Commented out core_width_analysis method.

pyscses/set_of_sites.py

@@ -246,40 +246,46 @@ def set_of_sites_from_input_data(cls: object,
                     line[4] = 0.0
         return SetOfSites([site_from_input_file(line, defect_species, site_charge, core, temperature) for line in site_data])
 
-    @ classmethod
-    def core_width_analysis(cls,
-                            input_data, limits, defect_species, site_charge, core, temperature ):
-        """
-        Calculated the width of the 'core' region. This is given as the region where the segregation energies in the system are within a region of positive to negative kT.
-
-        Args:
-        input_data (file): A .txt file where each line includes information about a site.
-        limits (list): Minimum and maximum x coordinates defining the calculation region.
-        defect_species (object): Class object containing information about the defect species present in the system.
-            site_charge (bool): The site charge refers to the contribution to the overall charge of a site given by the original, non-defective species present at that site. True if the site charge contribution is to be included in the calculation, False if it is not to be included.
-            core (str): Core definition. Allowed keywords: 'single' = Single segregation energy used to define the core. 'multi-site' = Layered segregation energies used to define the core while the energies fall in the region of positive and negative kT. 'all' = All sites between a minimum and maximum x coordinate used in calculation.
-        temperature (float): Temperature that the calculation is being run at.
-
-        Returns:
-            float: Distance between the minimum and maximum x coordinates where the segregation energy is in the range of positive to negative kT.
-
-        """
-        site_data = load_site_data( input_data, limits[0], limits[1], site_charge )
-        energies = [ line[4] for line in site_data ]
-        min_energy = min(energies)
-        if core == 'single':
-            for line in site_data:
-                if line[4] > min_energy:
-                    line[4] = 0.0
-        #print(boltzmann_eV * temperature, flush=True)
-        if core == 'multi_site':
-            for line in site_data:
-                if ( -boltzmann_eV * temperature) <= line[4] <= ( boltzmann_eV * temperature ):
-                    line[4] = 0.0
-        energies = [line[4] for line in site_data ]
-        x = [line[2] for line in site_data ]
-        x_seg = np.column_stack(( x, energies ))
-        minval = np.min(x_seg[:,0][np.nonzero(x_seg[:,1])])
-        maxval = np.max(x_seg[:,0][np.nonzero(x_seg[:,1])])
-        core_width = maxval-minval
-        return core_width
+# BEN: Is this used?
+#     @ classmethod
+#     def core_width_analysis(cls,
+#                             input_data,
+#                             limits,
+#                             defect_species,
+#                             site_charge,
+#                             core,
+#                             temperature):
+#         """
+#         Calculated the width of the 'core' region. This is given as the region where the segregation energies in the system are within a region of positive to negative kT.
+#
+#         Args:
+#             input_data (file): A .txt file where each line includes information about a site.
+#             limits (list): Minimum and maximum x coordinates defining the calculation region.
+#             defect_species (object): Class object containing information about the defect species present in the system.
+#             site_charge (bool): The site charge refers to the contribution to the overall charge of a site given by the original, non-defective species present at that site. True if the site charge contribution is to be included in the calculation, False if it is not to be included.
+#             core (str): Core definition. Allowed keywords: 'single' = Single segregation energy used to define the core. 'multi-site' = Layered segregation energies used to define the core while the energies fall in the region of positive and negative kT. 'all' = All sites between a minimum and maximum x coordinate used in calculation.
+#             temperature (float): Temperature that the calculation is being run at.
+#
+#         Returns:
+#             float: Distance between the minimum and maximum x coordinates where the segregation energy is in the range of positive to negative kT.
+#
+#         """
+#         site_data = load_site_data( input_data, limits[0], limits[1], site_charge )
+#         energies = [ line[4] for line in site_data ]
+#         min_energy = min(energies)
+#         if core == 'single':
+#             for line in site_data:
+#                 if line[4] > min_energy:
+#                     line[4] = 0.0
+#         #print(boltzmann_eV * temperature, flush=True)
+#         if core == 'multi_site':
+#             for line in site_data:
+#                 if ( -boltzmann_eV * temperature) <= line[4] <= ( boltzmann_eV * temperature ):
+#                     line[4] = 0.0
+#         energies = [line[4] for line in site_data ]
+#         x = [line[2] for line in site_data ]
+#         x_seg = np.column_stack(( x, energies ))
+#         minval = np.min(x_seg[:,0][np.nonzero(x_seg[:,1])])
+#         maxval = np.max(x_seg[:,0][np.nonzero(x_seg[:,1])])
+#         core_width = maxval-minval
+#         return core_width