def test_muon_set_frac(self):
self._sample._reset(cell=True, sym=True, magdefs=True, muon=True)
# check that missing cell raises error
with self.assertRaises(CellError):
muon_set_frac(self._sample, "0 0 0")
# ugly way to load a lattice with its symetry
co_lattice.seek(0)
atoms, sym = read_cif(co_lattice, 0) # selectd index 0
if atoms:
self._sample._reset(muon=True, sym=True)
self._sample.cell = atoms
self._sample.sym = sym
else:
raise RuntimeError
muon_set_frac(self._sample, "0 0 0")
np.testing.assert_array_almost_equal(np.array([0, 0, 0.]),
self._sample.muons[0])
muon_set_frac(self._sample, "0.125 0.125 0.125")
np.testing.assert_array_almost_equal(np.array([0.125, 0.125, 0.125]),
self._sample.muons[1])
def setUp(self):
self._sample = Sample()
self._sample._reset(cell=True, sym=True, magdefs=True, muon=True)
co_lattice.seek(0)
atoms, sym = read_cif(co_lattice, 0) # selectd index 0
if atoms:
self._sample._reset(muon=True, sym=True)
self._sample.cell = atoms
self._sample.sym = sym
else:
raise RuntimeError
def setUp(self):
self._sample = Sample()
self._sample._reset(cell=True,sym=True,magdefs=True,muon=True)
co_lattice.seek(0)
atoms, sym = read_cif(co_lattice,0) # selectd index 0
if atoms:
self._sample._reset(muon=True,sym=True)
self._sample.cell = atoms
self._sample.sym = sym
else:
raise RuntimeError
def test_muon_reset(self):
# ugly way to load a lattice with its symetry
co_lattice.seek(0)
atoms, sym = read_cif(co_lattice,0) # selectd index 0
if atoms:
self._sample._reset(muon=True,sym=True)
self._sample.cell = atoms
self._sample.sym = sym
else:
raise RuntimeError
muon_set_frac(self._sample, "0 0 0")
np.testing.assert_array_almost_equal(np.array([0,0,0.]),self._sample.muons[0])
muon_set_frac(self._sample, "0.125 0.125 0.125")
np.testing.assert_array_almost_equal(np.array([0.125,0.125,0.125]),self._sample.muons[1])
def test_find_equiv(self):
# ugly way to load a lattice with its symetry
co_lattice.seek(0)
atoms, sym = read_cif(co_lattice,0) # selectd index 0
if atoms:
self._sample._reset(cell=True, muon=True, sym=True, magdefs=True)
self._sample.cell = atoms
self._sample.sym = sym
else:
raise RuntimeError
#tests throw error if no muon positions defined
with self.assertRaises(MuonError):
muon_find_equiv(self._sample)
muon_set_frac(self._sample, "0 0 0")
muon_find_equiv(self._sample)
muon_positions = self._sample.muons
self.assertEqual(len(muon_positions),atoms.get_number_of_atoms())
for atm in atoms:
self.assertTrue(np.any(np.all((muon_positions-atm[2])==0, axis=1)))
self._sample._reset(muon=True)
muon_set_frac(self._sample, "0.2 0.3 0.4")
muon_find_equiv(self._sample)
muon_positions = self._sample.muons
#positions calculated with VESTA
eqpositions = np.array([[ 0.200000 , 0.300000 , 0.400000],
[ 0.800000 , 0.700000 , 0.600000],
[ 0.800000 , 0.700000 , 0.400000],
[ 0.200000 , 0.300000 , 0.600000],
[ 0.800000 , 0.300000 , 0.600000],
[ 0.200000 , 0.700000 , 0.400000],
[ 0.200000 , 0.700000 , 0.600000],
[ 0.800000 , 0.300000 , 0.400000],
[ 0.400000 , 0.200000 , 0.300000],
[ 0.600000 , 0.800000 , 0.700000],
[ 0.400000 , 0.800000 , 0.700000],
[ 0.600000 , 0.200000 , 0.300000],
[ 0.600000 , 0.800000 , 0.300000],
[ 0.400000 , 0.200000 , 0.700000],
[ 0.600000 , 0.200000 , 0.700000],
[ 0.400000 , 0.800000 , 0.300000],
[ 0.300000 , 0.400000 , 0.200000],
[ 0.700000 , 0.600000 , 0.800000],
[ 0.700000 , 0.400000 , 0.800000],
[ 0.300000 , 0.600000 , 0.200000],
[ 0.300000 , 0.600000 , 0.800000],
[ 0.700000 , 0.400000 , 0.200000],
[ 0.700000 , 0.600000 , 0.200000],
[ 0.300000 , 0.400000 , 0.800000],
[ 0.300000 , 0.200000 , 0.600000],
[ 0.700000 , 0.800000 , 0.400000],
[ 0.700000 , 0.800000 , 0.600000],
[ 0.300000 , 0.200000 , 0.400000],
[ 0.300000 , 0.800000 , 0.400000],
[ 0.700000 , 0.200000 , 0.600000],
[ 0.700000 , 0.200000 , 0.400000],
[ 0.300000 , 0.800000 , 0.600000],
[ 0.200000 , 0.400000 , 0.700000],
[ 0.800000 , 0.600000 , 0.300000],
[ 0.800000 , 0.400000 , 0.300000],
[ 0.200000 , 0.600000 , 0.700000],
[ 0.800000 , 0.600000 , 0.700000],
[ 0.200000 , 0.400000 , 0.300000],
[ 0.200000 , 0.600000 , 0.300000],
[ 0.800000 , 0.400000 , 0.700000],
[ 0.400000 , 0.300000 , 0.800000],
[ 0.600000 , 0.700000 , 0.200000],
[ 0.400000 , 0.700000 , 0.200000],
[ 0.600000 , 0.300000 , 0.800000],
[ 0.600000 , 0.300000 , 0.200000],
[ 0.400000 , 0.700000 , 0.800000],
[ 0.600000 , 0.700000 , 0.800000],
[ 0.400000 , 0.300000 , 0.200000],
[ 0.200000 , 0.800000 , 0.900000],
[ 0.800000 , 0.200000 , 0.100000],
[ 0.800000 , 0.200000 , 0.900000],
[ 0.200000 , 0.800000 , 0.100000],
[ 0.800000 , 0.800000 , 0.100000],
[ 0.200000 , 0.200000 , 0.900000],
[ 0.200000 , 0.200000 , 0.100000],
[ 0.800000 , 0.800000 , 0.900000],
[ 0.300000 , 0.900000 , 0.700000],
[ 0.700000 , 0.100000 , 0.300000],
[ 0.700000 , 0.900000 , 0.300000],
[ 0.300000 , 0.100000 , 0.700000],
[ 0.300000 , 0.100000 , 0.300000],
[ 0.700000 , 0.900000 , 0.700000],
[ 0.700000 , 0.100000 , 0.700000],
[ 0.300000 , 0.900000 , 0.300000],
[ 0.300000 , 0.700000 , 0.100000],
[ 0.700000 , 0.300000 , 0.900000],
[ 0.700000 , 0.300000 , 0.100000],
[ 0.300000 , 0.700000 , 0.900000],
[ 0.300000 , 0.300000 , 0.900000],
[ 0.700000 , 0.700000 , 0.100000],
[ 0.700000 , 0.700000 , 0.900000],
[ 0.300000 , 0.300000 , 0.100000],
[ 0.200000 , 0.900000 , 0.200000],
[ 0.800000 , 0.100000 , 0.800000],
[ 0.800000 , 0.900000 , 0.800000],
[ 0.200000 , 0.100000 , 0.200000],
[ 0.800000 , 0.100000 , 0.200000],
[ 0.200000 , 0.900000 , 0.800000],
[ 0.200000 , 0.100000 , 0.800000],
[ 0.800000 , 0.900000 , 0.200000],
[ 0.900000 , 0.200000 , 0.800000],
[ 0.100000 , 0.800000 , 0.200000],
[ 0.900000 , 0.800000 , 0.200000],
[ 0.100000 , 0.200000 , 0.800000],
[ 0.100000 , 0.800000 , 0.800000],
[ 0.900000 , 0.200000 , 0.200000],
[ 0.100000 , 0.200000 , 0.200000],
[ 0.900000 , 0.800000 , 0.800000],
[ 0.900000 , 0.300000 , 0.300000],
[ 0.100000 , 0.700000 , 0.700000],
[ 0.900000 , 0.700000 , 0.700000],
[ 0.100000 , 0.300000 , 0.300000],
[ 0.100000 , 0.300000 , 0.700000],
[ 0.900000 , 0.700000 , 0.300000],
[ 0.100000 , 0.700000 , 0.300000],
[ 0.900000 , 0.300000 , 0.700000]])
for p in eqpositions:
self.assertTrue(np.any(np.all(np.abs(muon_positions-p)<1e-10, axis=1)))
def test_open_file(self):
s = Sample()
MnSi_cif.seek(0)
read_cif(MnSi_cif, 0)
def test_find_equiv(self):
# ugly way to load a lattice with its symetry
co_lattice.seek(0)
atoms, sym = read_cif(co_lattice, 0) # selectd index 0
if atoms:
self._sample._reset(cell=True, muon=True, sym=True, magdefs=True)
self._sample.cell = atoms
self._sample.sym = sym
else:
raise RuntimeError
#tests throw error if no muon positions defined
with self.assertRaises(MuonError):
muon_find_equiv(self._sample)
muon_set_frac(self._sample, "0 0 0")
muon_find_equiv(self._sample)
muon_positions = self._sample.muons
self.assertEqual(len(muon_positions), atoms.get_number_of_atoms())
for atm in atoms:
self.assertTrue(
np.any(np.all((muon_positions - atm[2]) == 0, axis=1)))
self._sample._reset(muon=True)
muon_set_frac(self._sample, "0.2 0.3 0.4")
muon_find_equiv(self._sample)
muon_positions = self._sample.muons
#positions calculated with VESTA
eqpositions = np.array([[0.200000, 0.300000, 0.400000],
[0.800000, 0.700000, 0.600000],
[0.800000, 0.700000, 0.400000],
[0.200000, 0.300000, 0.600000],
[0.800000, 0.300000, 0.600000],
[0.200000, 0.700000, 0.400000],
[0.200000, 0.700000, 0.600000],
[0.800000, 0.300000, 0.400000],
[0.400000, 0.200000, 0.300000],
[0.600000, 0.800000, 0.700000],
[0.400000, 0.800000, 0.700000],
[0.600000, 0.200000, 0.300000],
[0.600000, 0.800000, 0.300000],
[0.400000, 0.200000, 0.700000],
[0.600000, 0.200000, 0.700000],
[0.400000, 0.800000, 0.300000],
[0.300000, 0.400000, 0.200000],
[0.700000, 0.600000, 0.800000],
[0.700000, 0.400000, 0.800000],
[0.300000, 0.600000, 0.200000],
[0.300000, 0.600000, 0.800000],
[0.700000, 0.400000, 0.200000],
[0.700000, 0.600000, 0.200000],
[0.300000, 0.400000, 0.800000],
[0.300000, 0.200000, 0.600000],
[0.700000, 0.800000, 0.400000],
[0.700000, 0.800000, 0.600000],
[0.300000, 0.200000, 0.400000],
[0.300000, 0.800000, 0.400000],
[0.700000, 0.200000, 0.600000],
[0.700000, 0.200000, 0.400000],
[0.300000, 0.800000, 0.600000],
[0.200000, 0.400000, 0.700000],
[0.800000, 0.600000, 0.300000],
[0.800000, 0.400000, 0.300000],
[0.200000, 0.600000, 0.700000],
[0.800000, 0.600000, 0.700000],
[0.200000, 0.400000, 0.300000],
[0.200000, 0.600000, 0.300000],
[0.800000, 0.400000, 0.700000],
[0.400000, 0.300000, 0.800000],
[0.600000, 0.700000, 0.200000],
[0.400000, 0.700000, 0.200000],
[0.600000, 0.300000, 0.800000],
[0.600000, 0.300000, 0.200000],
[0.400000, 0.700000, 0.800000],
[0.600000, 0.700000, 0.800000],
[0.400000, 0.300000, 0.200000],
[0.200000, 0.800000, 0.900000],
[0.800000, 0.200000, 0.100000],
[0.800000, 0.200000, 0.900000],
[0.200000, 0.800000, 0.100000],
[0.800000, 0.800000, 0.100000],
[0.200000, 0.200000, 0.900000],
[0.200000, 0.200000, 0.100000],
[0.800000, 0.800000, 0.900000],
[0.300000, 0.900000, 0.700000],
[0.700000, 0.100000, 0.300000],
[0.700000, 0.900000, 0.300000],
[0.300000, 0.100000, 0.700000],
[0.300000, 0.100000, 0.300000],
[0.700000, 0.900000, 0.700000],
[0.700000, 0.100000, 0.700000],
[0.300000, 0.900000, 0.300000],
[0.300000, 0.700000, 0.100000],
[0.700000, 0.300000, 0.900000],
[0.700000, 0.300000, 0.100000],
[0.300000, 0.700000, 0.900000],
[0.300000, 0.300000, 0.900000],
[0.700000, 0.700000, 0.100000],
[0.700000, 0.700000, 0.900000],
[0.300000, 0.300000, 0.100000],
[0.200000, 0.900000, 0.200000],
[0.800000, 0.100000, 0.800000],
[0.800000, 0.900000, 0.800000],
[0.200000, 0.100000, 0.200000],
[0.800000, 0.100000, 0.200000],
[0.200000, 0.900000, 0.800000],
[0.200000, 0.100000, 0.800000],
[0.800000, 0.900000, 0.200000],
[0.900000, 0.200000, 0.800000],
[0.100000, 0.800000, 0.200000],
[0.900000, 0.800000, 0.200000],
[0.100000, 0.200000, 0.800000],
[0.100000, 0.800000, 0.800000],
[0.900000, 0.200000, 0.200000],
[0.100000, 0.200000, 0.200000],
[0.900000, 0.800000, 0.800000],
[0.900000, 0.300000, 0.300000],
[0.100000, 0.700000, 0.700000],
[0.900000, 0.700000, 0.700000],
[0.100000, 0.300000, 0.300000],
[0.100000, 0.300000, 0.700000],
[0.900000, 0.700000, 0.300000],
[0.100000, 0.700000, 0.300000],
[0.900000, 0.300000, 0.700000]])
for p in eqpositions:
self.assertTrue(
np.any(np.all(np.abs(muon_positions - p) < 1e-10, axis=1)))