Minor tests updates

SMTG-Bham · Oct 9, 2024 · b303e97 · b303e97
1 parent ca32f47
commit b303e97
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Showing 288 changed files with 306 additions and 307 deletions.
diff --git a/doped/corrections.py b/doped/corrections.py
@@ -35,6 +35,7 @@
 eFNV) were developed, they should be used here.
 """
 
+import contextlib
 import os
 import warnings
 from typing import Optional, Union
@@ -518,12 +519,16 @@ def doped_make_efnv_correction(
 
     core_potentials_dict = {}
     for key, outcar in zip(["defect", "bulk"], [defect_outcar, bulk_outcar]):
-        total_energy = [
-            defect_entry.sc_entry.energy if key == "defect" else defect_entry.bulk_entry.energy,
-            defect_entry.calculation_metadata["run_metadata"][f"{key}_vasprun_dict"]["output"][
-                "ionic_steps"
-            ][-1]["electronic_steps"][-1]["e_0_energy"],
-        ]
+        total_energy = []
+        with contextlib.suppress(Exception):
+            total_energy.append(
+                defect_entry.sc_entry.energy if key == "defect" else defect_entry.bulk_entry.energy
+            )
+            total_energy.append(
+                defect_entry.calculation_metadata["run_metadata"][f"{key}_vasprun_dict"]["output"][
+                    "ionic_steps"
+                ][-1]["electronic_steps"][-1]["e_0_energy"]
+            )
 
         if outcar is not None:
             core_potentials_dict[key] = _check_if_pathlike_and_get_locpot_or_core_pots(

diff --git a/doped/generation.py b/doped/generation.py
@@ -1102,7 +1102,7 @@ def __init__(
         generate_supercell: bool = True,
         charge_state_gen_kwargs: Optional[dict] = None,
         supercell_gen_kwargs: Optional[dict[str, Union[int, float, bool]]] = None,
-        interstitial_gen_kwargs: Optional[dict] = None,
+        interstitial_gen_kwargs: Optional[Union[dict, bool]] = None,
         target_frac_coords: Optional[list] = None,
         processes: Optional[int] = None,
     ):
@@ -1210,7 +1210,7 @@ def __init__(
                 (such as ``min_dist``, ``clustering_tol``, ``symmetry_preference``,
                 ``stol`` and ``tight_stol`` -- see its docstring), or
                 ``InterstitialGenerator`` if ``interstitial_coords`` is specified.
-                If set to False, interstitial generation will be skipped entirely.
+                If set to ``False``, interstitial generation will be skipped entirely.
             target_frac_coords (list):
                 Defects are placed at the closest equivalent site to these fractional
                 coordinates in the generated supercells. Default is [0.5, 0.5, 0.5]
@@ -1265,7 +1265,7 @@ def __init__(
             "force_diagonal": False,
         }
         self.supercell_gen_kwargs.update(supercell_gen_kwargs if supercell_gen_kwargs is not None else {})
-        self.interstitial_gen_kwargs: dict[str, Union[int, float, bool]] = (
+        self.interstitial_gen_kwargs: Union[dict[str, Union[int, float, bool]], bool] = (
             interstitial_gen_kwargs if interstitial_gen_kwargs is not None else {}
         )
         self.target_frac_coords = target_frac_coords if target_frac_coords is not None else [0.5, 0.5, 0.5]
@@ -1511,6 +1511,9 @@ def __init__(
             # Interstitials:
             self._element_list = host_element_list + extrinsic_elements  # all elements in system
             if self.interstitial_gen_kwargs is not False:  # skip interstitials
+                self.interstitial_gen_kwargs = (
+                    self.interstitial_gen_kwargs if isinstance(self.interstitial_gen_kwargs, dict) else {}
+                )
                 pbar.set_description("Generating interstitials")
                 if self.interstitial_coords:
                     # map interstitial coords to primitive structure, and get multiplicities

diff --git a/doped/utils/parsing.py b/doped/utils/parsing.py
@@ -226,7 +226,7 @@ def _get_core_potentials_from_outcar_obj(
 def _check_outcar_energy(
     outcar: Union[Outcar, PathLike], total_energy: Optional[Union[list, float]] = None
 ):
-    if total_energy is not None:
+    if total_energy:
         outcar_energy = (
             outcar.final_energy if isinstance(outcar, Outcar) else _get_final_energy_from_outcar(outcar)
         )

diff --git a/tests/data/CdTe/CdTe_bulk/vasp_gam/INCAR b/tests/data/CdTe/CdTe_bulk/vasp_gam/INCAR
@@ -18,7 +18,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 486.0
 NSW = 0
 NUPDOWN = 0

diff --git a/tests/data/CdTe/CdTe_bulk/vasp_ncl/INCAR b/tests/data/CdTe/CdTe_bulk/vasp_ncl/INCAR
@@ -20,7 +20,7 @@ LREAL = Auto
 LSORBIT = True
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 486.0
 NSW = 0
 NUPDOWN = 0

diff --git a/tests/data/CdTe/CdTe_bulk/vasp_nkred_std/INCAR b/tests/data/CdTe/CdTe_bulk/vasp_nkred_std/INCAR
@@ -19,7 +19,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 486.0
 NKRED = 2
 NSW = 0

diff --git a/tests/data/CdTe/CdTe_bulk/vasp_std/INCAR b/tests/data/CdTe/CdTe_bulk/vasp_std/INCAR
@@ -19,7 +19,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 486.0
 NSW = 0
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_Te_+1/vasp_gam/INCAR b/tests/data/CdTe/Cd_Te_+1/vasp_gam/INCAR
@@ -20,7 +20,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 491.0
 NSW = 200
 NUPDOWN = 1

diff --git a/tests/data/CdTe/Cd_Te_+1/vasp_ncl/INCAR b/tests/data/CdTe/Cd_Te_+1/vasp_ncl/INCAR
@@ -20,7 +20,7 @@ LREAL = Auto
 LSORBIT = True
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 491.0
 NSW = 0
 NUPDOWN = 1

diff --git a/tests/data/CdTe/Cd_Te_+1/vasp_nkred_std/INCAR b/tests/data/CdTe/Cd_Te_+1/vasp_nkred_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 491.0
 NKRED = 2
 NSW = 200

diff --git a/tests/data/CdTe/Cd_Te_+1/vasp_std/INCAR b/tests/data/CdTe/Cd_Te_+1/vasp_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 491.0
 NSW = 200
 NUPDOWN = 1

diff --git a/tests/data/CdTe/Cd_Te_+2/vasp_gam/INCAR b/tests/data/CdTe/Cd_Te_+2/vasp_gam/INCAR
@@ -20,7 +20,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 490.0
 NSW = 200
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_Te_+2/vasp_ncl/INCAR b/tests/data/CdTe/Cd_Te_+2/vasp_ncl/INCAR
@@ -20,7 +20,7 @@ LREAL = Auto
 LSORBIT = True
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 490.0
 NSW = 0
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_Te_+2/vasp_nkred_std/INCAR b/tests/data/CdTe/Cd_Te_+2/vasp_nkred_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 490.0
 NKRED = 2
 NSW = 200

diff --git a/tests/data/CdTe/Cd_Te_+2/vasp_std/INCAR b/tests/data/CdTe/Cd_Te_+2/vasp_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 490.0
 NSW = 200
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_Te_+3/vasp_gam/INCAR b/tests/data/CdTe/Cd_Te_+3/vasp_gam/INCAR
@@ -20,7 +20,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 489.0
 NSW = 200
 NUPDOWN = 1

diff --git a/tests/data/CdTe/Cd_Te_+3/vasp_ncl/INCAR b/tests/data/CdTe/Cd_Te_+3/vasp_ncl/INCAR
@@ -20,7 +20,7 @@ LREAL = Auto
 LSORBIT = True
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 489.0
 NSW = 0
 NUPDOWN = 1

diff --git a/tests/data/CdTe/Cd_Te_+3/vasp_nkred_std/INCAR b/tests/data/CdTe/Cd_Te_+3/vasp_nkred_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 489.0
 NKRED = 2
 NSW = 200

diff --git a/tests/data/CdTe/Cd_Te_+3/vasp_std/INCAR b/tests/data/CdTe/Cd_Te_+3/vasp_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 489.0
 NSW = 200
 NUPDOWN = 1

diff --git a/tests/data/CdTe/Cd_Te_+4/vasp_gam/INCAR b/tests/data/CdTe/Cd_Te_+4/vasp_gam/INCAR
@@ -20,7 +20,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 488.0
 NSW = 200
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_Te_+4/vasp_ncl/INCAR b/tests/data/CdTe/Cd_Te_+4/vasp_ncl/INCAR
@@ -20,7 +20,7 @@ LREAL = Auto
 LSORBIT = True
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 488.0
 NSW = 0
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_Te_+4/vasp_nkred_std/INCAR b/tests/data/CdTe/Cd_Te_+4/vasp_nkred_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 488.0
 NKRED = 2
 NSW = 200

diff --git a/tests/data/CdTe/Cd_Te_+4/vasp_std/INCAR b/tests/data/CdTe/Cd_Te_+4/vasp_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 488.0
 NSW = 200
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_Te_0/vasp_gam/INCAR b/tests/data/CdTe/Cd_Te_0/vasp_gam/INCAR
@@ -20,7 +20,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 492.0
 NSW = 200
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_Te_0/vasp_ncl/INCAR b/tests/data/CdTe/Cd_Te_0/vasp_ncl/INCAR
@@ -20,7 +20,7 @@ LREAL = Auto
 LSORBIT = True
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 492.0
 NSW = 0
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_Te_0/vasp_nkred_std/INCAR b/tests/data/CdTe/Cd_Te_0/vasp_nkred_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 492.0
 NKRED = 2
 NSW = 200

diff --git a/tests/data/CdTe/Cd_Te_0/vasp_std/INCAR b/tests/data/CdTe/Cd_Te_0/vasp_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 492.0
 NSW = 200
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_i_C3v_+1/vasp_gam/INCAR b/tests/data/CdTe/Cd_i_C3v_+1/vasp_gam/INCAR
@@ -20,7 +20,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 497.0
 NSW = 200
 NUPDOWN = 1

diff --git a/tests/data/CdTe/Cd_i_C3v_+1/vasp_ncl/INCAR b/tests/data/CdTe/Cd_i_C3v_+1/vasp_ncl/INCAR
@@ -20,7 +20,7 @@ LREAL = Auto
 LSORBIT = True
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 497.0
 NSW = 0
 NUPDOWN = 1

diff --git a/tests/data/CdTe/Cd_i_C3v_+1/vasp_nkred_std/INCAR b/tests/data/CdTe/Cd_i_C3v_+1/vasp_nkred_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 497.0
 NKRED = 2
 NSW = 200

diff --git a/tests/data/CdTe/Cd_i_C3v_+1/vasp_std/INCAR b/tests/data/CdTe/Cd_i_C3v_+1/vasp_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 497.0
 NSW = 200
 NUPDOWN = 1

diff --git a/tests/data/CdTe/Cd_i_C3v_+2/vasp_gam/INCAR b/tests/data/CdTe/Cd_i_C3v_+2/vasp_gam/INCAR
@@ -20,7 +20,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 496.0
 NSW = 200
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_i_C3v_+2/vasp_ncl/INCAR b/tests/data/CdTe/Cd_i_C3v_+2/vasp_ncl/INCAR
@@ -20,7 +20,7 @@ LREAL = Auto
 LSORBIT = True
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 496.0
 NSW = 0
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_i_C3v_+2/vasp_nkred_std/INCAR b/tests/data/CdTe/Cd_i_C3v_+2/vasp_nkred_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 496.0
 NKRED = 2
 NSW = 200

diff --git a/tests/data/CdTe/Cd_i_C3v_+2/vasp_std/INCAR b/tests/data/CdTe/Cd_i_C3v_+2/vasp_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 496.0
 NSW = 200
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_i_C3v_0/vasp_gam/INCAR b/tests/data/CdTe/Cd_i_C3v_0/vasp_gam/INCAR
@@ -20,7 +20,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 498.0
 NSW = 200
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_i_C3v_0/vasp_ncl/INCAR b/tests/data/CdTe/Cd_i_C3v_0/vasp_ncl/INCAR
@@ -20,7 +20,7 @@ LREAL = Auto
 LSORBIT = True
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 498.0
 NSW = 0
 NUPDOWN = 0

diff --git a/tests/data/CdTe/Cd_i_C3v_0/vasp_nkred_std/INCAR b/tests/data/CdTe/Cd_i_C3v_0/vasp_nkred_std/INCAR
@@ -21,7 +21,7 @@ LORBIT = 11
 LREAL = Auto
 LVHAR = False
 NCORE = 10
-NEDOS = 2000
+NEDOS = 3000
 NELECT = 498.0
 NKRED = 2
 NSW = 200