- sample() - Method in class starfish.core.diagnostics.AveragingModule
-
adds a new sample to the averaging
- sample(boolean) - Method in class starfish.core.diagnostics.AveragingModule
-
adds a new sample to the averaging
- sample_mesh - Variable in class starfish.core.source.VolumeSource
-
- sampleFluid() - Method in class starfish.core.source.ParticleListSource
-
- sampleFluid() - Method in class starfish.core.source.Source
-
updates boundaries for fluid-based species
- sampleFluid() - Method in class starfish.core.source.VolumeSource
-
- sampleFluid() - Method in class starfish.sources.AmbientSource
-
- sampleFluid() - Method in class starfish.sources.ColdBeamSource
-
- sampleFluid() - Method in class starfish.sources.CosineSource
-
- sampleFluid() - Method in class starfish.sources.MaxwellianSource
-
- sampleFluid() - Method in class starfish.sources.UniformSource
-
- sampleFluid() - Method in class starfish.sources.VolumePreloadSource
-
- SampleMaxw1D(double) - Static method in class starfish.core.common.Utils
-
- SampleMaxw3D(double) - Static method in class starfish.core.common.Utils
-
- sampleMaxwellianVelocity(Mesh, double[], double) - Method in class starfish.core.materials.Material
-
- SampleMaxwSpeed(double) - Static method in class starfish.core.common.Utils
-
- sampleParticle() - Method in class starfish.core.source.ParticleListSource
-
- sampleParticle() - Method in class starfish.core.source.Source
-
returns a new particle
- sampleParticle() - Method in class starfish.core.source.VolumeSource
-
- sampleParticle() - Method in class starfish.sources.AmbientSource
-
- sampleParticle() - Method in class starfish.sources.ColdBeamSource
-
- sampleParticle() - Method in class starfish.sources.CosineSource
-
- sampleParticle() - Method in class starfish.sources.MaxwellianSource
-
- sampleParticle() - Method in class starfish.sources.UniformSource
-
- sampleSources() - Method in class starfish.core.source.SourceModule
-
samples sources and adds particles or updates boundaries
- sampleVelocity(Mesh, double[]) - Method in class starfish.core.materials.Material
-
- save(String) - Method in class starfish.core.boundaries.Contour
-
- save() - Method in class starfish.core.common.RestartModule
-
- save(boolean) - Method in class starfish.core.common.RestartModule
-
- save() - Method in class starfish.core.diagnostics.AnimationModule
-
- save(String) - Method in class starfish.core.domain.Mesh
-
saves the mesh, useful for debuggin
- save(String, LinkedHashMap<String, Field2D>) - Method in class starfish.core.domain.Mesh
-
- saveBoundaries(String, String[]) - Method in class starfish.core.io.Writer
-
convenience method for one stop writin
- saveRestartData() - Method in class starfish.core.common.RestartModule
-
saves restart data
At present only saves particle positions
TODO: add save for fields and fluid materials
- saveRestartData(DataOutputStream) - Method in class starfish.core.materials.KineticMaterial
-
- saveRestartData(DataOutputStream) - Method in class starfish.core.materials.Material
-
- saveStats() - Method in class starfish.core.diagnostics.StatsModule
-
- sc - Variable in class starfish.core.io.TecplotReader
-
- scaleByVol() - Method in class starfish.core.domain.Field2D
-
scales each node value by node volume
- scatter(double[], double) - Method in class starfish.core.boundaries.Field1D
-
- scatter(double, double) - Method in class starfish.core.boundaries.Field1D
-
Scatter
Distributes val to surroudning nodes
- scatter(double[], double) - Method in class starfish.core.domain.Field2D
-
- scatter(double, double, double) - Method in class starfish.core.domain.Field2D
-
Scatter
Distributes val to surrounding node
- seg_list - Variable in class starfish.core.boundaries.BoundaryModule
-
- Segment - Class in starfish.core.boundaries
-
Segment is the basic building block of a spline.
- Segment() - Constructor for class starfish.core.boundaries.Segment
-
- segmentArea(int) - Method in class starfish.core.boundaries.Spline
-
- segmentInBox(double[], double[]) - Method in class starfish.core.boundaries.Segment
-
- segments - Variable in class starfish.core.boundaries.Spline
-
- segments - Variable in class starfish.core.domain.Mesh.Node
-
- segments_in_box - Variable in class starfish.core.boundaries.Contour
-
- set(int, double) - Method in class starfish.core.boundaries.Field1D
-
set: sets value at i,
- set(int, int, double) - Method in class starfish.core.domain.Field2D
-
set: sets value at i,
- set(int, int, double) - Method in class starfish.core.solver.Matrix
-
sets value at row i, column j in full matri
- setAccomodationCoefficient(double) - Method in class starfish.core.interactions.MaterialInteraction
-
- setBoundaries(ArrayList<Boundary>) - Method in class starfish.core.domain.Mesh
-
- SetCell(Field2D, int, int, int, Spline) - Method in class starfish.core.boundaries.Contour
-
SetCell
this function adds control point on cell specified by
i,j, skipping over ignore edge (counterclockwise from XMAX)
function returns the edge that was set or -1 if not foun
- setDataShallow(double[]) - Method in class starfish.core.boundaries.Field1D
-
replaces field data, shallow replace (reference only
- setDataShallow(double[][]) - Method in class starfish.core.domain.Field2D
-
replaces field data, shallow replace (reference only
- setDt(double) - Method in class starfish.core.common.TimeModule
-
- setElectronModel(FluidElectronsMaterial.ElectronModel) - Method in class starfish.pic.FluidElectronsMaterial
-
- setInitValues(String[]) - Method in class starfish.core.materials.Material
-
- setInterfaceNodeLocation() - Method in class starfish.core.domain.Mesh
-
- setIt(int) - Method in class starfish.core.common.TimeModule
-
- setJpanel(JPanel) - Method in class starfish.core.gui.InputTextBox
-
- setMeshBCType(Mesh.Face, Mesh.NodeType, double) - Method in class starfish.core.domain.Mesh
-
- setMeshNeighbors() - Method in class starfish.core.domain.Mesh
-
sets neighbors boundary cells
- setName(String) - Method in class starfish.core.domain.Mesh
-
- setName(String) - Method in class starfish.core.gui.InputTextBox
-
- setNodeControlVolumes(ArrayList<Boundary>) - Method in class starfish.core.domain.Mesh
-
- setNumIt(int) - Method in class starfish.core.common.TimeModule
-
- setOrigin(double, double) - Method in class starfish.core.domain.UniformMesh
-
- setParentInfo(Boundary, int) - Method in class starfish.core.boundaries.Segment
-
- setPath(String, Matrix, boolean) - Method in class starfish.core.boundaries.Spline
-
Sets the spline using a SVG-like path syntax:
M x y : moves the current position to x y
L x y : creates a linear segment from current position to (x,y)
C k1x k1y k2x k2y x y : creates a cubic segment from current position to (x,y) using knots k1 and k2
S x y : creates a smooth segment from current position to (x,y)
Z : adds discontinuity into the spline
Unlike SVG, the cubic path is specified only by the final position.
- setPos(double[][], double[][]) - Method in class starfish.core.domain.QuadrilateralMesh
-
- setProbability(double) - Method in class starfish.core.interactions.MaterialInteraction
-
sets probabilit
- setProductMatIndex(int) - Method in class starfish.core.interactions.MaterialInteraction
-
- setRestitutionCoefficient(double) - Method in class starfish.core.interactions.MaterialInteraction
-
- setSourceMatIndex(int) - Method in class starfish.core.interactions.MaterialInteraction
-
- setSpacing(double, double) - Method in class starfish.core.domain.UniformMesh
-
- setSurfaceImpactHandler(MaterialInteraction.SurfaceImpactHandler) - Method in class starfish.core.interactions.MaterialInteraction
-
- setTargetMatIndex(int) - Method in class starfish.core.interactions.MaterialInteraction
-
- setValue(double) - Method in class starfish.core.boundaries.Field1D
-
sets all data to the same valu
- setValue(double) - Method in class starfish.core.boundaries.FieldCollection1D
-
sets the entire collection to a constant valu
- setValue(double) - Method in class starfish.core.domain.Field2D
-
sets all data to the same valu
- setValue(double) - Method in class starfish.core.domain.FieldCollection2D
-
sets the entire collection to a constant valu
- setXd() - Method in class starfish.core.domain.UniformMesh
-
- Sigma - Class in starfish.core.interactions
-
Collision cross-sections
- Sigma() - Constructor for class starfish.core.interactions.Sigma
-
- Sigma(double[]) - Constructor for class starfish.core.interactions.Sigma
-
- Sigma.SigmaConst - Class in starfish.core.interactions
-
sigma = [c0]
- Sigma.SigmaFactory - Interface in starfish.core.interactions
-
- Sigma.SigmaInv - Class in starfish.core.interactions
-
sigma = c[0]/g
- SigmaPlus - Class in starfish.collisions
-
- SigmaPlus() - Constructor for class starfish.collisions.SigmaPlus
-
- SigmaPlus.SigmaBird463 - Class in starfish.collisions
-
- SolidMaterial - Class in starfish.core.materials
-
solid material, does not change in density
- SolidMaterial(String, double) - Constructor for class starfish.core.materials.SolidMaterial
-
- SolidMaterialParser - Static variable in class starfish.core.materials.SolidMaterial
-
- solveLinearGS(Solver.MeshData[]) - Method in class starfish.core.solver.Solver
-
solves Ax=b for x using the GS method
- solveLinearMultigrid(Matrix, double[], double[]) - Method in class starfish.core.solver.Solver
-
solves Ax=b for x using the Multigrid method
- solveLinearPCG(Solver.MeshData[]) - Method in class starfish.core.solver.Solver
-
solves Ax=b for x using the PCG metho
- solveLU(Solver.MeshData[]) - Method in class starfish.core.solver.Solver
-
- solveNonLinearNR(Solver.MeshData[], Solver.NL_Eval) - Method in class starfish.core.solver.Solver
-
solves the nonlinear problem Ax-b=0 using the Newtons method
This method is based on the algorithm on page 614 in Numerical Analysis
F(x)=Ax-b
J(x)=dF/dx=A-db/dx=A-P
solve Jy=F
update x=x-y
also b=b0+b(x) where b0 is constant
- solvePotentialLin() - Method in class starfish.pic.PoissonSolver
-
- solvePotentialNL() - Method in class starfish.pic.PoissonSolver
-
- Solver - Class in starfish.core.solver
-
Finite volume Matrix solver for Ax=b using the Gauss-Seidel method (for now)
- Solver() - Constructor for class starfish.core.solver.Solver
-
- Solver.MeshData - Class in starfish.core.solver
-
- Solver.NL_Eval - Interface in starfish.core.solver
-
- solver_module - Static variable in class starfish.core.common.Starfish
-
- SolverModule - Class in starfish.core.solver
-
- SolverModule() - Constructor for class starfish.core.solver.SolverModule
-
- SolverModule.SolverFactory - Interface in starfish.core.solver
-
- Source - Class in starfish.core.source
-
Base class for particle sources
- Source(String, Material, Spline, double, int) - Constructor for class starfish.core.source.Source
-
constructor
- Source(String, Material, Spline, double, int, int) - Constructor for class starfish.core.source.Source
-
- Source(String, Material) - Constructor for class starfish.core.source.Source
-
constructor for sources not associated with a spline
- Source(String, Material, Spline, double) - Constructor for class starfish.core.source.Source
-
constructor without start-it
- source_coeff - Variable in class starfish.core.interactions.ChemicalReaction
-
- source_interactions - Variable in class starfish.core.materials.Material
-
list of interactions that affect the source particle: diffuse, absorb, etc..
- source_list - Variable in class starfish.core.boundaries.Boundary
-
source list
- source_mat - Variable in class starfish.core.interactions.ChemicalReaction
-
- source_mat - Variable in class starfish.core.source.Source
-
- source_module - Static variable in class starfish.core.common.Starfish
-
- SourceModule - Class in starfish.core.source
-
Handles < source\ > command
- SourceModule() - Constructor for class starfish.core.source.SourceModule
-
- SourceModule.SurfaceSourceFactory - Interface in starfish.core.source
-
interfaces for source factories
- SourceModule.VolumeSourceFactory - Interface in starfish.core.source
-
- spawnParticles(double[], double[], int) - Method in class starfish.core.source.ParticleListSource
-
- Spline - Class in starfish.core.boundaries
-
Defines a spline, collection of line segments
Segments can be linear or smooth cubic bezier curves
The parametric position along the spline is t=[0,np] where np is the
number of points.
- Spline() - Constructor for class starfish.core.boundaries.Spline
-
general constructor
- Spline(ArrayList<Spline>) - Constructor for class starfish.core.boundaries.Spline
-
constructs a spline made of other spline
- Spline(double[], double[]) - Constructor for class starfish.core.boundaries.Spline
-
constructs a spline composed of a single linear segmen
- spline - Variable in class starfish.core.source.Source
-
- Spline.SetPathMode - Enum in starfish.core.boundaries
-
- splines - Variable in class starfish.core.domain.EllipticMesh
-
- splitSpline(int, boolean) - Method in class starfish.core.boundaries.Spline
-
this function returns an array of parametric position [0,1] that split
a multisegment spline into nn-1 segments.
- spwt - Variable in class starfish.core.materials.KineticMaterial.Particle
-
- spwt0 - Variable in class starfish.core.materials.KineticMaterial
-
- SQRT2 - Static variable in class starfish.core.common.Constants
-
- ss_countdown - Variable in class starfish.core.common.TimeModule
-
- ss_time - Variable in class starfish.core.common.TimeModule
-
- Starfish - Class in starfish.core.common
-
- Starfish() - Constructor for class starfish.core.common.Starfish
-
- starfish.collisions - package starfish.collisions
-
- starfish.core.boundaries - package starfish.core.boundaries
-
- starfish.core.common - package starfish.core.common
-
- starfish.core.diagnostics - package starfish.core.diagnostics
-
- starfish.core.domain - package starfish.core.domain
-
- starfish.core.gui - package starfish.core.gui
-
- starfish.core.interactions - package starfish.core.interactions
-
- starfish.core.io - package starfish.core.io
-
- starfish.core.materials - package starfish.core.materials
-
- starfish.core.solver - package starfish.core.solver
-
- starfish.core.source - package starfish.core.source
-
- Starfish.Log - Class in starfish.core.common
-
convenience functions for logging
- starfish.pic - package starfish.pic
-
- starfish.sources - package starfish.sources
-
- start() - Method in class starfish.core.boundaries.BoundaryModule
-
- start() - Method in class starfish.core.common.CommandModule
-
function called prior to main loop
- start() - Method in class starfish.core.common.RestartModule
-
- start(String[], List<Plugin>) - Method in class starfish.core.common.Starfish
-
- start() - Method in class starfish.core.common.Starfish
-
- start() - Method in class starfish.core.common.TimeModule
-
- start() - Method in class starfish.core.diagnostics.AveragingModule
-
- start() - Method in class starfish.core.diagnostics.ParticleTraceModule
-
- start() - Method in class starfish.core.diagnostics.StatsModule
-
- start() - Method in class starfish.core.domain.DomainModule
-
- start() - Method in class starfish.core.interactions.InteractionsModule
-
- start() - Method in class starfish.core.io.LoadFieldModule
-
- start() - Method in class starfish.core.io.LoggerModule
-
- start() - Method in class starfish.core.io.NoteModule
-
- start() - Method in class starfish.core.io.OutputModule
-
- start() - Method in class starfish.core.materials.MaterialsModule
-
- start() - Method in class starfish.core.solver.SolverModule
-
- start() - Method in class starfish.core.source.Source
-
- start() - Method in class starfish.core.source.SourceModule
-
- start() - Method in class starfish.sources.AmbientSource
-
- StartModules() - Method in class starfish.core.common.Starfish
-
calls start subroutines
- stats_module - Static variable in class starfish.core.common.Starfish
-
- stats_skip - Variable in class starfish.core.diagnostics.StatsModule
-
- StatsModule - Class in starfish.core.diagnostics
-
- StatsModule() - Constructor for class starfish.core.diagnostics.StatsModule
-
- steady_state() - Static method in class starfish.core.common.Starfish
-
- steady_state - Variable in class starfish.core.common.TimeModule
-
- StopModule - Class in starfish.core.common
-
implements lt; stop > command
- StopModule() - Constructor for class starfish.core.common.StopModule
-
- stripArea(double, double) - Method in class starfish.core.boundaries.Spline
-
- subtract(double[], double[]) - Static method in class starfish.core.common.Vector
-
returns r = v1-v
- subtract(int, int, double) - Method in class starfish.core.solver.Matrix
-
add value to row r, column c in full matri
- subtract(Matrix) - Method in class starfish.core.solver.Matrix
-
returns A-
- subtractDiag(double[]) - Method in class starfish.core.solver.Matrix
-
returns A-diag(B), for now defined only for identical matrices (nv is equal
- subtractInclusive(double[], double[]) - Static method in class starfish.core.common.Vector
-
computes v1 = v1-v
- surface_model_factories - Static variable in class starfish.core.interactions.SurfaceInteraction
-
- surface_source_factories - Static variable in class starfish.core.source.SourceModule
-
- SurfaceEmissionAbsorb - Static variable in class starfish.core.interactions.SurfaceInteraction
-
absorbs particles
- SurfaceEmissionCosine - Static variable in class starfish.core.interactions.SurfaceInteraction
-
Reflects particles in direction following cosine law
- SurfaceEmissionDiffuse - Static variable in class starfish.core.interactions.SurfaceInteraction
-
Reflects particles using Bird's diffuse reflection model
- SurfaceEmissionNone - Static variable in class starfish.core.interactions.SurfaceInteraction
-
doesn't do anything - particles will pass
- SurfaceEmissionSpecular - Static variable in class starfish.core.interactions.SurfaceInteraction
-
specularly reflects all particles
- SurfaceInteraction - Class in starfish.core.interactions
-
particle-surface interaction handler
- SurfaceInteraction() - Constructor for class starfish.core.interactions.SurfaceInteraction
-
- SurfaceInteraction.SurfaceModelFactory - Interface in starfish.core.interactions
-
- syncMeshBoundaries() - Method in class starfish.core.domain.FieldCollection2D
-
creates continuity across mesh boundaries