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main.cu
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main.cu
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#include <stdio.h>
#include <stdlib.h>
#include <vector>
#include <iostream>
#include <GL/glew.h>
#include <GL/glut.h>
#include <GL/freeglut.h>
#include <cuda_runtime_api.h>
#include <cuda_gl_interop.h>
#include "typeDefinition.cuh"
// #include "globalVariables.cuh"
// Performance libraries
#include "./common/CudaSafeCall.h"
#include "./common/profile_time.h"
// Function protoypes
#include "hostPrototypes.h"
#include "devicePrototypes.cuh"
#include "openGLPrototypes.h"
using namespace std;
/*------------------------------------------------------------------------
* Decalre global variables
*------------------------------------------------------------------------
*/
size_t pitch;
fileVar strAdress;
paramVar param;
// Constants for device
__constant__ int nx_d, ny_d;
__constant__ REAL dt_d, rx_d, ry_d, hx_d, hy_d, Lx_d, Ly_d, qx4_d, qy4_d, fx4_d, fy4_d;
__constant__ REAL rxy_d, rbx_d, rby_d, rscale_d;
__constant__ REAL invdx_d, invdy_d;
__constant__ REAL tc_d, alpha_d, beta_d, delta_d, eps_d, mu_d, gamma_d, theta_d;
__constant__ REAL boundaryVal_d;
__constant__ bool solidSwitch_d, neumannBC_d, gateDiff_d, anisotropy_d, tipGrad_d;
__constant__ int tipOffsetX_d, tipOffsetY_d;
__constant__ float minVarColor_d, maxVarColor_d;
__constant__ float tipx0_d, tipy0_d;
__constant__ REAL Uth_d, conTh1_d, conTh2_d, conTh3_d;
__constant__ int lap4_d, timeIntOrder_d;
// Kernel setup
dim3 grid0D, block0D, grid1D, block1D, grid2D, block2D;
// Voltage and gate arrays
stateVar gate_h, gateIn_d, gateOut_d, J_d;
// Slices (templates) for the integrals
REAL3 c, c0, phi, phi0;
sliceVar slice, slice0;
stateVar velTan;
REAL *integrals;
std::vector<REAL3> clist;
std::vector<REAL3> philist;
// Advection arrays
advVar advect;
// BFECC (advection integration) arrays
stateVar uf_d, ub_d, ue_d;
// Solid holes //
bool *solid, *solid_d; // For the PDEs
REAL *coeffTrapz, *coeffTrapz_d; // For the integrals
bool *intglArea, *intglArea_d; // For the slices (derivatives)
// Arrays for the tip trajectory
int *tip_count_d;
vec5dyn *tip_vector_d; // Holds the tip trajectory
bool *tip_plot;
// Single cell recordings
std::vector<electrodeVar> electrode;
std::vector<REAL> contourLength;
REAL *point_h, *point_d;
stateVar timeSeries;
// Arrays for the contour tracking
int *contour_count_d;
float3 *contour_vector_d; // Holds the contours
bool *stimArea, *stimArea_d; // Area considered for APD(x,y)
REAL *APD1_d, *APD2_d, *sAPD_d, *dAPD_d, *back_d, *front_d; // sAPD_d: APD spatial field
bool *first_APD_d, *contour_plot; // Auxiliary array. Contour plots
REAL *stimulus, *stimulus_d; // Stimulus area
int sampleIt; // Sample period in iterations per unit time
int stimPeriodIt;
int stimDurationIt;
int stimCount = 0;
bool stimLock = false, stimLockKey = false, stimLockMouse = false;
REAL *timeSeriesContourLength;
// Figures/shapes
float2 *trapzAreaCircle, *stimAreaCircle;
// OpenGL pixel buffer object and texture //
GLuint gl_PBO, gl_Tex;
unsigned int *cmap_rgba; // rgba arrays for plotting
unsigned int *cmap_rgba_data, *plot_rgba_data;
float width, height;
int nsolid, nstep, nsteps, ncol;
GLint window1, window2;
bool timeScreen = true, phaseScreen = false, contourScreen = false;
REAL *timeSeriesCx, *timeSeriesCy, *timeSeriesCt;
// Timer for simulation
int base;
float FPS = 1.0;
int initial_time = time(NULL); // Timer for controlling the fps
int final_time, frame_count; // More fram/fps stuff
int fps;
/*------------------------------------------------------------------------
* Program starts here
*------------------------------------------------------------------------
*/
int main(int argc, char *argv[]) {
if (argc > 1) {
printf("%d VALUES(s) has been introduced form the EXECUTABLE COMMAND line\n",argc-1);
}
param = startMenu(&strAdress,param,argc,argv);
if ( param.save ) {
strAdress = saveFileNames(strAdress,¶m);
}
/*------------------------------------------------------------------------
* Parameters form command line
*------------------------------------------------------------------------
*/
if (argc > 1) param.stimPeriod = atof(argv[1]);
// Commonly changed variables
param.dt = param.reduceSym ? 0.5*param.dt : param.dt;
param.rx = param.dt*param.Dxx/(param.hx*param.hx);
param.ry = param.dt*param.Dyy/(param.hy*param.hy);
param.rxy = 2.0*param.Dxy*param.dt/(4.0*param.hx*param.hy);
param.qx4 = param.dt*param.Dyy/(param.hy*param.hy*12.0);
param.qy4 = param.dt*param.Dxx/(param.hx*param.hx*12.0);
param.fx4 = param.dt/12.0;
param.fy4 = param.dt/12.0;
sampleIt = round(param.sample/param.dt);
stimPeriodIt = floor(param.stimPeriod/param.dt);
stimDurationIt = floor(param.stimDuration/param.dt);
// Symmetry variables (also for predictor scheme)
c.x = 0.0; c.y = 0.0; c.t = 0.0;
c0.x = 0.0; c0.y = 0.0; c0.t = 0.0;
phi.x = 0.0; phi.y = 0.0; phi.t = 0.0;
phi0.x = 0.0; phi0.y = 0.0; phi0.t = 0.0;
// Kernel setup
grid0D = dim3(1,1,1);
block0D = dim3(1,1,1);
grid1D = dim3(GRIDSIZE_1D,1,1);
block1D = dim3(BLOCKSIZE_1D,1,1);
grid2D = dim3(iDivUp(param.nx,BLOCK_DIM_X),iDivUp(param.ny,BLOCK_DIM_Y),1);
block2D = dim3(BLOCK_DIM_X, BLOCK_DIM_Y,1);
printf("\n**Parameter values**\n");
printf("dt = %f ms \n", param.dt);
printf("rx = %f \n", param.rx);
printf("ry = %f \n", param.ry);
printf("Lx = %f cm \n", param.Lx);
printf("Ly = %f cm \n", param.Ly);
printf("nx = %d \n", param.nx);
printf("ny = %d \n", param.ny);
printf("hx = %f cm \n", param.hx);
printf("hy = %f cm \n", param.hy);
printf("Dx = %f cm^2/ms \n",param.Dxx);
printf("Dy = %f cm^2/ms \n",param.Dyy);
printf("\n");
pressEnterKey();
printf("\n**Keyboard options**\n");
printf("m --> Menu\n");
printf("Esc --> Close application\n");
printf("Space bar --> Pause simulation\n");
printf("r --> Restart simulation\n");
printf("q --> Pace/stimulate\n");
printf("s --> Symmetry reduction\n");
printf("t --> Tip tracjectory recordings\n");
printf("c --> Contour recordings\n");
printf("p --> Print screenshot\n");
printf("/ --> Conduction block\n");
printf("x --> Stimulate all tissue once\n");
printf("x --> Stimulate circle tissue once\n");
printf("z --> Clear screen\n");
printf("1 --> Screen 1 (electrodes)\n");
printf("2 --> Screen 2 (SR velocities)\n");
printf("3 --> Screen 3 (Contour length)\n");
/*------------------------------------------------------------------------
* Array allocation
*------------------------------------------------------------------------
*/
param.memSize = param.nx*param.ny*sizeof(REAL);
// Array allocation
gate_h.u = (REAL*)malloc(param.memSize);
gate_h.v = (REAL*)malloc(param.memSize);
// Holds the results of the slice integrals
integrals = (REAL*)malloc(12*sizeof(REAL));
// Circular boundary
solid = new bool[param.nx*param.ny];
coeffTrapz = (REAL*)malloc(param.memSize);
intglArea = new bool[param.nx*param.ny];
// Stimulation area
stimArea = new bool[param.nx*param.ny];
stimulus = (REAL*)malloc(param.memSize);
// Electrode recordings
point_h = (REAL*)malloc(param.eSize*sizeof(REAL));
timeSeries.u = (REAL*)malloc(param.wnx*sizeof(REAL));
timeSeries.v = (REAL*)malloc(param.wnx*sizeof(REAL));
// Array for figures/shapes
trapzAreaCircle = (float2*)malloc(param.nc*sizeof(float2));
stimAreaCircle = (float2*)malloc(param.nc*sizeof(float2));
// Plotting cx, cy, ct
timeSeriesCx = (REAL*)malloc(param.wnx*sizeof(REAL));
timeSeriesCy = (REAL*)malloc(param.wnx*sizeof(REAL));
timeSeriesCt = (REAL*)malloc(param.wnx*sizeof(REAL));
// Contour length
timeSeriesContourLength = (REAL*)malloc(param.wnx*sizeof(REAL));
// Allocate device memory arrays
CudaSafeCall(cudaMalloc(&gateIn_d.u,param.memSize));
CudaSafeCall(cudaMalloc(&gateIn_d.v,param.memSize));
CudaSafeCall(cudaMalloc(&gateOut_d.u,param.memSize));
CudaSafeCall(cudaMalloc(&gateOut_d.v,param.memSize));
CudaSafeCall(cudaMalloc(&J_d.u,param.memSize));
CudaSafeCall(cudaMalloc(&J_d.v,param.memSize));
CudaSafeCall(cudaMalloc(&slice.ux,param.memSize));
CudaSafeCall(cudaMalloc(&slice.uy,param.memSize));
CudaSafeCall(cudaMalloc(&slice.ut,param.memSize));
CudaSafeCall(cudaMalloc(&slice.vx,param.memSize));
CudaSafeCall(cudaMalloc(&slice.vy,param.memSize));
CudaSafeCall(cudaMalloc(&slice.vt,param.memSize));
CudaSafeCall(cudaMalloc(&slice0.ux,param.memSize));
CudaSafeCall(cudaMalloc(&slice0.uy,param.memSize));
CudaSafeCall(cudaMalloc(&slice0.ut,param.memSize));
CudaSafeCall(cudaMalloc(&slice0.vx,param.memSize));
CudaSafeCall(cudaMalloc(&slice0.vy,param.memSize));
CudaSafeCall(cudaMalloc(&slice0.vt,param.memSize));
CudaSafeCall(cudaMalloc(&advect.x,param.memSize));
CudaSafeCall(cudaMalloc(&advect.y,param.memSize));
CudaSafeCall(cudaMalloc(&velTan.u,param.memSize));
CudaSafeCall(cudaMalloc(&velTan.v,param.memSize));
CudaSafeCall(cudaMalloc(&tip_plot, param.nx*param.ny*sizeof(bool)));
CudaSafeCall(cudaMalloc(&uf_d.u,param.memSize));
CudaSafeCall(cudaMalloc(&ub_d.u,param.memSize));
CudaSafeCall(cudaMalloc(&ue_d.u,param.memSize));
CudaSafeCall(cudaMalloc(&uf_d.v,param.memSize));
CudaSafeCall(cudaMalloc(&ub_d.v,param.memSize));
CudaSafeCall(cudaMalloc(&ue_d.v,param.memSize));
CudaSafeCall(cudaMalloc(&tip_count_d,sizeof(int)));
CudaSafeCall(cudaMalloc(&tip_vector_d,TIPVECSIZE*sizeof(vec5dyn)));
CudaSafeCall(cudaMalloc(&solid_d, param.nx*param.ny*sizeof(bool)));
CudaSafeCall(cudaMalloc(&coeffTrapz_d,param.memSize));
CudaSafeCall(cudaMalloc(&intglArea_d,param.nx*param.ny*sizeof(bool)));
CudaSafeCall(cudaMalloc(&APD1_d,param.memSize));
CudaSafeCall(cudaMalloc(&APD2_d,param.memSize));
CudaSafeCall(cudaMalloc(&sAPD_d,param.memSize));
CudaSafeCall(cudaMalloc(&dAPD_d,param.memSize));
CudaSafeCall(cudaMalloc(&back_d,param.memSize));
CudaSafeCall(cudaMalloc(&front_d,param.memSize));
CudaSafeCall(cudaMalloc(&first_APD_d, param.nx*param.ny*sizeof(bool)));
CudaSafeCall(cudaMalloc(&contour_plot, param.nx*param.ny*sizeof(bool)));
CudaSafeCall(cudaMalloc(&stimArea_d, param.nx*param.ny*sizeof(bool)));
CudaSafeCall(cudaMalloc(&stimulus_d,param.memSize));
CudaSafeCall(cudaMalloc(&contour_count_d,sizeof(int)));
CudaSafeCall(cudaMalloc(&contour_vector_d,param.nx*param.ny*sizeof(float3)));
CudaSafeCall(cudaMalloc(&point_d,param.eSize*sizeof(REAL)));
/*------------------------------------------------------------------------
* Set GPU constants
*------------------------------------------------------------------------
*/
CudaSafeCall(cudaMemcpyToSymbol(nx_d, ¶m.nx, sizeof(int), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(ny_d, ¶m.ny, sizeof(int), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(rx_d, ¶m.rx, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(ry_d, ¶m.ry, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(qx4_d, ¶m.qx4, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(qy4_d, ¶m.qy4, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(fx4_d, ¶m.fx4, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(fy4_d, ¶m.fy4, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(hx_d, ¶m.hx, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(hy_d, ¶m.hy, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(dt_d, ¶m.dt, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(invdx_d, ¶m.invdx, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(invdy_d, ¶m.invdy, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(Lx_d, ¶m.Lx, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(Ly_d, ¶m.Ly, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(rxy_d, ¶m.rxy, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(rbx_d, ¶m.rbx, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(rby_d, ¶m.rby, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(rscale_d, ¶m.rscale, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(boundaryVal_d, ¶m.boundaryVal, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(solidSwitch_d, ¶m.solidSwitch, sizeof(bool), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(neumannBC_d, ¶m.neumannBC, sizeof(bool), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(gateDiff_d, ¶m.gateDiff, sizeof(bool), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(anisotropy_d, ¶m.anisotropy, sizeof(bool), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(tipGrad_d, ¶m.tipGrad, sizeof(bool), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(lap4_d, ¶m.lap4, sizeof(int), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(timeIntOrder_d, ¶m.timeIntOrder, sizeof(int), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(tipOffsetX_d, ¶m.tipOffsetX, sizeof(int), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(tipOffsetY_d, ¶m.tipOffsetY, sizeof(int), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(minVarColor_d, ¶m.minVarColor, sizeof(float), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(maxVarColor_d, ¶m.maxVarColor, sizeof(float), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(tipx0_d, ¶m.tipx, sizeof(float), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(tipy0_d, ¶m.tipy, sizeof(float), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(conTh1_d, ¶m.contourThresh1, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(conTh2_d, ¶m.contourThresh2, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(conTh3_d, ¶m.contourThresh3, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(Uth_d, ¶m.Uth, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(tc_d, ¶m.tc, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(alpha_d, ¶m.alpha, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(beta_d, ¶m.beta, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(gamma_d, ¶m.gamma, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(delta_d, ¶m.delta, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(eps_d, ¶m.eps, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(mu_d, ¶m.mu, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpyToSymbol(theta_d, ¶m.theta, sizeof(REAL), 0,
cudaMemcpyHostToDevice));
printf("Finished allocating device arrays\n");
/*------------------------------------------------------------------------
* Initializing physical arrays. Copy from host to device
*------------------------------------------------------------------------
*/
initGates(pitch,gate_h);
/*------------------------------------------------------------------------
* Initialize device arrays to 0
*------------------------------------------------------------------------
*/
CudaSafeCall(cudaMemset(slice.ux, 0.0, param.memSize));
CudaSafeCall(cudaMemset(slice.uy, 0.0, param.memSize));
CudaSafeCall(cudaMemset(slice.ut, 0.0, param.memSize));
CudaSafeCall(cudaMemset(slice.vx, 0.0, param.memSize));
CudaSafeCall(cudaMemset(slice.vy, 0.0, param.memSize));
CudaSafeCall(cudaMemset(slice.vt, 0.0, param.memSize));
CudaSafeCall(cudaMemset(slice0.ux, 0.0, param.memSize));
CudaSafeCall(cudaMemset(slice0.uy, 0.0, param.memSize));
CudaSafeCall(cudaMemset(slice0.ut, 0.0, param.memSize));
CudaSafeCall(cudaMemset(slice0.vx, 0.0, param.memSize));
CudaSafeCall(cudaMemset(slice0.vy, 0.0, param.memSize));
CudaSafeCall(cudaMemset(slice0.vt, 0.0, param.memSize));
CudaSafeCall(cudaMemset(advect.x, 0.0, param.memSize));
CudaSafeCall(cudaMemset(advect.y, 0.0, param.memSize));
CudaSafeCall(cudaMemset(velTan.u, 0.0, param.memSize));
CudaSafeCall(cudaMemset(velTan.v, 0.0, param.memSize));
CudaSafeCall(cudaMemset(J_d.u, 0.0, param.memSize));
CudaSafeCall(cudaMemset(J_d.v, 0.0, param.memSize));
CudaSafeCall(cudaMemset(APD1_d, 0.0f, param.memSize));
CudaSafeCall(cudaMemset(APD2_d, 0.0f, param.memSize));
CudaSafeCall(cudaMemset(tip_plot,0,param.nx*param.ny*sizeof(bool)));
CudaSafeCall(cudaMemset(first_APD_d,0,param.nx*param.ny*sizeof(bool)));
CudaSafeCall(cudaMemset(contour_plot,0,param.nx*param.ny*sizeof(bool)));
CudaSafeCall(cudaMemset(contour_vector_d,0.0,param.nx*param.ny*sizeof(float3)));
CudaSafeCall(cudaMemset(tip_vector_d,0.0,TIPVECSIZE*sizeof(vec5dyn)));
printf("Finished initalizing variables\n");
printf("Starting simulation\n\n");
/*------------------------------------------------------------------------
* Load color RGB
*------------------------------------------------------------------------
*/
loadcmap();
/*------------------------------------------------------------------------
* Create masks for domain, stimulus range and measurements
*------------------------------------------------------------------------
*/
domainObjects(solid,coeffTrapz,intglArea,stimArea,
stimulus,param.stimMag,argc,argv);
/*------------------------------------------------------------------------
* Copy form host to device
*------------------------------------------------------------------------
*/
// Copy data from host to device
CudaSafeCall(cudaMemcpy((void *)gateIn_d.u,(void *)gate_h.u,param.memSize,
cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpy((void *)gateIn_d.v,(void *)gate_h.v,param.memSize,
cudaMemcpyHostToDevice));
/*------------------------------------------------------------------------
* Copy masks for domain, stimulus range and measurements to device
*------------------------------------------------------------------------
*/
CudaSafeCall(cudaMemcpy(solid_d,solid,param.nx*param.ny*sizeof(bool),cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpy(coeffTrapz_d,coeffTrapz,param.memSize,cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpy(intglArea_d,intglArea, param.nx*param.ny*sizeof(bool),cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpy(stimArea_d,stimArea,param.nx*param.ny*sizeof(bool),cudaMemcpyHostToDevice));
CudaSafeCall(cudaMemcpy(stimulus_d,stimulus, param.memSize, cudaMemcpyHostToDevice));
free(solid);
free(coeffTrapz);
free(intglArea);
free(stimArea);
free(stimulus);
free(cmap_rgba);
/*------------------------------------------------------------------------
* Allocating and initializing OpenGL objects
*------------------------------------------------------------------------
*/
CudaSafeCall(cudaMemcpy((void *)cmap_rgba_data,
(void *)cmap_rgba, sizeof(unsigned int)*ncol,
cudaMemcpyHostToDevice));
if (false == initGL(&argc, argv)) exit(0);
/*------------------------------------------------------------------------
* Glut loop initialization. Rendering starts here
*------------------------------------------------------------------------
*/
// Return control to the program
glutSetOption(GLUT_ACTION_ON_WINDOW_CLOSE, GLUT_ACTION_GLUTMAINLOOP_RETURNS);
//glutCloseFunc(cleanup);
glutMainLoop();
/*------------------------------------------------------------------------
* Copy from device to host
*------------------------------------------------------------------------
*/
CudaSafeCall(cudaMemcpy((void *)gate_h.u,(void *)gateOut_d.u,param.memSize,
cudaMemcpyDeviceToHost));
CudaSafeCall(cudaMemcpy((void *)gate_h.v,(void *)gateOut_d.v,param.memSize,
cudaMemcpyDeviceToHost));
/*------------------------------------------------------------------------
* Save data in files
*------------------------------------------------------------------------
*/
if ( param.save && param.savePackage ) {
saveFile(strAdress,¶m,gate_h,electrode,contourLength,param.dt,
tip_count_d,tip_vector_d,clist,philist,true,contour_count_d,contour_vector_d);
}
/*------------------------------------------------------------------------
* Deallocate all arrays
*------------------------------------------------------------------------
*/
// Free gate host and device memory
free(gate_h.u);
free(gate_h.v);
CudaSafeCall(cudaFree(gateIn_d.u));
CudaSafeCall(cudaFree(gateIn_d.v));
CudaSafeCall(cudaFree(gateOut_d.u));
CudaSafeCall(cudaFree(gateOut_d.v));
CudaSafeCall(cudaFree(cmap_rgba_data));
CudaSafeCall(cudaFree(plot_rgba_data));
CudaSafeCall(cudaFree(slice.ux));
CudaSafeCall(cudaFree(slice.uy));
CudaSafeCall(cudaFree(slice.ut));
CudaSafeCall(cudaFree(slice.vx));
CudaSafeCall(cudaFree(slice.vy));
CudaSafeCall(cudaFree(slice.vt));
CudaSafeCall(cudaFree(slice0.ux));
CudaSafeCall(cudaFree(slice0.uy));
CudaSafeCall(cudaFree(slice0.ut));
CudaSafeCall(cudaFree(slice0.vx));
CudaSafeCall(cudaFree(slice0.vy));
CudaSafeCall(cudaFree(slice0.vt));
CudaSafeCall(cudaFree(advect.x));
CudaSafeCall(cudaFree(advect.y));
CudaSafeCall(cudaFree(velTan.u));
CudaSafeCall(cudaFree(velTan.v));
CudaSafeCall(cudaFree(J_d.u));
CudaSafeCall(cudaFree(J_d.v));
printf("Simulation ended\n");
printf("Physical time: %f ms\n", param.physicalTime);
printf("Real time: %f s\n", param.tiempo);
return 0;
}
void initGates(size_t pitch, stateVar g_h) {
/*------------------------------------------------------------------------
* Initialize host arrays
*------------------------------------------------------------------------
*/
if ( param.load ) {
loadData(g_h,strAdress,¶m);
} else {
int i, j, idx;
// Array initialization
memset(g_h.u, 0.0, param.memSize);
memset(g_h.v, 0.0, param.memSize);
// Initial condition
// for (j=(int)floor(0);j<(int)floor(param.ny);j++) {
// for (i=(int)floor(0);i<(int)floor(40);i++) {
// idx = i + param.nx*j;
// g_h.u[idx] = 1.0;
// }
// }
// Cross-field stimulation
for (j=(int)floor(0);j<(int)floor(param.ny);j++) {
for (i=(int)floor(0);i<(int)floor(param.nx/8);i++) {
idx = i + param.nx*j;
g_h.u[idx] = 1.0;
}
}
for (j=(int)floor(param.ny/2);j<(int)floor(param.ny);j++) {
for (i=(int)floor(0);i<(int)floor(param.nx);i++) {
idx = i + param.nx*j;
g_h.v[idx] = 1.0;
}
}
}
}
void domainObjects(bool *solid, REAL *coeffTrapz, bool *intglArea, bool *stimArea,
REAL *stimulus, REAL stimMag, int argc, char *argv[]) {
int i, j, idx;
/*------------------------------------------------------------------------
* Load unexcitable holes
* Heterogeneous media
*------------------------------------------------------------------------
*/
if ( param.solidSwitch ) {
float mesh;
memset(solid, false, param.nx*param.ny*sizeof(bool));
/*------------------------------------------------------------------------
* Load domain boundary
*------------------------------------------------------------------------
*/
FILE *fp_img;
char strPath[128];
if ( param.nx == 512 ) {
// fp_img = fopen("./common/cBoundary512.dat","r");
fp_img = fopen("./common/holes512.dat","r");
}
if ( param.nx == 800 ) {
if ( argc>2) {
sprintf(strPath, "./common/%s",argv[4]);
fp_img = fopen(strPath,"r");
} else {
fp_img = fopen("./common/holes800_1.dat","r");
}
}
if ( param.nx == 1000 ) {
fp_img = fopen("./common/holes1000.dat","r");
}
if ( param.nx == 1024 ) {
// fp_img = fopen("./common/cBoundary1024.dat","r");
fp_img = fopen("./common/holes1024.dat","r");
}
if ( fp_img==NULL ) {
printf("Error: can't open circleBoundary file \n");
exit(0);
}
for (i=0;i<param.nx*param.ny;i++){
fscanf(fp_img, "%f", &mesh);
// printf("mesh: %d\n", mesh);
solid[i] = mesh > 0.5 ? true : false;
// printf("solid %d\n", (int)solid[i]);
}
fclose(fp_img);
}
/*------------------------------------------------------------------------
* Slice (derivative) boundary (integration area)
*------------------------------------------------------------------------
*/
// Be sure that the radius of the slice boundary is always smaller than
// the radius of the domain. If it's not, the derivatives will be
// discontinious at the boundary.
float x0, y0;
// rdom = 0.5*(Lx-250.0*hx);
// param.rdomTrapz = 0.5*(param.Lx-(param.tipOffsetX+param.tipOffsetY)*param.hx);
param.rdomTrapz = 0.5*((param.tipOffsetX+param.tipOffsetY)*param.hx); // Integral area radius
for (j=0;j<param.ny;j++) {
for (i=0;i<param.nx;i++) {
idx = I2D(param.nx,i,j);
x0 = (float)i*param.hx - 0.5*param.Lx ;
y0 = (float)j*param.hy - 0.5*param.Ly ;
intglArea[idx] = ( (x0*x0 + y0*y0) < param.rdomTrapz*param.rdomTrapz ) ? true : false;
}
}
// Points for OpenGL
for (i=0;i<param.nc;i++) {
trapzAreaCircle[i].x = (float)( param.nx/2.f+(param.nx-1)/param.Lx*
param.rdomTrapz*sin((float)i*(2.0*pi)/(param.nc-1)) );
trapzAreaCircle[i].y = (float)( param.ny/2.f+(param.ny-1)/param.Ly*
param.rdomTrapz*cos((float)i*(2.0*pi)/(param.nc-1)) );
}
/*------------------------------------------------------------------------
* Load trapezoidal coefficients
*------------------------------------------------------------------------
*/
REAL *coeffx, *coeffy;
coeffx = (REAL*)malloc(param.memSize);
coeffy = (REAL*)malloc(param.memSize);
memset(coeffx, 0.0, param.memSize);
memset(coeffy, 0.0, param.memSize);
memset(coeffTrapz, 0.0, param.nx*param.ny*sizeof(REAL));
for (i=0;i<param.nx*param.ny;i++) {
if ( intglArea[i] == true ) {
coeffx[i] = 2.0;
}
if ( intglArea[i] == true && intglArea[i-1] == false ) {
coeffx[i] = 1.0;
}
if ( intglArea[i] == true && intglArea[i+1] == false ) {
coeffx[i] = 1.0;
}
}
// transpose matrix
for (j=0;j<param.ny;++j) {
for (i=0;i<param.nx;++i) {
coeffy[(i * param.ny) + j] = coeffx[(j * param.nx) + i];
}
}
for (i=0;i<param.nx*param.ny;i++) {
coeffTrapz[i] = coeffx[i]*coeffy[i];
}
free(coeffx);
free(coeffy);
/*------------------------------------------------------------------------
* Define the stimulus area
*------------------------------------------------------------------------
*/
param.stcx = 0.25*param.Lx; // Stimulus position
param.stcy = 0.25*param.Ly;
param.rdomStim = 0.03*param.Lx; // Stimulus radius
for (j=0;j<param.ny;j++) {
for (i=0;i<param.nx;i++) {
idx = I2D(param.nx,i,j);
x0 = (float)i*param.hx - 0.5*param.Lx ;
y0 = (float)j*param.hy - 0.5*param.Ly ;
if ( param.solidSwitch ) {
// bool sc = solid[idx];
// bool sw = solid[I2D(param.nx,i-1,j)];
// bool se = solid[I2D(param.nx,i+1,j)];
// // Electric field from left to right
// stimulus[idx] = sc && !sw ? param.stimMag : 0.0 ; // to the right
// stimulus[idx] = sc && !se ? -param.stimMag : 0.0 ; // to the left
// stimulus[idx] = param.stimMag;
// point stimulus
stimulus[idx] = ( ((x0-param.stcx)*(x0-param.stcx)+(y0-param.stcy)*(y0-param.stcy))
< param.rdomStim*param.rdomStim ) ? param.stimMag : 0.0;
} else {
// For contour stimulation
// stimulus[idx] = param.stimMag;
// point stimulus
stimulus[idx] = ( ((x0-param.stcx)*(x0-param.stcx)+(y0-param.stcy)*(y0-param.stcy))
< param.rdomStim*param.rdomStim ) ? param.stimMag : 0.0;
// Rectangular stimulus
// stimulus[idx] = ( (j>20) && (j<30) ) ? param.stimMag : 0.0;
}
}
}
// Point for OpenGL
param.pointStim.x = param.nx/2+(param.nx-1)/param.Lx*param.stcx;
param.pointStim.y = param.ny/2+(param.ny-1)/param.Ly*param.stcy;
/*------------------------------------------------------------------------
* Define the area arround the stimulus point where we are measureing the APD(x,y) (OPTIONAL)
*------------------------------------------------------------------------
*/
for (j=0;j<param.ny;j++) {
for (i=0;i<param.nx;i++) {
idx = I2D(param.nx,i,j);
x0 = (float)i*param.hx - 0.5*param.Lx ;
y0 = (float)j*param.hy - 0.5*param.Ly ;
if ( param.solidSwitch ) {
// bool sc = solid[idx];
// stimArea[idx] = sc ? true : false;
// Point stimulus
stimArea[idx] = ( ((x0-param.stcx)*(x0-param.stcx)+(y0-param.stcy)*(y0-param.stcy))
< param.rdomAPD*param.rdomAPD ) ? false : true;
} else {
// stimArea[idx] = true;
// Point stimulus
// stimArea[idx] = ( ((x0-param.stcx)*(x0-param.stcx)+(y0-param.stcy)*(y0-param.stcy))
// < param.rdomAPD*param.rdomAPD ) ? false : true;
// Rectangular stimulus
stimArea[idx] = (j<35) ? false : true;
}
}
}
// Points for OpenGL
for (i=0;i<param.nc;i++) {
stimAreaCircle[i].x = param.nx/2+(param.nx-1)/param.Lx*param.stcx+(param.nx-1)/param.Lx*
param.rdomAPD*sin((float)i*(2.0*pi)/(param.nc-1));
stimAreaCircle[i].y = param.ny/2+(param.ny-1)/param.Ly*param.stcy+(param.nx-1)/param.Ly*
param.rdomAPD*cos((float)i*(2.0*pi)/(param.nc-1));
}
}
/*------------------------------------------------------------------------
* Here is where all the kernel calls and tip tracking, etc. are made
*------------------------------------------------------------------------
*/
// This function is called automatically, over and over again, by GLUT
void display(void) {
glutSetWindow(window1);
if (param.animate) {
#pragma unroll
for (int i=0;i<(param.itPerFrame);i++) {
/*------------------------------------------------------------------------
* Reaction-diffusion Solver
*------------------------------------------------------------------------
*/
if ( !param.reduceSym ) {
/* Reaction diffusion */
reactionDiffusion_wrapper(pitch,grid2D,block2D,gateOut_d,gateIn_d,J_d,
velTan,param.reduceSym,solid_d,stimLock,stimulus_d,stimLockMouse,param.point);
swapSoA(&gateIn_d,&gateOut_d);
param.count++;
param.physicalTime = param.dt*(REAL)param.count;
}
/*------------------------------------------------------------------------
* Symmetry reduction Solver
*------------------------------------------------------------------------
*/
if ( param.reduceSym ) {
reactionDiffusion_wrapper(pitch,grid2D,block2D,gateOut_d,gateIn_d,J_d,
velTan,param.reduceSym,solid_d,stimLock,stimulus_d,stimLockMouse,param.point);
// if ( (param.count%sampleIt == 0) ) {
tip_wrapper(pitch,grid2D,block2D,gateIn_d,gateOut_d,velTan,param.physicalTime,
param.tipAlgorithm,param.recordTip,tip_plot,tip_count_d,tip_vector_d);
clist.push_back(c);
philist.push_back(phi);
// }
slice_wrapper(pitch,grid2D,block2D,gateIn_d,
slice,slice0,param.reduceSym,param.reduceSymStart,advect,2,intglArea_d,
tip_count_d,tip_vector_d,param.count);
if ( param.count == 0 ) {
trapz_wrapper(grid1D,block2D,slice,slice0,velTan,integrals,coeffTrapz_d,
tip_count_d,tip_vector_d,param.count);
c = solve_matrix(c,phi,integrals);
Cxy_field_wrapper(pitch,grid2D,block2D,advect,c,phi,solid_d);
slice_wrapper(pitch,grid2D,block2D,gateIn_d,
slice,slice0,param.reduceSym,param.reduceSymStart,advect,2,intglArea_d,
tip_count_d,tip_vector_d,param.count);
}
trapz_wrapper(grid1D,block1D,slice,slice0,velTan,integrals,coeffTrapz_d
,tip_count_d,tip_vector_d,param.count);
c = solve_matrix(c,phi,integrals);
// c.y = integrals[10]/integrals[4]; // Translational symmetry in y
// c.x = integrals[9]/integrals[0]; // Translational symmetry in x
Cxy_field_wrapper(pitch,grid2D,block2D,advect,c,phi,solid_d);
advFDBFECC_wrapper(pitch,grid2D,block2D,gateIn_d,gateOut_d,advect,
uf_d,ub_d,ue_d,solid_d);
if ( param.reduceSymStart ) {
phi.x = phi.x+c.x*param.dt;
phi.y = phi.y+c.y*param.dt;
phi.t = phi.t+c.t*param.dt;
c0.x = c.x;
c0.y = c.y;
c0.t = c.t;
} else {
phi.x = phi.x+param.dt*(1.5*c.x-0.5*c0.x);
phi.y = phi.y+param.dt*(1.5*c.y-0.5*c0.y);
phi.t = phi.t+param.dt*(1.5*c.t-0.5*c0.t);
c0.x = c.x;
c0.y = c.y;
c0.t = c.t;
}
param.count++;
param.physicalTime = param.dt*(REAL)param.count;
}
/*------------------------------------------------------------------------
* Special functions
*------------------------------------------------------------------------
*/
if ( param.count%sampleIt == 0 ) {
if ( param.plotTip && !param.reduceSym ) {
tip_wrapper(pitch,grid2D,block2D,gateIn_d,gateOut_d,velTan,param.physicalTime,
param.tipAlgorithm,param.recordTip,tip_plot,tip_count_d,tip_vector_d);
}
if ( param.recordTip ) {
saveFile(strAdress,¶m,gate_h,electrode,contourLength,param.dt,tip_count_d,tip_vector_d,
clist,philist,false,contour_count_d,contour_vector_d);
}
if ( param.plotContour ) {
if ( param.contourMode==1 ) {
countour_wrapper(pitch,grid2D,block2D,gateOut_d.u,sAPD_d,contour_plot,stimArea_d,
contour_count_d,contour_vector_d,param.physicalTime,param.contourMode);
}
if ( ( param.contourMode==2 ) || ( param.contourMode==3 ) ) {
countour_wrapper(pitch,grid2D,block2D,gateOut_d.u,gateOut_d.v,contour_plot,stimArea_d,
contour_count_d,contour_vector_d,param.physicalTime,param.contourMode);
}
if ( param.recordContour ) {
saveFile(strAdress,¶m,gate_h,electrode,contourLength,param.dt,tip_count_d,tip_vector_d,
clist,philist,false,contour_count_d,contour_vector_d);
}
}
if ( param.saveEveryIt && (param.physicalTime>param.startRecTime) ) {
CudaSafeCall(cudaMemcpy((void *)gate_h.u,(void *)gateOut_d.u,param.memSize,
cudaMemcpyDeviceToHost));
saveFile(strAdress,¶m,gate_h,electrode,contourLength,param.dt,tip_count_d,tip_vector_d,
clist,philist,false,contour_count_d,contour_vector_d);
}
}
// Automatic periodic pacing
if ( param.stimulate ) {
if ( (param.count%stimPeriodIt == 0) || (stimCount > 0) ) {
stimLock = true;
stimCount++;
if ( stimCount>stimDurationIt ) {
param.leapShocks++;
stimLock = false;
stimCount = 0;