java.lang.Object
- HAL.GridsAndAgents.PDEGrid3D

All Implemented Interfaces:

Grid3D, java.io.Serializable
```
public class PDEGrid3D
extends java.lang.Object
implements Grid3D, java.io.Serializable
```
PDEGrid3D class facilitates 3D diffusion with two arrays of doubles called fields the intended usage is that during a diffusion tick, the current values will be read, and the next values will be written to after updates, Update is called to set the delta field as the current field.

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field	Description
`double[]`	`deltas`
`double[]`	`field`
`int`	`length`
`double[]`	`maxDifscratch`
`double[]`	`scratch`
`double[]`	`scratch2`
`boolean`	`wrapX`
`boolean`	`wrapY`
`boolean`	`wrapZ`
`int`	`xDim`
`int`	`yDim`
`int`	`zDim`

Constructor Summary

Constructors
Constructor	Description
`PDEGrid3D(int xDim, int yDim, int zDim)`
`PDEGrid3D(int xDim, int yDim, int zDim, boolean wrapX, boolean wrapY, boolean wrapZ)`

Method Summary

Modifier and Type	Method	Description
`void`	`Add(double x, double y, double z, double val)`
`void`	`Add(int i, double val)`	adds to the delta field value at the specified index
`void`	`Add(int x, int y, int z, double val)`	adds to the delta field value at the specified index
`void`	`AddAll(double val)`	adds specified value to all entries of the delta field
`void`	`Advection(double[] xVels, double[] yVels, double[] zVels)`	runs discontinuous advection
`void`	`Advection(double[] xVels, double[] yVels, double[] zVels, Coords3DDouble BoundaryConditionFn, Coords3DDouble BoundaryXvels, Coords3DDouble BondaryYvels, Coords3DDouble BoundaryZvels)`	runs discontinuous advection
`void`	`Advection(double xVel, double yVel, double zVel)`
`void`	`Advection(double xVel, double yVel, double zVel, double boundaryVal)`	runs advection as described above with a boundary value, meaning that the boundary value will advect in from the upwind direction, and the concentration will disappear in the downwind direction.
`void`	`Advection(double xVel, double yVel, double zVel, Coords3DDouble BoundaryConditionFn)`	runs advection as described above with a boundary condition function, which will be evaluated with the out of bounds coordinates as arguments whenever a boundary value is needed, and should return the boundary value
`void`	`Advection(Grid2Ddouble xVels, Grid2Ddouble yVels, Grid2Ddouble zVels)`	runs discontinuous advection
`void`	`Advection(Grid2Ddouble xVels, Grid2Ddouble yVels, Grid2Ddouble zVels, Coords3DDouble BoundaryConditionFn, Coords3DDouble BoundaryXvels, Coords3DDouble BondaryYvels, Coords3DDouble BoundaryZvels)`	runs discontinuous advection
`void`	`BoundAllSwap(double min, double max)`	Bounds all values in the delta field between min and max
`void`	`Diffusion(double diffCoef)`	/** runs diffusion on the current field, adding the deltas to the delta field.
`void`	`Diffusion(double[] diffRatesX, double[] diffRatesY, double[] diffRatesZ)`	runs diffusion with discontinuous diffusion rates
`void`	`Diffusion(double[] diffRatesX, double[] diffRatesY, double[] diffRatesZ, Coords3DDouble BoundaryConditionFn, Coords3DDouble BoundaryDiffusionRatesX, Coords3DDouble BoundaryDiffusionRatesY, Coords3DDouble BoundaryDiffusionRatesZ)`	runs diffusion with discontinuous diffusion rates
`void`	`Diffusion(double diffCoef, double boundaryValue)`	has the same effect as the above diffusion function without the boundary value argument, except rather than assuming zero flux, the boundary condition is set to either the boundaryValue, or wrap around
`void`	`Diffusion(double diffCoef, Coords3DDouble BoundaryConditionFn)`	has the same effect as the above diffusion function with a boundary condition function, which will be evaluated with the out of bounds coordinates as arguments whenever a boundary value is needed, and should return the boundary value
`void`	`Diffusion(Grid3Ddouble diffRatesX, Grid3Ddouble diffRatesY, Grid3Ddouble diffRatesZ)`	runs diffusion with discontinuous diffusion rates
`void`	`Diffusion(Grid3Ddouble diffRatesX, Grid3Ddouble diffRatesY, Grid3Ddouble diffRatesZ, Coords3DDouble BoundaryConditionFn, Coords3DDouble BoundaryDiffusionRatesX, Coords3DDouble BoundaryDiffusionRatesY, Coords3DDouble BoundaryDiffusionRatesZ)`	runs diffusion with discontinuous diffusion rates
`void`	`DiffusionADI(double diffRate)`
`void`	`DiffusionADI(double diffRate, double boundaryValue)`
`double`	`Get(double x, double y, double z)`
`double`	`Get(int i)`	gets the delta field value at the specified index
`double`	`Get(int x, int y, int z)`	gets to the current field value at the specified coordinates
`double`	`GetAvg()`	gets the average value of all squares in the current field
`double[]`	`GetDeltas()`
`double[]`	`GetField()`
`double`	`GradientX(double x, double y, double z)`
`double`	`GradientX(double x, double y, double z, double boundaryCond)`
`double`	`GradientX(int x, int y, int z)`	returns the gradient of the diffusible in the X direction at the coordinates specified
`double`	`GradientX(int x, int y, int z, double boundaryCond)`	returns the gradient of the diffusible in the X direction at the coordinates specified, will use the boundary condition value if computing the gradient next to the boundary
`double`	`GradientY(double x, double y, double z)`
`double`	`GradientY(double x, double y, double z, double boundaryCond)`
`double`	`GradientY(int x, int y, int z)`	returns the gradient of the diffusible in the Y direction at the coordinates specified
`double`	`GradientY(int x, int y, int z, double boundaryCond)`	returns the gradient of the diffusible in the Y direction at the coordinates specified, will use the boundary condition value if computing the gradient next to the boundary
`double`	`GradientZ(double x, double y, double z)`
`double`	`GradientZ(double x, double y, double z, double boundaryCond)`
`double`	`GradientZ(int x, int y, int z)`	returns the gradient of the diffusible in the Z direction at the coordinates specified
`double`	`GradientZ(int x, int y, int z, double boundaryCond)`	returns the gradient of the diffusible in the Z direction at the coordinates specified, will use the boundary condition value if computing the gradient next to the boundary
`boolean`	`IsWrapX()`
`boolean`	`IsWrapY()`
`boolean`	`IsWrapZ()`
`int`	`Length()`
`double`	`MaxDelta()`	returns the maximum difference as stored on the delta field, call right before calling Update()
`double`	`MaxDeltaScaled(double denomOffset)`	like MaxDelta only the differences are scaled relative to the value in the current field.
`double`	`MaxDifInternal()`	returns the maximum difference between the field passed in and the current field.
`void`	`Mul(double x, double y, double z, double val)`
`void`	`Mul(int i, double val)`	multiplies a value in the “current field” and adds the change to the “delta field”
`void`	`Mul(int x, int y, int z, double val)`	multiplies a value in the “current field” and adds the change to the “delta field”
`void`	`MulAll(double val)`	multiplies all values in the “current field” and puts the results into the “delta field”
`void`	`Set(double x, double y, double z, double val)`
`void`	`Set(int i, double val)`	sets the current field value at the specified index
`void`	`Set(int x, int y, int z, double val)`	sets to the current field value at the specified coordinates
`void`	`SetAll(double val)`	sets all squares in the delta field using the vals array
`void`	`SetNonNegative()`	ensures that all values will be non-negative on the next timestep, call before Update
`void`	`Update()`	adds the delta field into the current field, also increments the tick.
`int`	`UpdateCt()`
`int`	`Xdim()`
`int`	`Ydim()`
`int`	`Zdim()`

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface HAL.Interfaces.Grid3D
ApplyHood, ApplyHood, ApplyHoodMapped, ApplyRectangle, BoundaryIs, ContainsValidI, ContainsValidI, ConvI, ConvXpt, ConvXsq, ConvYpt, ConvYsq, ConvZpt, ConvZsq, DispX, DispY, DispZ, Dist, DistSquared, GetHoodI, I, I, In, In, InWrap, InWrap, ItoX, ItoY, ItoZ, MapHood, MapHood, MapHood, MapHood, RandomHoodI, WrapI

Field Detail

xDim
```
public final int xDim
```

yDim
```
public final int yDim
```

zDim
```
public final int zDim
```

length
```
public final int length
```

wrapX
```
public boolean wrapX
```

wrapY
```
public boolean wrapY
```

wrapZ
```
public boolean wrapZ
```

field
```
public double[] field
```

deltas
```
public double[] deltas
```

scratch
```
public double[] scratch
```

scratch2
```
public double[] scratch2
```

maxDifscratch
```
public double[] maxDifscratch
```

Constructor Detail

PDEGrid3D

public PDEGrid3D(int xDim,
                 int yDim,
                 int zDim,
                 boolean wrapX,
                 boolean wrapY,
                 boolean wrapZ)

PDEGrid3D

public PDEGrid3D(int xDim,
                 int yDim,
                 int zDim)

Method Detail

GetField
```
public double[] GetField()
```

GetDeltas
```
public double[] GetDeltas()
```

Get

public double Get(int x,
                  int y,
                  int z)

gets to the current field value at the specified coordinates

Get

public double Get(double x,
                  double y,
                  double z)

Get
```
public double Get(int i)
```
gets the delta field value at the specified index

Set

public void Set(int x,
                int y,
                int z,
                double val)

sets to the current field value at the specified coordinates

Set

public void Set(double x,
                double y,
                double z,
                double val)

Set

public void Set(int i,
                double val)

sets the current field value at the specified index

Add

public void Add(int x,
                int y,
                int z,
                double val)

adds to the delta field value at the specified index

Add

public void Add(double x,
                double y,
                double z,
                double val)

Add

public void Add(int i,
                double val)

adds to the delta field value at the specified index

Mul
```
public void Mul(int i,
                double val)
```
multiplies a value in the “current field” and adds the change to the “delta field”

Mul

public void Mul(int x,
                int y,
                int z,
                double val)

multiplies a value in the “current field” and adds the change to the “delta field”

Mul

public void Mul(double x,
                double y,
                double z,
                double val)

Update
```
public void Update()
```
adds the delta field into the current field, also increments the tick.

UpdateCt
```
public int UpdateCt()
```

BoundAllSwap

public void BoundAllSwap(double min,
                         double max)

Bounds all values in the delta field between min and max

Diffusion
```
public void Diffusion(double diffCoef)
```
/** runs diffusion on the current field, adding the deltas to the delta field. This form of the function assumes either a reflective or wrapping boundary (depending on how the PDEGrid was specified). the diffCoef variable is the nondimensionalized diffusion conefficient. If the dimensionalized diffusion coefficient is x then diffCoef can be found by computing (x*SpaceStep)/TimeStep^2 Note that if the diffCoef exceeds 0.25, this diffusion method will become numerically unstable.

Diffusion
```
public void Diffusion(double diffCoef,
                      double boundaryValue)
```
has the same effect as the above diffusion function without the boundary value argument, except rather than assuming zero flux, the boundary condition is set to either the boundaryValue, or wrap around

Diffusion
```
public void Diffusion(double diffCoef,
                      Coords3DDouble BoundaryConditionFn)
```
has the same effect as the above diffusion function with a boundary condition function, which will be evaluated with the out of bounds coordinates as arguments whenever a boundary value is needed, and should return the boundary value

Diffusion

public void Diffusion(double[] diffRatesX,
                      double[] diffRatesY,
                      double[] diffRatesZ)

runs diffusion with discontinuous diffusion rates

Diffusion

public void Diffusion(Grid3Ddouble diffRatesX,
                      Grid3Ddouble diffRatesY,
                      Grid3Ddouble diffRatesZ)

runs diffusion with discontinuous diffusion rates

Diffusion

public void Diffusion(double[] diffRatesX,
                      double[] diffRatesY,
                      double[] diffRatesZ,
                      Coords3DDouble BoundaryConditionFn,
                      Coords3DDouble BoundaryDiffusionRatesX,
                      Coords3DDouble BoundaryDiffusionRatesY,
                      Coords3DDouble BoundaryDiffusionRatesZ)

runs diffusion with discontinuous diffusion rates

Diffusion

public void Diffusion(Grid3Ddouble diffRatesX,
                      Grid3Ddouble diffRatesY,
                      Grid3Ddouble diffRatesZ,
                      Coords3DDouble BoundaryConditionFn,
                      Coords3DDouble BoundaryDiffusionRatesX,
                      Coords3DDouble BoundaryDiffusionRatesY,
                      Coords3DDouble BoundaryDiffusionRatesZ)

runs diffusion with discontinuous diffusion rates

MaxDelta
```
public double MaxDelta()
```
returns the maximum difference as stored on the delta field, call right before calling Update()

MaxDeltaScaled
```
public double MaxDeltaScaled(double denomOffset)
```
like MaxDelta only the differences are scaled relative to the value in the current field. the denomOffset is used to prevent a division by zero

Advection

public void Advection(double xVel,
                      double yVel,
                      double zVel)

Advection
```
public void Advection(double xVel,
                      double yVel,
                      double zVel,
                      double boundaryVal)
```
runs advection as described above with a boundary value, meaning that the boundary value will advect in from the upwind direction, and the concentration will disappear in the downwind direction.

Advection
```
public void Advection(double xVel,
                      double yVel,
                      double zVel,
                      Coords3DDouble BoundaryConditionFn)
```
runs advection as described above with a boundary condition function, which will be evaluated with the out of bounds coordinates as arguments whenever a boundary value is needed, and should return the boundary value

Advection

public void Advection(double[] xVels,
                      double[] yVels,
                      double[] zVels)

runs discontinuous advection

Advection

public void Advection(Grid2Ddouble xVels,
                      Grid2Ddouble yVels,
                      Grid2Ddouble zVels)

runs discontinuous advection

Advection

public void Advection(double[] xVels,
                      double[] yVels,
                      double[] zVels,
                      Coords3DDouble BoundaryConditionFn,
                      Coords3DDouble BoundaryXvels,
                      Coords3DDouble BondaryYvels,
                      Coords3DDouble BoundaryZvels)

runs discontinuous advection

Advection

public void Advection(Grid2Ddouble xVels,
                      Grid2Ddouble yVels,
                      Grid2Ddouble zVels,
                      Coords3DDouble BoundaryConditionFn,
                      Coords3DDouble BoundaryXvels,
                      Coords3DDouble BondaryYvels,
                      Coords3DDouble BoundaryZvels)

runs discontinuous advection

MaxDifInternal
```
public double MaxDifInternal()
```
returns the maximum difference between the field passed in and the current field. call right after Update()

DiffusionADI

public void DiffusionADI(double diffRate)

DiffusionADI

public void DiffusionADI(double diffRate,
                         double boundaryValue)

SetAll
```
public void SetAll(double val)
```
sets all squares in the delta field using the vals array

SetNonNegative
```
public void SetNonNegative()
```
ensures that all values will be non-negative on the next timestep, call before Update

GetAvg
```
public double GetAvg()
```
gets the average value of all squares in the current field

AddAll
```
public void AddAll(double val)
```
adds specified value to all entries of the delta field

MulAll
```
public void MulAll(double val)
```
multiplies all values in the “current field” and puts the results into the “delta field”

GradientX

public double GradientX(int x,
                        int y,
                        int z)

returns the gradient of the diffusible in the X direction at the coordinates specified

GradientX

public double GradientX(double x,
                        double y,
                        double z)

GradientY

public double GradientY(int x,
                        int y,
                        int z)

returns the gradient of the diffusible in the Y direction at the coordinates specified

GradientY

public double GradientY(double x,
                        double y,
                        double z)

GradientZ

public double GradientZ(int x,
                        int y,
                        int z)

returns the gradient of the diffusible in the Z direction at the coordinates specified

GradientZ

public double GradientZ(double x,
                        double y,
                        double z)

GradientX
```
public double GradientX(int x,
                        int y,
                        int z,
                        double boundaryCond)
```
returns the gradient of the diffusible in the X direction at the coordinates specified, will use the boundary condition value if computing the gradient next to the boundary

GradientX

public double GradientX(double x,
                        double y,
                        double z,
                        double boundaryCond)

GradientY
```
public double GradientY(int x,
                        int y,
                        int z,
                        double boundaryCond)
```
returns the gradient of the diffusible in the Y direction at the coordinates specified, will use the boundary condition value if computing the gradient next to the boundary

GradientY

public double GradientY(double x,
                        double y,
                        double z,
                        double boundaryCond)

GradientZ
```
public double GradientZ(int x,
                        int y,
                        int z,
                        double boundaryCond)
```
returns the gradient of the diffusible in the Z direction at the coordinates specified, will use the boundary condition value if computing the gradient next to the boundary

GradientZ

public double GradientZ(double x,
                        double y,
                        double z,
                        double boundaryCond)

Xdim
```
public int Xdim()
```
Specified by:

Xdim in interface Grid3D

Ydim
```
public int Ydim()
```
Specified by:

Ydim in interface Grid3D

Zdim
```
public int Zdim()
```
Specified by:

Zdim in interface Grid3D

Length
```
public int Length()
```
Specified by:

Length in interface Grid3D

IsWrapX
```
public boolean IsWrapX()
```
Specified by:

IsWrapX in interface Grid3D

IsWrapY
```
public boolean IsWrapY()
```
Specified by:

IsWrapY in interface Grid3D

IsWrapZ
```
public boolean IsWrapZ()
```
Specified by:

IsWrapZ in interface Grid3D

Class PDEGrid3D

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface HAL.Interfaces.Grid3D

Field Detail

xDim

yDim

zDim

length

wrapX

wrapY

wrapZ

field

deltas

scratch

scratch2

maxDifscratch

Constructor Detail

PDEGrid3D

PDEGrid3D

Method Detail

GetField

GetDeltas

Get

Get

Get

Set

Set

Set

Add

Add

Add

Mul

Mul

Mul

Update

UpdateCt

BoundAllSwap

Diffusion

Diffusion

Diffusion

Diffusion

Diffusion

Diffusion

Diffusion

MaxDelta

MaxDeltaScaled

Advection

Advection

Advection

Advection

Advection

Advection

Advection

MaxDifInternal

DiffusionADI

DiffusionADI

SetAll

SetNonNegative

GetAvg

AddAll

MulAll

GradientX

GradientX

GradientY

GradientY

GradientZ

GradientZ

GradientX

GradientX

GradientY

GradientY

GradientZ

GradientZ

Xdim

Ydim

Zdim

Length