fix(GraphNetwork): working on loads of small bugs

Fized stoichiometry matrix initialization, added penames to reablib reactions, began work on LogicalReaction to sum the contributions of different fitting functions provided by reaclib

assets/static/reaclib/include/gridfire/reaclib.h

@@ -5,7 +5,7 @@
 #include <string>
 #include <iostream>
 #include <unordered_map>
-#include "atomicSpecies.h"
+#include "fourdst/composition/atomicSpecies.h"
 
 #include "cppad/cppad.hpp"
 
@@ -32,6 +32,7 @@ namespace gridfire::reaclib {
     class REACLIBReaction {
     private:
         std::string m_id; ///< Unique identifier for the reaction, generated by the Python script.
+        std::string_view m_peName; ///< Name of the reaction in (projectile, ejectile)  notation (e.g. p(p, g)d)
         int m_chapter;    ///< Chapter number from the REACLIB database, defining the reaction structure.
         std::vector<fourdst::atomic::Species> m_reactantNames; ///< Names of the reactant species involved in the reaction.
         std::vector<fourdst::atomic::Species> m_productNames;  ///< Names of the product species produced by the reaction.
@@ -56,6 +57,7 @@ namespace gridfire::reaclib {
          */
         REACLIBReaction(
             std::string id,
+            std::string_view peName,
             int chapter,
             std::vector<fourdst::atomic::Species> reactants,
             std::vector<fourdst::atomic::Species> products,
@@ -64,6 +66,7 @@ namespace gridfire::reaclib {
             RateFitSet sets,
             bool reverse = false)
             : m_id(std::move(id)),
+              m_peName(peName),
               m_chapter(chapter),
               m_reactantNames(std::move(reactants)),
               m_productNames(std::move(products)),
@@ -87,6 +90,8 @@ namespace gridfire::reaclib {
 
         [[nodiscard]] const std::string& id() const { return m_id; }
 
+        [[nodiscard]] std::string_view peName() const { return m_peName; }
+
         [[nodiscard]] int chapter() const { return m_chapter; }
 
         [[nodiscard]] const std::vector<fourdst::atomic::Species>& reactants() const { return m_reactantNames; }
@@ -99,8 +104,10 @@ namespace gridfire::reaclib {
 
         [[nodiscard]] bool is_reverse() const { return m_reverse; }
 
+        [[nodiscard]] RateFitSet rateFits() const { return m_rateSets; }
+
         friend std::ostream& operator<<(std::ostream& os, const REACLIBReaction& reaction) {
-            os << "REACLIBReaction(" << reaction.m_id << ", "
+            os << "REACLIBReaction(" << reaction.m_peName << ", "
                << "Chapter: " << reaction.m_chapter << ")";
             return os;
         }
@@ -234,6 +241,7 @@ namespace gridfire::reaclib {
     inline bool operator!=(const REACLIBReactionSet& lhs, const REACLIBReactionSet& rhs) {
         return !(lhs == rhs);
     }
+
 }
 
 namespace std {

assets/static/reaclib/meson.build

@@ -1,14 +1,20 @@
 required_headers = [
-    'reaclib.h',
-    'reactions.h',
+    'gridfire/reaclib.h',
+    'gridfire/reactions.h',
 ]
 
 foreach h : required_headers
     if not cpp.has_header(h, include_directories: include_directories('include'))
-        error('SERiF requires the header file ' + h + ' to be present in the assets/static/reaclib/include directory.')
+        error('GridFire requires the header file ' + h + ' to be present in the assets/static/reaclib/include/gridfire directory.')
     endif
 endforeach
 reaclib_reactions_dep = declare_dependency(
     include_directories: include_directories('include'),
 )
-message('✅ SERiF reaclib_reactions dependency declared')
+message('✅ GridFire reaclib_reactions dependency declared')
+
+to_install_headers = [
+    'include/gridfire/reaclib.h',
+    'include/gridfire/reactions.h',
+]
+install_headers(to_install_headers, subdir: 'gridfire/gridfire')