Minor updates to match most recent pymatgen

SMTG-Bham · May 4, 2024 · 4886aa0 · 4886aa0
1 parent e1f05d6
commit 4886aa0
Show file tree

Hide file tree

Showing 20 changed files with 76 additions and 74 deletions.
diff --git a/doped/utils/supercells.py b/doped/utils/supercells.py
@@ -72,8 +72,8 @@ def _get_min_image_distance_from_matrix(matrix: np.ndarray) -> float:
     eff_cubic_length = lattice.volume ** (1 / 3)
     max_min_dist = eff_cubic_length * (2 ** (1 / 6))  # max hypothetical min image distance in 3D lattice
 
-    zipped_fcoords_dist_idx_image = lattice.get_points_in_sphere(
-        [[0, 0, 0]], [0, 0, 0], r=max_min_dist * 1.01
+    zipped_fcoords_dist_idx_image = list(
+        lattice.get_points_in_sphere([[0, 0, 0]], [0, 0, 0], r=max_min_dist * 1.01)
     )
 
     # sort zipped list by dist:

diff --git a/doped/vasp.py b/doped/vasp.py
@@ -81,11 +81,11 @@ def _test_potcar_functional_choice(
         symbols = ["Mg"]
     try:
         test_potcar = _get_potcar(tuple(symbols), potcar_functional=potcar_functional)
-    except OSError as e:
+    except (OSError, RuntimeError) as e:  # updated to RuntimeError in pymatgen 2024.5.1
         # try other functional choices:
         if potcar_functional.startswith("PBE"):
             for pbe_potcar_string in ["PBE", "PBE_52", "PBE_54"]:
-                with contextlib.suppress(OSError):
+                with contextlib.suppress(OSError, RuntimeError):
                     potcar_functional = pbe_potcar_string
                     test_potcar = _get_potcar(tuple(symbols), potcar_functional=potcar_functional)
                     break

diff --git a/examples/CdTe/CdTe_example_defect_dict.json b/examples/CdTe/CdTe_example_defect_dict.json
diff --git a/examples/CdTe/CdTe_example_thermo.json b/examples/CdTe/CdTe_example_thermo.json
diff --git a/examples/Sb2Si2Te6/Sb2Si2Te6_example_defect_dict.json b/examples/Sb2Si2Te6/Sb2Si2Te6_example_defect_dict.json
diff --git a/examples/Sb2Si2Te6/Sb2Si2Te6_example_thermo.json b/examples/Sb2Si2Te6/Sb2Si2Te6_example_thermo.json
diff --git a/examples/YTOS/YTOS_example_defect_dict.json b/examples/YTOS/YTOS_example_defect_dict.json
diff --git a/examples/YTOS/YTOS_example_thermo.json b/examples/YTOS/YTOS_example_thermo.json
diff --git a/tests/data/N_diamond_defect_gen.json b/tests/data/N_diamond_defect_gen.json
diff --git a/tests/data/Sb2Se3/Sb2Se3_O_example_thermo.json b/tests/data/Sb2Se3/Sb2Se3_O_example_thermo.json
diff --git a/tests/data/Sb2Se3/defect/Sb2Se3_O_example_defect_dict.json b/tests/data/Sb2Se3/defect/Sb2Se3_O_example_defect_dict.json
diff --git a/tests/data/V2O5/V2O5_example_defect_dict.json b/tests/data/V2O5/V2O5_example_defect_dict.json
diff --git a/tests/data/V2O5/V2O5_example_thermo.json b/tests/data/V2O5/V2O5_example_thermo.json
diff --git a/tests/data/ZnS/ZnS_thermo.json b/tests/data/ZnS/ZnS_thermo.json
diff --git a/tests/data/agcu_defect_gen.json b/tests/data/agcu_defect_gen.json
diff --git a/tests/data/cd_i_supercell_defect_gen.json b/tests/data/cd_i_supercell_defect_gen.json
diff --git a/tests/data/lmno_defect_gen.json b/tests/data/lmno_defect_gen.json
diff --git a/tests/data/ytos_defect_gen.json b/tests/data/ytos_defect_gen.json
diff --git a/tests/test_generation.py b/tests/test_generation.py
@@ -339,7 +339,7 @@ def setUp(self):
 v_Cd_Cs_Te2.83Cd4.62Cd5.36    [+1,0,-1]          [0.555,0.111,0.111]  9b
 v_Cd_Cs_Te2.83Cd4.62Te5.42a   [+1,0,-1]          [0.222,0.111,0.111]  9b
 v_Cd_Cs_Te2.83Cd4.62Te5.42b   [+1,0,-1]          [0.111,0.222,0.222]  9b
-v_Cd_Cs_Te2.83Cd4.62Te5.42c   [+1,0,-1]          [0.444,0.222,0.222]  9b
+v_Cd_Cs_Te2.83Cd4.62Te5.42c   [+1,0,-1]          [0.445,0.222,0.222]  9b
 v_Te_C1                       [+1,0,-1]          [0.333,0.333,0.250]  18c
 v_Te_C3v_Cd2.83Cd4.25         [+1,0,-1]          [0.000,0.000,0.583]  3a
 v_Te_C3v_Cd2.83Te4.62Cd5.42a  [+1,0,-1]          [0.000,0.000,0.250]  3a
@@ -373,7 +373,7 @@ def setUp(self):
 Te_Cd_Cs_Te2.83Cd4.62Cd5.36    [+4,+3,+2,+1,0,-1,-2]  [0.555,0.111,0.111]  9b
 Te_Cd_Cs_Te2.83Cd4.62Te5.42a   [+4,+3,+2,+1,0,-1,-2]  [0.222,0.111,0.111]  9b
 Te_Cd_Cs_Te2.83Cd4.62Te5.42b   [+4,+3,+2,+1,0,-1,-2]  [0.111,0.222,0.222]  9b
-Te_Cd_Cs_Te2.83Cd4.62Te5.42c   [+4,+3,+2,+1,0,-1,-2]  [0.444,0.222,0.222]  9b
+Te_Cd_Cs_Te2.83Cd4.62Te5.42c   [+4,+3,+2,+1,0,-1,-2]  [0.445,0.222,0.222]  9b
 
 Interstitials                 Guessed Charges        Conv. Cell Coords    Wyckoff
 ----------------------------  ---------------------  -------------------  ---------
@@ -384,7 +384,7 @@ def setUp(self):
 Cd_i_C1_Cd2.71Te2.71Cd4.25c   [+2,+1,0]              [0.167,0.167,0.625]  18c
 Cd_i_C1_Cd2.71Te2.71Cd4.25d   [+2,+1,0]              [0.167,0.167,0.958]  18c
 Cd_i_C1_Cd2.71Te2.71Cd4.25e   [+2,+1,0]              [0.056,0.278,0.069]  18c
-Cd_i_C1_Cd2.71Te2.71Cd4.25f   [+2,+1,0]              [0.278,0.056,0.180]  18c
+Cd_i_C1_Cd2.71Te2.71Cd4.25f   [+2,+1,0]              [0.278,0.055,0.180]  18c
 Cd_i_C1_Cd2.71Te2.71Cd4.25g   [+2,+1,0]              [0.389,0.111,0.069]  18c
 Cd_i_C1_Cd2.71Te2.71Cd4.25h   [+2,+1,0]              [0.445,0.056,0.180]  18c
 Cd_i_C1_Cd2.83                [+2,+1,0]              [0.333,0.333,0.083]  18c
@@ -429,7 +429,7 @@ def setUp(self):
 Te_i_C1_Cd2.71Te2.71Cd4.25c   [+4,+3,+2,+1,0,-1,-2]  [0.167,0.167,0.625]  18c
 Te_i_C1_Cd2.71Te2.71Cd4.25d   [+4,+3,+2,+1,0,-1,-2]  [0.167,0.167,0.958]  18c
 Te_i_C1_Cd2.71Te2.71Cd4.25e   [+4,+3,+2,+1,0,-1,-2]  [0.056,0.278,0.069]  18c
-Te_i_C1_Cd2.71Te2.71Cd4.25f   [+4,+3,+2,+1,0,-1,-2]  [0.278,0.056,0.180]  18c
+Te_i_C1_Cd2.71Te2.71Cd4.25f   [+4,+3,+2,+1,0,-1,-2]  [0.278,0.055,0.180]  18c
 Te_i_C1_Cd2.71Te2.71Cd4.25g   [+4,+3,+2,+1,0,-1,-2]  [0.389,0.111,0.069]  18c
 Te_i_C1_Cd2.71Te2.71Cd4.25h   [+4,+3,+2,+1,0,-1,-2]  [0.445,0.056,0.180]  18c
 Te_i_C1_Cd2.83                [+4,+3,+2,+1,0,-1,-2]  [0.333,0.333,0.083]  18c
@@ -484,10 +484,10 @@ def setUp(self):
 v_C_C1_C1.54C2.52C2.95c   [+1,0,-1]          [0.278,0.222,0.222]  18c
 v_C_C1_C1.54C2.52C2.95d   [+1,0,-1]          [0.333,0.333,0.028]  18c
 v_C_C1_C1.54C2.52C2.95e   [+1,0,-1]          [0.333,0.333,0.111]  18c
-v_C_C1_C1.54C2.52C2.95f   [+1,0,-1]          [0.167,0.167,0.444]  18c
-v_C_C1_C1.54C2.52C2.95g   [+1,0,-1]          [0.167,0.167,0.694]  18c
+v_C_C1_C1.54C2.52C2.95f   [+1,0,-1]          [0.167,0.167,0.445]  18c
+v_C_C1_C1.54C2.52C2.95g   [+1,0,-1]          [0.167,0.167,0.695]  18c
 v_C_C1_C1.54C2.52C2.95h   [+1,0,-1]          [0.167,0.167,0.778]  18c
-v_C_C1_C1.54C2.52C2.95i   [+1,0,-1]          [0.055,0.278,0.000]  18c
+v_C_C1_C1.54C2.52C2.95i   [+1,0,-1]          [0.056,0.278,0.000]  18c
 v_C_C1_C1.54C2.52C2.95j   [+1,0,-1]          [0.278,0.056,0.139]  18c
 v_C_C1_C1.54C2.52C2.95k   [+1,0,-1]          [0.056,0.278,0.250]  18c
 v_C_C1_C1.54C2.52C2.95l   [+1,0,-1]          [0.389,0.111,0.000]  18c
@@ -497,43 +497,43 @@ def setUp(self):
 v_C_C1_C1.54C2.52C2.95p   [+1,0,-1]          [0.445,0.056,0.139]  18c
 v_C_C1_C1.54C2.52C2.95q   [+1,0,-1]          [0.389,0.111,0.250]  18c
 v_C_C1_C1.54C2.52C2.95r   [+1,0,-1]          [0.445,0.056,0.222]  18c
-v_C_C1_C1.54C2.52C2.95s   [+1,0,-1]          [0.056,0.445,0.250]  18c
+v_C_C1_C1.54C2.52C2.95s   [+1,0,-1]          [0.056,0.444,0.250]  18c
 v_C_C1_C1.54C2.52N2.52    [+1,0,-1]          [0.167,0.167,0.361]  18c
 v_C_C3v_C1.54C2.52C2.95a  [+1,0,-1]          [0.000,0.000,0.028]  3a
 v_C_C3v_C1.54C2.52C2.95b  [+1,0,-1]          [0.000,0.000,0.111]  3a
-v_C_C3v_C1.54C2.52C2.95c  [+1,0,-1]          [0.000,0.000,0.694]  3a
+v_C_C3v_C1.54C2.52C2.95c  [+1,0,-1]          [0.000,0.000,0.695]  3a
 v_C_C3v_C1.54C2.52C2.95d  [+1,0,-1]          [0.000,0.000,0.778]  3a
-v_C_C3v_C1.54N1.54        [+1,0,-1]          [0.000,0.000,0.444]  3a
+v_C_C3v_C1.54N1.54        [+1,0,-1]          [0.000,0.000,0.445]  3a
 v_C_Cs_C1.54C2.52C2.95a   [+1,0,-1]          [0.111,0.222,0.222]  9b
-v_C_Cs_C1.54C2.52C2.95b   [+1,0,-1]          [0.445,0.222,0.222]  9b
+v_C_Cs_C1.54C2.52C2.95b   [+1,0,-1]          [0.444,0.222,0.222]  9b
 v_C_Cs_C1.54C2.52C2.95c   [+1,0,-1]          [0.611,0.222,0.222]  9b
 v_C_Cs_C1.54C2.52C2.95d   [+1,0,-1]          [0.500,0.500,0.028]  9b
 v_C_Cs_C1.54C2.52C2.95e   [+1,0,-1]          [0.500,0.500,0.111]  9b
 v_C_Cs_C1.54C2.52C2.95f   [+1,0,-1]          [0.500,0.500,0.361]  9b
-v_C_Cs_C1.54C2.52C2.95g   [+1,0,-1]          [0.500,0.500,0.445]  9b
+v_C_Cs_C1.54C2.52C2.95g   [+1,0,-1]          [0.500,0.500,0.444]  9b
 v_C_Cs_C1.54C2.52C2.95h   [+1,0,-1]          [0.500,0.500,0.694]  9b
 v_C_Cs_C1.54C2.52C2.95i   [+1,0,-1]          [0.500,0.500,0.778]  9b
 v_C_Cs_C1.54C2.52C2.95j   [+1,0,-1]          [0.056,0.111,0.000]  9b
-v_C_Cs_C1.54C2.52C2.95k   [+1,0,-1]          [0.111,0.055,0.139]  9b
+v_C_Cs_C1.54C2.52C2.95k   [+1,0,-1]          [0.111,0.056,0.139]  9b
 v_C_Cs_C1.54C2.52C2.95l   [+1,0,-1]          [0.222,0.111,0.000]  9b
-v_C_Cs_C1.54C2.52C2.95m   [+1,0,-1]          [0.111,0.055,0.222]  9b
+v_C_Cs_C1.54C2.52C2.95m   [+1,0,-1]          [0.111,0.056,0.222]  9b
 v_C_Cs_C1.54C2.52C2.95n   [+1,0,-1]          [0.111,0.222,0.139]  9b
 v_C_Cs_C1.54C2.52C2.95o   [+1,0,-1]          [0.222,0.111,0.250]  9b
 v_C_Cs_C1.54C2.52C2.95p   [+1,0,-1]          [0.222,0.111,0.333]  9b
-v_C_Cs_C1.54C2.52C2.95q   [+1,0,-1]          [0.445,0.222,0.139]  9b
+v_C_Cs_C1.54C2.52C2.95q   [+1,0,-1]          [0.444,0.222,0.139]  9b
 v_C_Cs_C1.54C2.52C2.95r   [+1,0,-1]          [0.111,0.222,0.472]  9b
-v_C_Cs_C1.54C2.52C2.95s   [+1,0,-1]          [0.222,0.445,0.250]  9b
-v_C_Cs_C1.54C2.52C2.95t   [+1,0,-1]          [0.556,0.111,0.000]  9b
-v_C_Cs_C1.54C2.52C2.95u   [+1,0,-1]          [0.111,0.055,0.556]  9b
-v_C_Cs_C1.54C2.52C2.95v   [+1,0,-1]          [0.055,0.111,0.583]  9b
-v_C_Cs_C1.54C2.52C2.95w   [+1,0,-1]          [0.111,0.222,0.556]  9b
-v_C_Cs_C1.54C2.52C2.95x   [+1,0,-1]          [0.555,0.111,0.250]  9b
+v_C_Cs_C1.54C2.52C2.95s   [+1,0,-1]          [0.222,0.444,0.250]  9b
+v_C_Cs_C1.54C2.52C2.95t   [+1,0,-1]          [0.555,0.111,0.000]  9b
+v_C_Cs_C1.54C2.52C2.95u   [+1,0,-1]          [0.111,0.056,0.556]  9b
+v_C_Cs_C1.54C2.52C2.95v   [+1,0,-1]          [0.056,0.111,0.583]  9b
+v_C_Cs_C1.54C2.52C2.95w   [+1,0,-1]          [0.111,0.555,0.222]  9b
+v_C_Cs_C1.54C2.52C2.95x   [+1,0,-1]          [0.556,0.111,0.250]  9b
 v_C_Cs_C1.54C2.52C2.95y   [+1,0,-1]          [0.556,0.278,0.000]  9b
 v_C_Cs_C1.54C2.52C2.95z   [+1,0,-1]          [0.611,0.222,0.139]  9b
 v_C_Cs_C1.54C2.52C2.95{   [+1,0,-1]          [0.556,0.278,0.250]  9b
-v_C_Cs_C1.54C2.52N2.52a   [+1,0,-1]          [0.055,0.111,0.250]  9b
-v_C_Cs_C1.54C2.52N2.52b   [+1,0,-1]          [0.111,0.055,0.472]  9b
-v_C_Cs_C1.54N1.54         [+1,0,-1]          [0.055,0.111,0.333]  9b
+v_C_Cs_C1.54C2.52N2.52a   [+1,0,-1]          [0.056,0.111,0.250]  9b
+v_C_Cs_C1.54C2.52N2.52b   [+1,0,-1]          [0.111,0.056,0.472]  9b
+v_C_Cs_C1.54N1.54         [+1,0,-1]          [0.056,0.111,0.333]  9b
 v_N                       [+1,0,-1]          [0.000,0.000,0.361]  3a
 
 Substitutions             Guessed Charges    Conv. Cell Coords    Wyckoff
@@ -544,10 +544,10 @@ def setUp(self):
 N_C_C1_C1.54C2.52C2.95c   [+1,0,-1]          [0.278,0.222,0.222]  18c
 N_C_C1_C1.54C2.52C2.95d   [+1,0,-1]          [0.333,0.333,0.028]  18c
 N_C_C1_C1.54C2.52C2.95e   [+1,0,-1]          [0.333,0.333,0.111]  18c
-N_C_C1_C1.54C2.52C2.95f   [+1,0,-1]          [0.167,0.167,0.444]  18c
-N_C_C1_C1.54C2.52C2.95g   [+1,0,-1]          [0.167,0.167,0.694]  18c
+N_C_C1_C1.54C2.52C2.95f   [+1,0,-1]          [0.167,0.167,0.445]  18c
+N_C_C1_C1.54C2.52C2.95g   [+1,0,-1]          [0.167,0.167,0.695]  18c
 N_C_C1_C1.54C2.52C2.95h   [+1,0,-1]          [0.167,0.167,0.778]  18c
-N_C_C1_C1.54C2.52C2.95i   [+1,0,-1]          [0.055,0.278,0.000]  18c
+N_C_C1_C1.54C2.52C2.95i   [+1,0,-1]          [0.056,0.278,0.000]  18c
 N_C_C1_C1.54C2.52C2.95j   [+1,0,-1]          [0.278,0.056,0.139]  18c
 N_C_C1_C1.54C2.52C2.95k   [+1,0,-1]          [0.056,0.278,0.250]  18c
 N_C_C1_C1.54C2.52C2.95l   [+1,0,-1]          [0.389,0.111,0.000]  18c
@@ -557,43 +557,43 @@ def setUp(self):
 N_C_C1_C1.54C2.52C2.95p   [+1,0,-1]          [0.445,0.056,0.139]  18c
 N_C_C1_C1.54C2.52C2.95q   [+1,0,-1]          [0.389,0.111,0.250]  18c
 N_C_C1_C1.54C2.52C2.95r   [+1,0,-1]          [0.445,0.056,0.222]  18c
-N_C_C1_C1.54C2.52C2.95s   [+1,0,-1]          [0.056,0.445,0.250]  18c
+N_C_C1_C1.54C2.52C2.95s   [+1,0,-1]          [0.056,0.444,0.250]  18c
 N_C_C1_C1.54C2.52N2.52    [+1,0,-1]          [0.167,0.167,0.361]  18c
 N_C_C3v_C1.54C2.52C2.95a  [+1,0,-1]          [0.000,0.000,0.028]  3a
 N_C_C3v_C1.54C2.52C2.95b  [+1,0,-1]          [0.000,0.000,0.111]  3a
-N_C_C3v_C1.54C2.52C2.95c  [+1,0,-1]          [0.000,0.000,0.694]  3a
+N_C_C3v_C1.54C2.52C2.95c  [+1,0,-1]          [0.000,0.000,0.695]  3a
 N_C_C3v_C1.54C2.52C2.95d  [+1,0,-1]          [0.000,0.000,0.778]  3a
-N_C_C3v_C1.54N1.54        [+1,0,-1]          [0.000,0.000,0.444]  3a
+N_C_C3v_C1.54N1.54        [+1,0,-1]          [0.000,0.000,0.445]  3a
 N_C_Cs_C1.54C2.52C2.95a   [+1,0,-1]          [0.111,0.222,0.222]  9b
-N_C_Cs_C1.54C2.52C2.95b   [+1,0,-1]          [0.445,0.222,0.222]  9b
+N_C_Cs_C1.54C2.52C2.95b   [+1,0,-1]          [0.444,0.222,0.222]  9b
 N_C_Cs_C1.54C2.52C2.95c   [+1,0,-1]          [0.611,0.222,0.222]  9b
 N_C_Cs_C1.54C2.52C2.95d   [+1,0,-1]          [0.500,0.500,0.028]  9b
 N_C_Cs_C1.54C2.52C2.95e   [+1,0,-1]          [0.500,0.500,0.111]  9b
 N_C_Cs_C1.54C2.52C2.95f   [+1,0,-1]          [0.500,0.500,0.361]  9b
-N_C_Cs_C1.54C2.52C2.95g   [+1,0,-1]          [0.500,0.500,0.445]  9b
+N_C_Cs_C1.54C2.52C2.95g   [+1,0,-1]          [0.500,0.500,0.444]  9b
 N_C_Cs_C1.54C2.52C2.95h   [+1,0,-1]          [0.500,0.500,0.694]  9b
 N_C_Cs_C1.54C2.52C2.95i   [+1,0,-1]          [0.500,0.500,0.778]  9b
 N_C_Cs_C1.54C2.52C2.95j   [+1,0,-1]          [0.056,0.111,0.000]  9b
-N_C_Cs_C1.54C2.52C2.95k   [+1,0,-1]          [0.111,0.055,0.139]  9b
+N_C_Cs_C1.54C2.52C2.95k   [+1,0,-1]          [0.111,0.056,0.139]  9b
 N_C_Cs_C1.54C2.52C2.95l   [+1,0,-1]          [0.222,0.111,0.000]  9b
-N_C_Cs_C1.54C2.52C2.95m   [+1,0,-1]          [0.111,0.055,0.222]  9b
+N_C_Cs_C1.54C2.52C2.95m   [+1,0,-1]          [0.111,0.056,0.222]  9b
 N_C_Cs_C1.54C2.52C2.95n   [+1,0,-1]          [0.111,0.222,0.139]  9b
 N_C_Cs_C1.54C2.52C2.95o   [+1,0,-1]          [0.222,0.111,0.250]  9b
 N_C_Cs_C1.54C2.52C2.95p   [+1,0,-1]          [0.222,0.111,0.333]  9b
-N_C_Cs_C1.54C2.52C2.95q   [+1,0,-1]          [0.445,0.222,0.139]  9b
+N_C_Cs_C1.54C2.52C2.95q   [+1,0,-1]          [0.444,0.222,0.139]  9b
 N_C_Cs_C1.54C2.52C2.95r   [+1,0,-1]          [0.111,0.222,0.472]  9b
-N_C_Cs_C1.54C2.52C2.95s   [+1,0,-1]          [0.222,0.445,0.250]  9b
-N_C_Cs_C1.54C2.52C2.95t   [+1,0,-1]          [0.556,0.111,0.000]  9b
-N_C_Cs_C1.54C2.52C2.95u   [+1,0,-1]          [0.111,0.055,0.556]  9b
-N_C_Cs_C1.54C2.52C2.95v   [+1,0,-1]          [0.055,0.111,0.583]  9b
-N_C_Cs_C1.54C2.52C2.95w   [+1,0,-1]          [0.111,0.222,0.556]  9b
-N_C_Cs_C1.54C2.52C2.95x   [+1,0,-1]          [0.555,0.111,0.250]  9b
+N_C_Cs_C1.54C2.52C2.95s   [+1,0,-1]          [0.222,0.444,0.250]  9b
+N_C_Cs_C1.54C2.52C2.95t   [+1,0,-1]          [0.555,0.111,0.000]  9b
+N_C_Cs_C1.54C2.52C2.95u   [+1,0,-1]          [0.111,0.056,0.556]  9b
+N_C_Cs_C1.54C2.52C2.95v   [+1,0,-1]          [0.056,0.111,0.583]  9b
+N_C_Cs_C1.54C2.52C2.95w   [+1,0,-1]          [0.111,0.555,0.222]  9b
+N_C_Cs_C1.54C2.52C2.95x   [+1,0,-1]          [0.556,0.111,0.250]  9b
 N_C_Cs_C1.54C2.52C2.95y   [+1,0,-1]          [0.556,0.278,0.000]  9b
 N_C_Cs_C1.54C2.52C2.95z   [+1,0,-1]          [0.611,0.222,0.139]  9b
 N_C_Cs_C1.54C2.52C2.95{   [+1,0,-1]          [0.556,0.278,0.250]  9b
-N_C_Cs_C1.54C2.52N2.52a   [+1,0,-1]          [0.055,0.111,0.250]  9b
-N_C_Cs_C1.54C2.52N2.52b   [+1,0,-1]          [0.111,0.055,0.472]  9b
-N_C_Cs_C1.54N1.54         [+1,0,-1]          [0.055,0.111,0.333]  9b
+N_C_Cs_C1.54C2.52N2.52a   [+1,0,-1]          [0.056,0.111,0.250]  9b
+N_C_Cs_C1.54C2.52N2.52b   [+1,0,-1]          [0.111,0.056,0.472]  9b
+N_C_Cs_C1.54N1.54         [+1,0,-1]          [0.056,0.111,0.333]  9b
 \n"""
             "The number in the Wyckoff label is the site multiplicity/degeneracy of that defect in the "
             "conventional ('conv.') unit cell, which comprises 3 formula unit(s) of C215N.\n"
@@ -2694,9 +2694,9 @@ def agcu_defect_gen_check(self, agcu_defect_gen, generate_supercell=True):
         assert self.structure_matcher.fit(agcu_defect_gen.primitive_structure, self.agcu)
 
         supercell_matrix = np.array(
-            [[2, 2, -2], [-4, 4, 0], [-4, 0, 4]]
+            [[2, -2, 2], [4, 0, 0], [0, 4, 0]]
             if generate_supercell
-            else [[-1, 1, 1], [1, -1, 1], [1, 1, -1]]
+            else [[1, -1, 1], [0, -2, 0], [2, 0, 0]]
         )
         assert any(np.isclose(agcu_defect_gen.min_image_distance, i, atol=0.01) for i in [10.21, 5.11])
         np.testing.assert_allclose(agcu_defect_gen.supercell_matrix, supercell_matrix)
@@ -2737,7 +2737,9 @@ def agcu_defect_gen_check(self, agcu_defect_gen, generate_supercell=True):
         )
         assert agcu_defect_gen.defect_entries["Cu_i_C3v_Cu1.56Ag1.56Cu2.99b_+1"].wyckoff == "6c"
         assert agcu_defect_gen.defect_entries["Cu_i_C3v_Cu1.56Ag1.56Cu2.99b_+1"].defect.multiplicity == 2
-        sc_frac_coords = np.array([0.4375, 0.4375, 0.375] if generate_supercell else [0.375, 0.375, 0.375])
+        sc_frac_coords = np.array(
+            [0.4375, 0.4375, 0.5625] if generate_supercell else [0.125, 0.625, 0.625]
+        )
         np.testing.assert_allclose(
             agcu_defect_gen.defect_entries["Cu_i_C3v_Cu1.56Ag1.56Cu2.99b_+1"].sc_defect_frac_coords,
             sc_frac_coords,  # closest to [0.5, 0.5, 0.5]
@@ -2756,7 +2758,7 @@ def agcu_defect_gen_check(self, agcu_defect_gen, generate_supercell=True):
         )
         np.testing.assert_allclose(
             agcu_defect_gen.defect_entries["Cu_i_C3v_Cu1.56Ag1.56Cu2.99b_+1"].defect.site.frac_coords,
-            np.array([0.375, 0.375, 0.375]),
+            np.array([0.375, 0.625, 0.125]),
             rtol=1e-2,
         )
 

diff --git a/tests/test_vasp.py b/tests/test_vasp.py
@@ -297,7 +297,7 @@ def _generate_and_check_dds(self, struct, incar_check=True, **dds_kwargs):
 
     def kpts_nelect_nupdown_check(self, dds, kpt, nelect, nupdown):
         if isinstance(kpt, int):
-            assert dds.kpoints.kpts == [[kpt, kpt, kpt]]
+            assert dds.kpoints.kpts == [(kpt, kpt, kpt)]
         else:
             assert dds.kpoints.kpts == kpt
         if _potcars_available():
@@ -451,7 +451,7 @@ def test_file_writing_with_without_POTCARs(self):
             self._write_and_check_dds_files(dds)
             self._write_and_check_dds_files(dds, potcar_spec=True)  # can only test potcar_spec w/neutral
             self._write_and_check_dds_files(dds, unperturbed_poscar=False)
-        self.kpts_nelect_nupdown_check(dds, [[2, 2, 1]], 1584, 0)
+        self.kpts_nelect_nupdown_check(dds, [(2, 2, 1)], 1584, 0)
         # reciprocal_density = 100/Å⁻³ for YTOS
 
         if not _potcars_available():
@@ -463,7 +463,7 @@ def test_file_writing_with_without_POTCARs(self):
 
         # check changing charge state
         dds = self._generate_and_check_dds(self.ytos_bulk_supercell.copy(), charge_state=1)
-        self.kpts_nelect_nupdown_check(dds, [[2, 2, 1]], 1583, 1)
+        self.kpts_nelect_nupdown_check(dds, [(2, 2, 1)], 1583, 1)
         # reciprocal_density = 100/Å⁻³ for YTOS
         self._write_and_check_dds_files(dds, output_path="YTOS_test_dir")
         self._write_and_check_dds_files(dds, unperturbed_poscar=False)
@@ -1313,7 +1313,7 @@ def test_CdTe_files(self):
         # test DefectDictSet objects:
         for _defect_species, defect_relax_set in defects_set.defect_sets.items():
             for defect_dict_set in [defect_relax_set.vasp_gam, defect_relax_set.bulk_vasp_gam]:
-                assert defect_dict_set.kpoints.kpts == [[1, 1, 1]]
+                assert defect_dict_set.kpoints.kpts == [(1, 1, 1)]
             for defect_dict_set in [
                 defect_relax_set.vasp_std,
                 defect_relax_set.bulk_vasp_std,
@@ -1322,7 +1322,7 @@ def test_CdTe_files(self):
                 defect_relax_set.vasp_ncl,
                 defect_relax_set.bulk_vasp_ncl,
             ]:
-                assert defect_dict_set.kpoints.kpts == [[2, 2, 2]]
+                assert defect_dict_set.kpoints.kpts == [(2, 2, 2)]
 
         # test custom POTCAR and KPOINTS choices (INCAR already tested): also tests dictionary input to
         # DefectsSet
@@ -1350,7 +1350,7 @@ def test_CdTe_files(self):
 
                 for subfolder in ["vasp_std", "vasp_nkred_std", "vasp_ncl"]:
                     kpoints = Kpoints.from_file(f"{folder}/{subfolder}/KPOINTS")
-                    assert kpoints.kpts == [[4, 4, 4]]  # 4x4x4 with 54-atom 3x3x3 prim supercell,
+                    assert kpoints.kpts == [(4, 4, 4)]  # 4x4x4 with 54-atom 3x3x3 prim supercell,
                     # 3x3x3 with 64-atom 2x2x2 conv supercell
 
     def test_write_files_single_defect_entry(self):