Package | Description |
---|---|
simulation | |
simulation.dynamics | |
simulation.geometry.substrates | |
simulation.measurement |
Modifier and Type | Method and Description |
---|---|
Substrate |
DiffusionSimulation.getSubstrate() |
Modifier and Type | Method and Description |
---|---|
static StepAmender |
StepAmenderFactory.getStepAmender(StepAmenderFactory.AmenderType type,
Substrate substrate) |
static Walker |
WalkerFactory.getWalker(double[] r0,
StepGenerator stepGen,
Substrate substrate,
SyntheticScan synthScan,
java.io.DataOutputStream trajWriter,
SimulationParams simParams)
constructs the correct type of walker for the desired simulation
|
Constructor and Description |
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CylindricalSurfaceStepGenerator(Substrate substrate)
constructor that takes step length directly
|
ElasticReflector(Substrate substrate)
constructor
|
SpatiallyVaryingStepGenerator(SimulationParams simParams,
Substrate substrate)
constructor.
|
StickAndDiffuse(Substrate substrate)
constructor.
|
StickyWalker(double[] r0,
StepGenerator freeStepGen,
StepGenerator surfaceStepGen,
Substrate substrate,
SyntheticScan scan,
java.io.DataOutputStream trajWriter,
boolean free,
double p_unstick)
main constructor.
|
StickyWalker(double[] r0,
StepGenerator stepGen,
Substrate substrate,
boolean free)
test constructor with specified stick state.
|
Walker(double[] r0,
StepGenerator stepGen,
Substrate substrate,
SyntheticScan scan,
java.io.DataOutputStream trajWriter)
public constructor.
|
Walker(double[] r0,
Substrate substrate)
initialises a walker without a step generator.
|
Modifier and Type | Class and Description |
---|---|
class |
CellularLattice
Abstract class that implements a general cubic lattice geometry
initialisation of the geometry is left abstract so that inheriting
classes may implement any pattern they choose.
|
class |
CrossingCylinderSubstrate
substrate will two principle directions.
|
class |
CylinderSubstrate |
class |
DistributedRadiusCylinderSubstrate
implements a class of substrate whereby the radii of cylinders
are drawn from a specified distribution.
|
class |
EmptySubstrate
this is for debugging purposes.
|
class |
MeshSubstrate |
class |
ParallelCylinderSubstrate
Implements a class of substrates with a single population
of parallel cylinders with a single constant thickness.
|
class |
PercCellularLattice
Camino fibre reconstruction and tracking toolkit
PercCellularLattice (simulation)
Initialises a cellular lattice occupied like a using a
percolation-like technique.
|
class |
PercolationSubstrate |
class |
SquashyInflammationSubstrate |
class |
StickyCylinderSubstrate |
class |
StripedCellularLattice
Camino fibre reconstruction and tracking toolkit
StripedCellularLattice (simulation)
|
Modifier and Type | Method and Description |
---|---|
static Substrate |
SubstrateFactory.getSubstrate(SubstrateFactory.SubstrateType substrateType,
SimulationParams simParams)
factory method for making geometries.
|
Modifier and Type | Method and Description |
---|---|
static SyntheticScan |
ScanFactory.getMeasurementModule(SimulationParams simParams,
SimulableScheme scheme,
Substrate substrate,
Walker[] walker)
factory method.
|
Constructor and Description |
---|
AgnosticScan(SimulableScheme scheme,
Walker[] walker,
Substrate substrate)
constructor.
|