star-line

commit bafd3efb0869bb1da4762b89f5b7304831d3b280
parent 345d66bad759bd3b7ddbe6fc76740655ab30f1c4
Author: Vincent Forest <vincent.forest@meso-star.com>
Date:   Wed, 27 Apr 2022 11:23:35 +0200

Register the molecule parameters of the tree

i.e. concentration, cutoff and isotope abundances. Map them to the
molecule id and the isotope local id.

Diffstat:
M
src/sln_tree.c
 | 
60
+++++++++++++++++++++++++++++++++++++++++++++++++++++++-----
M
src/sln_tree_c.h
 | 
11
+++++++++++

2 files changed, 66 insertions(+), 5 deletions(-)
diff --git a/src/sln_tree.c b/src/sln_tree.c
@@ -23,6 +23,11 @@
 
 #include <star/shtr.h>
 
+STATIC_ASSERT(SLN_MAX_MOLECULES_COUNT <= SHTR_MAX_MOLECULES_COUNT,
+  Invalid_SLN_MAX_MOLECULES_COUNT);
+STATIC_ASSERT(SLN_MAX_ISOTOPES_COUNT <= SHTR_MAX_ISOTOPES_COUNT,
+  Invalid_SLN_MAX_ISOTOPES_COUNT);
+
 /*******************************************************************************
  * Helper functions
  ******************************************************************************/
@@ -204,11 +209,6 @@ create_lines_view
    const struct sln_tree_create_args* tree_args,
    struct shtr_lines_view** out_view)
 {
-  STATIC_ASSERT(SLN_MAX_MOLECULES_COUNT <= SHTR_MAX_MOLECULES_COUNT,
-    Invalid_SLN_MAX_MOLECULES_COUNT);
-  STATIC_ASSERT(SLN_MAX_ISOTOPES_COUNT <= SHTR_MAX_ISOTOPES_COUNT,
-    Invalid_SLN_MAX_ISOTOPES_COUNT);
-
   struct shtr_lines_view_create_args view_args = SHTR_LINES_VIEW_CREATE_ARGS_NULL;
   struct shtr_lines_view* view = NULL;
   size_t imol, iiso;
@@ -244,6 +244,54 @@ error:
 }
 
 static void
+molecules_params_reset(struct molecule_params params[SLN_MAX_MOLECULES_COUNT])
+{
+  size_t imol;
+  ASSERT(params);
+
+  /* Clean up the params */
+  FOR_EACH(imol, 0, SLN_MAX_MOLECULES_COUNT) {
+    size_t iiso;
+    params[imol].concentration = -1;
+    params[imol].cutoff = -1;
+    FOR_EACH(iiso, 0, SLN_MAX_ISOTOPES_COUNT) {
+      params[imol].isotopes_abundance[iiso] = -1;
+    }
+  }
+}
+
+static res_T
+setup_molecule_params
+  (struct sln_device* sln,
+   const struct sln_tree_create_args* args,
+   struct molecule_params params[SLN_MAX_MOLECULES_COUNT])
+{
+  size_t imol;
+  ASSERT(sln && args && params);
+  (void)sln;
+
+  molecules_params_reset(params);
+
+  FOR_EACH(imol, 0, args->nmolecules) {
+    const struct sln_molecule* mol = &args->molecules[imol];
+    size_t iiso;
+    ASSERT(mol->id < SLN_MAX_MOLECULES_COUNT);
+
+    params[mol->id].concentration = mol->concentration;
+    params[mol->id].cutoff = mol->cutoff;
+
+    FOR_EACH(iiso, 0, mol->nisotopes) {
+      const struct sln_isotope* iso = &mol->isotopes[iiso];
+      ASSERT(iso->id_local < SLN_MAX_ISOTOPES_COUNT);
+
+      params[mol->id].isotopes_abundance[iso->id_local] = iso->abundance;
+    }
+  }
+
+  return RES_OK;
+}
+
+static void
 release_tree(ref_T* ref)
 {
   struct sln_tree* tree = CONTAINER_OF(ref, struct sln_tree, ref);
@@ -286,6 +334,8 @@ sln_tree_create
 
   res = create_lines_view(sln, args, &tree->lines_view);
   if(res != RES_OK) goto error;
+  res = setup_molecule_params(sln, args, tree->molecules_params);
+  if(res != RES_OK) goto error;
   res = tree_build(tree, args);
   if(res != RES_OK) goto error;
 
diff --git a/src/sln_tree_c.h b/src/sln_tree_c.h
@@ -40,7 +40,18 @@ static const struct sln_node SLN_NODE_NULL = SLN_NODE_NULL__;
 #define DARRAY_NAME node
 #include <rsys/dynamic_array.h>
 
+struct molecule_params {
+  /* Map the isotope local identifier to its abundance */
+  double isotopes_abundance[SLN_MAX_ISOTOPES_COUNT];
+
+  double concentration;
+  double cutoff;
+};
+
 struct sln_tree {
+  /* Map the molecule id to its parameters (i.e. concentration, cutoff) */
+  struct molecule_params molecules_params[SLN_MAX_MOLECULES_COUNT];
+
   struct shtr_lines_view* lines_view; /* Set of lines */
   struct darray_node nodes; /* Nodes used to partition the lines */