def setUpClass(cls):
warnings.filterwarnings("ignore")
cls.Cu_conv = Structure.from_file(os.path.join(test_dir,
"Cu_mp-30_conventional_standard.cif"))
GB_Cu_conv = GrainBoundaryGenerator(cls.Cu_conv)
cls.Cu_GB1 = GB_Cu_conv.gb_from_parameters([1, 2, 3], 123.74898859588858,
expand_times=4, vacuum_thickness=1.5,
ab_shift=[0.0, 0.0], plane=[1, 3, 1],
rm_ratio=0.0)
cls.Cu_GB2 = GB_Cu_conv.gb_from_parameters([1, 2, 3], 123.74898859588858,
expand_times=4, vacuum_thickness=1.5,
ab_shift=[0.2, 0.2], rm_ratio=0.0)
def setUpClass(cls):
warnings.filterwarnings("ignore")
cls.Cu_conv = Structure.from_file(
os.path.join(test_dir, "Cu_mp-30_conventional_standard.cif"))
GB_Cu_conv = GrainBoundaryGenerator(cls.Cu_conv)
cls.Cu_GB1 = GB_Cu_conv.gb_from_parameters([1, 2, 3],
123.74898859588858,
expand_times=4,
vacuum_thickness=1.5,
ab_shift=[0.0, 0.0],
plane=[1, 3, 1],
rm_ratio=0.0)
cls.Cu_GB2 = GB_Cu_conv.gb_from_parameters([1, 2, 3],
123.74898859588858,
expand_times=4,
vacuum_thickness=1.5,
ab_shift=[0.2, 0.2],
rm_ratio=0.0)
def test_apply_transformation(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
Al_bulk = Structure.from_spacegroup("Fm-3m", Lattice.cubic(2.8575585),
["Al"], [[0, 0, 0]])
gb_gen_params_s5 = {"rotation_axis": [1, 0, 0], "rotation_angle": 53.13010235415599,
"expand_times": 3, "vacuum_thickness": 0.0, "normal": True,
"plane": [0, -1, -3], 'rm_ratio': 0.6}
gbg = GrainBoundaryGenerator(Al_bulk)
gb_from_generator = gbg.gb_from_parameters(**gb_gen_params_s5)
gbt_s5 = GrainBoundaryTransformation(**gb_gen_params_s5)
gb_from_trans = gbt_s5.apply_transformation(Al_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)
def test_apply_transformation(self):
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)
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)