def test_get_bond_distance_summary(self):
"""Test getting the bond distance summary"""
sa = SiteAnalyzer(self.tin_dioxide)
data = sa.get_bond_distance_summary(0)
self.assertEqual(len(data[2]), 6)
self.assertAlmostEqual(data[2][0], 2.0922101061490546)
def test_init(self):
"""Test to check SiteDescriber can be initialised"""
sa = SiteAnalyzer(self.tin_dioxide)
self.assertNotEqual(sa, None, msg="tin dioxide site analyzer could not be init")
# check different structure
sa = SiteAnalyzer(self.ba_n)
self.assertNotEqual(sa, None, msg="BaN2 site analyzer could not be initialized")
def test_connectivity_angle_summary(self):
"""Test getting the connectivity angle summary"""
sa = SiteAnalyzer(self.tin_dioxide)
data = sa.get_connectivity_angle_summary(0)
self.assertEqual(len(data[0]['corner']), 8)
self.assertEqual(len(data[0]['edge']), 4)
self.assertAlmostEqual(data[0]['edge'][0], 101.62287790513848)
def test_nnn_distance_summary(self):
"""Test getting the nnn distance summary"""
sa = SiteAnalyzer(self.tin_dioxide)
data = sa.get_nnn_distance_summary(0)
self.assertEqual(len(data[0]['corner']), 8)
self.assertEqual(len(data[0]['edge']), 2)
self.assertAlmostEqual(data[0]['edge'][0], 3.24322132)
def test_geometries_match(self):
"""Test geometry matching function."""
sa = SiteAnalyzer(self.tin_dioxide, use_symmetry_equivalent_sites=False)
geom_a = sa.get_site_geometry(0)
geom_b = sa.get_site_geometry(1)
geom_c = sa.get_site_geometry(4)
self.assertTrue(geometries_match(geom_a, geom_b))
self.assertFalse(geometries_match(geom_a, geom_c))
def test_get_site_summary(self):
"""Test getting the site summary"""
sa = SiteAnalyzer(self.tin_dioxide)
data = sa.get_site_summary(0)
self.assertEqual(data["element"], "Sn4+")
self.assertEqual(data["geometry"]["type"], "octahedral")
self.assertAlmostEqual(data["geometry"]["likeness"], 0.9349776258427136)
self.assertEqual(len(data["nn"]), 6)
self.assertEqual(len(data["nnn"]["corner"]), 8)
self.assertEqual(len(data["nnn"]["edge"]), 2)
self.assertEqual(data["poly_formula"], "O6")
self.assertEqual(data["sym_labels"], (1,))
def test_equivalent_sites(self):
"""Check equivalent sites instance variable set correctly."""
sa = SiteAnalyzer(self.ba_n, use_symmetry_equivalent_sites=False)
self.assertEqual(sa.equivalent_sites, [0, 0, 0, 0, 4, 4])
# test using symmetry to determine equivalent sites
sa = SiteAnalyzer(self.ba_n, use_symmetry_equivalent_sites=True)
self.assertIsInstance(sa.equivalent_sites, list)
self.assertEqual(sa.equivalent_sites, [0, 0, 0, 0, 4, 4])
# test symprec option works
sa = SiteAnalyzer(self.ba_n, use_symmetry_equivalent_sites=True, symprec=0.0001)
self.assertEqual(sa.equivalent_sites, [0, 1, 1, 0, 4, 4])
def test_get_site_summary(self):
"""Test getting the site summary"""
sa = SiteAnalyzer(self.tin_dioxide)
data = sa.get_site_summary(0)
self.assertEqual(data['element'], 'Sn4+')
self.assertEqual(data['geometry']['type'], 'octahedral')
self.assertAlmostEqual(data['geometry']['likeness'],
0.9349776258427136)
self.assertEqual(len(data['nn']), 6)
self.assertEqual(len(data['nnn']['corner']), 8)
self.assertEqual(len(data['nnn']['edge']), 2)
self.assertEqual(data['poly_formula'], 'O6')
self.assertEqual(data['sym_labels'], (1, ))
def test_get_next_nearest_neighbors(self):
"""Check getting next nearest neighbors."""
sa = SiteAnalyzer(self.tin_dioxide)
info = sa.get_next_nearest_neighbors(5)
self.assertEqual(len(info), 14)
self.assertEqual(info[0]["element"], "O2-")
self.assertEqual(info[0]["connectivity"], "edge")
self.assertEqual(info[0]["geometry"]["type"], "trigonal planar")
self.assertEqual(info[0]["inequiv_index"], 2)
info = sa.get_next_nearest_neighbors(0,
inc_inequivalent_site_index=False)
self.assertTrue('inequiv_index' not in info[0])
info = sa.get_next_nearest_neighbors(0)
self.assertEqual(info[0]["element"], 'Sn4+')
self.assertEqual(info[0]["connectivity"], "edge")
self.assertEqual(info[0]["geometry"]["type"], "octahedral")
self.assertEqual(len(info[0]['angles']), 2)
self.assertAlmostEqual(info[0]['angles'][0], 101.62287790513848)
# check different structure without oxi state
sa = SiteAnalyzer(self.ba_n)
info = sa.get_next_nearest_neighbors(0)
self.assertEqual(len(info), 36)
self.assertEqual(info[5]["element"], "N")
self.assertEqual(info[5]["connectivity"], "edge")
self.assertEqual(info[5]["geometry"]["type"], "6-coordinate")
self.assertEqual(len(info[5]['angles']), 2)
self.assertAlmostEqual(info[5]['angles'][0], 83.91397867959587)
def test_get_next_nearest_neighbors(self):
"""Check getting next nearest neighbors."""
sa = SiteAnalyzer(self.tin_dioxide)
info = sa.get_next_nearest_neighbors(5)
self.assertEqual(len(info), 14)
idx = [i for i, s in enumerate(info) if s["connectivity"] == "edge"][0]
self.assertEqual(info[idx]["element"], "O2-")
self.assertEqual(info[idx]["connectivity"], "edge")
self.assertEqual(info[idx]["geometry"]["type"], "trigonal planar")
self.assertEqual(info[idx]["inequiv_index"], 2)
info = sa.get_next_nearest_neighbors(0, inc_inequivalent_site_index=False)
self.assertTrue("inequiv_index" not in info[0])
info = sa.get_next_nearest_neighbors(0)
self.assertEqual(info[0]["element"], "Sn4+")
self.assertEqual(info[0]["connectivity"], "edge")
self.assertEqual(info[0]["geometry"]["type"], "octahedral")
self.assertEqual(len(info[0]["angles"]), 2)
self.assertAlmostEqual(info[0]["angles"][0], 101.62287790513848)
self.assertAlmostEqual(info[0]["distance"], 3.24322132)
# check different structure without oxi state
sa = SiteAnalyzer(self.ba_n)
info = sa.get_next_nearest_neighbors(0)
self.assertEqual(len(info), 36)
self.assertEqual(info[5]["element"], "N")
self.assertEqual(info[5]["connectivity"], "edge")
self.assertEqual(info[5]["geometry"]["type"], "6-coordinate")
self.assertEqual(len(info[5]["angles"]), 2)
self.assertAlmostEqual(info[5]["angles"][0], 83.91397867959587)
self.assertAlmostEqual(info[5]["distance"], 3.549136232944574)
def test_nnn_summaries_match(self):
"""Test nearest neighbour summary matching function."""
sa = SiteAnalyzer(self.ba_n, use_symmetry_equivalent_sites=True)
nnn_a = sa.get_next_nearest_neighbors(0)
nnn_b = sa.get_next_nearest_neighbors(3)
nnn_c = sa.get_next_nearest_neighbors(4)
self.assertTrue(nnn_summaries_match(nnn_a, nnn_b))
self.assertFalse(nnn_summaries_match(nnn_a, nnn_c))
# test not matching bond angles
self.assertTrue(
nnn_summaries_match(nnn_a,
nnn_b,
bond_angle_tol=1e-10,
match_bond_angles=False))
def test_get_inequivalent_site_indices(self):
sa = SiteAnalyzer(self.ba_n, use_symmetry_equivalent_sites=False)
inequiv_indices = sa.get_inequivalent_site_indices(list(range(6)))
self.assertEqual(inequiv_indices, [0, 0, 0, 0, 4, 4])
# test using symmetry to determine inequivalent sites.
sa = SiteAnalyzer(self.ba_n, use_symmetry_equivalent_sites=True)
inequiv_indices = sa.get_inequivalent_site_indices(list(range(6)))
self.assertEqual(inequiv_indices, [0, 0, 0, 0, 4, 4])
# test symprec option
sa = SiteAnalyzer(self.ba_n,
use_symmetry_equivalent_sites=True,
symprec=0.000001)
inequiv_indices = sa.get_inequivalent_site_indices(list(range(6)))
self.assertEqual(inequiv_indices, [0, 1, 1, 0, 4, 4])
def test_get_site_geometry(self):
"""Test site geometry description."""
sa = SiteAnalyzer(self.tin_dioxide)
geom_data = sa.get_site_geometry(0)
self.assertEqual(geom_data['type'], "octahedral")
self.assertAlmostEqual(geom_data['likeness'], 0.9349776258427136)
geom_data = sa.get_site_geometry(4)
self.assertEqual(geom_data['type'], "trigonal planar")
self.assertAlmostEqual(geom_data['likeness'], 0.6050243049545359)
# check different structure
sa = SiteAnalyzer(self.ba_n)
geom_data = sa.get_site_geometry(0)
self.assertEqual(geom_data['type'], "6-coordinate")
self.assertAlmostEqual(geom_data['likeness'], 1)
def test_get_nearest_neighbors(self):
"""Check getting nearest neighbors."""
sa = SiteAnalyzer(self.tin_dioxide)
info = sa.get_nearest_neighbors(4)
self.assertEqual(len(info), 3)
self.assertEqual(info[0]["element"], "Sn4+")
self.assertEqual(info[0]["inequiv_index"], 0)
self.assertAlmostEqual(info[0]["dist"], 2.0922101061490546)
info = sa.get_nearest_neighbors(0, inc_inequivalent_site_index=False)
self.assertTrue('inequiv_index' not in info[0])
# check different structure without oxi state
sa = SiteAnalyzer(self.ba_n)
info = sa.get_nearest_neighbors(0)
self.assertEqual(len(info), 6)
self.assertEqual(info[0]["element"], "N")
self.assertEqual(info[0]["inequiv_index"], 0)
self.assertAlmostEqual(info[0]["dist"], 1.2619877178483)
def test_symmetry_labels(self):
"""Check equivalent sites instance variable set correctly."""
sa = SiteAnalyzer(self.ba_n, use_symmetry_equivalent_sites=False)
self.assertEqual(sa.symmetry_labels, [1, 1, 1, 1, 1, 1])
def test_get_all_connectivity_angle_summaries(self):
sa = SiteAnalyzer(self.tin_dioxide)
data = sa.get_all_connectivity_angle_summaries()
self.assertEqual(len(data[0][0]['corner']), 8)
self.assertEqual(len(data[0][0]['edge']), 4)
self.assertAlmostEqual(data[0][0]['edge'][0], 101.62287790513848)
def test_get_all_bond_distance_summaries(self):
sa = SiteAnalyzer(self.tin_dioxide)
data = sa.get_all_bond_distance_summaries()
self.assertEqual(len(data[0][2]), 6)
self.assertEqual(len(data[2][0]), 3)
self.assertAlmostEqual(data[0][2][0], 2.0922101061490546)
def condense_structure(self, structure: Structure) -> Dict[str, Any]:
"""Condenses the structure into an intermediate dict representation.
Args:
structure: A pymatgen structure object.
Returns:
The condensed structure information. The data is formatted as a
:obj:`dict` with a fixed set of keys. An up-to-date example of the,
the condensed representation of MoS2 given in the documentation.
See: ``robocrystallographer/docs_rst/source/format.rst`` or
https://hackingmaterials.lbl.gov/robocrystallographer/format.html
"""
# sort so we can give proper symmetry labels
structure = structure.get_sorted_structure()
# wrap all site coords into unit cell
structure.translate_sites(range(structure.num_sites), [1, 1, 1])
sga = SpacegroupAnalyzer(structure, symprec=self.symprec)
if self.use_conventional_cell:
structure = sga.get_conventional_standard_structure()
else:
structure = sga.get_symmetrized_structure()
bonded_structure = self.near_neighbors.get_bonded_structure(structure)
components = get_structure_components(
bonded_structure,
inc_orientation=True,
inc_site_ids=True,
inc_molecule_graph=True,
)
dimensionality = max(c["dimensionality"] for c in components)
mineral = self._condense_mineral(structure, components)
formula = self._condense_formula(structure, components)
structure_data = {
"formula": formula,
"spg_symbol": sga.get_space_group_symbol(),
"crystal_system": sga.get_crystal_system(),
"mineral": mineral,
"dimensionality": dimensionality,
}
site_analyzer = SiteAnalyzer(
bonded_structure,
symprec=self.symprec,
use_symmetry_equivalent_sites=self.use_symmetry_equivalent_sites,
)
structure_data["sites"] = site_analyzer.get_all_site_summaries()
structure_data[
"distances"] = site_analyzer.get_all_bond_distance_summaries()
structure_data[
"angles"] = site_analyzer.get_all_connectivity_angle_summaries()
structure_data[
"nnn_distances"] = site_analyzer.get_all_nnn_distance_summaries()
component_summary, component_makeup = self._condense_components(
components, sga, site_analyzer)
structure_data["components"] = component_summary
structure_data["component_makeup"] = component_makeup
if components_are_vdw_heterostructure(components):
hs_info = get_vdw_heterostructure_information(
components,
use_iupac_formula=self.use_iupac_formula,
use_common_formulas=self.use_common_formulas,
)
else:
hs_info = None
structure_data["vdw_heterostructure_info"] = hs_info
return structure_data
def _condense_components(
self,
components: List[Component],
spacegroup_analyzer: SpacegroupAnalyzer,
site_analyzer: SiteAnalyzer,
) -> Tuple[Dict[int, Any], List[int]]:
"""Condenses the component data.
Args:
components: A list of structure components, generated using
:obj:`pymatgen.analysis.dimensionality.get_structure_components`
site_analyzer: A site analyzer object for the structure containing
the components.
spacegroup_analyzer: A space group analyzer object for the structure
containing the components.
Returns:
The condensed component data and the component makeup of the
structure. The condensed components have the form::
{
0: {
'formula': 'MoS2',
'sites': [0, 2]
'dimensionality': 2,
'molecule_name': None,
'orientation': (0, 0, 1)
}
}
Where the ``0`` key is the component identifier. The ``sites``
key gives a :obj:`list` of the indexes of the inequivalent sites
in the structure. If the component is zero-dimensional and
is a known molecule, the ``molecule_name`` key will be a :obj:`str`
with the molecule name. The ``orientation`` key is the miller
index (for two-dimensional components) or direction of propagation
(for one-dimensional components).
"""
if self.use_symmetry_equivalent_sites:
inequiv_components = get_sym_inequiv_components(
components, spacegroup_analyzer)
else:
inequiv_components = get_structure_inequiv_components(components)
molecule_namer = MoleculeNamer()
components = {}
component_makeup = []
for i, component in enumerate(inequiv_components):
formula = get_component_formula(
component,
use_iupac_formula=self.use_iupac_formula,
use_common_formulas=self.use_common_formulas,
)
sites = site_analyzer.get_inequivalent_site_indices(
component["site_ids"])
if component["dimensionality"] == 0:
molecule_name = molecule_namer.get_name_from_molecule_graph(
component["molecule_graph"])
else:
molecule_name = None
components[i] = {
"formula": formula,
"dimensionality": component["dimensionality"],
"orientation": component["orientation"],
"molecule_name": molecule_name,
"sites": sites,
}
component_makeup.extend([i] * component["count"])
return components, component_makeup
def test_get_all_nnn_distance_summaries(self):
sa = SiteAnalyzer(self.tin_dioxide)
data = sa.get_all_nnn_distance_summaries()
self.assertEqual(len(data[0][0]['corner']), 8)
self.assertEqual(len(data[0][0]['edge']), 2)
self.assertAlmostEqual(data[0][0]['edge'][0], 3.24322132)