merging cr-doped and additional validation caes

.github/workflows/codeql.yml

@@ -13,9 +13,9 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ "main" ]
+    branches: [ "patch-3" ]
   pull_request:
-    branches: [ "main" ]
+    branches: [ "patch-3" ]
   schedule:
     - cron: '29 23 * * 6'
 

.github/workflows/regression_test.yml

@@ -6,9 +6,9 @@ name: Python application test
 
 on:
   push:
-    branches: [ "main" ]
+    branches: [ "patch-3" ]
   pull_request:
-    branches: [ "main" ]
+    branches: [ "patch-3" ]
 
 jobs:
   build:

CMakeLists.txt

@@ -11,6 +11,14 @@
 
 cmake_minimum_required(VERSION 3.4.0)
 
+if(APPLE)
+    message(STATUS "Configuring on macOS, setting custom compilers...")
+    set(CMAKE_C_COMPILER /opt/homebrew/bin/gcc-14)
+    set(CMAKE_CXX_COMPILER /opt/homebrew/bin/g++-14)
+else()
+    message(STATUS "Not on macOS, using default compilers.")
+endif()
+
 # Name of the project created / existent in visual studio
 project(sciantix)
 
@@ -66,4 +74,4 @@ add_custom_command(TARGET sciantix POST_BUILD
 set(CPACK_PROJECT_NAME ${PROJECT_NAME})
 set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
 
-include(CPack)
+include(CPack)

include/classes/Matrix.h

@@ -55,6 +55,14 @@ class Matrix : virtual public Material
     double pore_nucleation_rate;
     double pore_resolution_rate;
     double pore_trapping_rate;
+    double chromium_content;
+	double chromium_solubility;
+	double Cr2O3_solubility;
+	double chromium_solution;
+	double chromium_precipitate;
+	double chromia_solution;
+	double chromia_precipitate;
+
 
     /**
      * @brief Sets the theoretical density of the matrix.
@@ -374,6 +382,83 @@ class Matrix : virtual public Material
         return healing_temperature_threshold;
     }
 
+    void setChromiumContent(double cc)
+	{
+		chromium_content = cc;
+	}
+
+	double getChromiumContent()
+	{	
+		/// Member function to set the chromium content (µg/g)
+		return chromium_content;
+	}
+
+	void setChromiumSolubility(double cs)
+	{
+		chromium_solubility = cs;
+	}
+
+	double getChroimumSolubility()
+	{
+		/// Member function to set the chromium solubility (weight%/UO2)	
+		return chromium_solubility;
+	}
+
+	void setChromiaSolubility(double crs)
+	{
+		Cr2O3_solubility = crs;
+	}
+
+	double getChromiaSolubility()
+	{
+		/// Member function to set the chromia (Cr2O3) solubility (weight%/UO2)	
+		return Cr2O3_solubility;
+	}
+
+	void setChromiumSolution(double cr_sol)
+	{
+		chromium_solution= cr_sol;
+	}
+
+	double getChromiumSolution()
+	{
+		/// Member function to set the chromium solution (kg)	
+		return chromium_solution;
+	}
+
+	void setChromiumPrecipitate(double cr_p)
+	{
+		chromium_precipitate= cr_p;
+	}
+
+	double getChromiumPrecipitate()
+	{
+		/// Member function to set the chromium precipitate (kg)	
+		return chromium_precipitate;
+	}
+
+	void setChromiaSolution(double chromia_sol)
+	{
+		chromia_solution = chromia_sol;
+	}
+
+	double getChromiaSolution()
+	{
+		/// Member function to set the chromia (Cr2O3) solution (kg)	
+		return chromia_solution;
+	}
+
+	void setChromiaPrecipitate(double chromia_p)
+	{
+		chromia_precipitate = chromia_p;
+	}
+
+	double getChromiaPrecipitate()
+	{
+		/// Member function to set the chromia (Cr2O3) precipitate (kg)	
+		return chromia_precipitate;
+	}
+
     /**
      * @brief Constructor
      */

include/classes/Simulation.h

@@ -295,6 +295,37 @@ class Simulation
      */
     void UO2Thermochemistry();
 
+	/**
+	 * @brief This function defines the Sciantix model *ChromiumSolubility*.
+	 * 
+     * @details
+	 * The model ChromiumSolubility is used to evaluate the chromium solubility accordingly to the temperature and the oxygen content.
+	 * Then the number of oxide chromium atoms is evaluated, accordingly to the oxygen content of the system. 
+	 * 
+	 * Solubility of Chromium is evaluated as log10(y_Cr) = p*log10(P_O2) + V + U/T
+	 * Coefficients U and V came from experimental fitting, in this way the Gibbs Potential is approximated as a function of 1/T
+	 * Metallic chromium shows two different phases with threshold temperature of 1651 °C
+	 * CrO is expected to be negligible, accordingly to Cr - O phase diagram
+	 * The exchange between Cr-metal phase and Cr-oxide phase is described accordingly to the empirical expression:
+	 * oxide_fraction  = 1 - exp(C1 * T - C1*C2)
+	 * 
+     * @author G. Nicodemo
+     * 
+     * @ref <a href="https://www.sciencedirect.com/science/article/pii/S0022311524004033" target="_blank">Nicodemo G. et al (2024). Journal of Nuclear Materials, 601, 155301.</a>
+	 */
+
+    void ChromiumSolubility();
+
+    /**
+	 * @brief The model Microstructure is used to evaluate the lattice parameter and the theoretical density, accordingly to chromium content.
+	 * 
+     * @author G. Nicodemo
+     * 
+     * @ref <a href="https://www.sciencedirect.com/science/article/pii/S0022311512000943" target="_blank">T. Cardinaels et al (2012), Journal of Nuclear Materials, 424 252-260.</a>
+	 */
+
+    void Microstructure();
+
     /**
      * @brief This method returns a pointer to the array of diffusion modes corresponding to the specified gas.
      * @param gas_name The name of the gas for which diffusion modes are required.

include/coupling/TUSrcCoupling.h

@@ -20,8 +20,9 @@
  * These two functions are also defined in TRANSURANUS, and are essentially required to create the
  * communication channel between the two codes.
  *
+ * @author M. Di Gennaro
  * @author E. Travaglia
- *
+ * 
  */
 
 #ifndef TUSRCCOUPLING_H
@@ -31,9 +32,8 @@
 extern "C"
 {
   #endif
-  void getSciantixOptions(int options[], double scaling_factors[]);
-  void callSciantix(int options[], double history[], double variables[],
-                    double scaling_factors[], double diffusion_modes[]);
+  void getSciantixOptions(int Sciantix_options[], double Sciantix_scaling_factors[]);
+  void callSciantix(int Sciantix_options[], double Sciantix_history[], double Sciantix_variables[], double Sciantix_scaling_factors[], double Sciantix_diffusion_modes[]);
 
   #ifdef __cplusplus
 }

include/namespaces/Constants.h

@@ -25,10 +25,15 @@
  * These constants are commonly used in various scientific and engineering calculations.
  * 
  * @author G. Zullo
+ * @author G. Nicodemo
  * 
  */
 
 const double boltzmann_constant = 1.380651e-23; // (J/K)
 const double avogadro_number = 6.02214076e23;   // (at/mol)
+const double molar_mass_Oxygen = 15.999; // g/mol
+const double molar_mass_Chromium = 51.9961; // g/mol
+const double calorie = 4.186; // J
+const double gas_constant = 8.3143; // J/(mol K)
 
 #endif

include/operations/SetVariablesFunctions.h

@@ -54,7 +54,8 @@ std::vector<std::string> getInputVariableNames()
         "iHighBurnupStructurePorosity",
         "iHeliumProductionRate",
         "iStoichiometryDeviation",
-        "iBubbleDiffusivity"
+        "iBubbleDiffusivity",
+        "iChromiumSolubility"
     };
 
     return names;
@@ -106,7 +107,8 @@ std::vector<SciantixVariable> initializeSciantixVariable(
     bool toOutputCracking,
     bool toOutputGrainBoundary,
     bool toOutputHighBurnupStructure,
-    bool toOutputStoichiometryDeviation
+    bool toOutputStoichiometryDeviation,
+    bool toOutputChromiumContent
 )
 {
     std::vector<SciantixVariable> init_sciantix_variable =
@@ -192,7 +194,7 @@ std::vector<SciantixVariable> initializeSciantixVariable(
         SciantixVariable("Intergranular fractional intactness", "(/)", Sciantix_variables[37], Sciantix_variables[37], toOutputCracking),
 
         SciantixVariable("Burnup", "(MWd/kgUO2)", Sciantix_variables[38], Sciantix_variables[38], 1),
-        SciantixVariable("FIMA", "(%)", Sciantix_variables[69], Sciantix_variables[69], toOutputHighBurnupStructure),
+        SciantixVariable("FIMA", "(%)", Sciantix_variables[69], Sciantix_variables[69], toOutputHighBurnupStructure || toOutputChromiumContent),
         SciantixVariable("Effective burnup", "(MWd/kgUO2)", Sciantix_variables[39], Sciantix_variables[39], toOutputHighBurnupStructure),
         SciantixVariable("Irradiation time", "(h)", Sciantix_variables[65], Sciantix_variables[65], 0),
         SciantixVariable("Fuel density", "(kg/m3)", Sciantix_variables[40], Sciantix_variables[40], 0),
@@ -224,7 +226,19 @@ std::vector<SciantixVariable> initializeSciantixVariable(
         SciantixVariable("Xe in HBS pores", "(at/m3)", Sciantix_variables[83], Sciantix_variables[83], toOutputHighBurnupStructure),
         SciantixVariable("Xe in HBS pores - variance", "(at^2/m3)", Sciantix_variables[85], Sciantix_variables[85], toOutputHighBurnupStructure),
         SciantixVariable("Xe atoms per HBS pore", "(at/pore)", Sciantix_variables[86], Sciantix_variables[86], toOutputHighBurnupStructure),
-        SciantixVariable("Xe atoms per HBS pore - variance", "(at^2/pore)", Sciantix_variables[88], Sciantix_variables[88], toOutputHighBurnupStructure)
+        SciantixVariable("Xe atoms per HBS pore - variance", "(at^2/pore)", Sciantix_variables[88], Sciantix_variables[88], toOutputHighBurnupStructure),
+
+        SciantixVariable("Chromium content", "(µg/g)", Sciantix_variables[150], Sciantix_variables[150], toOutputChromiumContent),
+        SciantixVariable("Lattice parameter", "(m)", Sciantix_variables[151], Sciantix_variables[151], 0),
+        SciantixVariable("Theoretical density", "(kg/m3)", Sciantix_variables[152], Sciantix_variables[152], 0),
+        SciantixVariable("Chromium solubility", "(% weight/UO2)", Sciantix_variables[153], Sciantix_variables[153], toOutputChromiumContent),
+        SciantixVariable("Chromia solubility", "(% weight/UO2)", Sciantix_variables[154], Sciantix_variables[154], toOutputChromiumContent),
+        SciantixVariable("Chromium solution", "(at/m3)", Sciantix_variables[155], Sciantix_variables[155], toOutputChromiumContent),
+        SciantixVariable("Chromium precipitate", "(at/m3)", Sciantix_variables[156], Sciantix_variables[156], toOutputChromiumContent),
+        SciantixVariable("Chromia solution", "(at/m3)", Sciantix_variables[157], Sciantix_variables[157], toOutputChromiumContent),
+        SciantixVariable("Chromia precipitate", "(at/m3)", Sciantix_variables[158], Sciantix_variables[158], toOutputChromiumContent),
+
+        SciantixVariable("Diffusion coefficient", "(m2/s)", Sciantix_variables[160], Sciantix_variables[160], 0),
     };
 
     return init_sciantix_variable;
@@ -243,6 +257,7 @@ std::vector<std::string> getScalingFactorsNames()
         "Trapping rate",
         "Nucleation rate",
         "Diffusivity",
+        "Diffusivity2",
         "Temperature",
         "Fission rate",
         "Cent parameter",

regression/regression.py

@@ -18,6 +18,8 @@
 from regression_oxidation import regression_oxidation
 from regression_kashibe import regression_kashibe
 from regression_hbs import regression_hbs
+from regression_chromium import regression_chromium
+from regression_cornell import regression_cornell
 
 def remove_output(file):
     os.chdir(file)
@@ -63,7 +65,9 @@ def main():
         ('Talip', regression_talip),
         ('CONTACT', regression_contact),
         ('oxidation', regression_oxidation),
-        ('HBS', regression_hbs)
+        ('HBS', regression_hbs),
+        ('Chromium', regression_chromium),
+        ('Cornell', regression_cornell)
     ]
 
     # Check if running in GitHub Actions environment
@@ -87,7 +91,7 @@ def main():
 
         # Option 2: Remove all output files
         if execution_option == 2:
-            directories = ["Baker", "Kashibe", "White", "Talip", "CONTACT", "oxidation", "HBS"]
+            directories = ["Baker", "Kashibe", "White", "Talip", "CONTACT", "oxidation", "HBS", "Chromium", "Cornell"]
             for file in os.listdir(wpath):
                 if any(dir_name in file for dir_name in directories) and os.path.isdir(file):
                     remove_output(file)
@@ -110,7 +114,7 @@ def main():
             print("Possible regression options \n")
             for i, (name, _) in enumerate(regression_modules):
                 print(f"{name} : {i}")
-            regression_mode = int(input("Enter the chosen regression (0, 1, 2, 3, 4, 5, 6) = "))
+            regression_mode = int(input("Enter the chosen regression (0, 1, 2, 3, 4, 5, 6, 7, 8) = "))
 
             mode_gold, mode_plot = get_mode_selections()