From 6eecc9d4460dc6ae205ab073b9af4d55324eda7c Mon Sep 17 00:00:00 2001
From: my-name <yuri.cho@epfl.ch>
Date: Tue, 7 Jan 2025 19:19:04 +0100
Subject: [PATCH] Update get_metal_poscharges

---
 cell2mol/charge_assignment.py | 36 ++++++++++++++++++++++++++++++++++-
 cell2mol/unitcell.py          |  7 +++++--
 2 files changed, 40 insertions(+), 3 deletions(-)

diff --git a/cell2mol/charge_assignment.py b/cell2mol/charge_assignment.py
index 633963d6..5152e58a 100644
--- a/cell2mol/charge_assignment.py
+++ b/cell2mol/charge_assignment.py
@@ -960,7 +960,6 @@ def get_metal_poscharges(metal: object, debug: int=0) -> list:
     at_charge[47] = [1]  # Ag
     at_charge[48] = [2]  # Cd
     # 3rd-row transition metals.
-    at_charge[57] = []  # La
     at_charge[72] = [4]  # Hf
     at_charge[73] = [2, 3, 4, 5]  # Ta
     at_charge[74] = [0, 2, 4, 5, 6]  # W
@@ -981,6 +980,41 @@ def get_metal_poscharges(metal: object, debug: int=0) -> list:
     at_charge[82] = [0, 2, 4]  # Pb
     at_charge[83] = [0, 3]  # Bi
 
+    # Lanthanides (atomic numbers 57 to 71)
+    at_charge[57] = [3]  # La
+    at_charge[58] = [3, 4]  # Ce
+    at_charge[59] = [3]  # Pr
+    at_charge[60] = [2, 3]  # Nd
+    at_charge[61] = [3]  # Pm
+    at_charge[62] = [2, 3]  # Sm
+    at_charge[63] = [3]  # Eu (some +2)
+    at_charge[64] = [3]  # Gd
+    at_charge[65] = [3]  # Tb (rare +4 in complexes)
+    at_charge[66] = [3]  # Dy
+    at_charge[67] = [3]  # Ho
+    at_charge[68] = [3]  # Er
+    at_charge[69] = [3]  # Tm
+    at_charge[70] = [2, 3]  # Yb
+    at_charge[71] = [3]  # Lu
+
+    # Actinides (atomic numbers 89 to 103)
+    at_charge[89] = [3]  # Ac
+    at_charge[90] = [3, 4]  # Th
+    at_charge[91] = [3, 4, 5]  # Pa
+    at_charge[92] = [3, 4, 5, 6]  # U
+    at_charge[93] = [3, 4, 5, 6]  # Np
+    at_charge[94] = [3, 4, 5, 6]  # Pu
+    at_charge[95] = [3, 4, 5, 6]  # Am
+    at_charge[96] = [3, 4]  # Cm
+    at_charge[97] = [3]  # Bk
+    at_charge[98] = [3]  # Cf
+    at_charge[99] = [3]  # Es
+    at_charge[100] = [2, 3]  # Fm
+    at_charge[101] = [2, 3]  # Md
+    at_charge[102] = [2, 3]  # No
+    at_charge[103] = [3]  # Lr
+
+
     poscharges = at_charge[atnum]
 
     list_of_zero_OS = ["Fe", "Ni", "Ru"]
diff --git a/cell2mol/unitcell.py b/cell2mol/unitcell.py
index 0bad3a2d..b5ad7e27 100644
--- a/cell2mol/unitcell.py
+++ b/cell2mol/unitcell.py
@@ -128,9 +128,12 @@ def perform_cell2mol(newcell, refcell, sym_ops, cell_fname, ref_cell_fname, debu
             refcell.assign_spin(debug=debug)
             refcell.create_bonds(debug=debug)
             refcell.save(ref_cell_fname)
+    
     print_refmoleclist(newcell)
-    print_unique_species(newcell)
-    print_moleclist(newcell)
+    if hasattr(newcell, "unique_species"):
+        print_unique_species(newcell)
+    if hasattr(newcell, "moleclist"):
+        print_moleclist(newcell)
     newcell.save(cell_fname)