void Absorption<EvalT, Traits>::
evaluateFields(typename Traits::EvalData workset)
{
if (is_constant) {
for (std::size_t cell=0; cell < workset.numCells; ++cell) {
for (std::size_t qp=0; qp < numQPs; ++qp) {
absorption(cell,qp) = constant_value;
}
}
}
/*else {
for (std::size_t cell=0; cell < workset.numCells; ++cell) {
for (std::size_t qp=0; qp < numQPs; ++qp) {
Teuchos::Array<MeshScalarT> point(numDims);
for (std::size_t i=0; i<numDims; i++)
point[i] = Sacado::ScalarValue<MeshScalarT>::eval(coordVec(cell,qp,i));
thermalCond(cell,qp) = exp_rf_kl->evaluate(point, rv);
}
}
}*/
}
Spectrum VolumeRegion::extinction(const Point3D &p, const Length3D &w,
double time) const {
return absorption(p, w, time) + scattering(p, w, time);
}
/*MONTE CARLO*/
void mc1m(int num_photons,double ma, double ms, double g, double *x0,double *x1, double *x2, double *u0, double *u1, double *u2,
double *na_fiber, double r_max, double x2_max,double n_tissue, double *n_fiber, double *fiber_radii, int t_grid,
double *th, double *ph,double tissue[],double fiber_tissue[], double r[],double depth[],double weight[],double path[],
double z[],double num_scatt[]) {
int i;
double s = 0;
/*Fiber NA*/
float na_clad = na_fiber[1];
float na_core = na_fiber[0];
/*Fiber refractive indices*/
float n_clad = n_fiber[1];
float n_core = n_fiber[0];
/*Maximum angle for detection*/
double theta_clad = asin(na_clad/n_tissue);
double Ralphi;
/*ran1 seed*/
srand ( time(NULL) );
long idum = -(rand() % 1000 +1);
/*Image array*/
int t_grid0 = t_grid*r_max;
int t_grid2 = t_grid*x2_max;
double dim_arr = t_grid0*t_grid2;
double *aux_tissue = malloc(dim_arr*sizeof(double));
double r_tissue;
/*Fibre geometry*/
double r_dclad = fiber_radii[2];
double r_clad = fiber_radii[1];
double r_core = fiber_radii[0];
/*Tissue and fiber_tissue initialization for each monte carlo run*/
int it,jt, count=0;
for (it = 0; it< t_grid2; it++){
for (jt = 0; jt< t_grid0; jt++){
*(tissue+count) = 0;
*(fiber_tissue+count) = 0;
count++;}}
/*Auxiliar arrays initialization*/
int ji,count2=0;
for (ji = 0; ji< num_photons; ji++){
*(r+count2) = 0;
*(depth+count2) = 0;
*(weight+count2) = 0;
*(path+count2) = 0;
*(z+count2) = 0;
*(num_scatt+count2)=0;
count2++;}
/*LAUNCHING*/
for (i=0;i<num_photons;i++) {
int status=1; /*Photon alive*/
double x[]={x0[i],x1[i],x2[i]}; /*Position*/
double u[]={u0[i],u1[i],u2[i]}; /*Direction*/
double path_pp=0; /*Pathlength*/
double weight_pp=1; /*Weigth*/
double num_pp = 0;
double depth_pp=0; /*Maximum depth*/
double dw=0; /*Weigth lost*/
double fiber_boundary;
double z_na, r_na, cone;
/*Specular reflection*/
specular(n_core, n_tissue,&weight_pp);
/*aux_ tissue initialization for each photon*/
int count1 = 0,j;
for (it = 0; it< t_grid2; it++){
for (jt = 0; jt< t_grid0; jt++){
*(aux_tissue+count1)=0;
count1++;}}
while (status==1) {
/*Propagation distance*/
if (s == 0){s=log(ran1(&idum))/(-(ma+ms));}
int tz0=0;
int tz2=0;
/*HIT FIBER BOUNDARY*/
fiber_boundary = -x[2]*(ma+ms)/u[2];
/*Position before updating*/
z_na = x[2];
r_na = r_tissue;
cone = theta_clad*z_na + r_clad;
if (u[2] < 0 && fiber_boundary <= s && z_na >0) {
move_s(x, u, fiber_boundary, &depth_pp, &path_pp, &s, &r_tissue,&num_pp);
/*whether the photon is internally reflected*/
reflection(u, n_core, n_tissue, &Ralphi);
if (ran1(&idum)<= Ralphi){u[2]=-u[2];}
}
else{
move_s(x, u, s, &depth_pp, &path_pp, &s, &r_tissue, &num_pp);
absorption(ma, ms,&weight_pp,&dw);
spin_thph(u, g, &idum,th,ph);
/*Absortion array updating*/
tz0=floor(r_tissue*t_grid);
tz2=floor(x[2]*t_grid);
if(tz0>t_grid0-1){tz0=t_grid0-1;}
if(tz0<0){tz0=0;}
if(tz2>t_grid2-1){tz2=t_grid2-1;}
if(tz2<0){tz2=0;}
*(tissue+(tz0*t_grid2+tz2))+=dw;
*(aux_tissue+(tz0*t_grid2+tz2))+=dw;
} /*else (the photon didn't reach the boundary)*/
/*PHOTON TERMINATION*/
if(x[2] > x2_max ){status=0;}
if(status==1 && weight_pp<0.00001 /*threshold*/ ){roulette(&weight_pp,&idum,&status);}
/*The photon reach the sensing area?*/
if(x[2] < 0 && r_tissue <= r_clad && r_tissue >= r_core && z_na >0 && r_na <= cone){
for(j=0;j<dim_arr;j++){fiber_tissue[j]+=aux_tissue[j];}
/*Final status of detected photons*/
r[i] = r_tissue;
z[i] = x[2];
path[i] = path_pp;
weight[i] = weight_pp;
depth[i] = depth_pp;
num_scatt[i] = num_pp;}
} /*while status is alive*/
} /*for i num_photons launched*/
return;
} /*mcml2m*/