added cornell

regression/regression.py

@@ -19,6 +19,7 @@
 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)
@@ -65,7 +66,8 @@ def main():
         ('CONTACT', regression_contact),
         ('oxidation', regression_oxidation),
         ('HBS', regression_hbs),
-        ('Chromium', regression_chromium)
+        ('Chromium', regression_chromium),
+        ('Cornell', regression_cornell)
     ]
 
     # Check if running in GitHub Actions environment
@@ -89,7 +91,7 @@ def main():
 
         # Option 2: Remove all output files
         if execution_option == 2:
-            directories = ["Baker", "Kashibe", "White", "Talip", "CONTACT", "oxidation", "HBS", "Chromium"]
+            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)
@@ -112,7 +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, 7) = "))
+            regression_mode = int(input("Enter the chosen regression (0, 1, 2, 3, 4, 5, 6, 7, 8) = "))
 
             mode_gold, mode_plot = get_mode_selections()
 

regression/regression_cornell.py

@@ -0,0 +1,168 @@
+"""
+This is a python script to execute the regression (running the validation database) of SCIANTIX.
+
+@author G. Zullo
+"""
+
+""" ------------------- Import Required Dependencies ------------------- """
+
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+from regression_functions import *
+from sklearn.linear_model import LinearRegression
+
+""" ------------------- Global Variables ------------------- """
+# Plot configuration
+font_size = 10
+
+plt.rcParams['axes.labelsize'] = font_size
+plt.rcParams['xtick.labelsize'] = font_size
+plt.rcParams['ytick.labelsize'] = font_size
+
+# Experimental data:
+# Temperature (K), intra-granular bubble radius (nm), density (bub/m3)
+exp_data = np.array([
+    [1133, 0.85, 3.80],
+    [1253, 0.90, 3.50],
+    [1333, 0.95, 3.30],
+    [1543, 1.00, 2.90],
+    [1698, 1.00, 2.46],
+    [1743, 1.15, 1.83],
+    [1783, 1.20, 1.32],
+    [1843, 1.30, 1.24],
+    [1853, 1.40, 1.18]
+])
+
+intraGranularBubbleDensitySciantix = []
+intraGranularBubbleRadiusSciantix = []
+
+number_of_tests_failed = 0
+gold = []
+sample_number = len(exp_data[:,0])
+
+""" ------------------- Functions ------------------- """
+
+def do_plot():
+    """Generate plots comparing experimental data with results."""
+
+    # Plot 1: Intragranular bubble radius
+    fig, ax = plt.subplots()
+    ax.scatter(exp_data[:,1], intraGranularBubbleRadiusSciantix, edgecolors='#757575', facecolors='brown', marker='^', s=30, label='SCIANTIX 2.0', zorder=1)
+    ax.plot([1e-3, 1e2], [1e-3, 1e2], '-', color='#757575')
+    ax.plot([1e-3, 1e2], [2e-3, 2e2], '--', color='#757575')
+    ax.plot([1e-3, 1e2], [5e-4, 5e1], '--', color='#757575')
+    ax.set_xlim(1e-1, 1.5e1)
+    ax.set_ylim(1e-1, 1.5e1)
+    ax.set_xscale('log')
+    ax.set_yscale('log')
+    ax.set_xlabel('Experimental (nm)', fontsize=font_size)
+    ax.set_ylabel('Calculated (nm)', fontsize=font_size)
+    ax.tick_params(axis='both', which='major', labelsize=font_size)
+    ax.legend()
+    plt.show()
+
+    # Plot 2: Intragranular bubble density
+    fig, ax = plt.subplots()
+    ax.scatter(exp_data[:,2], intraGranularBubbleDensitySciantix, edgecolors='#757575', facecolors='red', marker='^', s=30, label='SCIANTIX 2.0', zorder=1)
+    ax.plot([1e-3, 1e2], [1e-3, 1e2], '-', color='#757575')
+    ax.plot([1e-3, 1e2], [2e-3, 2e2], '--', color='#757575')
+    ax.plot([1e-3, 1e2], [5e-4, 5e1], '--', color='#757575')
+    ax.set_xlim(3e-1, 1.5e1)
+    ax.set_ylim(3e-1, 1.5e1)
+    ax.set_xscale('log')
+    ax.set_yscale('log')
+    ax.set_xlabel('Experimental (10^23 bub/m3)', fontsize=font_size)
+    ax.set_ylabel('Calculated (10^23 bub/m3)', fontsize=font_size)
+    ax.tick_params(axis='both', which='major', labelsize=font_size)
+    ax.legend()
+    plt.show()
+
+def regression_cornell(wpath, mode_Baker, mode_gold, mode_plot, folderList, number_of_tests, number_of_tests_failed):
+    """
+    Main function to perform the regression tests on SCIANTIX.
+
+    Parameters:
+        wpath (str): Working path to search for folders.
+        mode_Baker (int): Mode for executing tests.
+        mode_gold (int): Mode for using/golding results.
+        mode_plot (int): Mode for plotting results.
+        folderList (list): List to store folder names.
+        number_of_tests (int): Count of tests performed.
+        number_of_tests_failed (int): Count of failed tests.
+
+    Returns:
+        folderList (list): Updated list of folder names.
+        number_of_tests (int): Updated count of tests performed.
+        number_of_tests_failed (int): Updated count of failed tests.
+    """
+    if mode_Baker == 0:
+        return folderList, number_of_tests, number_of_tests_failed
+
+    files_and_dirs = os.listdir(wpath)
+    sorted_files_and_dirs = sorted(files_and_dirs)
+
+    for file in sorted_files_and_dirs:
+        if "Cornell" in file and os.path.isdir(file):
+            folderList.append(file)
+            os.chdir(file)
+            print(f"Now in folder {file}...")
+            number_of_tests += 1
+
+            if mode_gold == 0:
+                do_sciantix()
+                data, data_gold = check_output(file)
+                number_of_tests_failed = check_result(number_of_tests_failed)
+
+            elif mode_gold == 1:
+                do_sciantix()
+                data, data_gold = check_output(file)
+                print("...golding results.")
+                do_gold()
+
+            elif mode_gold == 2:
+                data, data_gold = check_output(file)
+                number_of_tests_failed = check_result(number_of_tests_failed)
+
+            elif mode_gold == 3:
+                data, data_gold = check_output(file)
+                print("...golding existing results.")
+                do_gold()
+
+            pos = findSciantixVariablePosition(data, "Intragranular bubble concentration (bub/m3)")
+            intraGranularBubbleDensitySciantix.append(data[-1, pos].astype(float)*1e-23)
+
+            pos = findSciantixVariablePosition(data, "Intragranular bubble radius (m)")
+            intraGranularBubbleRadiusSciantix.append(data[-1, pos].astype(float)*1e9)
+
+            os.chdir('..')
+
+    if mode_plot == 1:
+        do_plot()
+
+    # """ Statistical analysis """
+    # print(f"Experimental data - mean: ", np.mean(igSwellingBaker))
+    # print(f"Experimental data - median: ", np.median(igSwellingBaker))
+    # print(f"Experimental data - Q1: ", np.percentile(igSwellingBaker, 25))
+    # print(f"Experimental data - Q3: ", np.percentile(igSwellingBaker, 75))
+
+    # print(f"SCIANTIX 1.0 - mean: ", np.mean(intraGranularSwellingSciantix1))
+    # print(f"SCIANTIX 1.0 - median: ", np.median(intraGranularSwellingSciantix1))
+    # print(f"SCIANTIX 1.0 - Q1: ", np.percentile(intraGranularSwellingSciantix1, 25))
+    # print(f"SCIANTIX 1.0 - Q3: ", np.percentile(intraGranularSwellingSciantix1, 75))
+
+    # print(f"SCIANTIX 2.0 - mean: ", np.mean(intraGranularSwellingSciantix))
+    # print(f"SCIANTIX 2.0 - median: ", np.median(intraGranularSwellingSciantix))
+    # print(f"SCIANTIX 2.0 - Q1: ", np.percentile(intraGranularSwellingSciantix, 25))
+    # print(f"SCIANTIX 2.0 - Q3: ", np.percentile(intraGranularSwellingSciantix, 75))
+
+    # deviations_1 = abs(np.array(igSwellingBaker) - intraGranularSwellingSciantix1)
+    # deviations_2 = abs(np.array(igSwellingBaker) - intraGranularSwellingSciantix)
+    # print(f"SCIANTIX 1.0 - MAD: ", np.median(deviations_1))
+    # print(f"SCIANTIX 2.0 - MAD: ", np.median(deviations_2))
+
+    # print(f"SCIANTIX 1.0 - RMSE: ", np.mean(np.array(igSwellingBaker) - intraGranularSwellingSciantix1)**2)
+    # print(f"SCIANTIX 2.0 - RMSE: ", np.mean(np.array(igSwellingBaker) - intraGranularSwellingSciantix)**2)
+    # print("\n")
+
+    return folderList, number_of_tests, number_of_tests_failed

regression/test_Cornell1969_1133K/input_history.txt

@@ -0,0 +1,2 @@
+0	1133	9.26e18	0
+960	1133	9.26e18	0

regression/test_Cornell1969_1133K/input_initial_conditions.txt

@@ -0,0 +1,28 @@
+5.0e-06
+#	initial grain radius (m)
+0.0	0.0	0.0	0.0	0.0	0.0
+#	initial Xe (at/m3) produced, intragranular, intragranular in solution, intragranular in bubbles, grain boundary, released
+0.0	0.0	0.0	0.0	0.0	0.0
+#	initial Kr (at/m3) produced, intragranular, intragranular in solution, intragranular in bubbles, grain boundary, released
+0.0	0.0	0.0	0.0	0.0	0.0
+#	initial He (at/m3) produced, intragranular, intragranular in solution, intragranular in bubbles, grain boundary, released
+0.0 0.0
+# initial intragranular bubble concentration (at/m3), radius (m)
+0.0
+#	initial fuel burn-up (MWd/kgUO2)
+0.0
+#	initial fuel effective burn-up (MWd/kgUO2)
+0.0
+#	initial irradiation time (h)
+10641.0
+#	initial fuel density (kg/m3)
+0.0	3.0	0.0	0.0	97.0
+#	initial U234 U235 U236 U237 U238 (% of heavy atoms) content
+0.0	0.0	0.0	0.0	0.0	0.0 0.0
+#	initial Xe133 (at/m3) produced, intragranular, intragranular in solution, intragranular in bubbles, decayed, grain boundary, released
+0.0	0.0	0.0	0.0	0.0	0.0 0.0
+#	initial Kr85m (at/m3) produced, intragranular, intragranular in solution, intragranular in bubbles, decayed, grain boundary, released
+0.0
+#   initial fuel stoichiometry deviation (\)
+1000
+#   Cr content (ppm)

regression/test_Cornell1969_1133K/input_scaling_factors.txt

@@ -0,0 +1,18 @@
+1.0
+# scaling factor - resolution rate
+1.0
+# scaling factor - trapping rate
+1.0
+# scaling factor - nucleation rate
+1.0
+# scaling factor - diffusivity
+1.0
+# scaling factor - temperature
+1.0
+# scaling factor - fission rate
+1.0
+# scaling factor - cent parameter
+1.0
+# scaling factor - helium production rate
+1.0
+# scaling factor - dummy

regression/test_Cornell1969_1133K/input_settings.txt

@@ -0,0 +1,22 @@
+1    #    iGrainGrowth (0= no grain growth, 1= Ainscough et al. (1973), 2= Van Uffelen et al. (2013))
+1    #    iFissionGasDiffusivity (0= constant value, 1= Turnbull et al. (1988))
+1    #    iDiffusionSolver (1= SDA with quasi-stationary hypothesis, 2= SDA without quasi-stationary hypothesis)
+1    #    iIntraGranularBubbleBehavior (1= Pizzocri et al. (2018))
+1    #    iResolutionRate (0= constant value, 1= Turnbull (1971), 2= Losonen (2000), 3= thermal resolution, Cognini et al. (2021))
+1    #    iTrappingRate (0= constant value, 1= Ham (1958))
+1    #    iNucleationRate (0= constant value, 1= Olander, Wongsawaeng (2006))
+1    #    iOutput (1= default output files)
+1    #    iGrainBoundaryVacancyDiffusivity (0= constant value, 1= Reynolds and Burton (1979), 2= White (2004))
+1    #    iGrainBoundaryBehaviour (0= no grain boundary bubbles, 1= Pastore et al (2013))
+1    #    iGrainBoundaryMicroCracking (0= no model considered, 1= Barani et al. (2017))
+0    #    iFuelMatrix (0= UO2, 1= UO2 + HBS)
+0    #    iGrainBoundaryVenting (0= no model considered, 1= Pizzocri et al., D6.4 (2020), H2020 Project INSPYRE)
+0    #    iRadioactiveFissionGas (0= not considered)
+0    #    iHelium (0= not considered)
+0    #    iHeDiffusivity (0= null value, 1= limited lattice damage, Luzzi et al. (2018), 2= significant lattice damage, Luzzi et al. (2018))
+0    #    iGrainBoundarySweeping (0= no model considered, 1= TRANSURANUS swept volume model)
+0    #    iHighBurnupStructureFormation (0= no model considered, 1= fraction of HBS-restructured volume from Barani et al. (2020))
+0    #    iHighBurnupStructurePorosity (0= no evolution of HBS porosity, 1= HBS porosity evolution based on Spino et al. (2006) data)
+0    #    iHeliumProductionRate (0= zero production rate, 1= helium from ternary fissions, 2= linear with burnup (FR))
+0    #    iStoichiometryDeviation (0= not considered, 1= Cox et al. 1986, 2= Bittel et al. 1969, 3= Abrefah et al. 1994, 4= Imamura et al. 1997, 5= Langmuir-based approach)
+0    #    iBubbleDiffusivity (0= not considered, 1= volume diffusivity)