fix(engine_multiscale): resolved a major species index ordering bug

All jacobian calculations were broken because the indexing used to record the AD tape was broken (see not parallel to) the indexing used by the composition object. A fix for this was to sort the network species by mass. However, more generally we should introduce a mechanism to ensure these two indexed sets always remain parallel

src/lib/engine/procedures/construction.cpp

@@ -120,6 +120,9 @@ namespace gridfire {
         LOG_INFO(logger, "Starting network construction with {} available species.", availableSpecies.size());
 
         for (int layer = 0; layer < depth && !remainingReactions.empty(); ++layer) {
+            size_t collectedThisLayer = 0;
+            size_t collectedStrong = 0;
+            size_t collectedWeak = 0;
             LOG_TRACE_L1(logger, "Collecting reactions for layer {} with {} remaining reactions. Currently there are {} available species", layer, remainingReactions.size(), availableSpecies.size());
             std::vector<Reaction*> reactionsForNextPass;
             std::unordered_set<Species> newProductsThisLayer;
@@ -138,6 +141,12 @@ namespace gridfire {
 
                 if (allReactantsAvailable) {
                     collectedReactionPtrs.push_back(reaction);
+                    if (reaction->type() == reaction::ReactionType::WEAK) {
+                        collectedWeak++;
+                    } else {
+                        collectedStrong++;
+                    }
+                    collectedThisLayer++;
                     newReactionsAdded = true;
 
                     for (const auto& product : reaction->products()) {
@@ -153,14 +162,18 @@ namespace gridfire {
                 break;
             }
 
+            size_t oldProductCount = availableSpecies.size();
+            availableSpecies.insert(newProductsThisLayer.begin(), newProductsThisLayer.end());
+            size_t newProductCount = availableSpecies.size() - oldProductCount;
             LOG_TRACE_L1(
                 logger,
-                "Layer {}: Collected {} new reactions. New products this layer: {}",
+                "Layer {}: Collected {} new reactions ({} strong, {} weak). New products this layer: {}",
                 layer,
-                collectedReactionPtrs.size() - collectedReactionPtrs.size(),
-                newProductsThisLayer.size()
+                collectedThisLayer,
+                collectedStrong,
+                collectedWeak,
+                newProductCount
             );
-            availableSpecies.insert(newProductsThisLayer.begin(), newProductsThisLayer.end());
             remainingReactions = std::move(reactionsForNextPass);
         }