LISE agreement

Armory/anasenMS.cpp

@@ -104,6 +104,7 @@ int main(int argc, char **argv){
   transfer.Setb(1, 1);                 // outgoing proton from the primary transfer
   transfer.SetB(30, 14);               // 21Na* heavy product
   const double beamA = 27;                   // mass number of 27Al beam
+  const double beamE = 72.0 / 27.0;                // beam energy in MeV
 
   bool enableSequentialDecay = false; // turning to false to disable sequential decay for now, can be set to true to enable
   const int decayDaughterA = 20;
@@ -363,6 +364,7 @@ int main(int argc, char **argv){
     beamEnergy = elossBeam->Eval(beamPath_cm); // MeV
     beamEnergyLoss = elossBeam->Eval(0.0) - beamEnergy;
     KEA = beamEnergy / beamA;
+    //KEA = gRandom->Uniform(0, beamE);
     transfer.SetIncidentEnergyAngle(KEA, 0, 0);
     transfer.CalReactionConstant();
 

ELoss/PCEnergyAnalysis.py

@@ -84,6 +84,17 @@ def get_loss_table_path(medium, particle_label):
     return os.path.join(script_dir, f"{medium}Loss", f"E_vs_x_{particle_label}.dat")
 
 
+def normalize_particle_label(particle):
+    """Return the canonical table label for a particle or isotope name."""
+    if isinstance(particle, str):
+        try:
+            _, _, _, label = resolve_particle(particle)
+            return label
+        except Exception:
+            return particle.strip()
+    return str(particle)
+
+
 def clear_interpolator_cache():
     """Drop cached energy-loss interpolators and force Python to release memory."""
     global interp_cache
@@ -111,30 +122,23 @@ def make_E_vs_x(
     p_pa = P_TORR * 133.322
     molar_density = p_pa / (R * TEMP_K)  # mol/m^3
 
-    # ---------------------------
     # Medium definition
-    # ---------------------------
     if medium == "He":
 
         m_he = 4.0026
         m_c = 12.0000
         m_o = 15.9949
-
-        # FIX: do NOT double count oxygen
+        """
         material_def = [
             (m_he, 2, 0.96),
-            ((m_c + 2 * m_o), 18, 0.04)  # CO2 lumped correctly
-        ]
+            (m_c, 6, 0.04),
+            (m_o, 8, 0.08)
+        ] """
+        material_def = [(m_he, 2, 1.0)]
 
         #m_mix_avg = 0.96 * m_he + 0.04 * (m_c + 2 * m_o)
-        m_mix_avg = m_he
-
-        #rho_g_cm3 = (molar_density * m_mix_avg) / 1e6
-        if z == 2:
-            rho_g_cm3 = 0.00017
-            #rho_g_cm3 = 8.2928e-5
-        else:
-            rho_g_cm3 = 8.2928e-5
+        m_mix_avg = 1.0 * m_he
+        rho_g_cm3 = (molar_density * m_mix_avg) / 1e6
         
         gas = catima.Material(material_def)
         gas.density(rho_g_cm3)
@@ -156,10 +160,10 @@ def make_E_vs_x(
     E = np.linspace(0.1, emax_mev, npoints)
     S_mass = np.zeros_like(E)
     for i, energy in enumerate(E):
-        projectile.T(energy)
+        # CATIMA expects projectile energy in MeV/u, while the table axis stays in total MeV.
+        projectile.T(energy / mass_u)
         S_mass[i] = catima.dedx(projectile, gas)  # MeV/(g/cm^2)
 
-    # convert to MeV/cm
     S_linear = S_mass * rho_g_cm3
     invS = 1.0 / np.clip(S_linear, 1e-30, None)
     x = cumulative_trapezoid(invS[::-1], E[::-1], initial=0)
@@ -206,12 +210,38 @@ def load_table(filename):
 
 def get_interpolators(particle, medium):
 
-    cache_key = (particle.lower(), medium.lower())
+    canonical_particle = normalize_particle_label(particle)
+    cache_key = (canonical_particle.lower(), medium.lower())
 
     if cache_key in interp_cache:
         return interp_cache[cache_key]
 
-    filename = get_loss_table_path(medium, particle)
+    candidate_labels = [canonical_particle]
+    if isinstance(particle, str):
+        raw_particle = particle.strip()
+        candidate_labels.extend([
+            raw_particle,
+            canonical_particle.replace("-", "")
+        ])
+
+    filename = None
+    seen_candidates = set()
+    for label in candidate_labels:
+        normalized_label = label.strip()
+        if not normalized_label:
+            continue
+        key = normalized_label.lower()
+        if key in seen_candidates:
+            continue
+        seen_candidates.add(key)
+
+        candidate_filename = get_loss_table_path(medium, normalized_label)
+        if os.path.exists(candidate_filename):
+            filename = candidate_filename
+            break
+
+    if filename is None:
+        filename = get_loss_table_path(medium, canonical_particle)
 
     x, E = load_table(filename)
 
@@ -275,11 +305,29 @@ def resolve_particle(name):
     name = name.lower().strip().rstrip("s")
     if name in particles:
         return particles[name]
-    match = re.match(r"([a-zA-Z]+)[-\s]?(\d+)", name)
+    match = re.match(r"([a-zA-Z]+)[-\s]?(\d+)$", name)
     if match:
         element_symbol = match.group(1).capitalize()
         A = int(match.group(2))
 
+        try:
+            element = pt.elements.symbol(element_symbol)
+            isotope = element[A]
+
+            return (
+                isotope.number,   # Z
+                isotope.mass,     # mass in u
+                30.0,
+                f"{element_symbol}-{A}"
+            )
+        except Exception:
+            raise ValueError(f"Unknown isotope: {name}")
+
+    match = re.match(r"(\d+)[-\s]?([a-zA-Z]+)$", name)
+    if match:
+        A = int(match.group(1))
+        element_symbol = match.group(2).capitalize()
+
         try:
             element = pt.elements.symbol(element_symbol)
             isotope = element[A]
@@ -898,7 +946,7 @@ class MyInteractiveApp(cmd.Cmd):
                 if dl > 0:
                     print(f"\nChange in energy: {dE:.6f} MeV")
                     print(f"Distance travelled: {dl:.6f} cm\n")
-                    print(f"{(dl * 10000):.6f} microns")
+                    print(f"{(dl * 10):.6f} mm")
                 else:
                     print("Error: remake table with larger value, fallen off map")
             except:
@@ -1343,7 +1391,7 @@ class MyInteractiveApp(cmd.Cmd):
         
         plt.figure(figsize=(7,6))
         mask1 = ~np.isnan(Esx3) & ~np.isnan(Edet) & sx3_theta_plot_mask
-        plt.hist2d(Esx3[mask1], Edet[mask1], bins=300)
+        plt.hist2d(Esx3[mask1], Edet[mask1], bins=300, norm="log")
         plt.xlabel("Esx3")
         plt.ylabel("Edet")
         plt.title("Esx3 vs Edet")
@@ -1356,12 +1404,12 @@ class MyInteractiveApp(cmd.Cmd):
         
         mask1 = ~np.isnan(qqqE) & ~np.isnan(EdetQ) & qqq_theta_plot_mask
         plt.figure(figsize=(7,6))
-        plt.hist2d(qqqE[mask1], EdetQ[mask1], bins=300)
+        plt.hist2d(qqqE[mask1], EdetQ[mask1], bins=300, norm="log")
         plt.xlabel("Eqqq")
         plt.ylabel("Edet")
         plt.title("Eqqq vs Edet")
-        plt.yscale("log")
-        plt.xscale("log")
+        #plt.yscale("log")
+        #plt.xscale("log")
         plt.colorbar(label="counts")
         plt.tight_layout()
         plt.savefig(f"{base}/Eqqq_vs_Edet.png")
@@ -1418,6 +1466,7 @@ class MyInteractiveApp(cmd.Cmd):
                 plt.plot(theta_deg[order], path_cm[order], color='red', linewidth=2, label='0.1/sin(theta)')
                 plt.legend()
                 plt.tight_layout()
+                plt.gca().invert_xaxis()
                 plt.savefig(f"{base}/Range_vs_theta_with_path.png", dpi=300)
                 plt.show()
         except Exception: