Fix

lcmd-epfl · Jun 2, 2024 · 5439ec1 · 5439ec1
1 parent 1946ae3
commit 5439ec1
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/cell2mol/new_c2m_driver.py b/cell2mol/new_c2m_driver.py
@@ -124,7 +124,7 @@
 
         newcell = cell2mol(newcell, refcell, sym_ops, reconstruction, charge_assignment, spin_assignment, debug=debug)        
         newcell.assess_errors(mode="reconstruction")
-        """
+
         if newcell.error_case == 0 and reconstruction :
             reconstruction = False
             charge_assignment = True
@@ -145,7 +145,7 @@
 
                 # Update reference cell object
                 refcell.save(ref_cell_fname)
-        """
+
         # Save unit cell object
         newcell.save(cell_fname)
 

diff --git a/cell2mol/new_c2m_module.py b/cell2mol/new_c2m_module.py
@@ -17,6 +17,8 @@ def cell2mol(newcell: object, refcell: object, sym_ops, reconstruction: bool=Tru
             # Cell Reconstruction
             all_molecules, reconstructed_molecules = reconstuct(refcell, newcell, sym_ops, debug=debug)    
             all_molecules.extend(reconstructed_molecules)                                       
+            # Get moleclist for the unit cell
+            newcell = get_moleclist(newcell, refcell, all_molecules, debug=debug)
 
             if newcell.error_get_fragments:     return newcell
             elif newcell.error_reconstruction:  return newcell
@@ -30,9 +32,6 @@ def cell2mol(newcell: object, refcell: object, sym_ops, reconstruction: bool=Tru
         tini = time.time()
 
         if not newcell.error_reconstruction:
-            # Get moleclist for the unit cell
-            newcell = get_moleclist(newcell, refcell, all_molecules, debug=debug)
-
             # Get unique species for the reference cell
             refcell.get_unique_species(debug=debug)
             print("refcell.unique_species", [specie.formula for specie in refcell.unique_species], refcell.unique_indices)