void rawAtom(Atom *atom, char *atomFileName)
{
const char routineName[] = "rawAtom";
register int kr, kf, la, n;
char inputLine[MAX_LINE_SIZE], shapeStr[20], vdWstr[20], nuDepStr[20],
errorStr[80], symmStr[20], optionStr[20], *match;
bool_t exit_on_EOF;
int i, j, Nlevel, Nrad, Nline, Ncont, Nfixed, Nread, Nrequired,
checkPoint;
double f, C, lambda0, lambdamin, dlamb;
FILE *atomFile;
AtomicLine *line;
AtomicContinuum *continuum;
FixedTransition *fixed;
/* --- Open the data file for current model atom -- -------------- */
if ((atomFile = fopen(atomFileName, "r")) == NULL) {
sprintf(messageStr, "Unable to open input file %s", atomFileName);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Read atom ID and convert to uppercase -- -------------- */
getLine(atomFile, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%2s", atom->ID);
checkNread(Nread, Nrequired=1, routineName, checkPoint=1);
for (n = 0; n < (int) strlen(atom->ID); n++)
atom->ID[n] = toupper(atom->ID[n]);
if (strlen(atom->ID) == 1) strcat(atom->ID, " ");
/* --- Get the atomic weight -- -------------- */
for (n = 0; n < sizeof(atomweight)/sizeof(struct AtomWeight); n++) {
if ((match = strstr(atom->ID, atomweight[n].ID))) {
atom->weight = atomweight[n].weight;
break;
}
}
if (!match) {
sprintf(messageStr, "Found no matching element for %s", atom->ID);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Get Number of levels, lines fixed transitions, and continua */
getLine(atomFile, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%d %d %d %d",
&atom->Nlevel, &atom->Nline, &atom->Ncont, &atom->Nfixed);
checkNread(Nread, Nrequired=4, routineName, checkPoint=2);
Nlevel = atom->Nlevel;
Nline = atom->Nline; Ncont = atom->Ncont; Nfixed = atom->Nfixed;
Nrad = Nline + Ncont;
atom->E = (double *) malloc(Nlevel * sizeof(double));
atom->g = (double *) malloc(Nlevel * sizeof(double));
atom->stage = (int *) malloc(Nlevel * sizeof(int));
atom->label = (char **) malloc(Nlevel * sizeof(char *));
/* --- Read in the level energies, statistical weights, labels,
and ionization stage -- -------------- */
for (i = 0; i < Nlevel; i++) {
atom->label[i] = (char *) calloc((ATOM_LABEL_WIDTH+1), sizeof(char));
getLine(atomFile, COMMENT_CHAR, inputLine , exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%lf %lf '%20c' %d",
&atom->E[i], &atom->g[i], atom->label[i], &atom->stage[i]);
checkNread(Nread, Nrequired=4, routineName, checkPoint=3);
atom->E[i] *= (HPLANCK * CLIGHT) / CM_TO_M;
}
if (atom->stage[Nlevel-1] != (atom->stage[Nlevel-2] + 1)) {
sprintf(messageStr, "Found no overlying continuum for atom %s", atom->ID);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
C = 2 * PI * (Q_ELECTRON/EPSILON_0) * (Q_ELECTRON/M_ELECTRON) / CLIGHT;
/* --- Go through the bound-bound transitions -- -------------- */
atom->Nprd = 0;
atom->line = (AtomicLine *) malloc(Nline * sizeof(AtomicLine));
for (kr = 0; kr < Nline; kr++) {
line = atom->line + kr;
line->atom = atom;
line->isotope_frac = 1.0;
getLine(atomFile, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine,
"%d %d %lf %s %d %s %lf %lf %s %lf %lf %lf %lf %lf %lf %lf",
&j, &i, &f, shapeStr,
&line->Nlambda, symmStr, &line->qcore,
&line->qwing, vdWstr,
&line->cvdWaals[0], &line->cvdWaals[1],
&line->cvdWaals[2], &line->cvdWaals[3],
&line->Grad, &line->cStark, &line->g_Lande_eff);
checkNread(Nread, Nrequired=15, routineName, checkPoint=4);
if (Nread == 15) line->g_Lande_eff = 0.0;
line->j = MAX(i, j); line->i = MIN(i, j);
i = line->i;
j = line->j;
if (!strstr(shapeStr, "PRD") &&
!strstr(shapeStr, "VOIGT") && !strstr(shapeStr, "GAUSS")) {
sprintf(messageStr, "Invalid value for line-shape string: %s",
shapeStr);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
if (strstr(shapeStr, "PRD")) {
atom->Nprd++;
line->PRD = TRUE;
}
if (strstr(shapeStr, "GAUSS")) line->Voigt = FALSE;
lambda0 = (HPLANCK * CLIGHT) / (atom->E[j] - atom->E[i]);
line->Aji = C / SQ(lambda0) * (atom->g[i] / atom->g[j]) * f;
line->Bji = CUBE(lambda0) / (2.0 * HPLANCK * CLIGHT) * line->Aji;
line->Bij = (atom->g[j] / atom->g[i]) * line->Bji;
line->lambda0 = lambda0 / NM_TO_M;
if (strstr(vdWstr, "PARAMTR"))
line->vdWaals = RIDDER_RENSBERGEN;
else {
line->vdWaals = UNSOLD;
line->cvdWaals[3] = line->cvdWaals[1] = 0.0;
}
line->symmetric = (strstr(symmStr, "ASYMM")) ? FALSE : TRUE;
}
/* --- Go through the bound-free transitions -- -------------- */
atom->continuum =
(AtomicContinuum *) malloc(Ncont * sizeof(AtomicContinuum));
for (kr = 0; kr < Ncont; kr++) {
continuum = atom->continuum + kr;
continuum->atom = atom;
continuum->isotope_frac = 1.0;
getLine(atomFile, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%d %d %lf %d %s %lf",
&j, &i, &continuum->alpha0, &continuum->Nlambda,
nuDepStr, &lambdamin);
checkNread(Nread, Nrequired=6, routineName, checkPoint=5);
continuum->j = MAX(i, j); continuum->i = MIN(i, j);
j = continuum->j;
i = continuum->i;
lambda0 = (HPLANCK * CLIGHT)/(atom->E[j] - atom->E[i]);
continuum->lambda0 = lambda0 / NM_TO_M;
continuum->lambda =
(double *) malloc(continuum->Nlambda * sizeof(double));
continuum->alpha =
(double *) malloc(continuum->Nlambda * sizeof(double));
if (strstr(nuDepStr, "EXPLICIT")) {
continuum->hydrogenic = FALSE;
for (la = continuum->Nlambda-1; la >= 0; la--) {
getLine(atomFile, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%lf %lf",
&continuum->lambda[la], &continuum->alpha[la]);
checkNread(Nread, Nrequired=2, routineName, checkPoint=6);
}
for (la = 1; la < continuum->Nlambda; la++) {
if (continuum->lambda[la] < continuum->lambda[la-1]) {
sprintf(messageStr,
"Continuum %d does not have monotonous wavelengths",
kr - Nline);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
}
} else {
continuum->hydrogenic = TRUE;
if (lambdamin >= continuum->lambda0) {
sprintf(messageStr,
"Minimum wavelength for continuum %d too long", kr - Nline);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
dlamb = (continuum->lambda0 - lambdamin) / (continuum->Nlambda - 1);
continuum->lambda[0] = lambdamin;
for (la = 1; la < continuum->Nlambda; la++)
continuum->lambda[la] = continuum->lambda[la-1] + dlamb;
}
}
/* --- Go through fixed transitions -- -------------- */
if (atom->Nfixed > 0) {
atom->ft = (FixedTransition *) malloc(Nfixed * sizeof(FixedTransition));
for (kf = 0; kf < Nfixed; kf++) {
fixed = atom->ft + kf;
getLine(atomFile, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%d %d %lf %lf %s",
&j, &i, &fixed->strength,
&fixed->Trad, optionStr);
checkNread(Nread, Nrequired=5, routineName, checkPoint=7);
fixed->j = MAX(i, j); fixed->i = MIN(i, j);
j = fixed->j;
i = fixed->i;
for (kr = 0; kr < Nline; kr++) {
line = atom->line + kr;
if (line->i == i && line->j == j) {
sprintf(messageStr,
"Fixed transition j = %d, i = %d duplicates active line",
j, i);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
}
for (kr = 0; kr < Ncont; kr++) {
continuum = atom->continuum + kr;
if (continuum->i == i && continuum->j == j) {
sprintf(messageStr, "Fixed transition j = %d, i = %d"
" duplicates active continuum", j, i);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
}
lambda0 = (HPLANCK * CLIGHT) / (atom->E[j] - atom->E[i]);
fixed->lambda0 = lambda0 / NM_TO_M;
if (atom->stage[j] == atom->stage[i])
fixed->type = FIXED_LINE;
else
fixed->type = FIXED_CONTINUUM;
if (strstr(optionStr, "TRAD_ATMOSPHERIC"))
fixed->option = TRAD_ATMOSPHERIC;
else if (strstr(optionStr, "TRAD_PHOTOSPHERIC"))
fixed->option = TRAD_PHOTOSPHERIC;
else if (strstr(optionStr, "TRAD_CHROMOSPHERIC"))
fixed->option = TRAD_CHROMOSPHERIC;
else {
sprintf(messageStr, "Inavlid value for TRAD option: %s", optionStr);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
}
}
fclose(atomFile);
}
void readKuruczLines(char *inputFile)
{
const char routineName[] = "readKuruczLines";
const double C = 2.0*PI * (Q_ELECTRON/EPSILON_0) *
(Q_ELECTRON/M_ELECTRON) / CLIGHT;
char inputLine[RLK_RECORD_LENGTH+1], listName[MAX_LINE_SIZE],
filename[MAX_LINE_SIZE], Gvalues[18+1], elem_code[7],
labeli[RLK_LABEL_LENGTH+1], labelj[RLK_LABEL_LENGTH+1],
*commentChar = COMMENT_CHAR;
bool_t swap_levels, determined, useBarklem;
int Nline, Nread, Nrequired, checkPoint, hfs_i, hfs_j, gL_i, gL_j,
iso_dl;
double lambda0, Ji, Jj, Grad, GStark, GvdWaals, pti,
Ei, Ej, gf, lambda_air;
RLK_Line *rlk;
Barklemstruct bs_SP, bs_PD, bs_DF;
FILE *fp_Kurucz, *fp_linelist;
if (!strcmp(inputFile, "none")) return;
/* --- Read in the data files for Barklem collisional broadening -- */
readBarklemTable(SP, &bs_SP);
readBarklemTable(PD, &bs_PD);
readBarklemTable(DF, &bs_DF);
labeli[RLK_LABEL_LENGTH] = '\0';
labelj[RLK_LABEL_LENGTH] = '\0';
if ((fp_Kurucz = fopen(inputFile, "r")) == NULL) {
sprintf(messageStr, "Unable to open input file %s", inputFile);
Error(ERROR_LEVEL_1, routineName, messageStr);
return;
}
/* --- Go through each of the linelist files listed in input file - */
while (getLine(fp_Kurucz, commentChar, listName, FALSE) != EOF) {
Nread = sscanf(listName, "%s", filename);
if ((fp_linelist = fopen(filename, "r")) == NULL) {
sprintf(messageStr, "Unable to open input file %s", filename);
Error(ERROR_LEVEL_1, routineName, messageStr);
}
/* --- Count the number of lines in this file -- -------------- */
Nline = 0;
while (fgets(inputLine, RLK_RECORD_LENGTH+1, fp_linelist) != NULL)
if (*inputLine != *commentChar) Nline++;
rewind(fp_linelist);
if (atmos.Nrlk == 0) atmos.rlk_lines = NULL;
atmos.rlk_lines = (RLK_Line *)
realloc(atmos.rlk_lines, (Nline + atmos.Nrlk) * sizeof(RLK_Line));
/* --- Read lines from file -- -------------- */
rlk = atmos.rlk_lines + atmos.Nrlk;
while (fgets(inputLine, RLK_RECORD_LENGTH+1, fp_linelist) != NULL) {
if (*inputLine != *commentChar) {
initRLK(rlk);
Nread = sscanf(inputLine, "%lf %lf %s %lf",
&lambda_air, &gf, (char *) &elem_code, &Ei);
/* --- Ionization stage and periodic table index -- --------- */
sscanf(elem_code, "%d.%d", &rlk->pt_index, &rlk->stage);
Nread += sscanf(inputLine+53, "%lf", &Ej);
Ei = fabs(Ei) * (HPLANCK * CLIGHT) / CM_TO_M;
Ej = fabs(Ej) * (HPLANCK * CLIGHT) / CM_TO_M;
/* --- Beware: the Kurucz linelist has upper and lower levels
of a transition in random order. Therefore, we have to
check for the lowest energy of the two and use that as
lower level -- -------------- */
if (Ej < Ei) {
swap_levels = TRUE;
rlk->Ei = Ej;
rlk->Ej = Ei;
strncpy(labeli, inputLine+69, RLK_LABEL_LENGTH);
strncpy(labelj, inputLine+41, RLK_LABEL_LENGTH);
} else {
swap_levels = FALSE;
rlk->Ei = Ei;
rlk->Ej = Ej;
strncpy(labeli, inputLine+41, RLK_LABEL_LENGTH);
strncpy(labelj, inputLine+69, RLK_LABEL_LENGTH);
}
Nread += sscanf(inputLine+35, "%lf", &Ji);
Nread += sscanf(inputLine+63, "%lf", &Jj);
if (swap_levels) SWAPDOUBLE(Ji, Jj);
rlk->gi = 2*Ji + 1;
rlk->gj = 2*Jj + 1;
lambda0 = (HPLANCK * CLIGHT) / (rlk->Ej - rlk->Ei);
rlk->Aji = C / SQ(lambda0) * POW10(gf) / rlk->gj;
rlk->Bji = CUBE(lambda0) / (2.0 * HPLANCK * CLIGHT) * rlk->Aji;
rlk->Bij = (rlk->gj / rlk->gi) * rlk->Bji;
/* --- Store in nm -- -------------- */
rlk->lambda0 = lambda0 / NM_TO_M;
/* --- Get quantum numbers for angular momentum and spin -- - */
determined = RLKdeterminate(labeli, labelj, rlk);
rlk->polarizable = (atmos.Stokes && determined);
/* --- Line broadening -- -------------- */
strncpy(Gvalues, inputLine+79, 18);
Nread += sscanf(Gvalues, "%lf %lf %lf", &Grad, &GStark, &GvdWaals);
if (GStark != 0.0)
rlk->GStark = POW10(GStark) * CUBE(CM_TO_M);
else
rlk->GStark = 0.0;
if (GvdWaals != 0.0)
rlk->GvdWaals = POW10(GvdWaals) * CUBE(CM_TO_M);
else
rlk->GvdWaals = 0.0;
/* --- If possible use Barklem formalism -- -------------- */
useBarklem = FALSE;
if (determined) {
if ((rlk->Li == S_ORBIT && rlk->Lj == P_ORBIT) ||
(rlk->Li == P_ORBIT && rlk->Lj == S_ORBIT)) {
useBarklem = getBarklemcross(&bs_SP, rlk);
} else if ((rlk->Li == P_ORBIT && rlk->Lj == D_ORBIT) ||
(rlk->Li == D_ORBIT && rlk->Lj == P_ORBIT)) {
useBarklem = getBarklemcross(&bs_PD, rlk);
} else if ((rlk->Li == D_ORBIT && rlk->Lj == F_ORBIT) ||
(rlk->Li == F_ORBIT && rlk->Lj == D_ORBIT)) {
useBarklem = getBarklemcross(&bs_DF, rlk);
}
}
/* --- Else use good old Unsoeld -- -------------- */
if (!useBarklem) {
getUnsoldcross(rlk);
}
/* --- Radiative broadening -- -------------- */
if (Grad != 0.0) {
rlk->Grad = POW10(Grad);
} else {
/* --- Just take the Einstein Aji value, but only if either
Stark or vd Waals broadening is in effect -- ------- */
if (GStark != 0.0 || GvdWaals != 0.0)
rlk->Grad = rlk->Aji;
else {
rlk->Grad = 0.0;
/* --- In this case the line is not polarizable because
there is no way to determine its damping -- ------ */
rlk->polarizable = FALSE;
}
}
/* --- Isotope and hyperfine fractions and slpittings -- ---- */
Nread += sscanf(inputLine+106, "%d", &rlk->isotope);
Nread += sscanf(inputLine+108, "%lf", &rlk->isotope_frac);
rlk->isotope_frac = POW10(rlk->isotope_frac);
Nread += sscanf(inputLine+117, "%lf", &rlk->hyperfine_frac);
rlk->hyperfine_frac = POW10(rlk->hyperfine_frac);
Nread += sscanf(inputLine+123, "%5d%5d", &hfs_i, &hfs_j);
rlk->hfs_i = ((double) hfs_i) * MILLI * KBOLTZMANN;
rlk->hfs_j = ((double) hfs_j) * MILLI * KBOLTZMANN;
/* --- Effective Lande factors -- -------------- */
Nread += sscanf(inputLine+143, "%5d%5d", &gL_i, &gL_j);
rlk->gL_i = gL_i * MILLI;
rlk->gL_j = gL_j * MILLI;
if (swap_levels) {
SWAPDOUBLE(rlk->hfs_i, rlk->hfs_j);
SWAPDOUBLE(rlk->gL_i, rlk->gL_j);
}
/* Nread += sscanf(inputLine+154, "%d", &iso_dl); */
iso_dl = 0;
rlk->iso_dl = iso_dl * MILLI * ANGSTROM_TO_NM;
checkNread(Nread, Nrequired=17, routineName, checkPoint=1);
/*
printf(" Line: %f (vacuum), %f (air)\n"
" gi, gj: %f, %f\n"
" Ei, Ej: %e, %e\n"
" Aji: %e\n"
" Grad, GStark, GvdWaals: %e, %e, %e\n"
" VdWaals: %d\n"
" hyperfine_frac, isotope_frac: %f, %f\n"
" cross, alpha: %e, %e\n\n",
rlk->lambda0, lambda_air,
rlk->gi, rlk->gj, rlk->Ei, rlk->Ej, rlk->Aji,
rlk->Grad, rlk->GStark, rlk->GvdWaals,
rlk->vdwaals,
rlk->hyperfine_frac, rlk->isotope_frac,
rlk->cross, rlk->alpha);
*/
rlk++;
}
}
fclose(fp_linelist);
sprintf(messageStr, "Read %d Kurucz lines from file %s\n",
Nline, listName);
Error(MESSAGE, routineName, messageStr);
atmos.Nrlk += Nline;
}
fclose(fp_Kurucz);
free_BS(&bs_SP);
free_BS(&bs_PD);
free_BS(&bs_DF);
}
int main(int argc, char *argv[])
{
register int n, k;
char rayFileName[14], inputLine[MAX_LINE_SIZE];
bool_t result, exit_on_EOF, to_obs, initialize, crosscoupling,
analyze_output, equilibria_only;
int Nspect, Nread, Nrequired, checkPoint, *wave_index = NULL;
double muz, *S, *chi, *J;
FILE *fp_out, *fp_ray, *fp_stokes;
XDR xdrs;
ActiveSet *as;
setOptions(argc, argv);
getCPU(0, TIME_START, NULL);
SetFPEtraps();
/* --- Read input data and initialize -- -------------- */
readInput();
spectrum.updateJ = FALSE;
/* --- Read input data for atmosphere -- -------------- */
getCPU(1, TIME_START, NULL);
MULTIatmos(&atmos, &geometry);
/* --- Read direction cosine for ray -- -------------- */
if ((fp_ray = fopen(RAY_INPUT_FILE, "r")) == NULL) {
sprintf(messageStr, "Unable to open inputfile %s", RAY_INPUT_FILE);
Error(ERROR_LEVEL_2, argv[0], messageStr);
}
getLine(fp_ray, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%lf", &muz);
checkNread(Nread, Nrequired=1, argv[0], checkPoint=1);
if (muz <= 0.0 || muz > 1.0) {
sprintf(messageStr,
"Value of muz = %f does not lie in interval <0.0, 1.0]\n", muz);
Error(ERROR_LEVEL_2, argv[0], messageStr);
}
if (input.StokesMode == FIELD_FREE ||
input.StokesMode == POLARIZATION_FREE) {
input.StokesMode = FULL_STOKES;
}
/* --- redefine geometry for just this one ray -- -------------- */
atmos.Nrays = geometry.Nrays = 1;
geometry.muz[0] = muz;
geometry.mux[0] = sqrt(1.0 - SQ(geometry.muz[0]));
geometry.muy[0] = 0.0;
geometry.wmu[0] = 1.0;
if (atmos.Stokes) Bproject();
input.startJ = OLD_J;
readAtomicModels();
readMolecularModels();
SortLambda();
getBoundary(&geometry);
/* --- Open file with background opacities -- -------------- */
if (atmos.moving || input.StokesMode) {
strcpy(input.background_File, "background.ray");
Background(analyze_output=FALSE, equilibria_only=FALSE);
} else {
Background(analyze_output=FALSE, equilibria_only=TRUE);
if ((atmos.fd_background =
open(input.background_File, O_RDONLY, 0)) == -1) {
sprintf(messageStr, "Unable to open inputfile %s",
input.background_File);
Error(ERROR_LEVEL_2, argv[0], messageStr);
}
readBRS();
}
convertScales(&atmos, &geometry);
getProfiles();
initSolution();
initScatter();
getCPU(1, TIME_POLL, "Total initialize");
/* --- Solve radiative transfer equations -- -------------- */
solveSpectrum(FALSE, FALSE);
/* --- Write emergent spectrum to output file -- -------------- */
sprintf(rayFileName, "spectrum_%4.2f", muz);
if ((fp_out = fopen(rayFileName, "w" )) == NULL) {
sprintf(messageStr, "Unable to open output file %s", rayFileName);
Error(ERROR_LEVEL_2, argv[0], messageStr);
}
xdrstdio_create(&xdrs, fp_out, XDR_ENCODE);
result = xdr_double(&xdrs, &muz);
result = xdr_vector(&xdrs, (char *) spectrum.I[0], spectrum.Nspect,
sizeof(double), (xdrproc_t) xdr_double);
/* --- Read wavelength indices for which chi and S are to be
written out for the specified direction -- -------------- */
Nread = fscanf(fp_ray, "%d", &Nspect);
checkNread(Nread, 1, argv[0], checkPoint=2);
if (Nspect > 0) {
wave_index = (int *) malloc(Nspect * sizeof(int));
Nread = 0;
while (fscanf(fp_ray, "%d", &wave_index[Nread]) != EOF) Nread++;
checkNread(Nread, Nspect, argv[0], checkPoint=3);
fclose(fp_ray);
chi = (double *) malloc(atmos.Nspace * sizeof(double));
if (atmos.Stokes)
S = (double *) malloc(4 * atmos.Nspace * sizeof(double));
else
S = (double *) malloc(atmos.Nspace * sizeof(double));
}
result = xdr_int(&xdrs, &Nspect);
/* --- Go through the list of wavelengths -- -------------- */
if (Nspect > 0 && input.limit_memory)
J = (double *) malloc(atmos.Nspace * sizeof(double));
for (n = 0; n < Nspect; n++) {
if (wave_index[n] < 0 || wave_index[n] >= spectrum.Nspect) {
sprintf(messageStr, "Illegal value of wave_index[n]: %4d\n"
"Value has to be between 0 and %4d\n",
wave_index[n], spectrum.Nspect);
Error(ERROR_LEVEL_2, argv[0], messageStr);
continue;
}
sprintf(messageStr, "Processing n = %4d, lambda = %9.3f [nm]\n",
wave_index[n], spectrum.lambda[wave_index[n]]);
Error(MESSAGE, NULL, messageStr);
as = &spectrum.as[wave_index[n]];
alloc_as(wave_index[n], crosscoupling=FALSE);
Opacity(wave_index[n], 0, to_obs=TRUE, initialize=TRUE);
readBackground(wave_index[n], 0, to_obs=TRUE);
if (input.limit_memory) {
readJlambda(wave_index[n], J);
} else
J = spectrum.J[wave_index[n]];
/* --- Add the continuum opacity and emissivity -- -------------- */
for (k = 0; k < atmos.Nspace; k++) {
chi[k] = as->chi[k] + as->chi_c[k];
S[k] = (as->eta[k] + as->eta_c[k] + as->sca_c[k]*J[k]) / chi[k];
}
result = xdr_int(&xdrs, &wave_index[n]);
result = xdr_vector(&xdrs, (char *) chi, atmos.Nspace,
sizeof(double), (xdrproc_t) xdr_double);
result = xdr_vector(&xdrs, (char *) S, atmos.Nspace,
sizeof(double), (xdrproc_t) xdr_double);
free_as(wave_index[n], crosscoupling=FALSE);
}
/* --- If magnetic fields are present -- -------------- */
if (atmos.Stokes || input.backgr_pol) {
result = xdr_vector(&xdrs, (char *) spectrum.Stokes_Q[0],
spectrum.Nspect, sizeof(double),
(xdrproc_t) xdr_double);
result = xdr_vector(&xdrs, (char *) spectrum.Stokes_U[0],
spectrum.Nspect, sizeof(double),
(xdrproc_t) xdr_double);
result = xdr_vector(&xdrs, (char *) spectrum.Stokes_V[0],
spectrum.Nspect, sizeof(double),
(xdrproc_t) xdr_double);
}
if (Nspect > 0 && input.limit_memory)
free(J);
xdr_destroy(&xdrs);
fclose(fp_out);
printTotalCPU();
}
void MULTIatmos(Atmosphere *atmos, Geometry *geometry)
{
const char routineName[] = "MULTIatmos";
register int k, n, mu;
char scaleStr[20], inputLine[MAX_LINE_SIZE], *filename;
bool_t exit_on_EOF, enhanced_atmos_ID = FALSE;
int Nread, Ndep, Nrequired, checkPoint;
double *dscale, turbpress, turbelecpress, nbaryon, meanweight;
struct stat statBuffer;
getCPU(2, TIME_START, NULL);
/* --- Get abundances of background elements -- ------------ */
readAbundance(atmos);
/* --- Open the input file for model atmosphere in MULTI format - - */
if ((atmos->fp_atmos = fopen(input.atmos_input, "r")) == NULL) {
sprintf(messageStr, "Unable to open inputfile %s", input.atmos_input);
Error(ERROR_LEVEL_2, routineName, messageStr);
} else {
sprintf(messageStr, "\n -- reading input file: %s\n\n",
input.atmos_input);
Error(MESSAGE, NULL, messageStr);
}
atmos->NHydr = N_HYDROGEN_MULTI;
/* --- Boundary condition at TOP of atmosphere -- ------------ */
if (strcmp(input.Itop, "none"))
geometry->vboundary[TOP] = IRRADIATED;
else
geometry->vboundary[TOP] = ZERO;
/* --- Boundary condition at BOTTOM of atmosphere -- ------------ */
geometry->vboundary[BOTTOM] = THERMALIZED;
/* --- Read atmos ID, scale type, gravity, and number of depth
points -- ------------ */
getLine(atmos->fp_atmos, MULTI_COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
if (enhanced_atmos_ID) {
/* --- Construct atmosID from filename and last modification date */
stat(input.atmos_input, &statBuffer);
if ((filename = strrchr(input.atmos_input, '/')) != NULL)
filename++;
else
filename = input.atmos_input;
sprintf(atmos->ID, "%s (%.24s)", filename,
asctime(localtime(&statBuffer.st_mtime)));
Nread = 1;
} else
Nread = sscanf(inputLine, "%s", atmos->ID);
getLine(atmos->fp_atmos, MULTI_COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread += sscanf(inputLine, "%20s", scaleStr);
getLine(atmos->fp_atmos, MULTI_COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread += sscanf(inputLine, "%lf", &atmos->gravity);
getLine(atmos->fp_atmos, MULTI_COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread += sscanf(inputLine, "%d", &geometry->Ndep);
checkNread(Nread, Nrequired=4, routineName, checkPoint=1);
/* --- Keep duplicates of some of the geometrical quantities in
Atmos structure -- -------------- */
atmos->Ndim = 1;
atmos->N = (int *) malloc(atmos->Ndim * sizeof(int));
atmos->Nspace = Ndep = geometry->Ndep;
atmos->N[0] = Ndep;
atmos->gravity = POW10(atmos->gravity) * CM_TO_M;
/* --- Allocate space for arrays that define structure -- --------- */
geometry->tau_ref = (double *) malloc(Ndep * sizeof(double));
geometry->cmass = (double *) malloc(Ndep * sizeof(double));
geometry->height = (double *) malloc(Ndep * sizeof(double));
atmos->T = (double *) malloc(Ndep * sizeof(double));
atmos->ne = (double *) malloc(Ndep * sizeof(double));
atmos->vturb = (double *) malloc(Ndep * sizeof(double));
geometry->vel = (double *) malloc(Ndep * sizeof(double));
dscale = (double *) malloc(Ndep * sizeof(double));
for (k = 0; k < Ndep; k++) {
getLine(atmos->fp_atmos, MULTI_COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%lf %lf %lf %lf %lf",
&dscale[k], &atmos->T[k], &atmos->ne[k],
&geometry->vel[k], &atmos->vturb[k]);
checkNread(Nread, Nrequired=5, routineName, checkPoint=2);
}
switch(toupper(scaleStr[0])) {
case 'M':
geometry->scale = COLUMN_MASS;
for (k = 0; k < Ndep; k++)
geometry->cmass[k] = POW10(dscale[k]) * (G_TO_KG / SQ(CM_TO_M));
break;
case 'T':
geometry->scale = TAU500;
for (k = 0; k < Ndep; k++) geometry->tau_ref[k] = POW10(dscale[k]);
break;
case 'H':
geometry->scale = GEOMETRIC;
for (k = 0; k < Ndep; k++) geometry->height[k] = dscale[k] * KM_TO_M;
break;
default:
sprintf(messageStr, "Unknown depth scale string in file %s: %s",
input.atmos_input, scaleStr);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
free(dscale);
for (k = 0; k < Ndep; k++) {
geometry->vel[k] *= KM_TO_M;
atmos->vturb[k] *= KM_TO_M;
atmos->ne[k] /= CUBE(CM_TO_M);
}
atmos->moving = FALSE;
for (k = 0; k < Ndep; k++) {
if (fabs(geometry->vel[k]) >= atmos->vmacro_tresh) {
atmos->moving = TRUE;
break;
}
}
/* --- Get angle-quadrature and copy geometry independent quantity
wmu to atmos structure. -- -------------- */
getAngleQuad(geometry);
atmos->wmu = geometry->wmu;
/* --- Magnetic field is read here. -- -------------- */
atmos->Stokes = readB(atmos);
/* --- Read Hydrogen populations if present -- -------------- */
atmos->nH = matrix_double(atmos->NHydr, Ndep);
for (k = 0; k < Ndep; k++) {
if (getLine(atmos->fp_atmos, MULTI_COMMENT_CHAR, inputLine,
exit_on_EOF=FALSE) == EOF) break;
Nread = sscanf(inputLine, "%lf %lf %lf %lf %lf %lf",
&atmos->nH[0][k], &atmos->nH[1][k], &atmos->nH[2][k],
&atmos->nH[3][k], &atmos->nH[4][k], &atmos->nH[5][k]);
checkNread(Nread, Nrequired=6, routineName, checkPoint=3);
}
if (k > 0 && k < Ndep) {
sprintf(messageStr,
"Reached end of input file %s before all data was read",
input.atmos_input);
Error(ERROR_LEVEL_2, routineName, messageStr);
} else if (k == 0) {
/* --- No hydrogen populations supplied: use LTE populations
like MULTI does -- -------------- */
if (geometry->scale != COLUMN_MASS) {
sprintf(messageStr,
"Height scale should be COLUMNMASS when nH not supplied: "
"File %s", input.atmos_input);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
atmos->nHtot = (double *) calloc(Ndep, sizeof(double));
atmos->H_LTE = TRUE;
meanweight = atmos->avgMolWght * AMU;
for (k = 0; k < Ndep; k++) {
turbpress = 0.5 * meanweight * SQ(atmos->vturb[k]);
turbelecpress = 0.5 * M_ELECTRON * SQ(atmos->vturb[k]);
nbaryon =
(atmos->gravity * geometry->cmass[k] -
atmos->ne[k] *(KBOLTZMANN * atmos->T[k] + turbelecpress));
atmos->nHtot[k] = nbaryon /
(atmos->totalAbund * (KBOLTZMANN * atmos->T[k] + turbpress));
}
} else if (k == Ndep) {
atmos->nHtot = (double *) calloc(Ndep, sizeof(double));
for (n = 0; n < atmos->NHydr; n++) {
for (k = 0; k < Ndep; k++) {
atmos->nH[n][k] /= CUBE(CM_TO_M);
atmos->nHtot[k] += atmos->nH[n][k];
}
}
}
getCPU(2, TIME_POLL, "Read Atmosphere");
}