feat(Comoposition-Tracking): updated GridFire to use new, molar-abundance based, version of libcomposition (v2.0.6)

This entailed a major rewrite of the composition handling from each engine and engine view along with the solver and primer. The intent here is to let Compositions be constructed from the same extensive property which the solver tracks internally. This addressed C0 discontinuity issues in the tracked molar abundances of species which were introduced by repeadidly swaping from molar abundance space to mass fraction space and back. This also allowed for a simplification of the primeNetwork method. Specifically the mass borrowing system was dramatically simplified as molar abundances are extensive.

utils/reaclib/format.py

@@ -69,9 +69,11 @@ from collections import defaultdict
 from re import Match
 from typing import List, Tuple, Any, LiteralString
 import numpy as np
-from serif.atomic import species
-from serif.atomic import Species
-from serif.constants import Constants
+
+from fourdst.atomic import species
+from fourdst.atomic import Species
+from fourdst.constants import Constants
+
 import hashlib
 from collections import Counter
 import math
@@ -281,13 +283,13 @@ def translate_names_to_species(names: List[str]) -> List[Species]:
         try:
             sp.append(species[name])
         except Exception as e:
-            print("Error: Species not found in database:", name, e)
             raise ReaclibParseError(f"Species '{name}' not found in species database.", line_content=name)
     return sp
 
 def determine_reaction_type(reactants: List[str],
                             products: List[str],
-                            qValue: float
+                            qValue: float,
+                            chapter: int
                             ) -> Tuple[str, List[str], List[str], str, str, str]:
     """
     Analyze a reaction for quantum number conservation and classify projectiles/ejectiles.
@@ -323,8 +325,6 @@ def determine_reaction_type(reactants: List[str],
     - Identifies weak (leptonic) and photonic processes.
     - Determines projectiles/ejectiles based on mass and reaction type.
     """
-    if abs(qValue - 4.621) < 1e-6:
-        print("Looking at he3(he3, 2p)he4")
     # --- helper look-ups ----------------------------------------------------
     reactantSpecies = translate_names_to_species(reactants)
     productSpecies  = translate_names_to_species(products)
@@ -360,24 +360,41 @@ def determine_reaction_type(reactants: List[str],
     projectiles: List[str] = []
     ejectiles:   List[str] = []
 
+
+    debug = False
+    if reactants == ['b8'] and products == ['be8']:
+        debug = True
+
+    BETA_PLUS_THRESHOLD_ENERGY = 1.022 # MeV
+
     # -----------------------------------------------------------------------
     # 1.  Charged-lepton bookkeeping (|ΔZ| = 1) ------------------------------
     # -----------------------------------------------------------------------
-    if abs(dZ) == 1:
-        # Proton → neutron  (β⁻ / e- capture)
-        if dZ == -1:
-            # Electron capture when (i) exo-thermic and (ii) nucleus count unchanged
-            if qValue > 0 and dN == 0:
-                projectiles.append("e-")      # write e- as projectile
-            else:
-                ejectiles.append("e-")        # β⁻ decay: e- is an ejectile
+    if debug:
+        print("============")
+        print("Reactant Species: ", reactantSpecies)
+        print("Product Species: ", productSpecies)
+        print("Target Species: ", targetSpecies)
+        print("Residual Species: ", residualSpecies)
+        print("Nuclear Projectiles: ", nuclearProjectiles)
+        print("Nuclear Ejectiles: ", nuclearEjectiles)
+        print("aReact, aProd: ", aReact, aProd)
+        print("zReact, zProd: ", zReact, zProd)
+        print("nReact, nProd: ", nReact, nProd)
+        print("dA, dZ, dN: ", dA, dZ, dN)
+        print("qValue: ", qValue)
 
-        # Neutron → proton  (β⁺ / positron capture – capture is vanishingly rare)
-        elif dZ == 1:
-            ejectiles.append("e+")            # β⁺ / weak-proton capture
+    if dZ == -1 and chapter == 1:
+        ejectiles.append("e-") # β- decay
+    if dZ == -1 and chapter != 1:
+        projectiles.append("e+") # positron capture
+    if dZ == 1 and chapter == 1 and qValue >= BETA_PLUS_THRESHOLD_ENERGY:
+        ejectiles.append("e+") # β+ Decay
+    if dZ == 1 and chapter == 1 and qValue < BETA_PLUS_THRESHOLD_ENERGY:
+        projectiles.append("e-") # electron capture
+    if dZ == 1 and chapter != 1:
+        ejectiles.append("e+") # Positron as byproduct of two body reaction
 
-        # Neutrino companion is implicit – never written
-        # (dL is automatically fixed by hiding ν or ν̄)
 
     # -----------------------------------------------------------------------
     # 2.  Photon bookkeeping (ΔZ = 0) ----------------------------------------
@@ -452,12 +469,10 @@ def extract_groups(match: re.Match, reverse: bool) -> Reaction:
     chapter = int(groups[0].strip())
     rawGroup = groups[1].strip()
     rList, pList = get_rp(rawGroup, chapter)
-    if 'c12' in rList and 'mg24' in pList:
-        print("Found it!")
     if reverse:
         rList, pList = pList, rList
     qValue = float(groups[3].strip())
-    target, proj, ejec, residual, key, rType = determine_reaction_type(rList, pList, qValue)
+    target, proj, ejec, residual, key, rType = determine_reaction_type(rList, pList, qValue, chapter)
     reaction = Reaction(
         reactants=rList,
         products=pList,