public class StickyCylinderSubstrate extends ParallelCylinderSubstrate
DISTRIBUTED, HEX, SQUARE
cylinder
a, border, factor, intersectsBoundary, spatialOptInitialised, voxToObjects
Constructor and Description |
---|
StickyCylinderSubstrate(SimulationParams simParams)
constructor from superclass
|
Modifier and Type | Method and Description |
---|---|
boolean |
crossesMembrane(Walker walker,
double[] offset,
double[] stepVector,
double[] normal,
double[] d,
boolean skipCurrent,
double origLength,
boolean[] in,
double[] p)
wrapper for crosses membrane method.
|
double |
getLogMagnetisationChange(Walker walker,
double t,
double tLast)
returns the change in magnetisation at a given location and time.
|
boolean |
intracellular(Walker walker)
override intracellular check to account for being stuck to the surface
which would otherwise cause annoying floating-point precision related
difficulties and spurious crossings
|
getCylinderSpacing, getDiffusivityAt, getPacking, getPackingString, getPeakCoord, getSubstrateCoords, getSubstrateSize, main
getCylinders, init, setSubstrateDims
amend, getBottomLeft, getN, getSubsObj, getSubVoxelIndex, getUpperRight, initBoundaryIntersectionArrays, initCandidates, initialiseSpatialOptimisation, mapStepIntoSubstrate, moreCandidates, nextCandidate, testAmendment, testStepAmendment, unmapStepFromSubstrate, voxelContains
public StickyCylinderSubstrate(SimulationParams simParams)
public boolean crossesMembrane(Walker walker, double[] offset, double[] stepVector, double[] normal, double[] d, boolean skipCurrent, double origLength, boolean[] in, double[] p)
crossesMembrane
in class CylinderSubstrate
walker
- the (stick) walker making the stepoffset
- net step made so farstepVector
- the step to checknormal
- space to store normal at intersection pointd
- space to store distance of int point to origin dot normalskipCurrent
- skip the membrane we're sitting on?origLength
- length fo original stepin
- space to store initially in flagp
- space to store permeability of interacting membranepublic double getLogMagnetisationChange(Walker walker, double t, double tLast)
getLogMagnetisationChange
in class Substrate
walker
- the walkert
- current time (end of timestep)tLast
- the last time we were here (beginning of timestep)public boolean intracellular(Walker walker)
intracellular
in class CylinderSubstrate
walker
- the walker to check. this will be explicitly cast into a StickyWalker