Package | Description |
---|---|
simulation | |
simulation.dynamics | |
simulation.geometry.substrates | |
simulation.measurement |
Modifier and Type | Method and Description |
---|---|
Walker[] |
DiffusionSimulation.getWalkers() |
Modifier and Type | Class and Description |
---|---|
class |
StickyWalker
This is a kind of Walker that stick to barriers and
diffuse around on the surface for a while.
|
Modifier and Type | Method and Description |
---|---|
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
|
Modifier and Type | Method and Description |
---|---|
void |
StickAndDiffuse.amendStep(Walker walker,
double[] subsCoords,
double[] offset,
double[] step,
double[] normal,
double[] d,
double origLength,
double[] toBarrier,
double[] amended,
double[] unamended,
double[] L,
double t,
int n)
if a walker is free, it sticks it with a fixed prob.
|
void |
StepAmender.amendStep(Walker walker,
double[] subsCoords,
double[] offset,
double[] step,
double[] normal,
double[] d,
double origLength,
double[] toBarrier,
double[] amended,
double[] unamended,
double[] L,
double t,
int i)
amend a step given necessary geometric information
and places to store results etc
|
void |
ElasticReflector.amendStep(Walker walker,
double[] subsCoords,
double[] rawOffset,
double[] rawStep,
double[] normal,
double[] d,
double origLength,
double[] toBarrier,
double[] amended,
double[] unamended,
double[] L,
double time,
int n)
amends the step for the walker by relecting it elastically off
the appropriate membrane.
|
double[] |
StepGenerator.getStep(Walker walker)
returns a step vector as array of doubles
|
double[] |
SpatiallyVaryingStepGenerator.getStep(Walker walker)
queries the substrate for the diffusivity at the current location,
the constructs a step of the appropriate length.
|
double[] |
FixedLengthStepGenerator.getStep(Walker walker)
generates a step of fixed length and uniformly distributed
orientation in D<4 dimensions
|
double[] |
CylindricalSurfaceStepGenerator.getStep(Walker walker)
Generates steps confined to the surface of the given cylinder.
|
Modifier and Type | Method and Description |
---|---|
void |
Substrate.amend(Walker walker,
double[] step,
double t,
int n) |
void |
CellularLattice.applyBoundaries(Walker[] walker)
applies periodic boundary conditions to walker positions
|
abstract boolean |
Substrate.crossesMembrane(Walker walker,
double[] offset,
double[] step,
double[] normal,
double[] d,
boolean skipCurrent,
double origLength,
boolean[] in,
double[] p)
checks if a step will cross a barrier or not
|
boolean |
StickyCylinderSubstrate.crossesMembrane(Walker walker,
double[] offset,
double[] stepVector,
double[] normal,
double[] d,
boolean skipCurrent,
double origLength,
boolean[] in,
double[] p)
wrapper for crosses membrane method.
|
boolean |
MeshSubstrate.crossesMembrane(Walker walker,
double[] offset,
double[] stepVector,
double[] normal,
double[] d,
boolean skipCurrent,
double origLength,
boolean[] in,
double[] p) |
boolean |
EmptySubstrate.crossesMembrane(Walker walker,
double[] offset,
double[] step,
double[] normal,
double[] d,
boolean skipCurrent,
double origLength,
boolean[] in,
double[] p) |
boolean |
CylinderSubstrate.crossesMembrane(Walker walker,
double[] offset,
double[] stepVector,
double[] normal,
double[] d,
boolean skipCurrent,
double origLength,
boolean[] in,
double[] p)
checks if a walker's step will take it across a membrane or not.
|
boolean |
CrossingCylinderSubstrate.crossesMembrane(Walker walker,
double[] rawOffset,
double[] rawStep,
double[] normal,
double[] d,
boolean skipCurrent,
double origLength,
boolean[] in,
double[] p)
checks if a walker's step will take it across a membrane or not.
|
boolean |
CellularLattice.crossesMembrane(Walker walker,
double[] offset,
double[] stepVector,
double[] normal,
double[] d,
boolean skipCurrent,
double origLength,
boolean[] in,
double[] p)
checks if a step will take a walker across a membrane or not
by comparing the cell coords before and after the step.
|
double |
Substrate.getLogMagnetisationChange(Walker walker,
double t,
double tLast)
returns the change in magnetisation at a given location and time
|
double |
StickyCylinderSubstrate.getLogMagnetisationChange(Walker walker,
double t,
double tLast)
returns the change in magnetisation at a given location and time.
|
int[] |
CellularLattice.getWindingNumbers(Walker walker)
wrapper for winding nimber routine using walker instead of position
|
void |
Substrate.initCandidates(Walker walker,
double[] offset,
double[] step) |
abstract boolean |
Substrate.intracellular(Walker walker)
checks if a walker is in intracellular (true) or
extracellular (false) space
|
boolean |
StickyCylinderSubstrate.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
|
boolean |
SquashyInflammationSubstrate.intracellular(Walker walker)
tests if a position is intracellular or not.
|
boolean |
MeshSubstrate.intracellular(Walker walker)
performs the ray test to check if a point is inside the
object or not.
|
boolean |
EmptySubstrate.intracellular(Walker walker) |
boolean |
CylinderSubstrate.intracellular(Walker walker) |
boolean |
CellularLattice.intracellular(Walker walker) |
double[] |
Substrate.mapStepIntoSubstrate(Walker walker,
double[] offset,
double[] step)
maps the given step into the substrate coordinates.
|
double[] |
CrossingCylinderSubstrate.mapStepIntoSubstrate(Walker walker,
double[] offset,
double[] step)
overrides the default step mapper to take account of the rotated patch
in the coordinate system.
|
void |
Substrate.testAmendment(Walker walker,
double[] step,
double[] normal,
double[] d,
double origLength,
double[] toBarrier,
double[] amended,
double[] unamended)
test access to the amender.
|
Modifier and Type | Method and Description |
---|---|
static SyntheticScan |
ScanFactory.getMeasurementModule(SimulationParams simParams,
SimulableScheme scheme,
Substrate substrate,
Walker[] walker)
factory method.
|
double |
SyntheticScan.getPhaseShift(Walker walker,
double t,
int dir,
double tLast)
returns the phase shift at a given location at a given time
|
double |
AgnosticScan.getPhaseShift(Walker walker,
double t,
int dir,
double last)
calculates a phase shift for the given spin at the given time in
the given direction
|
static StatisticsModule |
StatisticsModuleFactory.getStatsModule(Walker[] walker)
factory method
|
Constructor and Description |
---|
AgnosticScan(SimulableScheme scheme,
Walker[] walker,
Substrate substrate)
constructor.
|
MSdispStatsModule(Walker[] walker)
constructor, takes array of walkers
|
StatisticsModule(Walker[] walker)
constructor.
|
StickyStatsModule(Walker[] walker)
constructor, takes array of walkers
|