handling error exit_with_error_exception

cell2mol/final_c2m_driver.py

@@ -4,7 +4,7 @@
 from cell2mol.refcell import process_refcell
 from cell2mol.unitcell import process_unitcell
 from cell2mol.xyz_molecule import get_molecule
-from cell2mol.read_write import prefilter_cif, exit_with_error
+from cell2mol.read_write import prefilter_cif, exit_with_error_input, exit_with_error_exception
 
 def main():
     input, system_type, cell_para, debug_mode = parsing_arguments()
@@ -15,32 +15,35 @@ def main():
 
     print(input, input_path, system_type, cell_para, debug_mode, name, extension)
     if not os.path.exists(input_path):
-        exit_with_error(f"Input file not found: {input_path}")
+        exit_with_error_input(f"Input file not found: {input_path}")
     if extension == ".cif":
         if prefilter_cif(input_path):
             handle_cif_file(input_path, system_type, name, current_dir, debug_mode)
         else:
-            exit_with_error("CIF file is not suitable for processing")
+            exit_with_error_input("CIF file is not suitable for processing")
     elif extension == ".xyz":
         handle_xyz_file(input_path, system_type, name, cell_para, current_dir, debug_mode)
     else:
-        exit_with_error("Invalid file extension")
+        exit_with_error_input("Invalid file extension")
 
 def handle_cif_file(input_path, system_type, name, current_dir, debug_mode):
     if system_type == "reference":
         print("Processing reference (Wyckoff sites) from .cif file")
-        process_refcell(input_path, name, current_dir, debug_mode)
+        try:
+            process_refcell(input_path, name, current_dir, debug_mode)
+        except Exception as e:
+            exit_with_error_exception(e)
     elif system_type == "unitcell":
         print("Processing unit cell from .cif file")
         process_unitcell(input_path, name, current_dir, debug_mode)
     else:
-        exit_with_error("Invalid system type for .cif file", {"system_type": system_type})
+        exit_with_error_input("Invalid system type for .cif file", {"system_type": system_type})
 
 
 def handle_xyz_file(input_path, system_type, name, cell_para, current_dir, debug_mode):
     if system_type == "unitcell":
         if cell_para is None:
-            exit_with_error("Cell parameters must be provided for .xyz file of a unit cell")
+            exit_with_error_input("Cell parameters must be provided for .xyz file of a unit cell")
         else:
             print("Processing unit cell from .xyz file")
             # users should provide chemical formula (Fe-O2-H3) of refmoleculist
@@ -49,7 +52,7 @@ def handle_xyz_file(input_path, system_type, name, cell_para, current_dir, debug
         print("Processing molecule from .xyz file")
         get_molecule(input_path, name, current_dir, debug_mode)
     else:
-        exit_with_error("Invalid system type for .xyz file", {"system_type": system_type})
+        exit_with_error_input("Invalid system type for .xyz file", {"system_type": system_type})
 
 
 if __name__ == "__main__" or __name__ == "cell2mol.final_c2m_driver":

cell2mol/read_write.py

@@ -6,6 +6,7 @@
 import re
 from collections import defaultdict
 import os
+import traceback
 
 #######################
 def get_wyckoff_positions(file_path):
@@ -54,32 +55,48 @@ def get_wyckoff_positions(file_path):
     return ref_labels, ref_fracs
 
 #######################
-def exit_with_error(message):
+def exit_with_error_input(message):
     """Logs the error message to a file and exits the program."""
     error_log_path = os.path.join(os.getcwd(), "error_input.out")
     with open(error_log_path, "w") as error_log:
         error_log.write(f"Error: {message}\n")
     sys.exit(message)
 
+#######################    
+def exit_with_error_exception(e):
+    """Logs the error details to a file and exits the program."""
+    error_details = traceback.format_exc()
+    error_log_path = os.path.join(os.getcwd(), f"error_{type(e).__name__}.out")
+
+    # Write the full error details to the log file
+    with open(error_log_path, "w") as error_log:
+        error_log.write(f"Error message: {type(e).__name__} - {str(e)}\n")
+        error_log.write(f"Error details:\n{error_details}")
+
+    # Print the error details to the console
+    print(f"An error occurred. Details have been logged to {error_log_path}")
+    print(f"Error details:\n{error_details}")
+
+    sys.exit(e)
 #######################
 def prefilter_cif(input_path):
 
     with open(input_path, 'r') as ciffile:
         file_content = ciffile.read()
         if 'radical' in file_content:
-            exit_with_error("Radical found in cif file. STOPPING")                   
+            exit_with_error_input("Radical found in cif file. STOPPING")                   
             return False
         elif '_atom_site_fract_x' not in file_content:
-            exit_with_error("No fractional coordinates found in cif file. STOPPING")  
+            exit_with_error_input("No fractional coordinates found in cif file. STOPPING")  
             return False
         elif '?' in file_content:
             if "_diffrn_ambient_temperature ?" not in file_content and "_chemical_melting_point ?" not in file_content:
-                exit_with_error("Disorder found in cif file. STOPPING")
+                exit_with_error_input("Disorder found in cif file. STOPPING")
                 return False
             else:
                 num_greps = file_content.count('?')
                 if num_greps > 1:
-                    exit_with_error("Disorder found in cif file. STOPPING")                      
+                    exit_with_error_input("Disorder found in cif file. STOPPING")                      
                     return False
                 else:
                     return True