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Simulation.cpp
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#include "Simulation.h"
#include <stdio.h>
#include <math.h>
#include "Array.h"
#include "Cell.h"
#include "Cells.h"
#include "Compute.h"
#include "InputOutput.h"
#include "Constants.h"
#include "tools.h"
#include "UniformGrid.h"
#include "Nutrients.h"
#include "Neighbours.h"
#include "Forces.h"
#include "ClockIt.h"
#ifdef _WIN32
#include <windows.h>
#else
#include <unistd.h>
#endif
void SimSingleThread(int N_cells, Cell* old_cells, Cell* new_cells, int** NeighbourList, int maxNeighbours, UniformGrid& Grid, OutputFiles Files, bool append, DoubleArray2D& Height, DoubleArray3D& Density, DoubleArray3D& Density1, DoubleArray3D& Density2, DoubleArray2D& WallDensity,DoubleArray2D& WallDensity1,DoubleArray2D& WallDensity2,EnvArray3D& Environment, EnvArray3D& oldEnvironment, AgaArray3D** FieldAgar, AgaArray3D** oldFieldAgar, AgaArray2D** FieldWall, AgaArray2D** oldFieldWall, CoordArray2D& Normal);
int GetProcessorCount()
{
#ifdef _WIN32
SYSTEM_INFO info;
GetSystemInfo(&info);
return info.dwNumberOfProcessors;
#else
return sysconf(_SC_NPROCESSORS_ONLN);
#endif
}
void RunSimulation(int N_cells, Cell* old_cells, Cell* new_cells, int** NeighbourList, int maxNeighbours, UniformGrid& Grid, OutputFiles Files, bool append, DoubleArray2D& Height, DoubleArray3D& Density, DoubleArray3D& Density1, DoubleArray3D& Density2,DoubleArray2D& WallDensity,DoubleArray2D& WallDensity1,DoubleArray2D& WallDensity2, EnvArray3D& Environment, EnvArray3D& oldEnvironment, AgaArray3D** FieldAgar, AgaArray3D** oldFieldAgar, AgaArray2D** FieldWall, AgaArray2D** oldFieldWall, CoordArray2D& Normal)
{
SimSingleThread(N_cells, old_cells, new_cells, NeighbourList, maxNeighbours, Grid, Files, append, Height, Density, Density1, Density2, WallDensity, WallDensity1, WallDensity2, Environment, oldEnvironment, FieldAgar, oldFieldAgar, FieldWall, oldFieldWall, Normal);
}
void SimSingleThread(int N_cells, Cell* old_cells, Cell* new_cells, int** NeighbourList, int maxNeighbours, UniformGrid& Grid, OutputFiles Files, bool append, DoubleArray2D& Height, DoubleArray3D& Density, DoubleArray3D& Density1, DoubleArray3D& Density2, DoubleArray2D& WallDensity,DoubleArray2D& WallDensity1,DoubleArray2D& WallDensity2,EnvArray3D& Environment, EnvArray3D& oldEnvironment, AgaArray3D** FieldAgar, AgaArray3D** oldFieldAgar, AgaArray2D** FieldWall, AgaArray2D** oldFieldWall, CoordArray2D& Normal)
{
// initialize time (generations)
double dt = initial_dt; // time step
double t = t0; // current time
int minx, maxx, miny, maxy, maxz;
// **********************Initialize*******************************
// counter to determine when to output data
double NextOutTime = OutputTime;
double NextUpdateTime = UpdateTime;
double HeightDensityNextUpdateTime = UpdateTime/10.0;
double HeightDensityUpdateTime = UpdateTime/10.0;
bool OutFlag = true;
bool UpdateFlag = true;
bool HeightDensityUpdateFlag = true;
// filter for doing some smoothing and averaging of fields
DoubleArray2D Filter(FilterLen,FilterLen);
double value = 1.0/(double)(FilterLen*FilterLen);
for (int ii = 0; ii<FilterLen; ii++)
{
for (int jj = 0; jj<FilterLen; jj++)
{
Filter.Set(ii,jj,value);
}
}
int FilterDim = FilterLen/2;
// make filter function for averaging the density
/* DoubleArray3D Filter3D(3,3,3);
double filter3D[27] = { 0.0010, 0.0081, 0.0010,
0.0081, 0.0642, 0.0081,
0.0010, 0.0081, 0.0010,
0.0081, 0.0642, 0.0081,
0.0642, 0.5102, 0.0642,
0.0081, 0.0642, 0.0081,
0.0010, 0.0081, 0.0010,
0.0081, 0.0642, 0.0081,
0.0010, 0.0081, 0.0010 };
Filter3D.SetData(filter3D,27);*/
DoubleArray3D Filter3D(FilterLen,FilterLen,FilterLen);
double norm = 0;
for (int ii=0; ii<FilterLen; ii++)
{
for (int jj=0; jj<FilterLen; jj++)
{
for (int kk=0; kk<FilterLen; kk++)
{
value = exp(-(ii-FilterLen/2)*(ii-FilterLen/2)-(jj-FilterLen/2)*(jj-FilterLen/2)-(kk-FilterLen/2)*(kk-FilterLen/2));
norm = norm + value;
}
}
}
for (int ii=0; ii<FilterLen; ii++)
{
for (int jj=0; jj<FilterLen; jj++)
{
for (int kk=0; kk<FilterLen; kk++)
{
value = exp(-(ii-FilterLen/2)*(ii-FilterLen/2)-(jj-FilterLen/2)*(jj-FilterLen/2)-(kk-FilterLen/2)*(kk-FilterLen/2));
Filter3D.Set(ii,jj,kk,value/norm);
}
}
}
// *******************Calculate important fields******************
DoubleArray3D RoughDensity(Density.Size().x, Density.Size().y, Density.Size().z);
DoubleArray3D RoughDensity1(Density1.Size().x, Density1.Size().y, Density1.Size().z);
DoubleArray3D RoughDensity2(Density2.Size().x, Density2.Size().y, Density2.Size().z);
DoubleArray3D insideColonyDen(Density.Size().x, Density.Size().y, Density.Size().z);
DoubleArray2D RoughWallDensity(WallDensity.Size().x, WallDensity.Size().y);
DoubleArray2D RoughWallDensity1(WallDensity1.Size().x, WallDensity1.Size().y);
DoubleArray2D RoughWallDensity2(WallDensity2.Size().x, WallDensity2.Size().y);
DoubleArray3D RoughDensityShiftP(Density.Size().x, Density.Size().y, Density.Size().z);
DoubleArray3D RoughDensity1ShiftP(Density1.Size().x, Density1.Size().y, Density1.Size().z);
DoubleArray3D RoughDensity2ShiftP(Density2.Size().x, Density2.Size().y, Density2.Size().z);
DoubleArray2D RoughWallDensityShiftP(WallDensity.Size().x, WallDensity.Size().y);
DoubleArray2D RoughWallDensity1ShiftP(WallDensity1.Size().x, WallDensity1.Size().y);
DoubleArray2D RoughWallDensity2ShiftP(WallDensity2.Size().x, WallDensity2.Size().y);
DoubleArray3D DensityShiftP(Density.Size().x, Density.Size().y, Density.Size().z);
DoubleArray3D Density1ShiftP(Density1.Size().x, Density1.Size().y, Density1.Size().z);
DoubleArray3D Density2ShiftP(Density2.Size().x, Density2.Size().y, Density2.Size().z);
DoubleArray2D WallDensityShiftP(WallDensity.Size().x, WallDensity.Size().y);
DoubleArray2D WallDensity1ShiftP(WallDensity1.Size().x, WallDensity1.Size().y);
DoubleArray2D WallDensity2ShiftP(WallDensity2.Size().x, WallDensity2.Size().y);
DoubleArray2D RoughHeight(Height.Size().x, Height.Size().y);
RoughHeight.Initialize(cellRadius);
RoughDensity.Initialize(0.0);
RoughDensity1.Initialize(0.0);
RoughDensity2.Initialize(0.0);
insideColonyDen.Initialize(0.0);
RoughWallDensity.Initialize(0.0);
RoughWallDensity1.Initialize(0.0);
RoughWallDensity2.Initialize(0.0);
RoughDensityShiftP.Initialize(0.0);
RoughDensity1ShiftP.Initialize(0.0);
RoughDensity2ShiftP.Initialize(0.0);
RoughWallDensityShiftP.Initialize(0.0);
RoughWallDensity1ShiftP.Initialize(0.0);
RoughWallDensity2ShiftP.Initialize(0.0);
DensityShiftP.Initialize(0.0);
Density1ShiftP.Initialize(0.0);
Density2ShiftP.Initialize(0.0);
WallDensityShiftP.Initialize(0.0);
WallDensity1ShiftP.Initialize(0.0);
WallDensity2ShiftP.Initialize(0.0);
// Make rough wall
DoubleArray2D Wall(BoxX,BoxY);
for (int ii = 0; ii < BoxX; ii++)
{
for (int jj = 0; jj < BoxY; jj++)
{
Wall.Set(ii,jj,((float)rand()/RAND_MAX-0.5)*wall_rough);
}
}
printf("Created wall \n");
int* IDlist = new int[maxNeighbours];
int IDlen = 0;
// cell stress tensor
Tensor stressTensor;
// net force
DoubleCoord Fnet;
// dividing cells
int* dividingCells = new int[maxCells]; // list of cells that need to divide at the end of a timestep
int numDivide;
// calculate fields, output to file
CreateOutputFiles(0, Files, append);
GetDensity(RoughDensity, RoughDensity1, RoughDensity2, insideColonyDen, Height, Grid, old_cells, minx, maxx, miny, maxy, maxz);
ShiftDensity(RoughDensity, RoughDensity1, RoughDensity2, RoughWallDensity, RoughWallDensity1, RoughWallDensity2,RoughDensityShiftP, RoughDensity1ShiftP, RoughDensity2ShiftP,RoughWallDensityShiftP, RoughWallDensity1ShiftP, RoughWallDensity2ShiftP,BoxX, BoxY, BoxZ);
RoughDensityShiftP.Output(Files.roughDensity,3);
RoughDensity1ShiftP.Output(Files.roughDensity1,3);
RoughDensity2ShiftP.Output(Files.roughDensity2,3);
BoxAverage(RoughDensity, Density, RoughWallDensity, WallDensity, Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
BoxAverage(RoughDensity1, Density1,RoughWallDensity1, WallDensity1, Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
BoxAverage(RoughDensity2, Density2, RoughWallDensity2, WallDensity2,Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
BoxAverage(RoughDensityShiftP, DensityShiftP, RoughWallDensityShiftP, WallDensityShiftP, Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
BoxAverage(RoughDensity1ShiftP, Density1ShiftP,RoughWallDensity1ShiftP, WallDensity1ShiftP, Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
BoxAverage(RoughDensity2ShiftP, Density2ShiftP, RoughWallDensity2ShiftP, WallDensity2ShiftP,Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
DensityShiftP.Output(Files.density,3);
Density1ShiftP.Output(Files.density1,3);
Density2ShiftP.Output(Files.density2,3);
WallDensityShiftP.Output(Files.walldensity);
WallDensity1ShiftP.Output(Files.walldensity1);
WallDensity2ShiftP.Output(Files.walldensity2);
Height_Average(Height, RoughHeight, minx, maxx, miny, maxy);
RoughHeight.Output(Files.roughheight);
Smooth(RoughHeight, Height, Filter, FilterDim, minx, maxx, miny, maxy);
Height.Output(Files.height);
// find surface normal
GetSurfaceNormal(Normal, Height, minx, maxx, miny, maxy);
Normal.Output(Files.normal);
int Nconv = 0;
Nconv = UpdateEnvArray(&Environment, &oldEnvironment, FieldAgar, oldFieldAgar, FieldWall, oldFieldWall, DensityShiftP, Density1ShiftP, Density2ShiftP, WallDensityShiftP, WallDensity1ShiftP, WallDensity2ShiftP, minx, maxx, miny, maxy, maxz, Height, insideColonyDen);
//ShiftGrowthrate(&Environment, &FieldWall,BoxX, BoxY, BoxZ);
Environment.Output(Files.env,1);
for (int level=0;level<maxLevels;level++)
{
FieldAgar[level]->Append(Files.aga,1);
FieldWall[level]->Append(Files.wal);
}
for (int cellID=0;cellID<N_cells;cellID++)
{
// output cell data
if (OutFlag)
{
IntCoord XYAddress = Grid.GetXY( Grid.GetAddress(average(old_cells[cellID].Position)) );
DoubleCoord T(0,0,0);
F_surf_tension(old_cells[cellID], Grid, XYAddress, Height, Normal, Fnet, T);
Output(Files.cells, cellID, t, old_cells[cellID], Fnet);
//printf("%6f %6d %6d\n", t, N_cells, cellID);
}
}
fflush(Files.cells);
OutFlag = false;
CloseOutputFiles(Files);
// **************************** Loop through time and evolve colony ****************************
ClockIt t0, t1, t2, t3, t4, t00;
double s0, s1, s2, s3, s4, st, s00;
s0=0; s1=0; s2=0; s3=0; s4=0; st=0; s00=0;
int koutput=0;
rewind(Files.lineage);
while (t<=t_max)
{
numDivide = 0; // number of cells dividing
// update fields only when UpdateFlag is true
t0.start();
if (UpdateFlag)
{
UpdateFlag = false;
// find density
GetDensity(RoughDensity, RoughDensity1, RoughDensity2, insideColonyDen, Height, Grid, old_cells, minx, maxx, miny, maxy, maxz);
ShiftDensity(RoughDensity, RoughDensity1, RoughDensity2, RoughWallDensity, RoughWallDensity1, RoughWallDensity2,RoughDensityShiftP, RoughDensity1ShiftP, RoughDensity2ShiftP,RoughWallDensityShiftP, RoughWallDensity1ShiftP, RoughWallDensity2ShiftP,BoxX, BoxY, BoxZ);
BoxAverage(RoughDensity, Density, RoughWallDensity, WallDensity, Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
BoxAverage(RoughDensity1, Density1,RoughWallDensity1, WallDensity1, Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
BoxAverage(RoughDensity2, Density2, RoughWallDensity2, WallDensity2,Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
BoxAverage(RoughDensityShiftP, DensityShiftP, RoughWallDensityShiftP, WallDensityShiftP, Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
BoxAverage(RoughDensity1ShiftP, Density1ShiftP,RoughWallDensity1ShiftP, WallDensity1ShiftP, Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
BoxAverage(RoughDensity2ShiftP, Density2ShiftP, RoughWallDensity2ShiftP, WallDensity2ShiftP,Filter3D, int((Filter3D.m_Size.x)/2), minx, maxx, miny, maxy, maxz,BoxX,BoxY,BoxZ);
Height_Average(Height, RoughHeight, minx, maxx, miny, maxy);
// RoughHeight.Output(Files.height);
Smooth(RoughHeight, Height, Filter, FilterDim, minx, maxx, miny, maxy);
// Height.Output(Files.height);
// find surface normal
GetSurfaceNormal(Normal, Height, minx, maxx, miny, maxy);
// find nutrient concentrations
Nconv = UpdateEnvArray(&Environment, &oldEnvironment, FieldAgar, oldFieldAgar, FieldWall, oldFieldWall, DensityShiftP, Density1ShiftP, Density2ShiftP, WallDensityShiftP, WallDensity1ShiftP, WallDensity2ShiftP, minx, maxx, miny, maxy, maxz, Height, insideColonyDen);
//ShiftGrowthrate(&Environment, &FieldWall,BoxX, BoxY, BoxZ);
if (Nconv>=maxIter)
printf("Environment has not converged");
// MyAssert(Nconv<maxIter,"Environment has not converged");
// update neighbour lists
getNeighbours(old_cells, N_cells, Grid, NeighbourList, maxNeighbours);
}
s0+=t0.stop()/1000.0;
t00.start();
if (HeightDensityUpdateFlag)
{
HeightDensityUpdateFlag = false;
// find height
GetHeight(RoughDensity, Height, Grid, old_cells, minx, maxx, miny, maxy, maxz);
Height_Average(Height, RoughHeight, minx, maxx, miny, maxy);
Smooth(RoughHeight, Height, Filter, FilterDim, minx, maxx, miny, maxy);
// find surface normal
GetSurfaceNormal(Normal, Height, minx, maxx, miny, maxy);
// update neighbour lists
// getNeighbours(old_cells, N_cells, Grid, NeighbourList, maxNeighbours);
}
s00+=t00.stop()/1000.0;
t1.start();
// calculate forces and move cells
int cellID;
if (OutFlag)
{
//CreateOutputFiles(int(t*10), Files, append);
CreateOutputFiles(koutput++, Files, append);
for (cellID=0;cellID<N_cells;cellID++)
{
// output cell data
mean_stress(old_cells[cellID], old_cells, NeighbourList[cellID], Grid, Wall, Height, Normal, stressTensor, Fnet);
Output(Files.cells, cellID, t, old_cells[cellID], stressTensor);
}
}
#pragma omp parallel for default(shared) private(cellID) schedule(static)
for (cellID=0;cellID<N_cells;cellID++)
{
MoveCell(cellID, Grid, old_cells, new_cells, NeighbourList[cellID], dt, Height, Normal, Wall);
GrowCell(new_cells[cellID], cellID, dt, dividingCells, numDivide, Environment, FieldWall, Grid);
}
// fflush(Files.cells);
s1+=t1.stop()/1000.0;
t2.start();
// output fields to file
if (OutFlag)
{
OutFlag = false;
// save restart file with cell information
SaveCells(Files.restart, new_cells, N_cells, t, dt);
// save field data
RoughHeight.Output(Files.roughheight);
Height.Output(Files.height);
RoughDensityShiftP.Output(Files.roughDensity,3);
RoughDensity1ShiftP.Output(Files.roughDensity1,3);
RoughDensity2ShiftP.Output(Files.roughDensity2,3);
DensityShiftP.Output(Files.density,3);
Density1ShiftP.Output(Files.density1,3);
Density2ShiftP.Output(Files.density2,3);
WallDensityShiftP.Output(Files.walldensity);
WallDensity1ShiftP.Output(Files.walldensity1);
WallDensity2ShiftP.Output(Files.walldensity2);
Normal.Output(Files.normal);
Environment.Output(Files.env,1);
for (int level=0;level<maxLevels;level++)
{
FieldAgar[level]->Append(Files.aga,1);
FieldWall[level]->Append(Files.wal);
}
printf("t = %6f, %5d cells; ", t, N_cells);
st += s0+s1+s2+s3+s4+s00;
printf("sim time = %3d:%2d:%2d; ", int(st/60.0/60.0), int(st/60.0)%60, int(st)%60);
printf("time cost = %g %g %g %g %g %g. \n", s0, s00, s1, s2, s3, s4);
s0=0; s1=0; s2=0; s3=0; s4=0; s00=0;
fflush(stdout);
CloseOutputFiles(Files);
}
s2+=t2.stop()/1000.0;
t3.start();
// Division (must be done after integration step because new neighbours are created)
for (int cellCount = 0; cellCount < numDivide; cellCount++)
{
if (N_cells>(maxCells-1))
{
break;
printf("Too many cells!");
}
// ID of cell that is undergoing division
const int cellID = dividingCells[cellCount];
DivideCell(cellID, N_cells, new_cells, Grid, NeighbourList[cellID], Wall, Height, Normal, t);
fprintf(Files.lineage, "%d %d\n", cellID, N_cells);
N_cells++;
// make list of all neighbours, new cell, and old cell
IDlen = NeighbourList[cellID][0];
memcpy(IDlist, NeighbourList[cellID], (IDlen+1)*sizeof(int)); // copy neighbours
IDlist[0] = cellID;
IDlist[IDlen+1] = N_cells-1;
IDlen+=2;
// update the neighbours of all of these cells
getNeighbours(new_cells, Grid, NeighbourList, maxNeighbours, IDlist, IDlen);
}
s3+=t3.stop()/1000.0;
t4.start();
// switch positions of old and new cells
{
Cell* temp = new_cells;
new_cells = old_cells;
old_cells = temp;
}
t += dt;
// determine if we're writing output next time
OutFlag = (NextOutTime<=0);
NextOutTime = (OutFlag? OutputTime: NextOutTime) - dt;
// determine if we're updating fields
UpdateFlag = (NextUpdateTime<=0);
NextUpdateTime = (UpdateFlag? UpdateTime: NextUpdateTime) - dt;
HeightDensityUpdateFlag = (HeightDensityNextUpdateTime<=0);
HeightDensityNextUpdateTime = (HeightDensityUpdateFlag? HeightDensityUpdateTime: HeightDensityNextUpdateTime) - dt;
s4+=t4.stop()/1000.0;
}
fflush(Files.lineage);
printf("Done\n");
}