/* \fcnfh
Set hard coded values
*/
void
sethcdef(struct transit *tr,
struct atm_data *at,
prop_samp *rads)
{
//Hard coded values.
//'hc\_t' temperature.
//'hc\_meanmass' is both the mean mass and the mass of the only
//isotope.
//'hc\_abund' is the abundance of the first isotope, the rest are
//just set at zero in the hardcode modality.
PREC_ZREC hc_t=1350;
PREC_ATM hc_pres=1.0e3;
PREC_ATM hc_abund=6.5e-4;
PREC_ATM hc_meanmass=2.3;
int nrad=rads->n;
rads->v=(PREC_ATM *)calloc(nrad,sizeof(PREC_ATM));
at->atm.tfct=1;
at->atm.pfct=1;
at->atm.t= (PREC_ATM *)calloc(nrad,sizeof(PREC_ATM));
at->atm.p= (PREC_ATM *)calloc(nrad,sizeof(PREC_ATM));
at->mm= (PREC_ATM *)calloc(nrad,sizeof(PREC_ATM));
rads->v[0]=1.0;
at->n_niso=0;
struct isotopes *iso=tr->ds.iso;
int nmb=iso->n_e=iso->n_i+at->n_niso;
at->isov=(prop_isov *)calloc(nmb,sizeof(prop_isov));
at->atm.t[0]=hc_t;
at->atm.p[0]=hc_pres;
at->mm[0]=hc_meanmass;
for(int i=0; i<nmb; i++) {
at->isov[i].d=(PREC_ATM *)calloc(1,sizeof(PREC_ATM));
at->isov[i].d[0]=stateeqnford(at->mass,hc_abund,hc_meanmass,
hc_meanmass,hc_pres,hc_t);
hc_abund=0;
}
telldefaults(iso,at);
}
/* FUNCTION: Calculate opacities for the grid of wavenumber, radius,
and temperature arrays for each molecule. */
int
calcopacity(struct transit *tr,
FILE *fp){
struct opacity *op=tr->ds.op; /* Opacity struct */
struct isotopes *iso=tr->ds.iso; /* Isotopes struct */
struct molecules *mol=tr->ds.mol; /* Molecules struct */
struct lineinfo *li=tr->ds.li; /* Lineinfo struct */
long Nmol, Ntemp, Nlayer, Nwave; /* Opacity-grid dimension sizes */
int i, j, t, r, /* for-loop indices */
rn, iso1db;
double *z;
int k;
PREC_ATM *density = (PREC_ATM *)calloc(mol->nmol, sizeof(PREC_ATM));
double *Z = (double *)calloc(iso->n_i, sizeof(double));
/* Make temperature array from hinted values: */
maketempsample(tr);
Ntemp = op->Ntemp = tr->temp.n;
op->temp = (PREC_RES *)calloc(Ntemp, sizeof(PREC_RES));
for (i=0; i<Ntemp; i++)
op->temp[i] = tr->temp.v[i];
/* Temperature boundaries check: */
if (op->temp[0] < li->tmin) {
tr_output(TOUT_ERROR, "The opacity file attempted to sample a "
"temperature (%.1f K) below the lowest allowed "
"TLI temperature (%.1f K).\n", op->temp[0], li->tmin);
exit(EXIT_FAILURE);
}
if (op->temp[Ntemp-1] > li->tmax) {
tr_output(TOUT_ERROR, "The opacity file attempted to sample a "
"temperature (%.1f K) beyond the highest allowed "
"TLI temperature (%.1f K).\n", op->temp[Ntemp-1], li->tmax);
exit(EXIT_FAILURE);
}
tr_output(TOUT_RESULT, "There are %li temperature samples.\n", Ntemp);
/* Evaluate the partition at these temperatures: */
op->ziso = (PREC_ATM **)calloc(iso->n_i, sizeof(PREC_ATM *));
op->ziso[0] = (PREC_ATM *)calloc(iso->n_i*Ntemp, sizeof(PREC_ATM));
for(i=1; i<iso->n_i; i++)
op->ziso[i] = op->ziso[0] + i*Ntemp;
/* Interpolate the partition function: */
for(i=0; i<iso->n_db; i++){ /* For each database separately: */
iso1db = iso->db[i].s; /* Index of first isotope in current DB */
for(j=0; j < iso->db[i].i; j++){
transitASSERT(iso1db + j > iso->n_i-1, "Trying to reference an isotope "
"(%i) outside the extended limit (%i).\n", iso1db+j, iso->n_i-1);
z = calloc(li->db[i].t, sizeof(double));
spline_init(z, li->db[i].T, li->isov[iso1db+j].z, li->db[i].t);
for(k=0;k<Ntemp;k++)
op->ziso[iso1db+j][k] = splinterp_pt(z, li->db[i].t, li->db[i].T,
li->isov[iso1db+j].z, op->temp[k]);
free(z);
}
}
/* Get pressure array from transit (save in CGS units): */
Nlayer = op->Nlayer = tr->rads.n;
op->press = (PREC_RES *)calloc(Nlayer, sizeof(PREC_RES));
for (i=0; i<Nlayer; i++)
op->press[i] = tr->atm.p[i]*tr->atm.pfct;
tr_output(TOUT_RESULT, "There are %li radius samples.\n", Nlayer);
/* Make molecules array from transit: */
Nmol = op->Nmol = tr->ds.iso->nmol;
op->molID = (int *)calloc(Nmol, sizeof(int));
tr_output(TOUT_RESULT, "There are %li molecules with line "
"transitions.\n", Nmol);
for (i=0, j=0; i<iso->n_i; i++){
/* If this molecule is not yet in molID array, add it's universal ID: */
if (valueinarray(op->molID, mol->ID[iso->imol[i]], j) < 0){
op->molID[j++] = mol->ID[iso->imol[i]];
tr_output(TOUT_DEBUG, "Isotope's (%d) molecule ID: %d (%s) "
"added at position %d.\n", i, op->molID[j-1],
mol->name[iso->imol[i]], j-1);
}
}
/* Get wavenumber array from transit: */
Nwave = op->Nwave = tr->wns.n;
op->wns = (PREC_RES *)calloc(Nwave, sizeof(PREC_RES));
for (i=0; i<Nwave; i++)
op->wns[i] = tr->wns.v[i];
tr_output(TOUT_RESULT, "There are %li wavenumber samples.\n", Nwave);
/* Allocate opacity array: */
if (fp != NULL){
op->o = (PREC_RES ****) calloc(Nlayer, sizeof(PREC_RES ***));
for (r=0; r<Nlayer; r++){
op->o[r] = (PREC_RES ***) calloc(Ntemp, sizeof(PREC_RES **));
for (t=0; t<Ntemp; t++){
op->o[r][t] = (PREC_RES **) calloc(Nmol, sizeof(PREC_RES *));
for (i=0; i<Nmol; i++){
op->o[r][t][i] = (PREC_RES *)calloc(Nwave, sizeof(PREC_RES));
}
}
}
if (!op->o[0][0][0])
tr_output(TOUT_ERROR, "Allocation fail.\n");
/* Compute extinction: */
for (r=0; r<Nlayer; r++){ /* For each layer: */
tr_output(TOUT_DEBUG, "\nOpacity Grid at layer %03d/%03ld.\n",
r+1, Nlayer);
for (t=0; t<Ntemp; t++){ /* For each temperature: */
/* Get density and partition-function arrays: */
for (j=0; j < mol->nmol; j++)
density[j] = stateeqnford(tr->ds.at->mass, mol->molec[j].q[r],
tr->atm.mm[r], mol->mass[j], op->press[r], op->temp[t]);
for (j=0; j < iso->n_i; j++)
Z[j] = op->ziso[j][t];
if((rn=computemolext(tr, op->o[r][t], op->temp[t], density, Z, 1))
!= 0) {
tr_output(TOUT_ERROR, "extinction() returned error code %i.\n", rn);
exit(EXIT_FAILURE);
}
}
}
/* Save dimension sizes: */
fwrite(&Nmol, sizeof(long), 1, fp);
fwrite(&Ntemp, sizeof(long), 1, fp);
fwrite(&Nlayer, sizeof(long), 1, fp);
fwrite(&Nwave, sizeof(long), 1, fp);
/* Save arrays: */
fwrite(&op->molID[0], sizeof(int), Nmol, fp);
fwrite(&op->temp[0], sizeof(PREC_RES), Ntemp, fp);
fwrite(&op->press[0], sizeof(PREC_RES), Nlayer, fp);
fwrite(&op->wns[0], sizeof(PREC_RES), Nwave, fp);
/* Save opacity: */
for (r=0; r<Nlayer; r++)
for (t=0; t<Ntemp; t++)
for (i=0; i<Nmol; i++)
fwrite(op->o[r][t][i], sizeof(PREC_RES), Nwave, fp);
fclose(fp);
}
tr_output(TOUT_RESULT, "Done.\n");
return 0;
}
/* \fcnfh
Read abundances and pressure for each isotope and radius
@returns number of radius point
*/
int
readatmfile(FILE *fp, /* File */
struct transit *tr, /* transit info */
struct atm_data *at, /* atmosphere info */
prop_samp *rads, /* radius sampling */
int nrad) /* number of allocated radii, note that
is not returned updated */
{
//find abundance related quantities for each radius
int lines=at->begline;
PREC_NREC r=0;
PREC_RES tmp;
char rc;
float allowq=1-tr->allowrq;
double sumq;
char line[maxline],*lp,*lp2;
prop_isov *isov=at->isov;
int *isoeq=at->isoeq;
struct isotopes *iso=tr->ds.iso;
enum isodo *isodo=at->isodo;
int i,neiso=iso->n_e;
fseek(fp,at->begpos,SEEK_SET);
while(1){
//reallocate if necessary
if(r==nrad){
nrad<<=1;
rads->v=(PREC_ATM *)realloc(rads->v,nrad*sizeof(PREC_ATM));
at->atm.t= (PREC_ATM *)realloc(at->atm.t,nrad*sizeof(PREC_ATM));
at->atm.p= (PREC_ATM *)realloc(at->atm.p,nrad*sizeof(PREC_ATM));
at->mm=(double *)realloc(at->mm,nrad*sizeof(double));
for(i=0;i<neiso;i++){
isov[i].d=(PREC_ATM *)realloc(isov[i].d,
nrad*sizeof(PREC_ATM));
isov[i].q=(PREC_ATM *)realloc(isov[i].q,
nrad*sizeof(PREC_ATM));
isov[i].n=nrad;
}
}
//Skip comments and read next line
while((rc=fgetupto_err(lp=line,maxline,fp,&atmerr,atmfilename,lines++))
=='#'||rc=='\n');
//if it is end of file, stop loop
if(!rc)
break;
tmp=rads->v[r]=strtod(lp,&lp2)+zerorad;
checkposvalue(tmp,1,lines);
if(lp==lp2)
invalidfield(line, lines, 1, "radius");
tmp=at->atm.p[r]=strtod(lp2,&lp);
checkposvalue(tmp,2,lines);
if(lp==lp2)
invalidfield(line, lines, 2, "pressure");
tmp=at->atm.t[r]=strtod(lp,&lp2);
checkposvalue(tmp,3,lines);
if(lp==lp2)
invalidfield(line, lines, 3, "temperature");
//variables to be used by factor (except ieq which is general)
int ieq, feq;
double ref;
_Bool otherfct[neiso];
memset(otherfct,0,sizeof(otherfct));
//now read abundances for every isotope, but don't process
//factorized elements. Because they might be proportional to a fixed
//element which is set below.
for(i=0;i<at->n_aiso;i++){
ieq=isoeq[i];
switch(isodo[i]){
case fixed:
if(!r){
isov[ieq].q[0]=askforposd(" %s abundance for isotope %s: "
,at->mass?"Mass":"Number"
,iso->isof[ieq].n);
if(isov[ieq].q[0]>=1){
fprintf(stderr," Abundance for any single isotope has to be"
" less than one\n Try Again!\n");
i--;
}
}
else
isov[ieq].q[r]=isov[ieq].q[0];
break;
case factor:
//don't process yet those that will use whatever abundance is left
//to complete unity
feq=ieq;
ieq=isoprop[feq].eq;
if(strcasecmp(isoprop[feq].t,"other")==0){
otherfct[ieq]=1;
continue;
}
//find the reference value
ref=findfactq(isoprop[feq].t,iso->isof,isov,neiso,r);
isov[ieq].q[r]=isoprop[feq].f*ref;
break;
default:
transiterror(TERR_CRITICAL,
"Trying to read isotope in readatmfile() which is\n"
"not 'fixed', 'atmfile', 'ignored', nor 'factor'.\n"
);
exit(EXIT_FAILURE);
break;
case atmfile:
case ignore:
transitASSERT(ieq<0 ||
(isodo[i]==ignore&&ieq>=nfonly) ||
(isodo[i]!=ignore&&ieq>=iso->n_e),
"Assertion failed in file %s, line %i: %i!=[0,%i].\n"
" Fonly: %i\n"
,__FILE__, __LINE__, isoeq[i],
isodo[i]==ignore?nfonly:iso->n_e-1, isodo[i]==ignore);
//Read the abundance of the new element. There are two ways:
//If processing one of the factor only elements
if(isodo[i]==ignore)
tmp=fonly[ieq].q=strtod(lp2,&lp);
//otherwise if this element is going to be considered
else
tmp=isov[ieq].q[r]=strtod(lp2,&lp);
checkposvalue(tmp, i+4, lines);
if(lp==lp2)
invalidfield(line, lines, 4+i, "isotope abundance");
lp2=lp;
break;
}
}
//process factorized elements that will take care of the rest of the
//atmosphere
ref=1-addq(isov,iso->isodo,otherfct,neiso,r);
for(i=0;i<at->n_aiso;i++)
if(isodo[i]==factor){
feq=isoeq[i];
ieq=isoprop[feq].eq;
if(otherfct[ieq])
isov[ieq].q[r]=isoprop[feq].f*ref;
}
//calculate mean molecular mass and check whether abundances add up
//correctly, up to round off error of course
sumq=checkaddmm(at->mm+r,r,isov,iso->isof,neiso,at->mass,iso->isodo);
if((int)(sumq*ROUNDOFF+0.5)<(int)(allowq*ROUNDOFF+0.5))
transiterror(TERR_WARNING,
"In radius %g(%i: %g in file), abundances\n"
"don't add up to 1: %.9g\n"
,at->rads.v[r],r,at->rads.v[r]-zerorad,sumq);
//Calculate densities
for(i=0;i<neiso;i++)
isov[i].d[r]=stateeqnford(at->mass,
isov[i].q[r],
at->mm[r],
iso->isof[i].m,
at->atm.p[r]*at->atm.pfct,
at->atm.t[r]*at->atm.tfct);
r++;
}
//reduce array to the right number of radii
rads->n=nrad=r;
rads->v=(PREC_ATM *)realloc(rads->v,nrad*sizeof(PREC_ATM));
at->atm.t= (PREC_ATM *)realloc(at->atm.t,nrad*sizeof(PREC_ATM));
at->atm.p= (PREC_ATM *)realloc(at->atm.p,nrad*sizeof(PREC_ATM));
at->mm=(double *)realloc(at->mm,nrad*sizeof(double));
for(i=0;i<neiso;i++){
isov[i].d=(PREC_ATM *)realloc(isov[i].d,
nrad*sizeof(PREC_ATM));
isov[i].q=(PREC_ATM *)realloc(isov[i].q,
nrad*sizeof(PREC_ATM));
isov[i].n=nrad;
}
//free arrays that were used only to get the factorizing elements
free(fonly);
return nrad;
}
/* \fcnfh
Read radius, pressure, temperature, and abundances and store it into
at_data of transit. Calculate mean molecular mass and densities.
Detailed:
Read and store radius, pressure, and temperature from file.
Read abundances for each (non other-factor) isotope.
Sum fractional abundances. Calculate ramaining (other-factor) abundances.
Calculate mean molecular mass per radius.
Calculate densities per isotope at each radius.
Returns: number of sample radius */
int
readatmfile(FILE *fp, /* Atmospheric file */
struct transit *tr, /* transit struct */
struct atm_data *at, /* Atmosphere struct */
prop_samp *rads, /* Radius sampling */
int nrad, /* Size of allocated radius array */
PREC_ZREC *f_remainder){ /* Remainder molecules' factor */
transitprint(1, verblevel, "Start reading abundances.\n");
/* Find abundance related quantities for each radius */
int lines = at->begline;
PREC_NREC r = 0; /* Radius index (number of radii being read) */
char rc; /* File reading output */
float allowq = 1 - tr->allowrq;
int nabundances; /* Number of abundances in list */
double sumq; /* Sum of abundances per line */
char line[maxline], *lp, *lp2;
prop_mol *molec = at->molec;
struct molecules *mol = tr->ds.mol;
int i, j; /* Auxiliary for-loop indices */
/* Variables to be used by factor (except ieq which is general): */
/* Count the number of abundances in each line: */
fseek(fp, at->begpos, SEEK_SET); /* Go to position where data begins */
/* Skip comments: */
while((rc=fgetupto_err(lp=line, maxline, fp, &atmerr, atmfilename, lines++))
=='#' || rc=='\n');
/* Count values per line: */
nabundances = countfields(lp, ' ') - 3; /* Subtract rad, p, and T columns */
fseek(fp, at->begpos, SEEK_SET); /* Go to position where data begins */
while(1){
/* Reallocate if necessary: */
if(r==nrad){
nrad <<= 1;
rads->v = (PREC_ATM *)realloc(rads->v, nrad*sizeof(PREC_ATM));
at->atm.t = (PREC_ATM *)realloc(at->atm.t, nrad*sizeof(PREC_ATM));
at->atm.p = (PREC_ATM *)realloc(at->atm.p, nrad*sizeof(PREC_ATM));
at->mm = (double *)realloc(at->mm, nrad*sizeof(double));
for(i=0; i<at->n_aiso; i++){
molec[i].d = (PREC_ATM *)realloc(molec[i].d, nrad*sizeof(PREC_ATM));
molec[i].q = (PREC_ATM *)realloc(molec[i].q, nrad*sizeof(PREC_ATM));
molec[i].n = nrad;
}
}
/* Skip comments and read next line: */
while((rc=fgetupto_err(lp=line, maxline, fp, &atmerr, atmfilename, lines++))
=='#' || rc=='\n');
/* If it is end of file, stop loop: */
if(!rc)
break;
/* Read and store radius, pressure, and temperature from file: */
rads->v[r] = strtod(lp, &lp2) + zerorad; /* Radius */
checkposvalue(rads->v[r], 1, lines); /* Check value is positive */
if(lp==lp2)
invalidfield(line, lines, 1, "radius");
at->atm.p[r] = strtod(lp2, &lp); /* Pressure */
checkposvalue(at->atm.p[r], 2, lines);
if(lp==lp2)
invalidfield(line, lines, 2, "pressure");
at->atm.t[r] = strtod(lp, &lp2); /* Temperature */
checkposvalue(at->atm.t[r], 3, lines);
if(lp==lp2)
invalidfield(line, lines, 3, "temperature");
/* Read abundances for each isotope. Keep reading-in values
while there are numbers in line: */
for(i=0, sumq=0; i<nabundances; i++){
lp = lp2;
/* Read the abundance of the isotope: */
molec[i].q[r] = strtod(lp, &lp2);
if (r==0)
transitprint(30, verblevel, "density[%d, %li]: %.9f.\n",
i, r, molec[i].q[r]);
sumq += molec[i].q[r]; /* Add the abundances */
checkposvalue(molec[i].q[r], i+4, lines); /* Check that tmp is positive */
if(lp==lp2)
invalidfield(line, lines, 4+i, "isotope abundance");
}
/* Remainder of the sum of abundances: */
/* Set abundance of remainder molecules: */
for(j=0; i < at->n_aiso; i++, j++)
molec[i].q[r] = f_remainder[j]*(1-sumq);
transitASSERT(i!=at->n_aiso, "The line %s of file %s contains %d abundance "
"values, when there were %d expected.\n",
__LINE__, __FILE__, i, at->n_aiso);
/* Calculate mean molecular mass and check whether abundances add up
to one (within roundoff error): */
sumq = checkaddmm(at->mm+r, r, molec, mol, at->n_aiso, at->mass);
if((int)(sumq*ROUNDOFF+0.5)<(int)(allowq*ROUNDOFF+0.5))
transiterror(TERR_WARNING,
"In radius %g (%i: %g in file), abundances "
"don't add up to 1: %.9g\n",
at->rads.v[r], r, at->rads.v[r]-zerorad, sumq);
/* Calculate densities using ideal gas law: */
if (r>=0){
transitprint(30, verblevel, "Abund: %.9f, mmm: %.3f, mass: %.3f, "
"p: %.3f, T: %.3f.\n", molec[2].q[r], at->mm[r],
mol->mass[2], at->atm.p[r]*at->atm.pfct,
at->atm.t[r]*at->atm.tfct);
}
for(i=0; i<at->n_aiso; i++)
molec[i].d[r] = stateeqnford(at->mass, molec[i].q[r], at->mm[r],
mol->mass[i], at->atm.p[r]*at->atm.pfct,
at->atm.t[r]*at->atm.tfct);
transitprint(30, verblevel, "dens[%2li]: %.14f, ", r, molec[2].d[r]);
r++;
}
/* Re-allocate arrays to final size (nrad): */
rads->n = nrad = r;
rads->v = (PREC_ATM *)realloc(rads->v, nrad*sizeof(PREC_ATM));
at->atm.t = (PREC_ATM *)realloc(at->atm.t, nrad*sizeof(PREC_ATM));
at->atm.p = (PREC_ATM *)realloc(at->atm.p, nrad*sizeof(PREC_ATM));
at->mm = (double *)realloc(at->mm, nrad*sizeof(double));
for(i=0; i<at->n_aiso; i++){
molec[i].d = (PREC_ATM *)realloc(molec[i].d, nrad*sizeof(PREC_ATM));
molec[i].q = (PREC_ATM *)realloc(molec[i].q, nrad*sizeof(PREC_ATM));
molec[i].n = nrad;
}
/* Free arrays that were used only to get the factorizing elements: */
free(fonly);
nfonly = 0;
return nrad;
}