Package | Description |
---|---|
simulation | |
simulation.dynamics | |
simulation.geometry.elements | |
simulation.geometry.substrates | |
simulation.measurement | |
tools |
Constructor and Description |
---|
DiffusionSimulation(SimulationParams simParams) |
DiffusionSimulation(SimulationParams simParams,
SimulableScheme imParams)
debug file writers
|
Modifier and Type | Method and Description |
---|---|
static StepGenerator |
StepGeneratorFactory.getStepGenerator(SimulationParams simParams)
factory method
|
static double[] |
StepGeneratorFactory.getStepParamsArray(StepGeneratorFactory.StepType type,
SimulationParams simParams)
parameters array generator
|
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 |
---|
CylindricalSurfaceStepGenerator(SimulationParams simParams) |
CylindricalSurfaceStepGenerator(SimulationParams simParams,
StickyCylinderSubstrate substrate) |
FixedLengthStepGenerator(SimulationParams simParams)
constructor.
|
SpatiallyVaryingStepGenerator(SimulationParams simParams,
Substrate substrate)
constructor.
|
Modifier and Type | Method and Description |
---|---|
static Cylinder |
CylinderFactory.getCylinder(double[] V,
double[] P,
SimulationParams simParams) |
static Cylinder |
CylinderFactory.getCylinder(double[] P,
SimulationParams simParams) |
Modifier and Type | Method and Description |
---|---|
static Substrate |
SubstrateFactory.getSubstrate(SubstrateFactory.SubstrateType substrateType,
SimulationParams simParams)
factory method for making geometries.
|
Constructor and Description |
---|
CellularLattice(SimulationParams simParams) |
CrossingCylinderSubstrate(SimulationParams simParams)
constructor for default crossing angle.
|
CylinderSubstrate(double[] L,
SimulationParams simParams,
boolean useSpaceOpt) |
DistributedRadiusCylinderSubstrate(SimulationParams simParams)
constructor.
|
EmptySubstrate(SimulationParams simParams) |
MeshSubstrate(SimulationParams simParams)
read a substrate from the named PLY file and scale it to the
specified length.
|
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
|
PercCellularLattice(SimulationParams simParams) |
PercolationSubstrate(SimulationParams simParams)
constructor.
|
SquashyInflammationSubstrate(SimulationParams simParams)
constructor.
|
StickyCylinderSubstrate(SimulationParams simParams)
constructor from superclass
|
StripedCellularLattice(SimulationParams simParams)
initialises stripes of occupied cells of given thickness (given
in number of cells) stripes will be parallel to the second
coordinate direction.
|
Substrate(SimulationParams simParams,
double[] substrateDims)
constructor with p specified
|
Modifier and Type | Method and Description |
---|---|
static SyntheticScan |
ScanFactory.getMeasurementModule(SimulationParams simParams,
SimulableScheme scheme,
Substrate substrate,
Walker[] walker)
factory method.
|
Modifier and Type | Field and Description |
---|---|
static SimulationParams |
CL_Initializer.simParams
diffusion simulation parameters object
|