def setUp(self):
mock_defect_species = create_mock_defect_species(2)
mock_defects_at_site = create_mock_defects_at_site(2)
with patch('pyscses.site.DefectAtSite',
autospec=True) as mock_DefectAtSite:
mock_DefectAtSite.side_effect = mock_defects_at_site
self.site = Site(label='A',
x=1.5,
defect_species=mock_defect_species,
defect_energies=[-0.2, +0.2])
def form_continuum_sites( all_sites, x_min, x_max, n_points, b, c, defect_species, limits_for_laplacian, site_labels, defect_labels ):
"""
Creates a Set_of_Sites object for sites interpolated onto a regular grid, this is equivalent to assuming a continuum approximation.
Args:
all_sites (object): Orginal Set_of_Sites object from full data.
x_min (float): Minimum x coordinate value defining the calculation region.
x_max (float): Maximum x coordinate value defining the calculation region.
n_points (int): Number of points that the data should be interpolated on to.
b (float): b dimension for every grid point.
c (float): c dimension for every grid point.
defect_species (object): Class object containing information about the defect species present in the system.
limits for laplacian (list): distance between the endmost sites and the midpoint of the next site outside of the calculation region for the first and last sites respectively.
site_labels( list ): List of strings for the different site species.
defect_labels (list): List of strings for the different defect species.
Returns:
:obj:`Set_of_Sites`: Sites interpolated onto a regular grid.
"""
grid = np.linspace( x_min, x_max, n_points )
limits = [grid[1] - grid[0], grid[1] - grid[0]]
sites = []
for label, d_label in zip(site_labels, defect_labels):
scaling = len( all_sites.subset( label ) ) / len( grid )
continuum_grid = Grid( grid, b, c, limits, limits_for_laplacian, all_sites.subset( label ) )
average_energies = np.array( [ site.average_local_energy( method = 'mean' )[0] for site in all_sites.subset( label ) ] )
new_energies = griddata( ( [ site.x for site in all_sites.subset( label ) ] ), average_energies, grid, method = 'nearest' )
for x, e in zip( grid, new_energies):
sites.append( Site( label, x, [ defect_species[ d_label ] ], [e], scaling = np.array( scaling ) ) )
return Set_of_Sites( sites ), limits
def form_continuum_sites_new(all_sites, x_min, x_max, n_points, b, c,
defect_species, limits_for_laplacian,
site_labels, defect_labels):
limits = [x_min, x_max]
grid = np.linspace(x_min, x_max, n_points)
sites = []
for label, d_label in zip(site_labels, defect_labels):
scaling = len(all_sites.subset(label)) / len(grid)
continuum_grid = Grid(grid, b, c, limits, limits_for_laplacian,
all_sites.subset(label))
average_energies = np.array([
site.average_local_energy(method='mean')[0]
for site in all_sites.subset(label)
])
new_energies = griddata(
([site.x for site in all_sites.subset(label)]),
Vo.average_energies,
grid,
method='nearest')
for x, e in zip(grid, new_energies):
sites.append(
Site(label,
x, [defect_species[d_label]], [e],
scaling=np.array(scaling)))
return Set_of_Sites(sites)
def test_site_init_data_check_1(self):
"""Checks that initialising a Site object raises a ValueError if n(defect_species) != n(defect_energies)"""
mock_defect_species = create_mock_defect_species(1)
with patch('pyscses.site.DefectAtSite',
autospec=True) as mock_DefectAtSite:
with self.assertRaises(ValueError):
site = Site(label='A',
x=1.5,
defect_species=mock_defect_species,
defect_energies=[-0.2, +0.2])
def test_site_init_with_mixed_mobile_and_fixed_defects(self):
mock_defect_species = create_mock_defect_species(3)
mock_defects_at_site = create_mock_defects_at_site(3)
mock_defects_at_site[0].fixed = False
mock_defects_at_site[0].mole_fraction = 0.4
mock_defects_at_site[1].fixed = True
mock_defects_at_site[1].mole_fraction = 0.3
mock_defects_at_site[2].fixed = True
mock_defects_at_site[2].mole_fraction = 0.2
with patch('pyscses.site.DefectAtSite',
autospec=True) as mock_DefectAtSite:
mock_DefectAtSite.side_effect = mock_defects_at_site
site = Site(label='C',
x=1.5,
defect_species=mock_defect_species,
defect_energies=[-0.2, +0.2, 0.0])
self.assertEqual(site.fixed_defects,
(mock_defects_at_site[1], mock_defects_at_site[2]))
self.assertEqual(site.mobile_defects[0], mock_defects_at_site[0])
self.assertEqual(site.alpha, 0.5)
def test_site_is_initialised_with_optional_args(self):
mock_defect_species = create_mock_defect_species(2)
with patch('pyscses.site.DefectAtSite',
autospec=True) as mock_DefectAtSite:
mock_DefectAtSite.side_effect = create_mock_defects_at_site(2)
site = Site(label='B',
x=1.5,
defect_species=mock_defect_species,
defect_energies=[-0.2, +0.2],
scaling=[0.5, 0.4],
valence=-2.0,
saturation_parameter=0.1)
self.assertEqual(site.label, 'B')
self.assertEqual(site.x, 1.5)
self.assertEqual(site.defect_species, mock_defect_species)
self.assertEqual(site.defect_energies, [-0.2, +0.2])
np.testing.assert_equal(site.scaling, np.array([0.5, 0.4]))
self.assertEqual(site.valence, -2.0)
self.assertEqual(site.saturation_parameter, 0.1)
self.assertEqual(site.alpha, 0.1)
def test_site_is_initialised(self):
mock_defect_species = create_mock_defect_species(2)
mock_defects_at_site = create_mock_defects_at_site(2)
with patch('pyscses.site.DefectAtSite',
autospec=True) as mock_DefectAtSite:
mock_DefectAtSite.side_effect = mock_defects_at_site
site = Site(label='A',
x=1.5,
defect_species=mock_defect_species,
defect_energies=[-0.2, +0.2])
self.assertEqual(site.label, 'A')
self.assertEqual(site.x, 1.5)
self.assertEqual(site.defect_species, mock_defect_species)
self.assertEqual(site.defect_energies, [-0.2, +0.2])
np.testing.assert_equal(site.scaling, np.array([1.0, 1.0]))
self.assertEqual(site.valence, 0.0)
self.assertEqual(site.saturation_parameter, 1.0)
self.assertEqual(site.fixed_defects, ())
self.assertEqual(site.mobile_defects, tuple(mock_defects_at_site))
self.assertEqual(site.alpha, 1.0)
def site_from_input_file(site,
defect_species,
site_charge,
temperature,
zero_energies_less_than_kT=False):
"""
Takes the data from the input file and converts it into a site.
The input data file is a .txt file where each line in the file corresponds to a site. The values in each line are formatted and separated into the corresponding properties before creating a Site object for each site.
Args:
site (str): A line in the input file.
defect_species (object): Class object containing information about the defect species present in the system.
site_charge (bool): The site charge refers to the contribution to the overall charge of a site given by the original, non-defective species present at that site. True if the site charge contribution is to be included in the calculation, False if it is not to be included.
temperature (float): Temperature in Kelvin.
zero_energies_less_than_kT (optional(bool)): If True segregation energies with absolute values < kT will be set to zero.
Default is False.
Returns:
:obj:`Site`
"""
label = site[0]
if site_charge == True:
valence = float(site[1])
if site_charge == False:
valence = 0.0
x = float(site[2])
defect_labels = site[3::2]
defect_energies = [float(e) for e in site[4::2]]
if zero_energies_less_than_kT:
kT = boltzmann_eV * temperature
for d_e in defect_energies:
if abs(d_e) < kT:
d_e = 0.0
return Site(label,
x,
[defect_species[l] for l in defect_labels],\
defect_energies,
valence=valence)
def site_from_input_file(site, defect_species, site_charge, core, temperature):
"""
Takes the data from the input file and converts it into a site.
The input data file is a .txt file where each line in the file corresponds to a site. The values in each line are formatted and separated into the corresponding properties before creating a Site object for each site.
Args:
site (str): A line in the input file.
defect_species (object): Class object containing information about the defect species present in the system.
site_charge (bool): The site charge refers to the contribution to the overall charge of a site given by the original, non-defective species present at that site. True if the site charge contribution is to be included in the calculation, False if it is not to be included.
Returns:
:obj:`Site`
"""
label = site[0]
if site_charge == True:
valence = float(site[1])
if site_charge == False:
valence = 0.0
x = float(site[2])
defect_labels = site[3::2]
defect_energies = [float(e) for e in site[4::2]]
min_energy = min(defect_energies)
if core == 'single':
for d_e in defect_energies:
if d_e > min_energy:
d_e = 0.0
if core == 'multi-site':
for d_e in defect_energies:
if (-boltzmann_eV * temperature) <= d_e <= (boltzmann_eV *
temperature):
d_e = 0.0
#defect_energies = [ 0.0 for e in site[4::2] ]
return Site(label,
x, [defect_species[l] for l in defect_labels],
defect_energies,
valence=valence)
class TestSite(unittest.TestCase):
def setUp(self):
mock_defect_species = create_mock_defect_species(2)
mock_defects_at_site = create_mock_defects_at_site(2)
with patch('pyscses.site.DefectAtSite',
autospec=True) as mock_DefectAtSite:
mock_DefectAtSite.side_effect = mock_defects_at_site
self.site = Site(label='A',
x=1.5,
defect_species=mock_defect_species,
defect_energies=[-0.2, +0.2])
def test_defect_with_label(self):
self.site.defects[0].label = 'foo'
self.site.defects[1].label = 'bar'
self.assertEqual(self.site.defect_with_label('foo'),
self.site.defects[0])
self.assertEqual(self.site.defect_with_label('bar'),
self.site.defects[1])
def test_defect_with_label_2(self):
"""Checks that defect_with_label() raises a LabelError if the argument does not match any of the defect labels for this site."""
self.site.defects[0].label = 'foo'
self.site.defects[1].label = 'bar'
with self.assertRaises(LabelError):
self.site.defect_with_label('banana')
def test_energies(self):
self.site.defects[0].energy = -0.2
self.site.defects[1].energy = +0.2
self.assertEqual(self.site.energies(), [-0.2, +0.2])
def test_probabilities_one(self):
self.site.defects[0].boltzmann_factor = Mock(return_value=0.1)
self.site.defects[0].mole_fraction = 0.2
self.site.defects[0].label = 'A'
self.site.defects[1].boltzmann_factor = Mock(return_value=0.1)
self.site.defects[1].mole_fraction = 0.1
self.site.defects[1].label = 'B'
exp_A = ((0.2 * 0.1 / (1.0 + (0.2 * (0.1 - 1.0) + 0.1 * (0.1 - 1.0)))))
exp_B = ((0.1 * 0.1 / (1.0 + (0.2 * (0.1 - 1.0) + 0.1 * (0.1 - 1.0)))))
self.assertEqual(self.site.probabilities(phi=1.0, temp=298.0), {
'A': exp_A,
'B': exp_B
})
def test_probabilities_two(self):
self.site.defects[0].boltzmann_factor = Mock(return_value=0.1)
self.site.defects[0].mole_fraction = 0.2
self.site.defects[0].label = 'A'
self.site.defects[0].fixed = True
self.site.alpha = 0.8
self.site.fixed_defects = (self.site.defects[0], )
self.site.defects[1].boltzmann_factor = Mock(return_value=0.1)
self.site.defects[1].mole_fraction = 0.1
self.site.defects[1].label = 'B'
self.site.mobile_defects = (self.site.defects[1], )
exp_A = 0.2
exp_B = 0.8 * ((0.1 * 0.1 / (0.8 + (0.1 * (0.1 - 1.0)))))
self.assertEqual(self.site.probabilities(phi=1.0, temp=298.0), {
'A': exp_A,
'B': exp_B
})
def test_charge(self):
self.site.probabilities = Mock(return_value={'E': 0.1, 'D': 0.2})
self.site.defects[0].valence = 1.0
self.site.defects[1].valence = 2.0
self.site.scaling = 0.5
self.site.valence = 1.0
expected_value = (
(1.0 * 0.1 + 2.0 * 0.2) * 0.5 + 1.0) * fundamental_charge
self.assertEqual(self.site.charge(phi=1.0, temp=298.0), expected_value)