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commit f844c376ab4951c7b5e27ac0f57ae9b54df5f1c8
parent 1c0ac0cce49ddb62c08888af958782db8987f5d8
Author: Vincent Forest <vincent.forest@meso-star.com>
Date:   Tue, 26 Apr 2022 09:39:36 +0200

Check the isotope abundances of the sln_tree_build function

Diffstat:
M
src/sln_tree.c
 | 
44
++++++++++++++++++++++++++++++--------------

1 file changed, 30 insertions(+), 14 deletions(-)
diff --git a/src/sln_tree.c b/src/sln_tree.c
@@ -37,7 +37,7 @@ check_sln_isotope
 
   if(isotope->abundance < 0) {
     log_err(sln,
-      "%s: molecule `%d': isotope `%d': invalid abundance `%g'.\n",
+      "%s: molecule %d: isotope %d: invalid abundance %g.\n",
       func_name, id, isotope->id_local, isotope->abundance);
     return RES_BAD_ARG;
   }
@@ -51,6 +51,7 @@ check_sln_molecule
    struct shtr_isotope_metadata* metadata,
    const struct sln_molecule* molecule)
 {
+  double abundances_sum = 0;
   struct shtr_molecule mol = SHTR_MOLECULE_NULL;
   size_t i;
   ASSERT(sln && func_name && metadata && molecule);
@@ -58,8 +59,9 @@ check_sln_molecule
   SHTR(isotope_metadata_find_molecule(metadata, molecule->id, &mol));
   if(SHTR_MOLECULE_IS_NULL(&mol)) {
     log_warn(sln,
-      "%s: the molecule `%d' is not found in the isotope metadata.\n",
+      "%s: the molecule %d is not found in the isotope metadata.\n",
       func_name, molecule->id);
+    return RES_OK; /* Do not check the other parmeters */
   }
 
   if(molecule->nisotopes >= SLN_MAX_ISOTOPES_COUNT) {
@@ -72,19 +74,38 @@ check_sln_molecule
     return RES_BAD_ARG;
   }
 
+  abundances_sum = 0;
   FOR_EACH(i, 0, molecule->nisotopes) {
-    const res_T res = check_sln_isotope
-      (sln, func_name, molecule->id, molecule->isotopes+i);
+    res_T res = RES_OK;
+
+    if((size_t)molecule->isotopes[i].id_local >= mol.nisotopes) {
+      log_warn(sln,
+        "%s: molecule %d: the isotope local index %d exceeds "
+        "the overall number of isotopes %lu.\n",
+        func_name, molecule->id, molecule->isotopes[i].id_local,
+        molecule->nisotopes);
+      continue; /* Skip the isotope */
+    }
+    res = check_sln_isotope(sln, func_name, molecule->id, molecule->isotopes+i);
     if(res != RES_OK) return res;
+    abundances_sum += molecule->isotopes[i].abundance;
+  }
+
+  if(abundances_sum > 1) {
+    log_err(sln,
+      "%s: molecule %d: the sum of the isotope abundances %g is invalid. "
+      "It must be less than or equal to 1.\n",
+      func_name, molecule->id, abundances_sum);
+    return RES_BAD_ARG;
   }
 
   if(molecule->concentration < 0) {
-    log_err(sln, "%s: molecule `%d': invalid concentration `%g'.\n",
+    log_err(sln, "%s: molecule %d: invalid concentration %g.\n",
       func_name, molecule->id, molecule->concentration);
     return RES_BAD_ARG;
   }
   if(molecule->cutoff <= 0) {
-    log_err(sln, "%s: molecule `%d': invalid line cutoff `%g'.\n",
+    log_err(sln, "%s: molecule %d: invalid line cutoff %g.\n",
       func_name, molecule->id, molecule->concentration);
     return RES_BAD_ARG;
   }
@@ -107,12 +128,6 @@ check_sln_tree_create_args
     return RES_BAD_ARG;
   }
 
-  if(args->max_nlines_per_leaf == 0) {
-    log_err(sln, "%s: invalid maximum number of lines per leaf `%lu'.\n",
-      func_name, (unsigned long)args->max_nlines_per_leaf);
-    return RES_BAD_ARG;
-  }
-
   /* Check the list of molecules to be taken into account */
   if(args->nmolecules >= SLN_MAX_MOLECULES_COUNT) {
     log_err(sln,
@@ -141,11 +156,12 @@ check_sln_tree_create_args
   }
 
   if(args->pressure < 0) {
-    log_err(sln, "%s: invalid pressure `%g'.\n", func_name, args->pressure);
+    log_err(sln, "%s: invalid pressure %g.\n", func_name, args->pressure);
     return RES_BAD_ARG;
   }
+
   if(args->temperature < 0) {
-    log_err(sln, "%s: invalid temperature `%g'.\n", func_name, args->temperature);
+    log_err(sln, "%s: invalid temperature %g.\n", func_name, args->temperature);
     return RES_BAD_ARG;
   }
   return RES_OK;