class TestGroundStateFinderTwoActiveSublattices(unittest.TestCase):
"""Container for test of the class functionality for a system with
two active sublattices."""
def __init__(self, *args, **kwargs):
super(TestGroundStateFinderTwoActiveSublattices,
self).__init__(*args, **kwargs)
a = 4.0
self.chemical_symbols = [['Au', 'Pd'], ['Li', 'Na']]
self.cutoffs = [3.0]
structure_prim = bulk(self.chemical_symbols[0][0], a=a)
structure_prim.append(
Atom(self.chemical_symbols[1][0], position=(a / 2, a / 2, a / 2)))
structure_prim.wrap()
self.structure_prim = structure_prim
self.cs = ClusterSpace(self.structure_prim, self.cutoffs,
self.chemical_symbols)
parameters = [0.1, -0.45, 0.333, 2, -1.42, 0.98]
self.ce = ClusterExpansion(self.cs, parameters)
self.all_possible_structures = []
self.supercell = self.structure_prim.repeat(2)
self.sl1_indices = [
s for s, sym in enumerate(self.supercell.get_chemical_symbols())
if sym == self.chemical_symbols[0][0]
]
self.sl2_indices = [
s for s, sym in enumerate(self.supercell.get_chemical_symbols())
if sym == self.chemical_symbols[1][0]
]
for i in self.sl1_indices:
for j in self.sl2_indices:
structure = self.supercell.copy()
structure.symbols[i] = self.chemical_symbols[0][1]
structure.symbols[j] = self.chemical_symbols[1][1]
self.all_possible_structures.append(structure)
def shortDescription(self):
"""Silences unittest from printing the docstrings in test cases."""
return None
def setUp(self):
"""Setup before each test."""
self.gsf = icet.tools.ground_state_finder.GroundStateFinder(
self.ce, self.supercell, verbose=False)
def test_init(self):
"""Tests that initialization of tested class work."""
# initialize from ClusterExpansion instance
gsf = icet.tools.ground_state_finder.GroundStateFinder(self.ce,
self.supercell,
verbose=False)
self.assertIsInstance(gsf,
icet.tools.ground_state_finder.GroundStateFinder)
def test_get_ground_state(self):
"""Tests get_ground_state functionality."""
target_val = min([
self.ce.predict(structure)
for structure in self.all_possible_structures
])
# Provide counts for the first/first species
species_count = {
self.chemical_symbols[0][0]: len(self.sl1_indices) - 1,
self.chemical_symbols[1][0]: len(self.sl2_indices) - 1
}
ground_state = self.gsf.get_ground_state(species_count=species_count)
predicted_species00 = self.ce.predict(ground_state)
self.assertEqual(predicted_species00, target_val)
# Provide counts for the first/second species
species_count = {
self.chemical_symbols[0][0]: len(self.sl1_indices) - 1,
self.chemical_symbols[1][1]: 1
}
ground_state = self.gsf.get_ground_state(species_count=species_count)
predicted_species01 = self.ce.predict(ground_state)
self.assertEqual(predicted_species01, predicted_species00)
# Provide counts for second/second species
species_count = {
self.chemical_symbols[0][1]: 1,
self.chemical_symbols[1][1]: 1
}
ground_state = self.gsf.get_ground_state(species_count=species_count)
predicted_species11 = self.ce.predict(ground_state)
self.assertEqual(predicted_species11, predicted_species01)
def _test_ground_state_cluster_vectors_in_database(self, db_name):
"""Tests get_ground_state functionality by comparing the cluster
vectors for the structures in the databases."""
filename = inspect.getframeinfo(inspect.currentframe()).filename
path = os.path.dirname(os.path.abspath(filename))
db = db_connect(os.path.join(path, db_name))
# Select the structure set with the lowest pairwise correlations
selections = ['id={}'.format(i) for i in [7, 13, 15, 62, 76]]
for selection in selections:
row = db.get(selection)
structure = row.toatoms()
target_cluster_vector = self.cs.get_cluster_vector(structure)
species_count = {
self.chemical_symbols[0][0]:
structure.get_chemical_symbols().count(
self.chemical_symbols[0][0]),
self.chemical_symbols[1][0]:
structure.get_chemical_symbols().count(
self.chemical_symbols[1][0])
}
ground_state = self.gsf.get_ground_state(
species_count=species_count)
gs_cluster_vector = self.cs.get_cluster_vector(ground_state)
mean_diff = np.mean(abs(target_cluster_vector - gs_cluster_vector))
self.assertLess(mean_diff, 1e-8)
def test_ground_state_cluster_vectors(self):
"""Tests get_ground_state functionality by comparing the cluster
vectors for ground states obtained from simulated annealing."""
self._test_ground_state_cluster_vectors_in_database(
'../../../structure_databases/annealing_ground_states.db')
def test_get_ground_state_fails_for_faulty_species_to_count(self):
"""Tests that get_ground_state fails if species_to_count is faulty."""
# Check that get_ground_state fails if counts are provided for a both species on one
# of the active sublattices
species_count = {
self.chemical_symbols[0][0]: len(self.sl1_indices) - 1,
self.chemical_symbols[0][1]: 1,
self.chemical_symbols[1][1]: 1
}
with self.assertRaises(ValueError) as cm:
self.gsf.get_ground_state(species_count=species_count)
self.assertTrue(
'Provide counts for at most one of the species on each active sublattice '
'({}), not {}!'.format(self.gsf._active_species,
list(species_count.keys())) in str(
cm.exception))
# Check that get_ground_state fails if the count exceeds the number sites on the first
# sublattice
faulty_species = self.chemical_symbols[0][1]
faulty_count = len(self.supercell)
species_count = {
faulty_species: faulty_count,
self.chemical_symbols[1][1]: 1
}
n_active_sites = len([
sym for sym in self.supercell.get_chemical_symbols()
if sym == self.chemical_symbols[0][0]
])
with self.assertRaises(ValueError) as cm:
self.gsf.get_ground_state(species_count=species_count)
self.assertTrue(
'The count for species {} ({}) must be a positive integer and cannot '
'exceed the number of sites on the active sublattice '
'({})'.format(faulty_species, faulty_count, n_active_sites) in str(
cm.exception))
# Check that get_ground_state fails if the count exceeds the number sites on the second
# sublattice
faulty_species = self.chemical_symbols[1][1]
faulty_count = len(self.supercell)
species_count = {
faulty_species: faulty_count,
self.chemical_symbols[0][1]: 1
}
n_active_sites = len([
sym for sym in self.supercell.get_chemical_symbols()
if sym == self.chemical_symbols[1][0]
])
with self.assertRaises(ValueError) as cm:
self.gsf.get_ground_state(species_count=species_count)
self.assertTrue(
'The count for species {} ({}) must be a positive integer and cannot '
'exceed the number of sites on the active sublattice '
'({})'.format(faulty_species, faulty_count, n_active_sites) in str(
cm.exception))
def test_get_ground_state_passes_for_partial_species_to_count(self):
# Check that get_ground_state passes if a single count is provided
species_count = {self.chemical_symbols[0][1]: 1}
self.gsf.get_ground_state(species_count=species_count)
# Check that get_ground_state passes no counts are provided
gs = self.gsf.get_ground_state()
self.assertEqual(gs.get_chemical_formula(), "Au8Li8")
class TestGroundStateFinderTriplets(unittest.TestCase):
"""Container for test of the class functionality for a system with
triplets."""
def __init__(self, *args, **kwargs):
super(TestGroundStateFinderTriplets, self).__init__(*args, **kwargs)
self.chemical_symbols = ['Au', 'Pd']
self.cutoffs = [3.0, 3.0]
structure_prim = fcc111(self.chemical_symbols[0],
a=4.0,
size=(1, 1, 6),
vacuum=10,
periodic=True)
structure_prim.wrap()
self.structure_prim = structure_prim
self.cs = ClusterSpace(self.structure_prim, self.cutoffs,
self.chemical_symbols)
parameters = [0.0] * 4 + [0.1] * 6 + [-0.02] * 11
self.ce = ClusterExpansion(self.cs, parameters)
self.all_possible_structures = []
self.supercell = self.structure_prim.repeat((2, 2, 1))
for i in range(len(self.supercell)):
structure = self.supercell.copy()
structure.symbols[i] = self.chemical_symbols[1]
self.all_possible_structures.append(structure)
def shortDescription(self):
"""Silences unittest from printing the docstrings in test cases."""
return None
def setUp(self):
"""Setup before each test."""
self.gsf = icet.tools.ground_state_finder.GroundStateFinder(
self.ce, self.supercell, verbose=False)
def test_init(self):
"""Tests that initialization of tested class work."""
# initialize from ClusterExpansion instance
gsf = icet.tools.ground_state_finder.GroundStateFinder(self.ce,
self.supercell,
verbose=False)
self.assertIsInstance(gsf,
icet.tools.ground_state_finder.GroundStateFinder)
def test_get_ground_state(self):
"""Tests get_ground_state functionality."""
target_val = min([
self.ce.predict(structure)
for structure in self.all_possible_structures
])
# Provide counts for first species
species_count = {self.chemical_symbols[0]: len(self.supercell) - 1}
ground_state = self.gsf.get_ground_state(species_count=species_count,
threads=1)
predicted_species0 = self.ce.predict(ground_state)
self.assertEqual(predicted_species0, target_val)
# Provide counts for second species
species_count = {self.chemical_symbols[1]: 1}
ground_state = self.gsf.get_ground_state(species_count=species_count,
threads=1)
predicted_species1 = self.ce.predict(ground_state)
self.assertEqual(predicted_species0, predicted_species1)
# Check that get_ground_state finds 50-50 mix when no counts are provided
gsf = icet.tools.ground_state_finder.GroundStateFinder(self.ce,
self.supercell,
verbose=False)
gs = gsf.get_ground_state(threads=1)
self.assertEqual(gs.get_chemical_formula(), "Au12Pd12")
# Ensure that an exception is raised when no solution is found
gsf = icet.tools.ground_state_finder.GroundStateFinder(
self.ce, self.supercell, solver_name='CBC', verbose=False)
species_count = {self.chemical_symbols[1]: 1}
with self.assertRaises(Exception) as cm:
gsf.get_ground_state(species_count=species_count,
max_seconds=0.0,
threads=1)
self.assertTrue('Optimization failed' in str(cm.exception))
class TestGroundStateFinderZeroParameter(unittest.TestCase):
"""Container for test of the class functionality for a system with a zero parameter."""
def __init__(self, *args, **kwargs):
super(TestGroundStateFinderZeroParameter,
self).__init__(*args, **kwargs)
self.chemical_symbols = ['Ag', 'Au']
self.cutoffs = [4.3]
self.structure_prim = bulk(self.chemical_symbols[1], a=4.0)
self.cs = ClusterSpace(self.structure_prim, self.cutoffs,
self.chemical_symbols)
nonzero_ce = ClusterExpansion(self.cs, [0, 0, 0.1, -0.02])
lolg = LocalOrbitListGenerator(
self.cs.orbit_list, Structure.from_atoms(self.structure_prim),
self.cs.fractional_position_tolerance)
full_orbit_list = lolg.generate_full_orbit_list()
binary_parameters_zero = transform_parameters(self.structure_prim,
full_orbit_list,
nonzero_ce.parameters)
binary_parameters_zero[1] = 0
A = get_transformation_matrix(self.structure_prim, full_orbit_list)
Ainv = np.linalg.inv(A)
zero_parameters = np.dot(Ainv, binary_parameters_zero)
self.ce = ClusterExpansion(self.cs, zero_parameters)
self.all_possible_structures = []
self.supercell = self.structure_prim.repeat(2)
for i in range(len(self.supercell)):
structure = self.supercell.copy()
structure.symbols[i] = self.chemical_symbols[0]
self.all_possible_structures.append(structure)
def shortDescription(self):
"""Silences unittest from printing the docstrings in test cases."""
return None
def setUp(self):
"""Setup before each test."""
self.gsf = icet.tools.ground_state_finder.GroundStateFinder(
self.ce, self.supercell, verbose=False)
def test_init(self):
"""Tests that initialization of tested class work."""
# initialize from ClusterExpansion instance
gsf = icet.tools.ground_state_finder.GroundStateFinder(self.ce,
self.supercell,
verbose=False)
self.assertIsInstance(gsf,
icet.tools.ground_state_finder.GroundStateFinder)
def test_get_ground_state(self):
"""Tests get_ground_state functionality."""
target_val = min([
self.ce.predict(structure)
for structure in self.all_possible_structures
])
# Provide counts for first species
species_count = {self.chemical_symbols[0]: 1}
ground_state = self.gsf.get_ground_state(species_count=species_count,
threads=1)
predicted_species0 = self.ce.predict(ground_state)
self.assertEqual(predicted_species0, target_val)
# Provide counts for second species
species_count = {self.chemical_symbols[1]: len(self.supercell) - 1}
ground_state = self.gsf.get_ground_state(species_count=species_count,
threads=1)
predicted_species1 = self.ce.predict(ground_state)
self.assertEqual(predicted_species0, predicted_species1)
class TestGroundStateFinderInactiveSublatticeSameSpecies(unittest.TestCase):
"""Container for test of the class functionality for a system with an
inactive sublattice occupied by a species found on the active
sublattice."""
def __init__(self, *args, **kwargs):
super(TestGroundStateFinderInactiveSublatticeSameSpecies,
self).__init__(*args, **kwargs)
self.chemical_symbols = [['Ag', 'Au'], ['Ag']]
self.cutoffs = [4.3]
a = 4.0
structure_prim = bulk(self.chemical_symbols[0][1], a=a)
structure_prim.append(
Atom(self.chemical_symbols[1][0], position=(a / 2, a / 2, a / 2)))
self.structure_prim = structure_prim
self.cs = ClusterSpace(self.structure_prim, self.cutoffs,
self.chemical_symbols)
self.ce = ClusterExpansion(self.cs, [0, 0, 0.1, -0.02])
self.all_possible_structures = []
self.supercell = self.structure_prim.repeat(2)
sublattices = self.cs.get_sublattices(self.supercell)
self.n_active_sites = [
len(subl.indices) for subl in sublattices.active_sublattices
]
for i, sym in enumerate(self.supercell.get_chemical_symbols()):
if sym not in self.chemical_symbols[0]:
continue
structure = self.supercell.copy()
structure.symbols[i] = self.chemical_symbols[0][0]
self.all_possible_structures.append(structure)
def shortDescription(self):
"""Silences unittest from printing the docstrings in test cases."""
return None
def setUp(self):
"""Setup before each test."""
self.gsf = icet.tools.ground_state_finder.GroundStateFinder(
self.ce, self.supercell, verbose=False)
def test_init(self):
"""Tests that initialization of tested class work."""
# initialize from ClusterExpansion instance
gsf = icet.tools.ground_state_finder.GroundStateFinder(self.ce,
self.supercell,
verbose=False)
self.assertIsInstance(gsf,
icet.tools.ground_state_finder.GroundStateFinder)
def test_get_ground_state(self):
"""Tests get_ground_state functionality."""
target_val = min([
self.ce.predict(structure)
for structure in self.all_possible_structures
])
# Provide counts for first species
species_count = {self.chemical_symbols[0][0]: 1}
ground_state = self.gsf.get_ground_state(species_count=species_count,
threads=1)
predicted_species0 = self.ce.predict(ground_state)
self.assertEqual(predicted_species0, target_val)
species_count = {
self.chemical_symbols[0][1]: self.n_active_sites[0] - 1
}
ground_state = self.gsf.get_ground_state(species_count=species_count,
threads=1)
predicted_species1 = self.ce.predict(ground_state)
self.assertEqual(predicted_species0, predicted_species1)
def test_get_ground_state_fails_for_faulty_species_to_count(self):
"""Tests that get_ground_state fails if species_to_count is faulty."""
# Check that get_ground_state fails if counts are provided for multiple species
species_count = {
self.chemical_symbols[0][0]: 1,
self.chemical_symbols[0][1]: self.n_active_sites[0] - 1
}
with self.assertRaises(ValueError) as cm:
self.gsf.get_ground_state(species_count=species_count)
self.assertTrue(
'Provide counts for at most one of the species on each active sublattice '
'({}), not {}!'.format(self.gsf._active_species,
list(species_count.keys())) in str(
cm.exception))
# Check that get_ground_state fails if counts are provided for a
# species not found on the active sublattice
species_count = {'H': 1}
with self.assertRaises(ValueError) as cm:
self.gsf.get_ground_state(species_count=species_count)
self.assertTrue(
'The species {} is not present on any of the active sublattices'
' ({})'.format(
list(species_count.keys())[0],
self.gsf._active_species) in str(cm.exception))
# Check that get_ground_state fails if the count exceeds the number sites on the active
# sublattice
faulty_species = self.chemical_symbols[0][0]
faulty_count = len(self.supercell)
species_count = {faulty_species: faulty_count}
n_active_sites = len([
sym for sym in self.supercell.get_chemical_symbols()
if sym == self.chemical_symbols[0][1]
])
with self.assertRaises(ValueError) as cm:
self.gsf.get_ground_state(species_count=species_count)
self.assertTrue(
'The count for species {} ({}) must be a positive integer and cannot '
'exceed the number of sites on the active sublattice '
'({})'.format(faulty_species, faulty_count, n_active_sites) in str(
cm.exception))
def test_create_cluster_maps(self):
"""Tests _create_cluster_maps functionality """
gsf = icet.tools.ground_state_finder.GroundStateFinder(self.ce,
self.supercell,
verbose=False)
gsf._create_cluster_maps(self.structure_prim)
# Test cluster to sites map
target = [[0], [0, 0], [0, 0], [0, 0], [0, 0], [0, 0], [0, 0], [0, 0],
[0, 0], [0, 0]]
self.assertEqual(target, gsf._cluster_to_sites_map)
# Test cluster to orbit map
target = [0, 1, 1, 1, 1, 1, 1, 2, 2, 2]
self.assertEqual(target, gsf._cluster_to_orbit_map)
# Test ncluster per orbit map
target = [1, 1, 6, 3]
self.assertEqual(target, gsf._nclusters_per_orbit)
class TestGroundStateFinder(unittest.TestCase):
"""Container for test of the class functionality."""
def __init__(self, *args, **kwargs):
super(TestGroundStateFinder, self).__init__(*args, **kwargs)
self.chemical_symbols = ['Ag', 'Au']
self.cutoffs = [4.3]
self.structure_prim = bulk(self.chemical_symbols[1], a=4.0)
self.cs = ClusterSpace(self.structure_prim, self.cutoffs,
self.chemical_symbols)
self.ce = ClusterExpansion(self.cs, [0, 0, 0.1, -0.02])
self.all_possible_structures = []
self.supercell = self.structure_prim.repeat(2)
for i in range(len(self.supercell)):
structure = self.supercell.copy()
structure.symbols[i] = self.chemical_symbols[0]
self.all_possible_structures.append(structure)
def shortDescription(self):
"""Silences unittest from printing the docstrings in test cases."""
return None
def setUp(self):
"""Setup before each test."""
self.gsf = icet.tools.ground_state_finder.GroundStateFinder(
self.ce, self.supercell, verbose=False)
def test_mip_import(self):
"""Tests the Python-MIP import statement"""
# Test that an error is raised if Python-MIP is not installed
with self.assertRaises(ImportError) as cm:
with mock.patch.dict(sys.modules, {'mip': None}):
importlib.reload(icet.tools.ground_state_finder)
self.assertTrue(
'Python-MIP (https://python-mip.readthedocs.io/en/latest/) is required in '
'order to use the ground state finder.' in str(cm.exception))
# Test that an error is raised if the Python-MIP version is not sufficiently recent
with self.assertRaises(VersionConflict) as cm:
with mock.patch('mip.constants.VERSION', '1.6.2'):
importlib.reload(icet.tools.ground_state_finder)
self.assertTrue(
'Python-MIP version 1.6.3 or later is required in order to use the ground '
'state finder.' in str(cm.exception))
def test_init(self):
"""Tests that initialization of tested class work."""
# initialize from GroundStateFinder instance
gsf = icet.tools.ground_state_finder.GroundStateFinder(self.ce,
self.supercell,
verbose=False)
self.assertIsInstance(gsf,
icet.tools.ground_state_finder.GroundStateFinder)
def test_init_solver(self):
"""Tests that initialization of tested class work."""
# initialize from GroundStateFinder instance
# Set the solver explicitely
gsf = icet.tools.ground_state_finder.GroundStateFinder(
self.ce, self.supercell, solver_name='CBC', verbose=False)
self.assertEqual('CBC', gsf._model.solver_name.upper())
def test_init_fails_for_ternary_with_one_active_sublattice(self):
"""Tests that initialization fails for a ternary system with one active
sublattice."""
chemical_symbols = ['Au', 'Ag', 'Pd']
cs = ClusterSpace(self.structure_prim,
cutoffs=self.cutoffs,
chemical_symbols=chemical_symbols)
ce = ClusterExpansion(cs, [0.0] * len(cs))
with self.assertRaises(NotImplementedError) as cm:
icet.tools.ground_state_finder.GroundStateFinder(ce,
self.supercell,
verbose=False)
self.assertTrue(
'Currently, systems with more than two allowed species on any sublattice '
'are not supported.' in str(cm.exception))
def test_optimization_status_property(self):
"""Tests the optimization_status property."""
# Check that the optimization_status is None initially
self.assertIsNone(self.gsf.optimization_status)
# Check that the optimization_status is OPTIMAL if a ground state is found
species_count = {self.chemical_symbols[0]: 1}
self.gsf.get_ground_state(species_count=species_count, threads=1)
self.assertEqual(str(self.gsf.optimization_status),
'OptimizationStatus.OPTIMAL')
def test_model_property(self):
"""Tests the model property."""
self.assertEqual(self.gsf.model.name, 'CE')
def test_get_ground_state(self):
"""Tests get_ground_state functionality."""
target_val = min([
self.ce.predict(structure)
for structure in self.all_possible_structures
])
# Provide counts for first species
species_count = {self.chemical_symbols[0]: 1}
ground_state = self.gsf.get_ground_state(species_count=species_count,
threads=1)
predicted_species0 = self.ce.predict(ground_state)
self.assertEqual(predicted_species0, target_val)
# Provide counts for second species
species_count = {self.chemical_symbols[1]: len(self.supercell) - 1}
ground_state = self.gsf.get_ground_state(species_count=species_count,
threads=1)
predicted_species1 = self.ce.predict(ground_state)
self.assertEqual(predicted_species0, predicted_species1)
# Set the maximum run time
species_count = {self.chemical_symbols[0]: 1}
ground_state = self.gsf.get_ground_state(species_count=species_count,
max_seconds=0.5,
threads=1)
predicted_max_seconds = self.ce.predict(ground_state)
self.assertGreaterEqual(predicted_max_seconds, predicted_species0)
def test_get_ground_state_fails_for_faulty_species_to_count(self):
"""Tests that get_ground_state fails if species_to_count is faulty."""
# Check that get_ground_state fails if counts are provided for multiple
# species
species_count = {
self.chemical_symbols[0]: 1,
self.chemical_symbols[1]: len(self.supercell) - 1
}
with self.assertRaises(ValueError) as cm:
self.gsf.get_ground_state(species_count=species_count)
self.assertTrue(
'Provide counts for at most one of the species on each active sublattice '
'({}), not {}!'.format(self.gsf._active_species,
list(species_count.keys())) in str(
cm.exception))
# Check that get_ground_state fails if counts are provided for a
# species not found on the active sublattice
species_count = {'H': 1}
with self.assertRaises(ValueError) as cm:
self.gsf.get_ground_state(species_count=species_count)
self.assertTrue(
'The species {} is not present on any of the active sublattices'
' ({})'.format(
list(species_count.keys())[0],
self.gsf._active_species) in str(cm.exception))
# Check that get_ground_state fails if the count exceeds the number sites on the active
# sublattice
faulty_species = self.chemical_symbols[0]
faulty_count = len(self.supercell) + 1
species_count = {faulty_species: faulty_count}
with self.assertRaises(ValueError) as cm:
self.gsf.get_ground_state(species_count=species_count)
self.assertTrue(
'The count for species {} ({}) must be a positive integer and cannot '
'exceed the number of sites on the active sublattice '
'({})'.format(faulty_species, faulty_count, len(
self.supercell)) in str(cm.exception))
# Check that get_ground_state fails if the count is not a positive integer
species = self.chemical_symbols[0]
count = -1
species_count = {species: count}
with self.assertRaises(ValueError) as cm:
self.gsf.get_ground_state(species_count=species_count)
self.assertTrue(
'The count for species {} ({}) must be a positive integer and cannot '
'exceed the number of sites on the active sublattice '
'({})'.format(species, count, len(self.supercell)) in str(
cm.exception))
def test_create_cluster_maps(self):
"""Tests _create_cluster_maps functionality """
gsf = icet.tools.ground_state_finder.GroundStateFinder(self.ce,
self.supercell,
verbose=False)
gsf._create_cluster_maps(self.structure_prim)
# Test cluster to sites map
target = [[0], [0, 0], [0, 0], [0, 0], [0, 0], [0, 0], [0, 0], [0, 0],
[0, 0], [0, 0]]
self.assertEqual(target, gsf._cluster_to_sites_map)
# Test cluster to orbit map
target = [0, 1, 1, 1, 1, 1, 1, 2, 2, 2]
self.assertEqual(target, gsf._cluster_to_orbit_map)
# Test ncluster per orbit map
target = [1, 1, 6, 3]
self.assertEqual(target, gsf._nclusters_per_orbit)
class TestClusterExpansion(unittest.TestCase):
"""Container for tests of the class functionality."""
def __init__(self, *args, **kwargs):
super(TestClusterExpansion, self).__init__(*args, **kwargs)
self.structure = bulk('Au')
self.cutoffs = [3.0] * 3
chemical_symbols = ['Au', 'Pd']
self.cs = ClusterSpace(self.structure, self.cutoffs, chemical_symbols)
def shortDescription(self):
"""Silences unittest from printing the docstrings in test cases."""
return None
def setUp(self):
"""Setup before each test."""
params_len = len(self.cs)
self.parameters = np.arange(params_len)
self.ce = ClusterExpansion(self.cs, self.parameters)
def test_init(self):
"""Tests that initialization works."""
self.assertIsInstance(self.ce, ClusterExpansion)
# test whether method raises Exception
with self.assertRaises(ValueError) as context:
ClusterExpansion(self.cs, [0.0])
self.assertTrue('cluster_space (5) and parameters (1) must have the'
' same length' in str(context.exception))
def test_predict(self):
"""Tests predict function."""
predicted_val = self.ce.predict(self.structure)
self.assertEqual(predicted_val, 10.0)
def test_property_orders(self):
"""Tests orders property."""
self.assertEqual(self.ce.orders, list(range(len(self.cutoffs) + 2)))
def test_property_to_dataframe(self):
"""Tests to_dataframe() property."""
df = self.ce.to_dataframe()
self.assertIn('radius', df.columns)
self.assertIn('order', df.columns)
self.assertIn('eci', df.columns)
self.assertEqual(len(df), len(self.parameters))
def test_get__clusterspace_copy(self):
"""Tests get cluster space copy."""
self.assertEqual(str(self.ce.get_cluster_space_copy()), str(self.cs))
def test_property_parameters(self):
"""Tests parameters properties."""
self.assertEqual(list(self.ce.parameters), list(self.parameters))
def test_len(self):
"""Tests len functionality."""
self.assertEqual(self.ce.__len__(), len(self.parameters))
def test_read_write(self):
"""Tests read and write functionalities."""
# save to file
temp_file = tempfile.NamedTemporaryFile()
self.ce.write(temp_file.name)
# read from file
temp_file.seek(0)
ce_read = ClusterExpansion.read(temp_file.name)
# check cluster space
self.assertEqual(self.cs._input_structure,
ce_read._cluster_space._input_structure)
self.assertEqual(self.cs._cutoffs, ce_read._cluster_space._cutoffs)
self.assertEqual(self.cs._input_chemical_symbols,
ce_read._cluster_space._input_chemical_symbols)
# check parameters
self.assertIsInstance(ce_read.parameters, np.ndarray)
self.assertEqual(list(ce_read.parameters), list(self.parameters))
# check metadata
self.assertEqual(len(self.ce.metadata), len(ce_read.metadata))
self.assertSequenceEqual(sorted(self.ce.metadata.keys()),
sorted(ce_read.metadata.keys()))
for key in self.ce.metadata.keys():
self.assertEqual(self.ce.metadata[key], ce_read.metadata[key])
def test_read_write_pruned(self):
"""Tests read and write functionalities."""
# save to file
temp_file = tempfile.NamedTemporaryFile()
self.ce.prune(indices=[2, 3])
self.ce.prune(tol=3)
pruned_params = self.ce.parameters
pruned_cs_len = len(self.ce._cluster_space)
self.ce.write(temp_file.name)
# read from file
temp_file.seek(0)
ce_read = ClusterExpansion.read(temp_file.name)
params_read = ce_read.parameters
cs_len_read = len(ce_read._cluster_space)
# check cluster space
self.assertEqual(cs_len_read, pruned_cs_len)
self.assertEqual(list(params_read), list(pruned_params))
def test_prune_cluster_expansion(self):
"""Tests pruning cluster expansion."""
len_before = len(self.ce)
self.ce.prune()
len_after = len(self.ce)
self.assertEqual(len_before, len_after)
# Set all parameters to zero except three
self.ce._parameters = np.array([0.0] * len_after)
self.ce._parameters[0] = 1.0
self.ce._parameters[1] = 2.0
self.ce._parameters[2] = 0.5
self.ce.prune()
self.assertEqual(len(self.ce), 3)
self.assertNotEqual(len(self.ce), len_after)
def test_prune_cluster_expansion_tol(self):
"""Tests pruning cluster expansion with tolerance."""
len_before = len(self.ce)
self.ce.prune()
len_after = len(self.ce)
self.assertEqual(len_before, len_after)
# Set all parameters to zero except two, one of which is
# non-zero but below the tolerance
self.ce._parameters = np.array([0.0] * len_after)
self.ce._parameters[0] = 1.0
self.ce._parameters[1] = 0.01
self.ce.prune(tol=0.02)
self.assertEqual(len(self.ce), 1)
self.assertNotEqual(len(self.ce), len_after)
def test_prune_pairs(self):
"""Tests pruning pairs only."""
df = self.ce.to_dataframe()
pair_indices = df.index[df['order'] == 2].tolist()
self.ce.prune(indices=pair_indices)
df_new = self.ce.to_dataframe()
pair_indices_new = df_new.index[df_new['order'] == 2].tolist()
self.assertEqual(pair_indices_new, [])
def test_prune_zerolet(self):
"""Tests pruning zerolet."""
with self.assertRaises(ValueError) as context:
self.ce.prune(indices=[0])
self.assertTrue('zerolet may not be pruned' in str(context.exception))
def test_plot_ecis(self):
"""Tests plot_ecis."""
self.ce.plot_ecis()
def test_repr(self):
"""Tests repr functionality."""
retval = self.ce.__repr__()
target = """
================================================ Cluster Expansion =================================================
space group : Fm-3m (225)
chemical species : ['Au', 'Pd'] (sublattice A)
cutoffs : 3.0000 3.0000 3.0000
total number of parameters : 5
number of parameters by order : 0= 1 1= 1 2= 1 3= 1 4= 1
fractional_position_tolerance : 2e-06
position_tolerance : 1e-05
symprec : 1e-05
total number of nonzero parameters : 4
number of nonzero parameters by order : 0= 0 1= 1 2= 1 3= 1 4= 1
--------------------------------------------------------------------------------------------------------------------
index | order | radius | multiplicity | orbit_index | multi_component_vector | sublattices | parameter | ECI
--------------------------------------------------------------------------------------------------------------------
0 | 0 | 0.0000 | 1 | -1 | . | . | 0 | 0
1 | 1 | 0.0000 | 1 | 0 | [0] | A | 1 | 1
2 | 2 | 1.4425 | 6 | 1 | [0, 0] | A-A | 2 | 0.333
3 | 3 | 1.6657 | 8 | 2 | [0, 0, 0] | A-A-A | 3 | 0.375
4 | 4 | 1.7667 | 2 | 3 | [0, 0, 0, 0] | A-A-A-A | 4 | 2
====================================================================================================================
""" # noqa
self.assertEqual(strip_surrounding_spaces(target),
strip_surrounding_spaces(retval))
def test_get_string_representation(self):
"""Tests _get_string_representation functionality."""
retval = self.ce._get_string_representation(print_threshold=2,
print_minimum=1)
target = """
================================================ Cluster Expansion =================================================
space group : Fm-3m (225)
chemical species : ['Au', 'Pd'] (sublattice A)
cutoffs : 3.0000 3.0000 3.0000
total number of parameters : 5
number of parameters by order : 0= 1 1= 1 2= 1 3= 1 4= 1
fractional_position_tolerance : 2e-06
position_tolerance : 1e-05
symprec : 1e-05
total number of nonzero parameters : 4
number of nonzero parameters by order : 0= 0 1= 1 2= 1 3= 1 4= 1
--------------------------------------------------------------------------------------------------------------------
index | order | radius | multiplicity | orbit_index | multi_component_vector | sublattices | parameter | ECI
--------------------------------------------------------------------------------------------------------------------
0 | 0 | 0.0000 | 1 | -1 | . | . | 0 | 0
...
4 | 4 | 1.7667 | 2 | 3 | [0, 0, 0, 0] | A-A-A-A | 4 | 2
====================================================================================================================
""" # noqa
self.assertEqual(strip_surrounding_spaces(target),
strip_surrounding_spaces(retval))
def test_print_overview(self):
"""Tests print_overview functionality."""
with StringIO() as capturedOutput:
sys.stdout = capturedOutput # redirect stdout
self.ce.print_overview()
sys.stdout = sys.__stdout__ # reset redirect
self.assertTrue('Cluster Expansion' in capturedOutput.getvalue())