public class ParallelCylinderSubstrate extends CylinderSubstrate
Modifier and Type | Field and Description |
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static int |
DISTRIBUTED |
static int |
HEX |
static int |
SQUARE |
cylinder
a, border, factor, intersectsBoundary, spatialOptInitialised, voxToObjects
Constructor and Description |
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ParallelCylinderSubstrate(CylinderFactory.CylType type,
SimulationParams simParams)
constructor for thick-walled cylinders.
|
ParallelCylinderSubstrate(SimulationParams simParams)
construct a lattice of parallel simple cylinders of
given radius, orientation and spacing
|
Modifier and Type | Method and Description |
---|---|
double |
getCylinderSpacing()
gets the cylinder spacing
same as short axis length in hex packing cell.
|
double |
getDiffusivityAt(double[] walkerPos)
overrides getDiffusivityAt method in Substrate
so that we can do spatial variation in diffusivity.
|
int |
getPacking()
gets the packing type
|
java.lang.String |
getPackingString() |
double |
getPeakCoord() |
void |
getSubstrateCoords(double[] r,
double[] offset,
double[] subsCoords)
transforms the walker coords into the cell
|
double[] |
getSubstrateSize() |
static void |
main(java.lang.String[] args)
test code for barrier crossing with cylinders
instantiates a square lattice with R=2.0, r=0.5 and a
walker at r=(1.4,1) with a step of s=(0.2,0) which
should take it across the barrier at (1.5, 1.0)
giving t=0.1
|
crossesMembrane, getCylinders, init, intracellular, setSubstrateDims
amend, getBottomLeft, getLogMagnetisationChange, getN, getSubsObj, getSubVoxelIndex, getUpperRight, initBoundaryIntersectionArrays, initCandidates, initialiseSpatialOptimisation, mapStepIntoSubstrate, moreCandidates, nextCandidate, testAmendment, testStepAmendment, unmapStepFromSubstrate, voxelContains
public static final int SQUARE
public static final int HEX
public static final int DISTRIBUTED
public ParallelCylinderSubstrate(SimulationParams simParams)
R
- cylinder spacingr
- radius of cylinderspacking
- cylinder packing (HEX or SQUARE)public ParallelCylinderSubstrate(CylinderFactory.CylType type, SimulationParams simParams)
cylType
- which type of cylinder to usesimParams
- simulation parameters objectpublic double[] getSubstrateSize()
getSubstrateSize
in class CylinderSubstrate
public double getPeakCoord()
getPeakCoord
in class CylinderSubstrate
public final double getDiffusivityAt(double[] walkerPos)
getDiffusivityAt
in class Substrate
walkerPos
- position to check in world coordspublic double getCylinderSpacing()
public int getPacking()
public java.lang.String getPackingString()
public void getSubstrateCoords(double[] r, double[] offset, double[] subsCoords)
getSubstrateCoords
in class Substrate
r
- position in non-periodic spaceoffset
- the offset vector from walker positionpublic static void main(java.lang.String[] args)
args
-