void
predefinedLIMEGrid(inputPars *par, struct grid *g){
FILE *fp;
int i;
double x,y,z,scale,abun;
fp=fopen(par->pregridLIME,"r");
par->ncell=par->pIntensity+par->sinkPoints;
/* read in the grid file, which includes all the sink points so we don't need to generate them */
for(i=0;i<par->ncell;i++){
fscanf(fp,"%lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %d\n", &g[i].x[0], &g[i].x[1], &g[i].x[2], &g[i].dens[0], &g[i].t[0], &g[i].t[1], &g[i].abun[0], &g[i].vel[0], &g[i].vel[1], &g[i].vel[2], &g[i].dopb, &g[i].sink);
g[i].id=i;
g[i].nmol[0]=g[i].abun[0]*g[i].dens[0];
// This next step needs to be done, even though it looks stupid
g[i].dir=malloc(sizeof(point)*1);
g[i].ds =malloc(sizeof(double)*1);
g[i].neigh =malloc(sizeof(int)*1);
if(!silent) progressbar((double) i/((double)par->ncell-1), 4);
}
fclose(fp);
qhull(par,g);
distCalc(par,g);
// getArea(par,g, ran);
// getMass(par,g, ran);
getVelosplines_lin(par,g);
if(par->gridfile) write_VTK_unstructured_Points(par, g);
}
void
popsin(inputPars *par, struct grid **g, molData **m, int *popsdone){
FILE *fp;
int i,j,k;
double dummy;
if((fp=fopen(par->restart, "rb"))==NULL){
if(!silent) bail_out("Error reading binary output populations file!");
exit(1);
}
par->collPart=1;
fread(&par->radius, sizeof(double), 1, fp);
fread(&par->ncell, sizeof(int), 1, fp);
fread(&par->nSpecies, sizeof(int), 1, fp);
if( par->nSpecies < 0 || par->nSpecies > MAX_NSPECIES )
{
if(!silent) bail_out("Error reading binary output populations file : is this really a binary output file generated by lime ?");
exit(1);
}
*m=realloc(*m, sizeof(molData)*par->nSpecies);
for(i=0;i<par->nSpecies;i++){
(*m)[i].lcl = NULL;
(*m)[i].lcu = NULL;
(*m)[i].up = NULL;
(*m)[i].down = NULL;
(*m)[i].eterm = NULL;
(*m)[i].gstat = NULL;
(*m)[i].cmb = NULL;
fread(&(*m)[i].nlev, sizeof(int), 1,fp);
fread(&(*m)[i].nline, sizeof(int), 1,fp);
fread(&(*m)[i].npart, sizeof(int), 1,fp);
(*m)[i].ntrans=malloc(sizeof(int)*(*m)[i].npart);
for(j=0;j<(*m)[i].npart;j++) fread(&(*m)[i].ntrans[j], sizeof(int), 1,fp);
(*m)[i].lal=malloc(sizeof(int)*(*m)[i].nline);
for(j=0;j<(*m)[i].nline;j++) fread(&(*m)[i].lal[j], sizeof(int), 1,fp);
(*m)[i].lau=malloc(sizeof(int)*(*m)[i].nline);
for(j=0;j<(*m)[i].nline;j++) fread(&(*m)[i].lau[j], sizeof(int), 1,fp);
(*m)[i].aeinst=malloc(sizeof(double)*(*m)[i].nline);
for(j=0;j<(*m)[i].nline;j++) fread(&(*m)[i].aeinst[j], sizeof(double), 1,fp);
(*m)[i].freq=malloc(sizeof(double)*(*m)[i].nline);
for(j=0;j<(*m)[i].nline;j++) fread(&(*m)[i].freq[j], sizeof(double), 1,fp);
(*m)[i].beinstl=malloc(sizeof(double)*(*m)[i].nline);
for(j=0;j<(*m)[i].nline;j++) fread(&(*m)[i].beinstl[j],sizeof(double), 1,fp);
(*m)[i].beinstu=malloc(sizeof(double)*(*m)[i].nline);
for(j=0;j<(*m)[i].nline;j++) fread(&(*m)[i].beinstu[j],sizeof(double), 1,fp);
(*m)[i].local_cmb = malloc(sizeof(double)*(*m)[i].nline);
for(j=0;j<(*m)[i].nline;j++) fread(&(*m)[i].local_cmb[j],sizeof(double), 1,fp);
fread(&(*m)[i].norm, sizeof(double), 1,fp);
fread(&(*m)[i].norminv, sizeof(double), 1,fp);
}
*g=malloc(sizeof(struct grid)*par->ncell);
for(i=0;i<par->ncell;i++){
(*g)[i].a0 = NULL;
(*g)[i].a1 = NULL;
(*g)[i].a2 = NULL;
(*g)[i].a3 = NULL;
(*g)[i].a4 = NULL;
(*g)[i].dens = NULL;
(*g)[i].abun = NULL;
(*g)[i].nmol = NULL;
(*g)[i].dir = NULL;
(*g)[i].neigh = NULL;
(*g)[i].w = NULL;
(*g)[i].ds = NULL;
fread(&(*g)[i].id, sizeof (*g)[i].id, 1, fp);
fread(&(*g)[i].x, sizeof (*g)[i].x, 1, fp);
fread(&(*g)[i].vel, sizeof (*g)[i].vel, 1, fp);
fread(&(*g)[i].sink, sizeof (*g)[i].sink, 1, fp);
(*g)[i].nmol=malloc(par->nSpecies*sizeof(double));
for(j=0;j<par->nSpecies;j++) fread(&(*g)[i].nmol[j], sizeof(double), 1, fp);
fread(&(*g)[i].dopb, sizeof (*g)[i].dopb, 1, fp);
(*g)[i].mol=malloc(par->nSpecies*sizeof(struct populations));
for(j=0;j<par->nSpecies;j++){
(*g)[i].mol[j].pops=malloc(sizeof(double)*(*m)[j].nlev);
for(k=0;k<(*m)[j].nlev;k++) fread(&(*g)[i].mol[j].pops[k], sizeof(double), 1, fp);
(*g)[i].mol[j].knu=malloc(sizeof(double)*(*m)[j].nline);
for(k=0;k<(*m)[j].nline;k++) fread(&(*g)[i].mol[j].knu[k], sizeof(double), 1, fp);
(*g)[i].mol[j].dust=malloc(sizeof(double)*(*m)[j].nline);
for(k=0;k<(*m)[j].nline;k++) fread(&(*g)[i].mol[j].dust[k],sizeof(double), 1, fp);
fread(&(*g)[i].mol[j].dopb,sizeof(double), 1, fp);
fread(&(*g)[i].mol[j].binv,sizeof(double), 1, fp);
(*g)[i].mol[j].partner=NULL;
}
fread(&dummy, sizeof(double), 1, fp);
fread(&dummy, sizeof(double), 1, fp);
fread(&dummy, sizeof(double), 1, fp);
}
fclose(fp);
qhull(par, *g);
distCalc(par, *g);
getVelosplines(par,*g);
*popsdone=1;
}
void
predefinedGrid(inputPars *par, struct grid *g){
FILE *fp;
int i;
double x,y,z,scale;
gsl_rng *ran = gsl_rng_alloc(gsl_rng_ranlxs2);
#ifdef TEST
gsl_rng_set(ran,6611304);
#else
gsl_rng_set(ran,time(0));
#endif
fp=fopen(par->pregrid,"r");
par->ncell=par->pIntensity+par->sinkPoints;
for(i=0;i<par->pIntensity;i++){
// fscanf(fp,"%d %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf\n", &g[i].id, &g[i].x[0], &g[i].x[1], &g[i].x[2], &g[i].dens[0], &g[i].t[0], &abun, &g[i].dopb, &g[i].vel[0], &g[i].vel[1], &g[i].vel[2]);
// fscanf(fp,"%d %lf %lf %lf %lf %lf %lf %lf\n", &g[i].id, &g[i].x[0], &g[i].x[1], &g[i].x[2], &g[i].dens[0], &g[i].t[0], &abun, &g[i].dopb);
int nRead = fscanf(fp,"%d %lf %lf %lf %lf %lf %lf %lf %lf\n", &g[i].id, &g[i].x[0], &g[i].x[1], &g[i].x[2], &g[i].dens[0], &g[i].t[0], &g[i].vel[0], &g[i].vel[1], &g[i].vel[2]);
if( nRead != 9 || g[i].id < 0 || g[i].id > par->ncell)
{
if(!silent) bail_out("Reading Grid File error");
exit(0);
}
g[i].dopb=200;
g[i].abun[0]=1e-9;
g[i].sink=0;
g[i].t[1]=g[i].t[0];
g[i].nmol[0]=g[i].abun[0]*g[i].dens[0];
/* This next step needs to be done, even though it looks stupid */
g[i].dir=malloc(sizeof(point)*1);
g[i].ds =malloc(sizeof(double)*1);
g[i].neigh =malloc(sizeof(struct grid *)*1);
if(!silent) progressbar((double) i/((double)par->pIntensity-1), 4);
}
for(i=par->pIntensity;i<par->ncell;i++){
x=2*gsl_rng_uniform(ran)-1.;
y=2*gsl_rng_uniform(ran)-1.;
z=2*gsl_rng_uniform(ran)-1.;
if(x*x+y*y+z*z<1){
scale=par->radius*sqrt(1/(x*x+y*y+z*z));
g[i].id=i;
g[i].x[0]=scale*x;
g[i].x[1]=scale*y;
g[i].x[2]=scale*z;
g[i].sink=1;
g[i].abun[0]=0;
g[i].dens[0]=1e-30;
g[i].t[0]=par->tcmb;
g[i].t[1]=par->tcmb;
g[i].dopb=0.;
} else i--;
}
fclose(fp);
qhull(par,g);
distCalc(par,g);
// getArea(par,g, ran);
// getMass(par,g, ran);
getVelosplines_lin(par,g);
if(par->gridfile) write_VTK_unstructured_Points(par, g);
gsl_rng_free(ran);
}
/* Based on Lloyds Algorithm (Lloyd, S. IEEE, 1982) */
void
smooth(configInfo *par, struct grid *gp){
double mindist; /* Distance to closest neighbor */
int k=0,j,i; /* counters */
int sg; /* counter for smoothing the grid */
int cn;
double move[3]; /* Auxillary array for smoothing the grid */
double dist; /* Distance to a neighbor */
struct cell *dc=NULL; /* Not used at present. */
unsigned long numCells;
for(sg=0;sg<N_SMOOTH_ITERS;sg++){
delaunay(DIM, gp, (unsigned long)par->ncell, 0, 0, &dc, &numCells);
distCalc(par, gp);
for(i=0;i<par->pIntensity;i++){
mindist=1e30;
cn=-1;
for(k=0;k<gp[i].numNeigh;k++){
if(gp[i].neigh[k]->sink==0){
if(gp[i].ds[k]<mindist){
mindist=gp[i].ds[k];
cn=k;
}
}
}
if(par->radius-sqrt(gp[i].x[0]*gp[i].x[0] + gp[i].x[1]*gp[i].x[1] + gp[i].x[2]*gp[i].x[2])<mindist) cn=-1;
if(cn>-1) {
for(k=0;k<DIM;k++){
move[k] = gp[i].x[k] - gp[i].dir[cn].x[k]*0.20;
}
if((move[0]*move[0]+move[1]*move[1]+move[2]*move[2])<par->radiusSqu &&
(move[0]*move[0]+move[1]*move[1]+move[2]*move[2])>par->minScaleSqu){
for(k=0;k<DIM;k++) gp[i].x[k]=move[k];
}
}
}
for(i=par->pIntensity;i<par->ncell;i++){
mindist=1e30;
cn=-1;
for(k=0;k<gp[i].numNeigh;k++){
if(gp[i].neigh[k]->sink==1){
if(gp[i].ds[k]<mindist){
mindist=gp[i].ds[k];
cn=k;
}
}
}
j=gp[i].neigh[cn]->id;
for(k=0;k<DIM;k++){
gp[i].x[k] = gp[i].x[k] - (gp[j].x[k]-gp[i].x[k]) * 0.15;
}
dist=par->radius/sqrt(gp[i].x[0]*gp[i].x[0] + gp[i].x[1]*gp[i].x[1] + gp[i].x[2]*gp[i].x[2]);
for(k=0;k<DIM;k++){
gp[i].x[k] *= dist;
}
}
if(!silent) progressbar((double)(sg+1)/(double)N_SMOOTH_ITERS, 5);
free(dc);
}
}
