def test_previous_reconstructions(self):
# Test to see if we generated all reconstruction
# types correctly and nothing changes
m = StructureMatcher()
for n in self.rec_archive.keys():
if "base_reconstruction" in self.rec_archive[n].keys():
arch = self.rec_archive[self.rec_archive[n]
["base_reconstruction"]]
sg = arch["spacegroup"]["symbol"]
else:
sg = self.rec_archive[n]["spacegroup"]["symbol"]
if sg == "Fm-3m":
rec = ReconstructionGenerator(self.Ni, 20, 20, n)
el = self.Ni[0].species_string
elif sg == "Im-3m":
rec = ReconstructionGenerator(self.Fe, 20, 20, n)
el = self.Fe[0].species_string
elif sg == "Fd-3m":
rec = ReconstructionGenerator(self.Si, 20, 20, n)
el = self.Si[0].species_string
slabs = rec.build_slabs()
s = Structure.from_file(
get_path(os.path.join("reconstructions",
el + "_" + n + ".cif")))
self.assertTrue(
any([
len(m.group_structures([s, slab])) == 1 for slab in slabs
]))
def test_previous_reconstructions(self):
# Test to see if we generated all reconstruction
# types correctly and nothing changes
m = StructureMatcher()
for n in self.rec_archive.keys():
if "base_reconstruction" in self.rec_archive[n].keys():
arch = self.rec_archive[
self.rec_archive[n]["base_reconstruction"]]
sg = arch["spacegroup"]["symbol"]
else:
sg = self.rec_archive[n]["spacegroup"]["symbol"]
if sg == "Fm-3m":
rec = ReconstructionGenerator(self.Ni, 20, 20, n)
el = self.Ni[0].species_string
elif sg == "Im-3m":
rec = ReconstructionGenerator(self.Fe, 20, 20, n)
el = self.Fe[0].species_string
elif sg == "Fd-3m":
rec = ReconstructionGenerator(self.Si, 20, 20, n)
el = self.Si[0].species_string
slabs = rec.build_slabs()
s = Structure.from_file(get_path(os.path.join("reconstructions",
el + "_" + n + ".cif")))
self.assertTrue(any(
[len(m.group_structures([s, slab])) == 1 for slab in slabs]))
def test_build_slab(self):
# First lets test a reconstruction where we only remove atoms
recon = ReconstructionGenerator(self.Ni, 10, 10,
"fcc_110_missing_row_1x2")
slab = recon.get_unreconstructed_slabs()[0]
recon_slab = recon.build_slabs()[0]
self.assertTrue(recon_slab.reconstruction)
self.assertEqual(len(slab), len(recon_slab) + 2)
self.assertTrue(recon_slab.is_symmetric())
# Test if the ouc corresponds to the reconstructed slab
recon_ouc = recon_slab.oriented_unit_cell
ouc = slab.oriented_unit_cell
self.assertEqual(ouc.lattice.b * 2, recon_ouc.lattice.b)
self.assertEqual(len(ouc) * 2, len(recon_ouc))
# Test a reconstruction where we simply add atoms
recon = ReconstructionGenerator(self.Ni, 10, 10,
"fcc_111_adatom_t_1x1")
slab = recon.get_unreconstructed_slabs()[0]
recon_slab = recon.build_slabs()[0]
self.assertEqual(len(slab), len(recon_slab) - 2)
self.assertTrue(recon_slab.is_symmetric())
# If a slab references another slab,
# make sure it is properly generated
recon = ReconstructionGenerator(self.Ni, 10, 10,
"fcc_111_adatom_ft_1x1")
slab = recon.build_slabs()[0]
self.assertTrue(slab.is_symmetric)
# Test a reconstruction where it works on a specific
# termination (Fd-3m (111))
recon = ReconstructionGenerator(self.Si, 10, 10,
"diamond_111_1x2")
slab = recon.get_unreconstructed_slabs()[0]
recon_slab = recon.build_slabs()[0]
self.assertEqual(len(slab), len(recon_slab) - 8)
self.assertTrue(recon_slab.is_symmetric())
def test_build_slab(self):
# First lets test a reconstruction where we only remove atoms
recon = ReconstructionGenerator(self.Ni, 10, 10,
"fcc_110_missing_row_1x2")
slab = recon.get_unreconstructed_slabs()[0]
recon_slab = recon.build_slabs()[0]
self.assertTrue(recon_slab.reconstruction)
self.assertEqual(len(slab), len(recon_slab) + 2)
self.assertTrue(recon_slab.is_symmetric())
# Test if the ouc corresponds to the reconstructed slab
recon_ouc = recon_slab.oriented_unit_cell
ouc = slab.oriented_unit_cell
self.assertEqual(ouc.lattice.b * 2, recon_ouc.lattice.b)
self.assertEqual(len(ouc) * 2, len(recon_ouc))
# Test a reconstruction where we simply add atoms
recon = ReconstructionGenerator(self.Ni, 10, 10,
"fcc_111_adatom_t_1x1")
slab = recon.get_unreconstructed_slabs()[0]
recon_slab = recon.build_slabs()[0]
self.assertEqual(len(slab), len(recon_slab) - 2)
self.assertTrue(recon_slab.is_symmetric())
# If a slab references another slab,
# make sure it is properly generated
recon = ReconstructionGenerator(self.Ni, 10, 10,
"fcc_111_adatom_ft_1x1")
slab = recon.build_slabs()[0]
self.assertTrue(slab.is_symmetric)
# Test a reconstruction where it works on a specific
# termination (Fd-3m (111))
recon = ReconstructionGenerator(self.Si, 10, 10,
"diamond_111_1x2")
slab = recon.get_unreconstructed_slabs()[0]
recon_slab = recon.build_slabs()[0]
self.assertEqual(len(slab), len(recon_slab) - 8)
self.assertTrue(recon_slab.is_symmetric())