Fix

lcmd-epfl · Jun 2, 2024 · 7a07737 · 7a07737
1 parent d05e956
commit 7a07737
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Showing 2 changed files with 38 additions and 18 deletions.
diff --git a/cell2mol/classes.py b/cell2mol/classes.py
@@ -1880,14 +1880,23 @@ def assess_errors(self, mode):
             if self.has_isolated_H:             case = 1
             elif self.has_missing_H:            case = 2
             else :                              case = 0
-        elif mode == "unit_cell":
+        elif mode == "reconstruction":
             print("-------------------------------")
             print("Errors in Reference Molecules")
             print("-------------------------------")
             if self.has_isolated_H:             case = 1
             elif self.has_missing_H:            case = 2
             elif self.error_get_fragments:      case = 3
             elif self.error_reconstruction:     case = 4
+            else :                              case = 0
+        elif mode == "charge_assignment":
+            print("-------------------------------")
+            print("Errors in charge assignment")
+            print("-------------------------------")
+            if self.has_isolated_H:             case = 1
+            elif self.has_missing_H:            case = 2
+            elif self.error_get_fragments:      case = 3
+            elif self.error_reconstruction:     case = 4
             elif self.error_empty_poscharges :  case = 5
             elif self.error_multiple_distrib :  case = 6
             elif self.error_empty_distrib :     case = 7

diff --git a/cell2mol/new_c2m_driver.py b/cell2mol/new_c2m_driver.py
@@ -123,14 +123,15 @@
     error.close()
     sys.stdout = stdout
 
-
+    output = open(output_fname, "a")
+    sys.stdout = error
     ##########################################
     if refcell.error_case != 0:
         sys.exit(1)
     else:
         reconstruction = True
-        charge_assignment = True
-        spin_assignment = True
+        charge_assignment = False
+        spin_assignment = False
 
         # Define new cell object for the unit cell
         newcell = cell(name, cell_labels, cell_pos, cell_fracs, cell_vector, cell_param)
@@ -143,24 +144,34 @@
         newcell.assess_errors(mode="hydrogens")
 
         print(f"ENTERING cell2mol with {debug=}")
-        print(f"with mode {reconstruction=} {charge_assignment=} {spin_assignment=}")
 
         newcell = cell2mol(newcell, refcell, sym_ops, reconstruction, charge_assignment, spin_assignment, debug=debug)        
-        newcell.assess_errors(mode="unit_cell")
-
-        # Save cell object
+        newcell.assess_errors(mode="reconstruction")
+        """
+        if newcell.error_case == 0 and reconstruction :
+            reconstruction = False
+            charge_assignment = True
+            newcell = cell2mol(newcell, refcell, sym_ops, reconstruction, charge_assignment, spin_assignment, debug=debug)        
+            newcell.assess_errors(mode="charge_assignment")
+
+            if newcell.error_case == 0 and charge_assignment : 
+                reconstruction = False
+                charge_assignment = False
+                spin_assignment = True
+                newcell = cell2mol(newcell, refcell, sym_ops, reconstruction, charge_assignment, spin_assignment, debug=debug)
+
+                final_charge_distribution, final_charges = balance_charge(newcell.unique_indices, refcell.unique_species, debug=debug)
+                refcell.unique_species = assign_charge_state_for_unique_species(refcell.unique_species, final_charges[0], debug=debug)
+                refcell.assign_charges_for_refcell(debug=debug)
+                refcell.assign_spin(debug=debug)
+                refcell.create_bonds(debug=debug)
+            
+                # Update reference cell object
+                refcell.save(ref_cell_fname)
+        """
+        # Save unit cell object
         newcell.save(cell_fname)
 
-        if newcell.error_case == 0 and charge_assignment :          
-            final_charge_distribution, final_charges = balance_charge(newcell.unique_indices, refcell.unique_species, debug=debug)
-            refcell.unique_species = assign_charge_state_for_unique_species(refcell.unique_species, final_charges[0], debug=debug)
-            refcell.assign_charges_for_refcell(debug=debug)
-            refcell.assign_spin(debug=debug)
-            refcell.create_bonds(debug=debug)
-
-            # Update reference cell object
-            refcell.save(ref_cell_fname)
-
     output.close()
     sys.stdout = stdout