Debugging

lcmd-epfl · Jun 5, 2024 · 547ad56 · 547ad56
1 parent eda8773
commit 547ad56
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Showing 6 changed files with 383 additions and 345 deletions.
diff --git a/cell2mol/charge_assignment.py b/cell2mol/charge_assignment.py
@@ -401,7 +401,7 @@ def get_protonation_states_specie(specie: object, debug: int=0) -> list:
                     elif a.connec == 1:
                         elemlist[idx] = "Cl"
                         addedlist[idx] = 1
-                    else:
+                    elif a.connec > 1:
                         block[idx] = 1
                 # Nitrogen
                 elif a.label == "N":

diff --git a/cell2mol/new_cell_reconstruction.py b/cell2mol/new_cell_reconstruction.py
@@ -418,8 +418,7 @@ def get_updated_indices(sp_idx, new, cell_labels, cell_pos, cell_fracs, debug: i
             if n_l == l and np.allclose(n_p, p, atol=1e-4, rtol=1e-2):
                 if np.allclose(np.remainder(n_f, 1), np.remainder(f, 1), atol=1e-4, rtol=1e-2):
                     if debug > 2: 
-                        print(f"symmtry operation {sp_idx}:", f"atom of new (index: {jdx})", n_l, n_p, n_f, \
-                            f"is the same as the atom of the unit cell (index: {kdx})", l, p, f)
+                        print(f"symmtry operation {sp_idx}:", f"atom of new (index: {jdx})", n_l, n_p, n_f, f"is the same as the atom of the unit cell (index: {kdx})", l, p, f)
                 indices_lists.append((jdx, kdx))
     return indices_lists
 

diff --git a/cell2mol/test/Cell_reconstruction_Assign-Copy1.ipynb b/cell2mol/test/Cell_reconstruction_Assign-Copy1.ipynb
diff --git a/cell2mol/test/Cell_reconstruction_Assign.ipynb b/cell2mol/test/Cell_reconstruction_Assign.ipynb