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readmolecule.c
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readmolecule.c
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/* ------- file: -------------------------- readmolecule.c ----------
Version: rh2.0
Author: Han Uitenbroek (huitenbroek@nso.edu)
Modified: Wed Oct 12 20:00:35 2011 --
Last Modified: Oct 20, 2017 by serena criscuoli (scriscuo@nso.edu)
Additional electronic transitions for CO and SiO isotopes.
-------------------------- ----------RH-- */
/* --- Reads molecular data file.
In case of an active molecule the populations of the vibrational
levels are determined in Non-LTE, while the rotational levels
within each vibrational level are assumed to be given by their
respective Boltzmann factors -- -------------- */
#include <ctype.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "rh.h"
#include "atom.h"
#include "atmos.h"
#include "spectrum.h"
#include "background.h"
#include "constant.h"
#include "error.h"
#include "inputs.h"
#include "statistics.h"
#define COMMENT_CHAR "#"
#define N_MAX_CONFIG 10
/* --- Special case: C^13 fraction for CO -- -------------- */
#define C_13 0.011
/* --- Special case: Si fractions for SiO -- from Asplund 2009 -------------- */
#define SI_29 0.047
#define SI_30 0.031
/* --- Special case: Si fractions for MgH -- from Asplund 2009 -------------- */
#define MG_25 0.10
#define MG_26 0.11
/* --- Special case: TI fractions for TiO -- -------------- */
#define TI_46 0.08
#define TI_47 0.0743
#define TI_48 0.738
#define TI_49 0.055
#define TI_50 0.054
/* --- Function prototypes -- -------------- */
int countTokens(char *line, char *separator);
int mrt_ascend(const void *v1, const void *v2);
int stringcompare(const void *s1, const void *s2);
char *getMoleculeID(char *molecule_file);
/* --- Global variables -- -------------- */
extern InputData input;
extern Atmosphere atmos;
extern char messageStr[];
/* ------- begin -------------------------- readMolecule.c ---------- */
void readMolecule(Molecule *molecule, char *fileName, bool_t active)
{
const char routineName[] = "readMolecule";
register int k, m, n, kr, la, i;
char inputLine[MAX_LINE_SIZE], fitStr[20], line_data[MAX_LINE_SIZE],
elementID[ATOM_ID_WIDTH+1], *token,
popsFile[MAX_LINE_SIZE], labelStr[MAX_LINE_SIZE];
bool_t exit_on_EOF, match;
int Nread, Nrequired, checkPoint, J_max, v_max, Ji, Jj, nconfig;
double vtherm, dlambda, dlambda_wing, lambda;
FILE *fp_molecule;
MolecularLine *mrt;
getCPU(3, TIME_START, NULL);
/* --- Open the data file for current molecule -- -------------- */
if ((fp_molecule = fopen(fileName, "r")) == NULL) {
sprintf(messageStr, "Unable to open inputfile %s", fileName);
Error(ERROR_LEVEL_2, routineName, messageStr);
} else {
sprintf(messageStr, " -- reading input file: %s %s",
fileName, (active) ? "(active)\n\n" : "(passive)\n");
Error(MESSAGE, routineName, messageStr);
initMolecule(molecule);
}
/* --- Read molecule ID -- -------------- */
getLine(fp_molecule, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%s", molecule->ID);
checkNread(Nread, Nrequired=1, routineName, checkPoint=1);
getLine(fp_molecule, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%d", &molecule->charge);
checkNread(Nread, Nrequired=1, routineName, checkPoint=2);
/* --- We only allow molecules with 0 or +1 charge -- ------------- */
if (molecule->charge < 0 || molecule->charge > 1) {
sprintf(messageStr,
"Only neutral or singly charged positive molecules allowed"
" Molecule: %s", molecule->ID);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Read list of constituent atoms -- -------------- */
getLine(fp_molecule, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
molecule->Nelement = countTokens(inputLine, " ,");
if (molecule->Nelement == 0) {
sprintf(messageStr, "Could not identify constituents for molecule %s\n",
molecule->ID);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
molecule->pt_index =
(int *) malloc(molecule->Nelement * sizeof(int));
molecule->pt_count =
(int *) malloc(molecule->Nelement * sizeof(int));
molecule->Nnuclei = 0;
token = strtok(inputLine, " ,");
for (n = 0; n < molecule->Nelement; n++) {
Nread = sscanf(token, "%d%s", molecule->pt_count+n, elementID);
if (Nread == 0) {
molecule->pt_count[n] = 1;
Nread = sscanf(token, "%s", elementID);
}
UpperCase(elementID);
if (strlen(elementID) == 1) strcat(elementID, " ");
match = FALSE;
for (m = 0; m < atmos.Nelem; m++) {
if (strstr(elementID, atmos.elements[m].ID)) {
if (atmos.elements[m].abundance_set) {
molecule->pt_index[n] = m;
match = TRUE;
}
break;
}
}
if (!match) {
sprintf(messageStr, "Could not find element %s of molecule %s"
" in periodic table, or element abundance not specified\n",
elementID, molecule->ID);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
molecule->Nnuclei += molecule->pt_count[n];
token = strtok(NULL, " ,");
}
/* --- Read dissociation energy in eV, convert to Joule -- ------- */
getLine(fp_molecule, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%lf", &molecule->Ediss);
checkNread(Nread, Nrequired=1, routineName, checkPoint=3);
molecule->Ediss *= EV;
/* --- Read identification string for type of temperature fit for
partition function and molecular equilibrium constant -- -- */
getLine(fp_molecule, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%s", fitStr);
checkNread(Nread, Nrequired=1, routineName, checkPoint=4);
if (strstr(fitStr, "KURUCZ_70"))
molecule->fit = KURUCZ_70;
else if (strstr(fitStr, "KURUCZ_85"))
molecule->fit = KURUCZ_85;
else if (strstr(fitStr, "SAUVAL_TATUM_84"))
molecule->fit = SAUVAL_TATUM_84;
else if (strstr(fitStr, "IRWIN_81"))
molecule->fit = IRWIN_81;
else if (strstr(fitStr, "TSUJI_73"))
molecule->fit = TSUJI_73;
else {
sprintf(messageStr, "Unable to regognize keyword %s in file %s",
fitStr, fileName);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Charged molecules can only be in KURUCZ_{70,85} format -- -- *
if (molecule->charge > 0) {
if (molecule->fit != KURUCZ_70 && molecule->fit != KURUCZ_85) {
sprintf(messageStr,
"Positively charged molecules MUST be in format:\n"
" KURUCZ_70 or\n KURUCZ_85. Molecule: %s", molecule->ID);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
}
* --- Read minimum and maximum formation temperature -- ---------- */
getLine(fp_molecule, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%lf %lf", &molecule->Tmin, &molecule->Tmax);
checkNread(Nread, Nrequired=2, routineName, checkPoint=5);
/* --- Get fit parameters for partition function -- -------------- */
getLine(fp_molecule, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(strtok(inputLine, " "), "%d", &molecule->Npf);
if (molecule->Npf > 0) {
molecule->pf_coef = (double *) malloc(molecule->Npf * sizeof(double));
for (n = molecule->Npf-1; n >= 0; n--)
Nread += sscanf(strtok(NULL, " "), "%lf", molecule->pf_coef+n);
checkNread(Nread, molecule->Npf+1, routineName, checkPoint=6);
}
molecule->pf = (double *) malloc(atmos.Nspace * sizeof(double));
/* --- Get fit parameters for equilibrium constant -- ------------- */
getLine(fp_molecule, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(strtok(inputLine, " "), "%d", &molecule->Neqc);
if (molecule->Neqc > 0) {
molecule->eqc_coef = (double *) malloc(molecule->Neqc * sizeof(double));
for (n = molecule->Neqc-1; n >= 0; n--)
Nread += sscanf(strtok(NULL, " "), "%lf", molecule->eqc_coef+n);
checkNread(Nread, molecule->Neqc+1, routineName, checkPoint=7);
}
/* --- Get molecular weight from composing atoms and calculate
broadening velocity -- -------------- */
molecule->weight = 0.0;
for (n = 0; n < molecule->Nelement; n++)
molecule->weight += molecule->pt_count[n] *
atmos.elements[molecule->pt_index[n]].weight;
/* --- Allocate memory for total population numbers, broadening
velocity and partition function -- -------------- */
molecule->n = (double *) malloc(atmos.Nspace * sizeof(double));
molecule->vbroad = (double *) malloc(atmos.Nspace * sizeof(double));
vtherm = 2.0*KBOLTZMANN / (AMU * molecule->weight);
for (k = 0; k < atmos.Nspace; k++)
molecule->vbroad[k] = sqrt(vtherm*atmos.T[k] + SQ(atmos.vturb[k]));
/* --- Collect the line transitions from separate data files -- --- */
while (getLine(fp_molecule, COMMENT_CHAR, inputLine,
exit_on_EOF=FALSE) != EOF) {
Nread = sscanf(inputLine, "%s", line_data);
readMolecularLines(molecule, line_data);
}
/* --- Sort transitions within each molecule in wavelength -- ----- */
qsort(molecule->mrt, molecule->Nrt, sizeof(MolecularLine), mrt_ascend);
if (active) {
if (molecule->Nrt == 0) {
sprintf(messageStr, " No lines specified for active molecule %s\n",
molecule->ID);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
molecule->active = TRUE;
/* --- This particular implementation is for the case where the
rotational levels in each vibrational level are assumed to
have LTE ratio's. -- -------------- */
v_max = 0;
J_max = 0;
nconfig = 0;
molecule->configs = (char *) malloc(N_MAX_CONFIG * sizeof(char));
molecule->configs[0] = molecule->mrt[0].configi[0];
molecule->mrt[0].ecnoi = nconfig++;
for (kr = 0; kr < molecule->Nrt; kr++) {
mrt = molecule->mrt + kr;
v_max = MAX(v_max, MAX(mrt->vi, mrt->vj));
Ji = (int) ((mrt->gi - 1) / 2);
Jj = (int) ((mrt->gj - 1) / 2);
J_max = MAX(J_max, MAX(Ji, Jj));
/* --- Collect the unique electronic configurations -- -- */
match = FALSE;
for (i = 0; i < nconfig; i++) {
if (mrt->configi[0] == molecule->configs[i]) {
match = TRUE;
break;
}
}
if (!match) {
if (nconfig == N_MAX_CONFIG) {
sprintf(messageStr, "nconfig = %d > N_MAX_CONFIG", nconfig + 1);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
molecule->configs[nconfig] = mrt->configi[0];
mrt->ecnoi = nconfig++;
}
match = FALSE;
for (i = 0; i < nconfig; i++) {
if (mrt->configj[0] == molecule->configs[i]) {
match = TRUE;
break;
}
}
if (!match) {
if (nconfig == N_MAX_CONFIG) {
sprintf(messageStr, "nconfig = %d > N_MAX_CONFIG", nconfig + 1);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
molecule->configs[nconfig] = mrt->configj[0];
mrt->ecnoj = nconfig++;
}
}
molecule->NJ = J_max + 1;
molecule->Nv = v_max + 1;
molecule->Nconfig = nconfig;
molecule->configs = (char *) realloc(molecule->configs,
(molecule->Nconfig + 1) * sizeof(char));
molecule->configs[molecule->Nconfig] = '\0';
sprintf(messageStr,
" --- Found %d electronic configurations for molecule %s: %s\n\n",
molecule->Nconfig, molecule->ID, molecule->configs);
Error(MESSAGE, routineName, messageStr);
/* --- Allocate memory for the populations of each vibrational
state in each electronic configuration. Within each of these
the rotational states will be assumed to be in LTE -- --- */
molecule->nv = matrix_double(molecule->Nv * molecule->Nconfig,
atmos.Nspace);
molecule->nvstar = matrix_double(molecule->Nv * molecule->Nconfig,
atmos.Nspace);
molecule->pfv = matrix_double(molecule->Nv * molecule->Nconfig,
atmos.Nspace);
sprintf(popsFile, "pops_mol.%s.out", molecule->ID);
molecule->popsFile =
(char *) malloc((strlen(popsFile) + 1) * sizeof(char));
strcpy(molecule->popsFile, popsFile);
/* --- In this case vibrational partition functions for the molecule
and each of its vibrational states are calculated in routine
LTEmolecule -- -------------- */
LTEmolecule(molecule);
} else {
if (molecule->Npf > 0) {
/* --- Otherwise, the total partition function is interpolated
from a polynomial in T -- -------------- */
for (k = 0; k < atmos.Nspace; k++)
molecule->pf[k] = partfunction(molecule, atmos.T[k]);
}
}
/* --- Get wavelength grid for each line if active -- ------------- */
if (molecule->active) {
for (kr = 0; kr < molecule->Nrt; kr++) {
mrt = &molecule->mrt[kr];
dlambda_wing = mrt->qwing * atmos.vmicro_char / CLIGHT;
dlambda = 2.0*dlambda_wing * mrt->lambda0 / (mrt->Nlambda - 1);
mrt->lambda = (double *) malloc(mrt->Nlambda * sizeof(double));
lambda = mrt->lambda0 * (1.0 - dlambda_wing);
for (la = 0; la < mrt->Nlambda; la++) {
mrt->lambda[la] = lambda;
lambda += dlambda;
}
}
/* --- Allocate space for thread dependent quantities -- -------- */
molecule->rhth =
(rhthread *) malloc(input.Nthreads * sizeof(rhthread));
}
fclose(fp_molecule);
sprintf(labelStr, "Read %s %3s",
(molecule->active) ? "Active" : "Molecule", molecule->ID);
getCPU(3, TIME_POLL, labelStr);
}
/* ------- end ---------------------------- readMolecule.c ---------- */
/* ------- begin -------------------------- initMolecule.c ---------- */
void initMolecule(Molecule *molecule)
{
molecule->popsFile = NULL;
molecule->active = FALSE;
molecule->fit = KURUCZ_70;
molecule->pt_index = molecule->pt_count = 0;
molecule->Nelement = molecule->Nnuclei = 0;
molecule->Npf = molecule->Neqc = molecule->Nrt = 0;
molecule->charge = 0;
molecule->Nv = molecule->NJ = 0;
molecule->Nconfig = 0;
molecule->Ediss = molecule->Tmin = molecule->Tmax = molecule->weight = 0.0;
molecule->vbroad = NULL;
molecule->pf_coef = molecule->eqc_coef = molecule->pf = NULL;
molecule->pfv = NULL;
molecule->initial_solution = UNKNOWN;
molecule->n = NULL;
molecule->nv = molecule->nvstar = NULL;
molecule->C_ul = NULL;
molecule->Gamma = NULL;
molecule->mrt = NULL;
molecule->Ng_nv = NULL;
}
/* ------- end ---------------------------- initMolecule.c ---------- */
/* ------- begin -------------------------- freeMolecule.c ---------- */
void freeMolecule(Molecule *molecule)
{
register int kr;
if (molecule->pt_index != NULL) free(molecule->pt_index);
if (molecule->pt_count != NULL) free(molecule->pt_count);
if (molecule->vbroad != NULL) free(molecule->vbroad);
if (molecule->pf_coef != NULL) free(molecule->pf_coef);
if (molecule->eqc_coef != NULL) free(molecule->eqc_coef);
if (molecule->pf != NULL) free(molecule->pf);
if (molecule->pfv != NULL) freeMatrix((void **) molecule->pfv);
if (molecule->n != NULL) free(molecule->n);
if (molecule->nv != NULL) freeMatrix((void **) molecule->nv);
if (molecule->nvstar != NULL) freeMatrix((void **) molecule->nvstar);
if (molecule->C_ul != NULL) free(molecule->C_ul);
if (molecule->Gamma != NULL) freeMatrix((void **) molecule->Gamma);
if (molecule->mrt != NULL) {
for (kr = 0; kr < molecule->Nrt; kr++)
freeMolLine(molecule->mrt + kr);
free(molecule->mrt);
}
}
/* ------- end ---------------------------- freeMolecule.c ---------- */
/* ------- begin -------------------------- initMolLine.c ----------- */
void initMolLine(MolecularLine *mrt, enum type line_type)
{
/* --- Initialize transition data structure. Set pointers to NULL - */
mrt->type = line_type;
mrt->configi[0] = mrt->configj[0] = '\0';
mrt->symmetric = TRUE;
mrt->Voigt = TRUE;
mrt->vi = mrt->vj = 0;
mrt->Nlambda = mrt->Nblue = 0;
mrt->lambda0 = mrt->isotope_frac = 0.0;
mrt->lambda = NULL;
mrt->phi = NULL;
mrt->wphi = NULL;
mrt->Ei = mrt->Ej = mrt->gi = mrt->gj = 0.0;
mrt->Grad = mrt->qwing = mrt->qcore = 0.0;
mrt->Aji = mrt->Bji = mrt->Bij = 0.0;
mrt->polarizable = FALSE;
mrt->molecule = NULL;
mrt->zm = NULL;
mrt->g_Lande_eff = 0.0;
}
/* ------- end ---------------------------- initMolLine.c ----------- */
/* ------- begin -------------------------- freeMolLine.c ----------- */
void freeMolLine(MolecularLine *mrt)
{
/* --- Free allocated memory for active transition structure line - */
if (mrt->lambda != NULL) free(mrt->lambda);
if (mrt->phi != NULL) freeMatrix((void **) mrt->phi);
if (mrt->wphi != NULL) free(mrt->wphi);
mrt->molecule = NULL;
if (mrt->zm != NULL) {
free(mrt->zm->q);
free(mrt->zm->strength);
free(mrt->zm->shift);
}
free(mrt->zm);
mrt->zm = NULL;
}
/* ------- end ---------------------------- freeMolLine.c ----------- */
/* ------- begin -------------------------- mrt_ascend.c ------------ */
int mrt_ascend(const void *v1, const void *v2)
{
double f1, f2;
/* --- Used for sorting molecular transitions by wavelength -- ---- */
f1 = ((MolecularLine *) v1)->lambda0;
f2 = ((MolecularLine *) v2)->lambda0;
if (f1 < f2)
return -1;
else if (f1 > f2)
return 1;
else
return 0;
}
/* ------- end ---------------------------- mrt_ascend.c ------------ */
/* ------- begin -------------------------- stringcompare.c --------- */
int stringcompare(const void *s1, const void *s2)
{
/* --- Wrapper around strcmp to get the proper prototype for the
comparing function (ie., with void rather than char
parameters). -- -------------- */
return strcmp((const char *) s1, (const char *) s2);
}
/* ------- end ---------------------------- stringcompare.c --------- */
/* ------- begin -------------------------- readMolecularLines.c ---- */
/* --- Reads molecular line data and computes molecular opacities.
Recognized formats:
-- GOORVITCH94:
CO line data in the format of D. Goorvitch 1994, ApJS 95, 535
(vibration-rotation transitions of the X configuration).
-- KURUCZ_CD18:
Molecular line data from Bob Kurucz's CD 18
203.6264 -7.917 2.5 83.924 2.5 -49177.701 108X00F1 A07E1 16
| | | | | | | | | | | | | | | |
0 5 10 20 30 40 50 60 70
The numbers mean:
203.6264 -- Wavelength [nm]
-7.917 -- log(gf) value
2.5 -- J first level (usually lower level)
83.924 -- Energy first level (- indicates predicted, + observed)
in units of [cm^-1]
2.5 -- J second level (usually upper level)
-49177.701 -- Energy second level [cm^-1]
108X00F1 -- Molecule ID (OH in this case) plus ID first level:
X configuration, vibration level 0, F parity
A07E1 -- ID second level: A configuration, vibration level 7,
parity E
16 -- Isotope ID (16 refers to O16 in this case)
-- KURUCZ_TIO
Molecular line list for TiO molecules
708.9002 -1.213 68.0 9920.304 67.0 24022.776822a04p1 b08m1 46
| | | | | | | | | | | | | | | |
0 5 10 20 30 40 50 60 70
Meaning of the numbers as above.
Parity translation p --> E, and m --> F, for the orbital angular
momentum pointing parallel or anti-parallel to the internuclear axis.
-- -------------- */
void readMolecularLines(struct Molecule *molecule, char *line_data)
{
const char routineName[] = "readMolecularLines";
register int kr;
char inputLine[MAX_LINE_SIZE], branchStr[2], type_string[25],
format_string[15], Lambdai[2], Lambdaj[2], Hundi[2], Hundj[2];
bool_t exit_on_EOF;
enum type line_type;
int Nrt, Nread, Nrequired, checkPoint, isotope, Nlambda, Ji, Jj;
double dipole, C, strength, gf, qwing, lambda_air, log_gf, lambda0;
FILE *fp_lines;
MolecularLine *mrt;
C = 2.0*PI * (Q_ELECTRON/EPSILON_0) * (Q_ELECTRON/M_ELECTRON) / CLIGHT;
/* --- Open the data file -- -------------- */
if ((fp_lines = fopen(line_data, "r")) == NULL) {
sprintf(messageStr, "Unable to open inputfile %s", line_data);
Error(ERROR_LEVEL_2, routineName, messageStr);
} else {
sprintf(messageStr, " -- reading input file: %s\n", line_data);
Error(MESSAGE,routineName, messageStr);
}
/* --- Get count, type, and format of the lines in this file -- -- */
getLine(fp_lines, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%d %s %s", &Nrt,
type_string, format_string);
checkNread(Nread, Nrequired=3, routineName, checkPoint=1);
if (strstr(type_string, "VIBRATION_ROTATION"))
line_type = VIBRATION_ROTATION;
else if (strstr(type_string, "MOLECULAR_ELECTRONIC"))
line_type = MOLECULAR_ELECTRONIC;
else {
sprintf(messageStr, "Unknown molecular line type: %s", type_string);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
molecule->mrt = (MolecularLine *)
realloc(molecule->mrt, (molecule->Nrt + Nrt) * sizeof(MolecularLine));
getLine(fp_lines, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%d %lf", &Nlambda, &qwing);
checkNread(Nread, Nrequired=2, routineName, checkPoint=2);
/* --- Read line data line by line -- -------------- */
if (strstr(format_string, "GOORVITCH94")) {
for (kr = molecule->Nrt; kr < molecule->Nrt + Nrt; kr++) {
mrt = molecule->mrt + kr;
initMolLine(mrt, VIBRATION_ROTATION);
mrt->molecule = molecule;
strcpy(mrt->configi, "X");
strcpy(mrt->configj, "X");
mrt->Nlambda = Nlambda;
mrt->qwing = qwing;
getLine(fp_lines, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
Nread = sscanf(inputLine, "%lf %lf %lf %lf %lf %lf %d %d %s %d %d",
&mrt->lambda0, &dipole, &mrt->Aji, &mrt->Ei, &gf,
&strength, &mrt->vj, &mrt->vi, branchStr, &Ji,
&isotope);
checkNread(Nread, Nrequired=11, routineName, checkPoint=3);
mrt->lambda0 = (CM_TO_M / NM_TO_M) / mrt->lambda0;
mrt->Ei *= (HPLANCK * CLIGHT) / CM_TO_M;
mrt->Ej = mrt->Ei + HPLANCK*CLIGHT / (mrt->lambda0 * NM_TO_M);
mrt->gi = 2*Ji + 1;
switch (branchStr[0]) {
case 'P':
Jj = Ji - 1;
break;
case 'Q':
Jj = Ji;
break;
case 'R':
Jj = Ji + 1;
break;
default:
sprintf(messageStr, "Invalid value of branch stringin file %s: %s\n"
" Line: %f [nm]\n Valid options are P, R and Q",
line_data, branchStr, mrt->lambda0);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
mrt->gj = 2*Jj + 1;
mrt->Bji = CUBE(mrt->lambda0*NM_TO_M) /
(2.0*HPLANCK*CLIGHT) * mrt->Aji;
mrt->Bij = (mrt->gj / mrt->gi) * mrt->Bji;
/* --- Temporary measure to accommodate $^13$CO -- ------------ */
switch (isotope) {
case 12:
case 26: mrt->isotope_frac = 1.0 - C_13; break;
case 13:
case 36: mrt->isotope_frac = C_13; break;
default: mrt->isotope_frac = 1.0;
}
}
mrt->polarizable = FALSE;
} else if (strstr(format_string, "KURUCZ_CD18") ||
strstr(format_string, "KURUCZ_NEW") ||
strstr(format_string, "KURUCZ_SIO") ||
strstr(format_string, "KURUCZ_CN") ||
strstr(format_string, "KURUCZ_CH") ||
strstr(format_string, "KURUCZ_CO") ||
strstr(format_string, "KURUCZ_C2") ||
strstr(format_string, "KURUCZ_MGH") ||
strstr(format_string, "KURUCZ_TIO")) {
C = 2 * PI * (Q_ELECTRON/EPSILON_0) * (Q_ELECTRON/M_ELECTRON) / CLIGHT;
for (kr = molecule->Nrt; kr < molecule->Nrt + Nrt; kr++) {
mrt = &molecule->mrt[kr];
initMolLine(mrt, line_type);
mrt->molecule = molecule;
mrt->Nlambda = Nlambda;
mrt->qwing = qwing;
mrt->isotope_frac = 1.0;
getLine(fp_lines, COMMENT_CHAR, inputLine, exit_on_EOF=TRUE);
if (strstr(format_string, "KURUCZ_TIO")) {
Nread = sscanf(inputLine,
"%10lf %7lf %5lf %10lf %5lf %10lf",
&lambda_air, &log_gf,
&mrt->gi, &mrt->Ei, &mrt->gj, &mrt->Ej);
} else {
Nread = sscanf(inputLine,
"%10lf %7lf %5lf %10lf %5lf %11lf",
&lambda_air, &log_gf,
&mrt->gi, &mrt->Ei, &mrt->gj, &mrt->Ej);
}
checkNread(Nread, Nrequired=6, routineName, checkPoint=3);
mrt->Ei = (HPLANCK * CLIGHT) / CM_TO_M * fabs(mrt->Ei);
mrt->Ej = (HPLANCK * CLIGHT) / CM_TO_M * fabs(mrt->Ej);
mrt->gi = 2*mrt->gi + 1;
mrt->gj = 2*mrt->gj + 1;
lambda0 = (HPLANCK * CLIGHT) / (mrt->Ej - mrt->Ei);
mrt->Aji = C / SQ(lambda0) * POW10(log_gf)/mrt->gj;
mrt->Bji = CUBE(lambda0) / (2.0 * HPLANCK * CLIGHT) * mrt->Aji;
mrt->Bij = (mrt->gj / mrt->gi) * mrt->Bji;
mrt->lambda0 = lambda0 / NM_TO_M;
if (strstr(format_string, "KURUCZ_CD18")) {
/* --- Electronic configuration -- -------------- */
mrt->configi[0] = inputLine[52];
mrt->configj[0] = inputLine[60];
mrt->configi[1] = '\0';
mrt->configj[1] = '\0';
/* --- Parity designation -- -------------- */
mrt->parityi[0] = inputLine[55];
mrt->parityj[0] = inputLine[63];
mrt->parityi[1] = '\0';
mrt->parityj[1] = '\0';
/* --- Vibrational quantum numbers -- ------------ */
Nread = sscanf(inputLine+53, "%2d", &mrt->vi);
Nread = sscanf(inputLine+61, "%2d", &mrt->vj);
/* --- Subbranch (F1, F2, ...., E1, E2, ...etc) -- ---------- */
Nread = sscanf(inputLine+56, "%1d", &mrt->subi);
Nread = sscanf(inputLine+64, "%1d", &mrt->subj);
} else if (strstr(format_string, "KURUCZ_NEW")) {
/* --- Electronic configuration -- -------------- */
strncpy(mrt->configi, inputLine+52, 2);
strncpy(mrt->configj, inputLine+60, 2);
mrt->configi[2] = '\0';
mrt->configj[2] = '\0';
/* --- Parity designation -- -------------- */
mrt->parityi[0] = inputLine[56];
mrt->parityj[0] = inputLine[64];
mrt->parityi[1] = '\0';
mrt->parityj[1] = '\0';
/* --- Vibrational quantum numbers -- ------------ */
Nread = sscanf(inputLine+54, "%2d", &mrt->vi);
Nread = sscanf(inputLine+62, "%2d", &mrt->vj);
/* --- Subbranch (F1, F2, ...., E1, E2, ...etc) -- ---------- */
Nread = sscanf(inputLine+57, "%1d", &mrt->subi);
Nread = sscanf(inputLine+65, "%1d", &mrt->subj);
} else if (strstr(format_string, "KURUCZ_CN") ||
strstr(format_string, "KURUCZ_CH") ||
strstr(format_string, "KURUCZ_C2") ||
strstr(format_string, "KURUCZ_CO")) {
/* --- Electronic configuration -- -------------- */
strncpy(mrt->configi, inputLine+52, 2);
strncpy(mrt->configj, inputLine+60, 2);
mrt->configi[2] = '\0';
mrt->configj[2] = '\0';
/* --- Parity designation -- -------------- */
mrt->parityi[0] = inputLine[56];
mrt->parityj[0] = inputLine[64];
mrt->parityi[1] = '\0';
mrt->parityj[1] = '\0';
/* --- Vibrational quantum numbers -- ------------ */
Nread = sscanf(inputLine+54, "%2d", &mrt->vi);
Nread = sscanf(inputLine+62, "%2d", &mrt->vj);
/* --- Subbranch (F1, F2, ...., E1, E2, ...etc) -- ---------- */
Nread = sscanf(inputLine+57, "%1d", &mrt->subi);
Nread = sscanf(inputLine+65, "%1d", &mrt->subj);
Nread = sscanf(inputLine+67, "%2d", &isotope);
switch (isotope) {
case 13: mrt->isotope_frac = C_13; break;
default: mrt->isotope_frac = 1.0;
}
} else if (strstr(format_string, "KURUCZ_SIO")) {
/* --- Electronic configuration -- -------------- */
strncpy(mrt->configi, inputLine+52, 2);
strncpy(mrt->configj, inputLine+60, 2);
mrt->configi[2] = '\0';
mrt->configj[2] = '\0';
/* --- Parity designation -- -------------- */
mrt->parityi[0] = inputLine[56];
mrt->parityj[0] = inputLine[64];
mrt->parityi[1] = '\0';
mrt->parityj[1] = '\0';
/* --- Vibrational quantum numbers -- ------------ */
Nread = sscanf(inputLine+54, "%2d", &mrt->vi);
Nread = sscanf(inputLine+62, "%2d", &mrt->vj);
/* --- Subbranch (F1, F2, ...., E1, E2, ...etc) -- ---------- */
Nread = sscanf(inputLine+57, "%1d", &mrt->subi);
Nread = sscanf(inputLine+65, "%1d", &mrt->subj);
/* --- Isotope fraction for Si -- ------------ */
Nread = sscanf(inputLine+67, "%2d", &isotope);
switch (isotope) {
case 29: mrt->isotope_frac = SI_29; break;
case 30: mrt->isotope_frac = SI_30; break;
default: mrt->isotope_frac = 1.0;
}
} else if (strstr(format_string, "KURUCZ_MGH")) {
/* --- Electronic configuration -- -------------- */
strncpy(mrt->configi, inputLine+52, 2);
strncpy(mrt->configj, inputLine+60, 2);
mrt->configi[2] = '\0';
mrt->configj[2] = '\0';
/* --- Parity designation -- -------------- */
mrt->parityi[0] = inputLine[56];
mrt->parityj[0] = inputLine[64];
mrt->parityi[1] = '\0';
mrt->parityj[1] = '\0';
/* --- Vibrational quantum numbers -- ------------ */
Nread = sscanf(inputLine+54, "%2d", &mrt->vi);
Nread = sscanf(inputLine+62, "%2d", &mrt->vj);
/* --- Subbranch (F1, F2, ...., E1, E2, ...etc) -- ---------- */
Nread = sscanf(inputLine+57, "%1d", &mrt->subi);
Nread = sscanf(inputLine+65, "%1d", &mrt->subj);
/* --- Isotope fraction for Si -- ------------ */
Nread = sscanf(inputLine+67, "%2d", &isotope);
switch (isotope) {
case 25: mrt->isotope_frac = MG_25; break;
case 26: mrt->isotope_frac = MG_26; break;
default: mrt->isotope_frac = 1.0;
}
} else if (strstr(format_string, "KURUCZ_TIO")) {
/* --- Electronic configuration -- -------------- */
strncpy(mrt->configi, inputLine+50, 2);
strncpy(mrt->configj, inputLine+59, 2);
mrt->configi[2] = '\0';
mrt->configj[2] = '\0';
/* --- Parity designation -- -------------- */
mrt->parityi[0] = ((inputLine[53] == 'p') ? 'E' : 'F');
mrt->parityj[0] = ((inputLine[61] == 'p') ? 'E' : 'F');
mrt->parityi[1] = '\0';
mrt->parityj[1] = '\0';
/* --- Vibrational quantum numbers -- ------------ */
Nread = sscanf(inputLine+51, "%2d", &mrt->vi);
Nread = sscanf(inputLine+59, "%2d", &mrt->vj);
/* --- Subbranch (F1, F2, ...., E1, E2, ...etc) -- ---------- */
Nread = sscanf(inputLine+54, "%1d", &mrt->subi);
Nread = sscanf(inputLine+62, "%1d", &mrt->subj);
/* --- Isotope fraction for Ti -- ------------ */
Nread = sscanf(inputLine+66, "%2d", &isotope);
switch (isotope) {
case 46: mrt->isotope_frac = TI_46; break;
case 47: mrt->isotope_frac = TI_47; break;
case 48: mrt->isotope_frac = TI_48; break;
case 49: mrt->isotope_frac = TI_49; break;
case 50: mrt->isotope_frac = TI_50; break;
default: mrt->isotope_frac = 1.0;
}
}
/* --- read additional data for Zeeman polarization -- -------- */
if (strlen(inputLine) > 71) {
Nread = sscanf(inputLine+71, "%1s %1s %lf %1s %1s %lf",
Hundi, Lambdai, &mrt->Si,
Hundj, Lambdaj, &mrt->Sj);
/* --- Determine the coupling case according to Hund -- ----- */
switch (Hundi[0]) {
case 'A': mrt->Hundi = CASE_A; break;
case 'B': mrt->Hundi = CASE_B; break;
default:
sprintf(messageStr, "Unsupported Hund's case: %s\n", Hundi);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
switch (Hundj[0]) {
case 'A': mrt->Hundj = CASE_A; break;
case 'B': mrt->Hundj = CASE_B; break;
default:
sprintf(messageStr, "Unsupported Hund's case: %s\n", Hundj);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Orbital angular momemtum Lambda along nuclear axis
S --> Sigma
P --> Pi
D --> Delta
F --> Phi
-- -------------- */
switch (Lambdai[0]) {
case 'S': mrt->Lambdai = 0; break;
case 'P': mrt->Lambdai = 1; break;
case 'D': mrt->Lambdai = 2; break;
case 'F': mrt->Lambdai = 3; break;
default:
sprintf(messageStr,
"Unsupported orbital projection Lambda: %s\n", Lambdai);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
switch (Lambdaj[0]) {
case 'S': mrt->Lambdaj = 0; break;
case 'P': mrt->Lambdaj = 1; break;
case 'D': mrt->Lambdaj = 2; break;
case 'F': mrt->Lambdaj = 3; break;
default:
sprintf(messageStr,
"Unsupported orbital projection Lambda: %s\n", Lambdaj);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
/* --- Set the polarized flag only if the atmosphere has magnetic
fields -- -------------- */
if (atmos.Stokes) mrt->polarizable = TRUE;
} else
mrt->polarizable = FALSE;
}
} else {
sprintf(messageStr, "Unknown molecular line format: %s", format_string);
Error(ERROR_LEVEL_2, routineName, messageStr);
}
molecule->Nrt += Nrt;
fclose(fp_lines);
sprintf(messageStr, " --- read %d %s lines for molecule %2s\n\n",