleQuantity, double)

Specified by:

advance in interface DiffusionCalculator

Parameters:

difnet - the DiffusiveNet to evolve. Note that its properties object must be the same as that used to initialise the net diffuser.

dq - the diffusible quantity to use. One net may contain several different diffusing quantitites - membrane potential, ions, indicators and others. NB as yet dq is ignored ***

timestep - the timestep to be taken

fullNetDiffuse

private int fullNetDiffuse(OrderedNetMap ordNM,
                 double dt)

sparseNetDiffuse

private int sparseNetDiffuse(OrderedNetMap ordNM,
                   double dt)

calculateFixedNodeCurrents

private void calculateFixedNodeCurrents(NetMapNode[] node)