commit 31f5415ad97b4553a015099dc634a63bbe1b8d9f
parent 0d1212b9bba3dfa7589772b0beca126530e1a852
Author: Vincent Forest <vincent.forest@meso-star.com>
Date: Fri, 26 Jun 2026 16:20:07 +0200
Merge branch 'release_0.1'
Diffstat:
6 files changed, 63 insertions(+), 18 deletions(-)
diff --git a/README.md b/README.md
@@ -19,6 +19,13 @@ Edit config.mk as needed, then run:
## Release notes
+### Version 0.1
+
+- Add support for the molecules `H3+`, `CH3`, `S2`, `COFCl`, `HONO`, and
+ `ClNO2`.
+- Fix a library crash that occurred when the metadata list contained
+ unrecognized molecules.
+
### Version 0.0
- Initial version of the library for loading metadata and spectroscopic
diff --git a/config.mk b/config.mk
@@ -1,4 +1,4 @@
-VERSION = 0.0
+VERSION = 0.1
PREFIX = /usr/local
BINPREFIX = $(PREFIX)/bin
diff --git a/src/shtr.h b/src/shtr.h
@@ -60,7 +60,8 @@ enum shtr_molecule_id {
SHTR_HOBr, SHTR_C2H4, SHTR_CH3OH, SHTR_CH3Br, SHTR_CH3CN, SHTR_CF4,
SHTR_C4H2, SHTR_HC3N, SHTR_H2, SHTR_CS, SHTR_SO3, SHTR_C2N2,
SHTR_COCl2, SHTR_SO, SHTR_CH3F, SHTR_GeH4, SHTR_CS2, SHTR_CH3I,
- SHTR_NF3,
+ SHTR_NF3, SHTR_H3plus, SHTR_CH3, SHTR_S2, SHTR_COFCl, SHTR_HONO,
+ SHTR_ClNO2,
SHTR_MAX_MOLECULE_COUNT
};
@@ -78,7 +79,8 @@ static const char* SHTR_MOLECULE_CSTR__[SHTR_MAX_MOLECULE_COUNT] = {
"HOBr", "C2H4", "CH3OH", "CH3Br", "CH3CN", "CF4",
"C4H2", "HC3N", "H2", "CS", "SO3", "C2N2",
"COCl2", "SO", "CH3F", "GeH4", "CS2", "CH3I",
- "NF3"
+ "NF3", "H3+", "CH3", "S2", "COFCl", "HONO",
+ "ClNO2"
};
static INLINE const char*
diff --git a/src/shtr_isotope_metadata.c b/src/shtr_isotope_metadata.c
@@ -46,7 +46,8 @@ struct molecule {
size_t isotopes_range[2]; /* Range of the [1st and last[ isotopes */
int id; /* Unique identifier of the molecule */
};
-#define MOLECULE_IS_VALID(Molecule) ((Molecule)->id >= 0)
+#define MOLECULE_IS_VALID(Molecule) \
+ (((Molecule)->id > 0) && ((Molecule)->id < SHTR_MAX_MOLECULE_COUNT))
static INLINE void
molecule_clear(struct molecule* molecule)
@@ -155,7 +156,6 @@ flush_molecule
{
size_t nisotopes = 0;
size_t ientry = SIZE_MAX;
- size_t* pimolecule = NULL;
res_T res = RES_OK;
ASSERT(metadata && molecule && MOLECULE_IS_VALID(molecule));
@@ -195,16 +195,9 @@ flush_molecule
/* Register the molecule */
if(metadata->molid2idx[molecule->id] >= 0) {
- const struct molecule* molecule2 = NULL;
- molecule2 = darray_molecule_cdata_get(&metadata->molecules) + *pimolecule;
- ERROR(metadata->shtr,
- "%s: cannot register the %s molecule. "
- "The %s molecule has the same identifier %i.\n",
- txtrdr_get_name(txtrdr),
- str_cget(&molecule->name),
- str_cget(&molecule2->name),
- molecule->id);
- res = RES_OK;
+ ERROR(metadata->shtr, "%s: the molecule %s appears several times.\n",
+ txtrdr_get_name(txtrdr), str_cget(&molecule->name));
+ res = RES_BAD_ARG;
goto error;
}
ASSERT((size_t)((int)ientry) == ientry);
@@ -246,7 +239,7 @@ parse_molecule
res = str_set(&molecule->name, name);
if(res != RES_OK) {
ERROR(metadata->shtr,
- "%s:%lu: error seting the molecule name `%s' -- %s.\n",
+ "%s:%lu: error setting the molecule name `%s' -- %s.\n",
txtrdr_get_name(txtrdr), (unsigned long)txtrdr_get_line_num(txtrdr),
name, res_to_cstr(res));
goto error;
@@ -263,14 +256,33 @@ parse_molecule
id[len-1] = '\0'; /* Rm trailing parenthesis */
res = cstr_to_int(id+1/*Rm leading parenthesis*/, &molecule->id);
- if(res != RES_OK || !MOLECULE_IS_VALID(molecule)) {
+ if(res != RES_OK) {
id[len-1] = ')'; /* Re-add the trailing parenthesis */
- ERROR(metadata->shtr, "%s:%lu: invalid molecule identifier `%s'.\n",
+ ERROR(metadata->shtr,
+ "%s:%lu: invalid molecule identifier `%s'.\n",
txtrdr_get_name(txtrdr), (unsigned long)txtrdr_get_line_num(txtrdr), id);
res = RES_BAD_ARG;
goto error;
}
+ if(!MOLECULE_IS_VALID(molecule)) {
+ ERROR(metadata->shtr,
+ "%s:%lu: the `%s (%d)' molecule is not supported.\n",
+ txtrdr_get_name(txtrdr), (unsigned long)txtrdr_get_line_num(txtrdr),
+ name, molecule->id);
+ res = RES_BAD_ARG;
+ goto error;
+ }
+
+ if(strcmp(name, shtr_molecule_cstr(molecule->id))) {
+ ERROR(metadata->shtr,
+ "%s:%li: the molecule %d is named `%s' instead of `%s'.\n",
+ txtrdr_get_name(txtrdr), (unsigned long)txtrdr_get_line_num(txtrdr),
+ molecule->id, name, shtr_molecule_cstr(molecule->id));
+ res = RES_BAD_ARG;
+ goto error;
+ }
+
tk = strtok_r(NULL, " \t", &tk_ctx);
if(tk) {
WARN(metadata->shtr, "%s:%lu: unexpected text `%s'.\n",
diff --git a/src/test_shtr_isotope_metadata.c b/src/test_shtr_isotope_metadata.c
@@ -559,6 +559,24 @@ test_load_failures(struct shtr* shtr)
rewind(fp);
CHK(shtr_isotope_metadata_load_stream(shtr, fp, NULL, &mdata) == RES_MEM_ERR);
CHK(fclose(fp) == 0);
+
+ /* Duplicate molecule */
+ CHK(fp = tmpfile());
+ fprintf(fp, "Molecule # Iso Abundance Q(296K) gj Molar Mass(g)\n");
+ molecule_print(fp, &H2O);
+ molecule_print(fp, &H2O);
+ rewind(fp);
+ CHK(shtr_isotope_metadata_load_stream(shtr, fp, NULL, &mdata) == RES_BAD_ARG);
+ CHK(fclose(fp) == 0);
+
+ /* Invalid molecule name */
+ CHK(fp = tmpfile());
+ fprintf(fp, "Comment line\n");
+ fprintf(fp, "H_2O (1)\n");
+ isotope_print(fp, &H2O_isotopes[0]);
+ rewind(fp);
+ CHK(shtr_isotope_metadata_load_stream(shtr, fp, NULL, &mdata) == RES_BAD_ARG);
+ CHK(fclose(fp) == 0);
}
static void
diff --git a/src/test_shtr_molecule_id.c b/src/test_shtr_molecule_id.c
@@ -79,6 +79,12 @@ id2cstr(const enum shtr_molecule_id id)
case SHTR_CS2: cstr = "CS2"; break;
case SHTR_CH3I: cstr = "CH3I"; break;
case SHTR_NF3: cstr = "NF3"; break;
+ case SHTR_H3plus: cstr = "H3+"; break;
+ case SHTR_CH3: cstr = "CH3"; break;
+ case SHTR_S2: cstr = "S2"; break;
+ case SHTR_COFCl: cstr = "COFCl"; break;
+ case SHTR_HONO: cstr = "HONO"; break;
+ case SHTR_ClNO2: cstr = "ClNO2"; break;
default: FATAL("Unreachable code\n"); break;
}
return cstr;
