Update tests

SMTG-Bham · Oct 22, 2024 · d91d46a · d91d46a
1 parent f178b64
commit d91d46a
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Showing 2 changed files with 39 additions and 13 deletions.
diff --git a/doped/generation.py b/doped/generation.py
@@ -1225,7 +1225,7 @@ def __init__(
             interstitial_gen_kwargs (dict, bool):
                 Keyword arguments to be passed to ``get_Voronoi_interstitial_sites``
                 (such as ``min_dist``, ``clustering_tol``, ``symmetry_preference``,
-                ``stol`` and ``tight_stol`` -- see its docstring), or
+                ``stol``, ``tight_stol`` and ``symprec``  -- see its docstring), or
                 ``InterstitialGenerator`` if ``interstitial_coords`` is specified.
                 If set to ``False``, interstitial generation will be skipped entirely.
             target_frac_coords (list):
@@ -2435,6 +2435,9 @@ def get_Voronoi_interstitial_sites(
                 Structure matcher tolerance for looser site matching. Defaults to 0.32.
             - tight_stol (float):
                 Structure matcher tolerance for tighter site matching. Defaults to 0.02.
+            - symprec (float):
+                Symmetry precision for (symmetry-)equivalent site determination. Defaults
+                to 0.01.
 
     Returns:
         list: List of interstitial sites as fractional coordinates
@@ -2451,6 +2454,7 @@ def get_Voronoi_interstitial_sites(
         "symmetry_preference",
         "stol",
         "tight_stol",
+        "symprec",
     }
     if any(  # check interstitial_gen_kwargs and warn if any missing:
         i not in supported_interstitial_gen_kwargs for i in interstitial_gen_kwargs
@@ -2472,12 +2476,14 @@ def get_Voronoi_interstitial_sites(
     )
 
     label_equiv_fpos_dict: dict[int, list[np.ndarray[float]]] = {}
-    sga = symmetry.get_sga(host_structure)
+    sga = symmetry.get_sga(host_structure, symprec=interstitial_gen_kwargs.get("symprec", 0.01))
     symm_ops = sga.get_symmetry_operations()
     tight_dist = get_stol_equiv_dist(
         interstitial_gen_kwargs.get("tight_stol", 0.02), host_structure
     )  # 0.06 Å for CdTe, Sb2Si2Te6
 
+    # this now depends on symprec in `_get_all_equiv_sites` (doesn't matter in most cases,
+    # but e.g. changes results in Ag2Se where we have some slight differences in site coordinations)
     for i, frac_coords in enumerate(site_frac_coords_array.tolist()):
         match_found = False
         for equiv_fpos in list(label_equiv_fpos_dict.values()):
@@ -2488,7 +2494,12 @@ def get_Voronoi_interstitial_sites(
         if not match_found:  # try equiv sites:
             this_equiv_fpos = [
                 site.frac_coords
-                for site in symmetry._get_all_equiv_sites(frac_coords, host_structure, symm_ops=symm_ops)
+                for site in symmetry._get_all_equiv_sites(
+                    frac_coords,
+                    host_structure,
+                    symm_ops=symm_ops,
+                    symprec=interstitial_gen_kwargs.get("symprec", 0.01),
+                )
             ]
             for label, equiv_fpos in list(label_equiv_fpos_dict.items()):
                 if np.min(host_structure.lattice.get_all_distances(equiv_fpos, frac_coords)) < tight_dist:

diff --git a/tests/test_generation.py b/tests/test_generation.py
@@ -690,16 +690,28 @@ def setUp(self):
 Se_Ag_C2_Ag2.80  [+3,+2,+1,0,-1,-2,-3]  [0.391,0.000,0.000]  2a
 Se_Ag_C2_Ag2.85  [+3,+2,+1,0,-1,-2,-3]  [0.615,0.500,0.500]  2b
 
-Interstitials    Guessed Charges    Conv. Cell Coords    Wyckoff
----------------  -----------------  -------------------  ---------
-Ag_i_C1_Ag2.04   [+2,+1,0]          [0.335,0.435,0.002]  4e
-Ag_i_C1_Ag2.09   [+2,+1,0]          [0.435,0.123,0.251]  4e
-Ag_i_C2_Ag2.02   [+2,+1,0]          [0.500,0.250,0.319]  2d
-Ag_i_C2_Ag2.48   [+2,+1,0]          [0.091,0.500,0.500]  2b
-Se_i_C1_Ag2.04   [0,-1,-2]          [0.335,0.435,0.002]  4e
-Se_i_C1_Ag2.09   [0,-1,-2]          [0.435,0.123,0.251]  4e
-Se_i_C2_Ag2.02   [0,-1,-2]          [0.500,0.250,0.319]  2d
-Se_i_C2_Ag2.48   [0,-1,-2]          [0.091,0.500,0.500]  2b
+Interstitials                Guessed Charges    Conv. Cell Coords    Wyckoff
+---------------------------  -----------------  -------------------  ---------
+Ag_i_C1_Ag2.03               [+2,+1,0]          [0.341,0.438,0.498]  4e
+Ag_i_C1_Ag2.04               [+2,+1,0]          [0.335,0.435,0.002]  4e
+Ag_i_C1_Ag2.05               [+2,+1,0]          [0.570,0.589,0.250]  4e
+Ag_i_C1_Ag2.09               [+2,+1,0]          [0.435,0.123,0.251]  4e
+Ag_i_C2_Ag1.95Se1.95Ag2.98a  [+2,+1,0]          [0.500,0.250,0.668]  2d
+Ag_i_C2_Ag1.95Se1.95Ag2.98b  [+2,+1,0]          [0.500,0.750,0.171]  2d
+Ag_i_C2_Ag2.02Se2.02Ag2.88   [+2,+1,0]          [0.500,0.250,0.184]  2d
+Ag_i_C2_Ag2.02Se2.02Ag2.89   [+2,+1,0]          [0.500,0.250,0.319]  2d
+Ag_i_C2_Ag2.45               [+2,+1,0]          [0.899,0.000,0.000]  2a
+Ag_i_C2_Ag2.48               [+2,+1,0]          [0.091,0.500,0.500]  2b
+Se_i_C1_Ag2.03               [0,-1,-2]          [0.341,0.438,0.498]  4e
+Se_i_C1_Ag2.04               [0,-1,-2]          [0.335,0.435,0.002]  4e
+Se_i_C1_Ag2.05               [0,-1,-2]          [0.570,0.589,0.250]  4e
+Se_i_C1_Ag2.09               [0,-1,-2]          [0.435,0.123,0.251]  4e
+Se_i_C2_Ag1.95Se1.95Ag2.98a  [0,-1,-2]          [0.500,0.250,0.668]  2d
+Se_i_C2_Ag1.95Se1.95Ag2.98b  [0,-1,-2]          [0.500,0.750,0.171]  2d
+Se_i_C2_Ag2.02Se2.02Ag2.88   [0,-1,-2]          [0.500,0.250,0.184]  2d
+Se_i_C2_Ag2.02Se2.02Ag2.89   [0,-1,-2]          [0.500,0.250,0.319]  2d
+Se_i_C2_Ag2.45               [0,-1,-2]          [0.899,0.000,0.000]  2a
+Se_i_C2_Ag2.48               [0,-1,-2]          [0.091,0.500,0.500]  2b
 \n"""
             "The number in the Wyckoff label is the site multiplicity/degeneracy of that defect in "
             "the conventional ('conv.') unit cell, which comprises 4 formula unit(s) of Ag2Se.\n"
@@ -727,16 +739,19 @@ def setUp(self):
 Si_i_C1_Si2.21   [+4,+3,+2,+1,0]              [0.158,0.359,0.167]  18f
 Si_i_C1_Si2.48   [+4,+3,+2,+1,0]              [0.348,0.348,0.457]  18f
 Si_i_C1_Te2.44   [+4,+3,+2,+1,0]              [0.336,0.335,0.711]  18f
+Si_i_C3_Sb2.41   [+4,+3,+2,+1,0]              [0.000,0.000,0.050]  6c
 Si_i_C3_Si2.64   [+4,+3,+2,+1,0]              [0.000,0.000,0.318]  6c
 Si_i_C3i_Te2.81  [+4,+3,+2,+1,0]              [0.000,0.000,0.000]  3a
 Sb_i_C1_Si2.21   [+5,+4,+3,+2,+1,0,-1,-2,-3]  [0.158,0.359,0.167]  18f
 Sb_i_C1_Si2.48   [+5,+4,+3,+2,+1,0,-1,-2,-3]  [0.348,0.348,0.457]  18f
 Sb_i_C1_Te2.44   [+5,+4,+3,+2,+1,0,-1,-2,-3]  [0.336,0.335,0.711]  18f
+Sb_i_C3_Sb2.41   [+5,+4,+3,+2,+1,0,-1,-2,-3]  [0.000,0.000,0.050]  6c
 Sb_i_C3_Si2.64   [+5,+4,+3,+2,+1,0,-1,-2,-3]  [0.000,0.000,0.318]  6c
 Sb_i_C3i_Te2.81  [+5,+4,+3,+2,+1,0,-1,-2,-3]  [0.000,0.000,0.000]  3a
 Te_i_C1_Si2.21   [+4,+3,+2,+1,0,-1,-2]        [0.158,0.359,0.167]  18f
 Te_i_C1_Si2.48   [+4,+3,+2,+1,0,-1,-2]        [0.348,0.348,0.457]  18f
 Te_i_C1_Te2.44   [+4,+3,+2,+1,0,-1,-2]        [0.336,0.335,0.711]  18f
+Te_i_C3_Sb2.41   [+4,+3,+2,+1,0,-1,-2]        [0.000,0.000,0.050]  6c
 Te_i_C3_Si2.64   [+4,+3,+2,+1,0,-1,-2]        [0.000,0.000,0.318]  6c
 Te_i_C3i_Te2.81  [+4,+3,+2,+1,0,-1,-2]        [0.000,0.000,0.000]  3a
 \n"""