#include <pde.h>
Public Member Functions | |
PDE (const int layers, const int sizex, const int sizey) | |
Constructor for PDE object containing arbitrary number of planes. | |
virtual | ~PDE () |
void | Plot (Graphics *g, const int layer=0) |
Plots one layer of the PDE plane to a Graphics window. | |
void | Plot (Graphics *g, CellularPotts *cpm, const int layer=0) |
Plots one layer of the PDE to a Graphics window, but not over the cells. | |
void | ContourPlot (Graphics *g, int layer=0, int colour=1) |
Plots the PDE field using contour lines. | |
int | SizeX () const |
Returns the horizontal size of the PDE planes. | |
int | SizeY () const |
Returns the vertical size of the PDE planes. | |
int | Layers () const |
Returns the number of PDE layers in the PDE object. | |
double | Sigma (const int layer, const int x, const int y) const |
Returns the value of grid point x,y of PDE plane "layer". | |
void | setValue (const int layer, const int x, const int y, const double value) |
Sets grid point x,y of PDE plane "layer" to value "value". | |
void | addtoValue (const int layer, const int x, const int y, const double value) |
Adds a number to a PDE grid point. | |
double | Max (int l) |
Gets the maximum value of PDE layer l. | |
double | Min (int l) |
Returns the minimum value of PDE layer l. | |
void | Diffuse (int repeat) |
Carry out $n$ diffusion steps for all PDE planes. | |
void | NoFluxBoundaries (void) |
Implementation of no-flux boundaries. | |
void | AbsorbingBoundaries (void) |
Implementation of absorbing boundaries. | |
void | PeriodicBoundaries (void) |
Implementation of periodic boundaries. | |
void | Secrete (CellularPotts *cpm) |
Reaction and interaction of CPM plane with PDE planes. | |
double | TheTime (void) const |
Returns cumulative "simulated" time, i.e. number of time steps * dt. | |
double | GetChemAmount (const int layer=-1) |
Returns summed amount of chemical in PDE plane "layer". | |
void | GradC (int layer=0, int first_grad_layer=1) |
void | PlotVectorField (Graphics &g, int stride, int linelength, int first_grad_layer=1) |
Protected Member Functions | |
virtual int | MapColour (double val) |
Used in Plot. Takes a color and turns it into a grey value. | |
PDE (void) | |
empty constructor (necessary for derivation) | |
virtual double *** | AllocateSigma (const int layers, const int sx, const int sy) |
Allocates a PDE plane (internal use). | |
Protected Attributes | |
double *** | sigma |
double *** | alt_sigma |
int | sizex |
int | sizey |
int | layers |
Friends | |
class | Info |
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Constructor for PDE object containing arbitrary number of planes.
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empty constructor (necessary for derivation)
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Implementation of absorbing boundaries. Called internally (optionally) by Diffuse(). |
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Adds a number to a PDE grid point.
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Allocates a PDE plane (internal use). For internal use, can be reimplemented in derived class to change method of memory allocation. |
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Plots the PDE field using contour lines.
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Carry out $n$ diffusion steps for all PDE planes. We use a forward Euler method here. Can be replaced for better algorithm.
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Returns summed amount of chemical in PDE plane "layer".
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Calculates the first and second order gradients, i.e. gradx, grady, gradxx, gradxy and gradyy and puts them in the next three chemical fields. Not currently used and might need some redoing. Make sure you have allocated sufficient fields (this method generates five planes).
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Returns the number of PDE layers in the PDE object.
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Used in Plot. Takes a color and turns it into a grey value.
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Gets the maximum value of PDE layer l.
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Returns the minimum value of PDE layer l.
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Implementation of no-flux boundaries. Called internally (optionally) by Diffuse(). |
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Implementation of periodic boundaries. Called internally (optionally) by Diffuse(). |
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Plots one layer of the PDE to a Graphics window, but not over the cells.
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Plots one layer of the PDE plane to a Graphics window.
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Plots a field of the first order gradients, i.e. gradx and grady; assumes you have called GradC before. Not currently used and might need some redoing.
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Reaction and interaction of CPM plane with PDE planes.
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Sets grid point x,y of PDE plane "layer" to value "value".
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Returns the value of grid point x,y of PDE plane "layer". Warning, no range checking done.
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Returns the horizontal size of the PDE planes.
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Returns the vertical size of the PDE planes.
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Returns cumulative "simulated" time, i.e. number of time steps * dt.
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