Missed out on GB transformation.

materialsproject · Dec 14, 2018 · eb014d4 · eb014d4
1 parent 24ef7ae
commit eb014d4
Showing 1 changed file with 22 additions and 21 deletions.
diff --git a/pymatgen/transformations/tests/test_advanced_transformations.py b/pymatgen/transformations/tests/test_advanced_transformations.py
@@ -8,7 +8,7 @@
 import warnings
 import numpy as np
 
-from pymatgen import Lattice, Structure, Specie, Element
+from pymatgen import Lattice, Structure, Specie
 from pymatgen.transformations.standard_transformations import \
     OxidationStateDecorationTransformation, SubstitutionTransformation, \
     OrderDisorderedStructureTransformation, AutoOxiStateDecorationTransformation
@@ -17,7 +17,8 @@
     MultipleSubstitutionTransformation, ChargeBalanceTransformation, \
     SubstitutionPredictorTransformation, MagOrderingTransformation, \
     DopingTransformation, _find_codopant, SlabTransformation, \
-    MagOrderParameterConstraint, DisorderOrderedTransformation
+    MagOrderParameterConstraint, DisorderOrderedTransformation, \
+    GrainBoundaryTransformation
 from monty.os.path import which
 from pymatgen.io.vasp.inputs import Poscar
 from pymatgen.io.cif import CifParser
@@ -26,7 +27,6 @@
 from pymatgen.analysis.gb.grain import GrainBoundaryGenerator
 from pymatgen.util.testing import PymatgenTest
 from pymatgen.core.surface import SlabGenerator
-
 """
 Created on Jul 24, 2012
 """
@@ -99,12 +99,11 @@ def test_apply_transformation(self):
 
     @unittest.skipIf(not enumlib_present, "enum_lib not present.")
     def test_apply_transformation_mult(self):
-        #Test returning multiple structures from each transformation.
+        # Test returning multiple structures from each transformation.
         disord = Structure(np.eye(3) * 4.209, [{"Cs+": 0.5, "K+": 0.5}, "Cl-"],
                            [[0, 0, 0], [0.5, 0.5, 0.5]])
         disord.make_supercell([2, 2, 1])
 
-
         tl = [EnumerateStructureTransformation(),
               OrderDisorderedStructureTransformation()]
         t = SuperTransformation(tl, nstructures_per_trans=10)
@@ -576,23 +575,26 @@ def test_apply_transformation(self):
         self.assertArrayAlmostEqual(slab_from_gen.cart_coords, 
                                     slab_from_trans.cart_coords)
 
-from pymatgen.transformations.advanced_transformations import GrainBoundaryTransformation
+
 
 class GrainBoundaryTransformationTest(PymatgenTest):
     def test_apply_transformation(self):
-        Li_bulk = Structure.from_spacegroup("Im-3m", Lattice.cubic(2.96771),
-                                            ["Li"], [[0, 0, 0]])
-        gb_gen_params_s3 = {"rotation_axis": [1, 1, 1], "rotation_angle": 60.0,
-                            "expand_times": 2, "vacuum_thickness": 0.0, "normal": True,
-                            "ratio": None, "plane": None}
-        gbg = GrainBoundaryGenerator(Li_bulk)
-        gb_from_generator = gbg.gb_from_parameters(**gb_gen_params_s3)
-        gbt_s3 = GrainBoundaryTransformation(**gb_gen_params_s3)
-        gb_from_trans = gbt_s3.apply_transformation(Li_bulk)
-        self.assertArrayAlmostEqual(gb_from_generator.lattice.matrix,
-                                    gb_from_trans.lattice.matrix)
-        self.assertArrayAlmostEqual(gb_from_generator.cart_coords,
-                                    gb_from_trans.cart_coords)
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
+            Li_bulk = Structure.from_spacegroup("Im-3m", Lattice.cubic(2.96771),
+                                                ["Li"], [[0, 0, 0]])
+            gb_gen_params_s3 = {"rotation_axis": [1, 1, 1], "rotation_angle": 60.0,
+                                "expand_times": 2, "vacuum_thickness": 0.0, "normal": True,
+                                "ratio": None, "plane": None}
+            gbg = GrainBoundaryGenerator(Li_bulk)
+            gb_from_generator = gbg.gb_from_parameters(**gb_gen_params_s3)
+            gbt_s3 = GrainBoundaryTransformation(**gb_gen_params_s3)
+            gb_from_trans = gbt_s3.apply_transformation(Li_bulk)
+            self.assertArrayAlmostEqual(gb_from_generator.lattice.matrix,
+                                        gb_from_trans.lattice.matrix)
+            self.assertArrayAlmostEqual(gb_from_generator.cart_coords,
+                                        gb_from_trans.cart_coords)
+
 
 class DisorderedOrderedTransformationTest(PymatgenTest):
 
@@ -608,7 +610,6 @@ def test_apply_transformation(self):
         self.assertDictEqual(output.species_and_occu[-1].as_dict(),
                              {'Ni': 0.5, 'Ba': 0.5})
 
+
 if __name__ == "__main__":
-    import logging
-    # logging.basicConfig(level=logging.INFO)
     unittest.main()