/* \fcnfh
Wrapper for fgetupto() with error parameters previously stored
*/
inline char
fgetupto(char *line,
int max,
FILE *fp)
{
long zero=0;
if (!fgut_currline) fgut_currline = &zero;
return fgetupto_err(line, max, fp, fgut_errfcn, fgut_file,
*fgut_currline);
}
/* \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
get number of isotopes from file and set index
@returns number of lines read
*/
int
getmnfromfile(FILE *fp,
struct atm_data *at,
struct transit *tr,
int nmb)
{
char line[maxline],*lp;
int ison=0,i;
struct isotopes *iso=tr->ds.iso;
enum isodo *isodo=iso->isodo;
//Set variable to handle proportional to isotopes
int ipi=0,ipa=at->ipa=4;
isolineinatm=(_Bool *)calloc(iso->n_i,sizeof(_Bool));
isoprop=(struct atm_isoprop *)calloc(ipa,sizeof(struct atm_isoprop));
at->begline=0;
enum isodo atisodo;
at->isodo = (enum isodo *)calloc(nmb,sizeof(enum isodo));
at->isoeq = (int *) calloc(nmb,sizeof(int));
at->m = (PREC_ZREC *) calloc(nmb,sizeof(PREC_ZREC));
at->n = (char **) calloc(nmb,sizeof(char *));
at->n[0] = (char *) calloc(nmb*maxeisoname,sizeof(char));
at->isoeq[0]=-1;
for(i=1;i<nmb;i++){
at->n[i]=at->n[0]+i*maxeisoname;
at->isoeq[i]=-1;
}
//while t,p data doesn't start, check for the various modifiers
while(1){
switch(fgetupto_err(line,maxline,fp,&atmerr,atmfilename,
at->begline++)){
case '\n': //Ignore comments and
case '#': // blank lines
continue;
case 0: //Error if EOF
transiterror(TERR_SERIOUS|TERR_ALLOWCONT,
"readatminfo:: EOF unexpectedly found at line %i\n"
"of file %s while no t,p data points have been read\n"
,at->begline,atmfilename);
exit(EXIT_FAILURE);
continue;
case 'q': //Whether is mass or number abundance
lp=line+1;
while(*lp++==' ');
lp--;
switch(*lp|0x20){
case 'n':
at->mass=0;
break;
case 'm':
at->mass=1;
break;
default:
transiterror(TERR_SERIOUS,
"'q' option in the atmosphere file can only be followed\n"
"by 'm' (for abundances by mass) or 'n' (for abundances by\n"
"number). '%s' is invalid.\n"
,line);
break;
}
continue;
case 'z': //Zero radius value
zerorad=atof(line+1);
continue;
case 'f': //An isotope is to be taken as
//proportional to other.
lp=line+1;
while(*lp==' '||*lp=='\t') lp++;
if(ipi==ipa)
isoprop=(struct atm_isoprop *)realloc(isoprop,(ipa<<=1)*
sizeof(struct atm_isoprop));
isoprop[ipi].m=getds(lp,0,isoprop[ipi].n,maxeisoname-1);
//skip over recently read field, and go to next field.
lp=nextfield(lp);
//skip an optional equal '=' sign
if(*lp=='=' && lp[1]==' ')
lp=nextfield(lp);
//get factor, which has to be between 0 and 1
isoprop[ipi].f=strtod(lp,NULL);
if(isoprop[ipi].f<0 )
transiterror(TERR_CRITICAL,
"Abundance ratio has to be positive in atmosphere\n"
"file '%s' in line: %s"
,atmfilename,line);
lp=nextfield(lp);
//get name of reference and increase index
i=0;
while(*lp)
isoprop[ipi].t[i++]=*lp++;
isoprop[ipi].t[i]='\0';
//now check if that isotope is one of the given in the lineinfo
//file
isoprop[ipi].eq=-1;
isisoline(isoprop[ipi].n,isoprop[ipi].m,&isoprop[ipi].eq,factor,
iso->isof,isodo,iso->n_i);
//advance index and go for the next line
ipi++;
continue;
case 'u': //Change factorization of radius, temp,
//or press
switch(line[1]){
case 'r':
at->rads.fct=atof(line+2);
break;
case 'p':
at->atm.pfct=atof(line+2);
break;
case 't':
at->atm.tfct=atof(line+2);
break;
default:
transiterror(TERR_SERIOUS,
"Invalid unit factor indication in atmosphere file\n");
exit(EXIT_FAILURE);
}
continue;
case 'n': //Name or identifier for file data
storename(at,line+1);
continue;
case 'i': //Isotope information
lp=line+1;
while(*lp==' '||*lp=='\t') lp++;
//'i' has to come before 'f'
if(ipi)
transiterror(TERR_CRITICAL,
"In line '%s'.\n"
" 'f' lines have to come after all the 'i' lines in\n"
" atmosphere file '%s'"
,line,atmfilename);
//for each field
while(*lp){
atisodo=atmfile;
//Allocate if necessary
if(ison==nmb){
nmb<<=1;
at->isodo = (enum isodo *)realloc(at->isodo,nmb*sizeof(enum isodo));
at->isoeq = (int *) realloc(at->isoeq,nmb*sizeof(int));
at->m = (PREC_ZREC *) realloc(at->m, nmb*sizeof(PREC_ZREC));
at->n = (char **) realloc(at->n, nmb*sizeof(char *));
at->n[0] = (char *) realloc(at->n[0], nmb*maxeisoname*sizeof(char));
for(i=1;i<nmb;i++)
at->n[i]=at->n[0]+i*maxeisoname;
for(i=nmb/2;i<nmb;i++)
at->isoeq[i]=-1;
}
//get mass and name, checking that is correct. First see if this
//isotope wants to be ignored.
if(*lp=='!'){
lp++;
atisodo=ignore;
}
at->m[ison]=getds(lp,0,at->n[ison],maxeisoname-1);
if(at->m[ison]<0||at->n[ison]=='\0'){
transiterror(TERR_SERIOUS,
"Invalid field in file %s, line %i while reading isotope"
" info at:\n%s\n"
,atmfilename,at->begline,lp);
}
//now check if that isotope is one of the given in the lineinfo
//file
isisoline(at->n[ison],at->m[ison],at->isoeq+ison,atisodo,
iso->isof,isodo,iso->n_i);
at->isodo[ison++]=atisodo;
//skip over recently read field, and go to next field.
while(*lp!=' '&&*lp!='\0') lp++;
while(*lp==' '||*lp=='\t') lp++;
}
continue;
default: //T,P seems to be starting
break;
}
break;
}
transitprint(3,verblevel,
"Read all keywords in atmosphere file without problems\n");
//Check if there was at least an isotope identification and allocate new
//arrays
if(!ison)
transiterror(TERR_SERIOUS,
"No isotopes were found in atmosphere file, make sure to\n"
"specify them in a line starting with the letter 'i'.\n"
"First non-comment line read:\n%s\n"
,line);
at->begpos=ftell(fp)-strlen(line)-1;
//shorten extra length of arrays
fonly=(struct fonly *)calloc(nfonly,sizeof(struct fonly));
at->ipa=ipa=ipi;
isoprop=(struct atm_isoprop *)realloc(isoprop,ipa*
sizeof(struct atm_isoprop));
//Makes at arrays bigger, so that they can hold the factorized values.
nmb = at->n_aiso = ison + ipa;
at->isodo = (enum isodo *)realloc(at->isodo,nmb*sizeof(enum isodo) );
at->isoeq = (int *) realloc(at->isoeq,nmb*sizeof(int) );
at->m = (PREC_ZREC *) realloc(at->m, nmb*sizeof(PREC_ZREC) );
at->n = (char **) realloc(at->n, nmb*sizeof(char *) );
at->n[0] = (char *) realloc(at->n[0], nmb*maxeisoname*sizeof(char));
for(i=1;i<nmb;i++)
at->n[i] = at->n[0] + i * maxeisoname;
//initialize values for the factorized elements
for(i=ison;i<nmb;i++){
strncpy(at->n[i],isoprop[i-ison].n,maxeisoname-1);
at->n[i][maxeisoname-1] = '\0';
at->isoeq[i] = i-ison;
at->m[i] = isoprop[i-ison].m;
at->isodo[i] = factor;
}
//Resolve what to do with those isotopes that appear in the transition
//database, but not in the atmosphere file.
at->n_niso = checknonmatch(tr,at,isodo);
//Set full isotope info in the transit structure
nmb = iso->n_i + at->n_niso;
iso->isodo = (enum isodo *)realloc(iso->isodo,
nmb*sizeof(enum isodo));
iso->isof = (prop_isof *)realloc(iso->isof,
nmb*sizeof(prop_isof));
iso->isof[iso->n_i].n = (char *)realloc(iso->isof[iso->n_i].n,
(nmb-iso->n_i)*maxeisoname*
sizeof(char));
for(i=1;i<nmb-iso->n_i;i++)
iso->isof[iso->n_i+i].n = iso->isof[iso->n_i].n + i * maxeisoname;
//Look for isotopes who have not been associated and see whether they
//are supposed to be ignored.
nmb = iso->n_i;
ipi = 0;
int lineignore=0;
for(i=0 ; i<ison+ipa ; i++)
//If the isotope is not associated to the linedb isotopes, then
//associate it. Note that isotopes in linedb that are ignored will
//be associated (see comments for Line \label{isodbassoc}). Hence
//they won't be detected in this IF. Factor isotopes will also be
//associated, and will be handled below
if(at->isoeq[i] == -1){
//If they are not going to be ignored then associate them with the
//following index available of post linedb isotopes.
if(at->isodo[i] != ignore){
at->isoeq[i] = nmb;
iso->isodo[nmb] = at->isodo[i];
iso->isof[nmb].m = at->m[i];
strcpy(iso->isof[nmb++].n, at->n[i]);
}
//otherwise, they might only be used as a reference to factor.
else{
at->isoeq[i] = ipi;
strcpy(fonly[ipi++].n, at->n[i]);
}
}
//Just count the number of ignored isotopes that belonged to the line
//isotopes.
else if(at->isodo[i] == ignore)
lineignore++;
//If there is factor isotopes
else if(at->isodo[i] == factor && isoprop[at->isoeq[i]].eq == -1){
if(at->isodo[i]==ignore)
transiterror(TERR_CRITICAL,
"Trying to ignore an factor isotope, that is not\n"
"posible.\n");
isoprop[at->isoeq[i]].eq = nmb;
iso->isodo[nmb] = at->isodo[i];
iso->isof[nmb].m = at->m[i];
strcpy(iso->isof[nmb++].n, at->n[i]);
}
//Reduce the array to get rid of nonline-ignored isotopes. (isov has
//not even been allocated yet)
iso->n_e = nmb;
iso->isodo = (enum isodo *)realloc(iso->isodo,
nmb*sizeof(enum isodo));
iso->isof = (prop_isof *)realloc(iso->isof,
nmb*sizeof(prop_isof));
iso->isof[iso->n_i].n = (char *)realloc(iso->isof[iso->n_i].n,
nmb*maxeisoname*sizeof(char));
for(i=1;i<nmb-iso->n_i;i++)
iso->isof[iso->n_i+i].n = iso->isof[iso->n_i].n + i * maxeisoname;
//Check that everything makes sense
double cumulother=0;
for(i=0 ; i<at->n_aiso ; i++)
if(at->isodo[i]==factor){
int feq=at->isoeq[i];
if(strcasecmp(isoprop[feq].n,"other")==0)
cumulother+=isoprop[feq].f;
}
//It doesn't make sense for cumulother to be anything different from
//unity (except round-off error): you want to associate the
//remainder of the atmosphere to some isotopic properties.
if( cumulother!=0 && (int)(cumulother*ROUNDOFF+0.5)!=(int)(ROUNDOFF+0.5) )
transiterror(TERR_SERIOUS,
"If you are specifying isotopes proportional to 'other'\n"
"you have to complete unity (%g). It doesn't make sense\n"
"otherwise\n"
,cumulother);
transitASSERT(nmb+nfonly!=ison+ipa,
"Oooops, number of ignored-nonline elements (%i), plus the\n"
"number of ignored-line elements(%i), plus the number of\n"
"nonignored (%i), doesn't match the number of elements\n"
"found in fields 'i'(%i) and 'f'(%i) of the atmosphere\n"
"file '%s'\n"
,nfonly,lineignore,nmb-lineignore,ison,ipa,atmfilename);
transitASSERT(nmb!=iso->n_e,
"Uyuyuyuyu! Problem in file %s, line %i,\n"
"assertion failed: %i != %i!!\n"
,__FILE__,__LINE__,nmb,iso->n_e);
//free unused array, store factor info in at structure and return line
//where T,P start
free(isolineinatm);
at->isoprop=isoprop;
return at->begline;
}
/* \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;
}
/* \fcnfh
Get keyword variables from atmosphere file (mass/number abundance bool;
zero-radius offset; radius, temperature, and pressure units factor;
atmfile name/info; list isotopes; list of proportional-abundance isotopes).
Store molecules and proportional isotopes in atm_data struct.
Determine which linedb isotope corresponds to such atm_data isotope.
Solve non-matched linedb isotope cases.
Put all non-ignore isotopes in transit.ds.iso structure.
Return: Number of lines read */
int
getmnfromfile(FILE *fp, /* Pointer to atmospheric file */
struct atm_data *at, /* atmosphere structure */
struct transit *tr, /* transit structure */
PREC_ZREC *f_remainder){ /* Remainder molecules' factor */
struct molecules *mol=tr->ds.mol;
char line[maxline], *lp;
int nimol=0, /* Number of molecules with abundance profile */
nmol=0, /* Total number of molecules */
i; /* Auxiliary for-loop index */
double cumulother = 0; /* Cumulative remainder-molecules' factor */
int ipi = 0; /* Number of remainder molecules */
/* Is the isotope defined in the atm file?: */
//isoprop = (struct atm_isoprop *)calloc(ipa, sizeof(struct atm_isoprop));
at->begline = 0; /* Line where the info begins */
/* Read and store the keyword atmospheric variables: */
while(1){
switch(fgetupto_err(line, maxline, fp, &atmerr, atmfilename,
at->begline++)){
/* Ignore comments and blank lines: */
case '\n':
case '#':
continue;
case 0: /* Throw error if EOF */
transiterror(TERR_SERIOUS|TERR_ALLOWCONT,
"readatm :: EOF unexpectedly found at line %i "
"of file %s while no t,p data points have been read.\n",
at->begline, atmfilename);
exit(EXIT_FAILURE);
continue;
/* Determine whether abundance is by mass or number: */
case 'q':
lp = line + 1;
while(*lp++ == ' '); /* Skip blank spaces */
lp--;
switch(*lp|0x20){
case 'n':
at->mass = 0; /* Number abundance (mixing ratio) */
break;
case 'm':
at->mass = 1; /* Mass abundance (mass mixing ratio) */
break;
default:
transiterror(TERR_SERIOUS,
"'q' option in the atmosphere file can only be followed "
"by 'm' (for abundances by mass) or 'n' (for abundances "
"by number). '%s' is invalid.\n", line);
break;
}
continue;
/* Zero radius value: */
case 'z':
zerorad = atof(line+1);
continue;
/* Radius, temperature, or pressure units factor: */
case 'u':
switch(line[1]){
case 'r':
at->rads.fct = atof(line+2);
break;
case 'p':
at->atm.pfct = atof(line+2);
break;
case 't':
at->atm.tfct = atof(line+2);
break;
default:
transiterror(TERR_SERIOUS, "Invalid unit factor indication in "
"atmosphere file.\n");
exit(EXIT_FAILURE);
}
continue;
case 'n': /* Name or identifier for file data */
storename(at, line+1);
continue;
case 'i': /* Molecule names with an abundance profile: */
/* Count the number of wrds (molecules) in line: */
nimol = countfields(line+1, ' ');
transitprint(15, verblevel, "The number of molecules is %d.\n", nimol);
/* Allocate Molecules names: */
mol->name = (char **)calloc(nimol, sizeof(char *));
mol->name[0] = (char *)calloc(nimol*maxeisoname, sizeof(char));
for(i=1; i<nimol; i++)
mol->name[i] = mol->name[0] + i*maxeisoname;
transitprint(1, verblevel, "Molecules with abundance profile:\n ");
lp = line;
lp = nextfield(lp); /* Skip keyword */
/* Read and store names: */
for (i=0; i<nimol; i++){
getname(lp, mol->name[i]);
lp = nextfield(lp);
transitprint(1, verblevel, "%s, ", mol->name[i]);
}
transitprint(1, verblevel, "\b\b.\n");
continue;
/* Molecules with abundance proportional to the remainder: */
case 'f':
lp = line;
lp = nextfield(lp); /* Skip keyword */
/* Current total number of molecules: */
nmol = ++ipi + nimol;
/* Re-allocate to add the new molecule: */
mol->name = (char **)realloc(mol->name, nmol*sizeof(char *));
mol->name[0] = (char *)realloc(mol->name[0],
nmol*maxeisoname*sizeof(char));
for (i=1; i<nmol; i++)
mol->name[i] = mol->name[0] + i*maxeisoname;
/* Re-allocate remainder factors: */
f_remainder = (PREC_ZREC *)realloc(f_remainder, ipi*sizeof(PREC_ZREC));
/* Read and store the molecule's name: */
getname(lp, mol->name[nmol-1]);
lp = nextfield(lp); /* Move pointer to next field */
if(*lp == '=') /* Skip an optional equal '=' sign */
lp++;
/* Read and store factor: */
f_remainder[ipi-1] = strtod(lp, NULL);
transitprint(30, verblevel, "%s remainder factor: %.3f\n",
mol->name[nmol-1], f_remainder[ipi-1]);
if(f_remainder[ipi-1] < 0)
transiterror(TERR_CRITICAL,
"Abundance ratio has to be positive in atmosphere "
"file '%s' in line: '%s'.\n", atmfilename, line);
continue;
/* End of keyword variables: */
default:
break;
}
break;
}
transitprint(1, verblevel, "Molecules with abundance proportional to "
"remainder:\n ");
for(i=nimol; i<nmol; i++)
transitprint(1, verblevel, "%s, ", mol->name[i]);
transitprint(1, verblevel, "\b\b.\n");
transitprint(3, verblevel, "Read all keywords in atmosphere file without "
"problems.\n");
/* Set total number of molecules in atmosphere: */
mol->nmol = at->n_aiso = nmol;
/* Check that there was at least one isotope defined and re-allocate
array sizes to their final size: */
if(!nimol)
transiterror(TERR_SERIOUS, "No isotopes were found in atmosphere file, "
"make sure to specify them in a line starting "
"with the letter 'i'. First non-comment line "
"read:\n%s\n", line);
/* Set position of beginning of data: */
at->begpos = ftell(fp) - strlen(line) - 1;
/* Calculate cumulative fraction of remainder molecules: */
for(i=0; i < nmol-nimol; i++)
cumulother += f_remainder[i];
transitprint(30, verblevel, "Cumulative remainder fraction: %.4f.\n",
cumulother);
/* Check that cumulother sums to 1.0 (within allowed errors): */
if(nmol>nimol && abs(1.0 - cumulother) > ROUNDTHRESH)
transiterror(TERR_SERIOUS, "Sum of remainder-molecules fractional "
"abundance (%g) must add to 1.0 +/- %g.\n", cumulother, ROUNDTHRESH);
/* Resolve what to do with those isotopes that appear in the
line transition database, but not in the atmosphere file. Get
the number of non-ignored isotopes in atm_data without linelist: */
//at->n_niso = checknonmatch(tr, at, isodo);
/* FINDME: This will be a task in readline (if actually needed). */
return at->begline;
}
/* \fcnfh
Read CIA info from tabulated files.
Return: 0 on success */
int
readcia(struct transit *tr){
FILE *fp; /* Pointer to CIA file */
char *file, /* CIA file name */
*colname; /* CIA isotope names */
PREC_CIA **a, /* CIA cross sections sample */
*wn; /* CIA sampled wavenumber array */
static struct cia st_cia; /* CIA structure */
tr->ds.cia = &st_cia;
int npairs = tr->ds.cia->nfiles = tr->ds.th->ncia; /* Number of CIA files */
int p; /* Auxiliary wavenumber index */
long nt, wa; /* Number of temperature, wn samples in CIA file */
char rc;
char *lp, *lpa; /* Pointers in file */
int maxline=300, n; /* Max length of line. Counter */
long lines; /* Lines read counter */
long i; /* Auxiliary for indices */
char line[maxline+1]; /* Array to hold line being read */
struct molecules *mol=tr->ds.mol;
/* Make sure that radius and wavenumber samples exist: */
transitcheckcalled(tr->pi, "interpolatecia", 2, "makewnsample", TRPI_MAKEWN,
"makeradsample", TRPI_MAKERAD);
/* Allocate (output) transit extinction array (in cm-1): */
st_cia.e = (PREC_CIA **)calloc(tr->wns.n, sizeof(PREC_CIA *));
st_cia.e[0] = (PREC_CIA *)calloc(tr->wns.n*tr->rads.n, sizeof(PREC_CIA));
for(p=1; p < tr->wns.n; p++)
st_cia.e[p] = st_cia.e[0] + p*tr->rads.n;
memset(st_cia.e[0], 0, tr->wns.n*tr->rads.n*sizeof(double));
/* If there are no files, allocate tr.ds.cia.e (extinction) and return: */
if(!npairs){
return 0;
}
transitprint(1, verblevel, "Computing CIA opacities for %i database%s:\n",
npairs, npairs>1 ? "s":"");
/* Allocate string for molecule names: */
colname = (char *)calloc(maxline, sizeof(char));
/* Allocate molecules' ID: */
st_cia.mol1 = (int *)calloc(npairs, sizeof(int));
st_cia.mol2 = (int *)calloc(npairs, sizeof(int));
/* Number of temperature and wavenumber samples per file: */
st_cia.ntemp = (int *)calloc(npairs, sizeof(int));
st_cia.nwave = (int *)calloc(npairs, sizeof(int));
/* CIA, temperature and wavenumber samples: */
st_cia.cia = (PREC_CIA ***)calloc(npairs, sizeof(PREC_CIA **));
st_cia.temp = (PREC_CIA **)calloc(npairs, sizeof(PREC_CIA *));
st_cia.wn = (PREC_CIA **)calloc(npairs, sizeof(PREC_CIA *));
for(p=0; p < npairs; p++){
/* Copy file names from hint: */
file = xstrdup(tr->ds.th->ciafile[p]);
/* Attempt to open the files: */
if((fp=fopen(file, "r")) == NULL)
transiterror(TERR_SERIOUS, "Cannot read CIA file '%s'.\n", file);
transitprint(10, verblevel, " CIA file (%d/%d): '%s'\n",
p+1, npairs, file);
lines = 0; /* lines read counter */
lpa = 0;
/* Read the file headers: */
while(1){
/* Skip comments, blanks and read next line: */
while((rc=fgetupto_err(lp=line, maxline, fp, &ciaerr, file, lines++))
=='#' || rc=='\n');
/* If it is end of file, stop loop: */
if(!rc)
transiterror(TERR_SERIOUS, "File '%s' finished before opacity info.\n",
file);
switch(rc){
case 'i': /* Read the name of the isotopes: */
while(isblank(*++lp));
/* Check that there are exactly two isotopes: */
if(countfields(lp, ' ') != 2)
transiterror(TERR_SERIOUS,
"Wrong line %i in CIA file '%s', if it begins with a "
"'i', it should have the species separated by blank "
"spaces. Rest of line:\n'%s'\n", lines, file, lp);
st_cia.mol1[p] = st_cia.mol2[p] = -1;
/* Allocate and copy the name of the first moleculee: */
getname(lp, colname);
/* Find the ID of the first molecule: */
for(i=0; i<mol->nmol; i++)
if(strcmp(mol->name[i], colname)==0)
st_cia.mol1[p] = i;
/* If the molecule is not in the atmosphere file: */
if(st_cia.mol1[p] == -1)
transiterror(TERR_SERIOUS, "CIA molecule '%s' from file '%s' does "
"not match any in the atmsopheric file.\n", colname, file);
/* Allocate and store the name of the second isotope: */
lp = nextfield(lp);
getname(lp, colname);
for(i=0; i < mol->nmol; i++)
if(strcmp(mol->name[i], colname)==0)
st_cia.mol2[p] = i;
if(st_cia.mol2[p] == -1)
transiterror(TERR_SERIOUS, "CIA molecule '%s' from file '%s' does "
"not match any in the atmsopheric file.\n", colname, file);
transitprint(10, verblevel, " CIA molecules: [%s, %s]\n",
mol->name[st_cia.mol1[p]], mol->name[st_cia.mol2[p]]);
continue;
case 't': /* Read the sampling temperatures array: */
while(isblank(*++lp));
nt = st_cia.ntemp[p] = countfields(lp, ' '); /* Number of temps. */
transitprint(10, verblevel, " Number of temperature samples: %ld\n",
nt);
if(!nt)
transiterror(TERR_SERIOUS, "Wrong line %i in CIA file '%s', if it "
"begins with a 't' then it should have the "
"blank-separated fields with the temperatures. Rest "
"of line: %s.\n", lines, file, lp);
/* Allocate and store the temperatures array: */
st_cia.temp[p] = (PREC_CIA *)calloc(nt, sizeof(PREC_CIA));
n = 0; /* Count temperatures per line */
lpa = lp; /* Pointer in line */
transitprint(20, verblevel, " Temperatures (K) = [");
while(n < nt){
while(isblank(*lpa++));
st_cia.temp[p][n] = strtod(--lpa, &lp); /* Get value */
transitprint(20, verblevel, "%d, ", (int)st_cia.temp[p][n]);
if(lp==lpa)
transiterror(TERR_CRITICAL, "Less fields (%i) than expected (%i) "
"were read for temperature in the CIA file '%s'.\n",
n, nt, file);
if((lp[0]|0x20) == 'k') lp++; /* Remove trailing K if exists */
lpa = lp;
n++;
}
transitprint(20, verblevel, "\b\b]\n");
continue;
default:
break;
}
break;
}
/* Set an initial value for allocated wavenumber fields: */
wa = 32;
/* Allocate wavenumber array: */
wn = (PREC_CIA *)calloc(wa, sizeof(PREC_CIA));
/* Allocate input extinction array (in cm-1 amagat-2): */
a = (PREC_CIA **)calloc(wa, sizeof(PREC_CIA *));
a[0] = (PREC_CIA *)calloc(wa*nt, sizeof(PREC_CIA));
for(i=1; i<wa; i++)
a[i] = a[0] + i*nt;
n=0;
/* Read information for each wavenumber sample: */
while(1){
/* Skip comments and blanks; read next line: */
if (n)
while((rc=fgetupto_err(lp=line, maxline, fp, &ciaerr, file, lines++))
=='#'||rc=='\n');
/* Stop, if it is end of file: */
if(!rc)
break;
/* Re-allocate (double the size) if necessary: */
if(n==wa){
wn = (PREC_CIA *)realloc(wn, (wa<<=1) * sizeof(PREC_CIA));
a = (PREC_CIA **)realloc(a, wa * sizeof(PREC_CIA *));
a[0] = (PREC_CIA *)realloc(a[0], wa * nt * sizeof(PREC_CIA));
for(i=1; i<wa; i++)
a[i] = a[0] + i*nt;
}
/* Store new line: wavenumber first, then loop over cross sections: */
while(isblank(*lp++));
wn[n] = strtod(lp-1, &lpa); /* Store wavenumber */
if(lp==lpa+1)
transiterror(TERR_CRITICAL, "Invalid fields for the %ith wavenumber "
"in the CIA file '%s'.\n", n+1, file);
i = 0;
while(i<nt){
a[n][i] = strtod(lpa, &lp); /* Store cross section */
if(lp==lpa)
transiterror(TERR_CRITICAL, "Less fields (%i) than expected (%i) "
"were read for the %ith wavenumber in the CIA "
"file '%s'.\n", i, nt, n+1, file);
lpa = lp;
i++;
}
n++;
}
/* Re-allocate arrays to their final sizes: */
if(n<wa){
st_cia.wn[p] = (PREC_CIA *)realloc(wn, n* sizeof(PREC_CIA));
a = (PREC_CIA **)realloc(a, n* sizeof(PREC_CIA *));
a[0] = (PREC_CIA *)realloc(a[0], n*nt*sizeof(PREC_CIA));
for(i=1; i<n; i++)
a[i] = a[0] + i*nt;
}
transitprint(10, verblevel, " Number of wavenumber samples: %d\n", n);
transitprint(20, verblevel, " Wavenumber array (cm-1) = [%.1f, %.1f, "
"%.1f, ..., %.1f, %.1f, %.1f]\n", st_cia.wn[p][0], st_cia.wn[p][1],
st_cia.wn[p][2], st_cia.wn[p][n-3], st_cia.wn[p][n-2], st_cia.wn[p][n-1]);
st_cia.cia[p] = a;
st_cia.nwave[p] = n;
fclose(fp);
}
/* FINDME: The program breaks when I free colname, it makes no sense */
free(colname);
transitprint(1, verblevel, "Done.\n");
tr->pi |= TRPI_CIA;
return 0;
}
