def test_get_structure_components(self):
# test components are returned correctly with the right keys
components = get_structure_components(self.tricky_structure)
self.assertEqual(len(components), 1)
self.assertEqual(components[0]['dimensionality'], 3)
self.assertTrue(isinstance(components[0]['structure'], Structure))
self.assertEqual(components[0]['structure'].num_sites, 10)
# test 2D structure and get orientation information
components = get_structure_components(self.graphite,
inc_orientation=True)
self.assertEqual(len(components), 2)
self.assertEqual(components[0]['dimensionality'], 2)
self.assertTrue(isinstance(components[0]['structure'], Structure))
self.assertEqual(components[0]['structure'].num_sites, 2)
self.assertEqual(components[0]['orientation'], (0, 0, 1))
def test_get_vdw_heterostructure_information(self):
data = get_vdw_heterostructure_information(
self.vdw_hetero_components,
inc_ordered_components=True,
inc_intercalants=True,
)
self.assertEqual(len(data["ordered_components"]), 4)
self.assertAlmostEqual(
data["ordered_components"][0]
["structure_graph"].structure.frac_coords[0][0],
0.33330876,
)
self.assertAlmostEqual(
data["ordered_components"][3]
["structure_graph"].structure.frac_coords[0][0],
0.6666924,
)
self.assertEqual(data["repeating_unit"], ["MoS2", "WS2"])
self.assertEqual(data["num_repetitions"], 2)
self.assertEqual(data["intercalants"], [])
# test error catching
self.assertRaises(ValueError, get_vdw_heterostructure_information,
self.mapi_components)
self.assertRaises(
KeyError,
get_vdw_heterostructure_information,
get_structure_components(self.vdw_hetero),
)
def setUp(self):
cnn = CrystalNN()
self.mapi = cnn.get_bonded_structure(self.get_structure("mapi"))
self.mapi_components = get_structure_components(
self.mapi,
inc_molecule_graph=True,
inc_site_ids=True,
inc_orientation=True)
self.vdw_hetero = cnn.get_bonded_structure(self.get_structure("MoWS4"))
self.vdw_hetero_components = get_structure_components(
self.vdw_hetero,
inc_molecule_graph=True,
inc_site_ids=True,
inc_orientation=True,
)
def setUp(self):
cnn = CrystalNN()
mapi = cnn.get_bonded_structure(self.get_structure("mapi"))
mapi_components = get_structure_components(mapi,
inc_molecule_graph=True)
mol_components, _ = filter_molecular_components(mapi_components)
self.methylammonium = mol_components[0]['molecule_graph']
def test_get_formula_from_components(self):
formula = get_formula_from_components(self.mapi_components,
use_common_formulas=True,
use_iupac_formula=True)
self.assertTrue(formula, "CH3NH3PbI3")
# check not using common formulas
formula = get_formula_from_components(self.mapi_components,
use_common_formulas=False,
use_iupac_formula=True)
self.assertTrue(formula, "CNH6PbI3")
# check non-iupac ordering works
formula = get_formula_from_components(self.mapi_components,
use_iupac_formula=False,
use_common_formulas=False)
self.assertEqual(formula, "H6CNPbI3")
# test multiple groups of different numbers of compositions
s = CrystalNN().get_bonded_structure(self.get_structure("CuH8CN5Cl3"))
comps = get_structure_components(s)
formula = get_formula_from_components(comps,
use_iupac_formula=True,
use_common_formulas=True)
self.assertEqual(formula, "(CuCN4HCl)2(NH2)2(H2)3(HCl)4")
# test putting molecules first
s = CrystalNN().get_bonded_structure(
self.get_structure("ZrCuH8C2NCl6"))
comps = get_structure_components(s)
formula = get_formula_from_components(
comps,
molecules_first=False,
use_iupac_formula=True,
use_common_formulas=True,
)
self.assertEqual(formula, "ZrCuCl6(CH3)2NH2")
formula = get_formula_from_components(
comps,
molecules_first=True,
use_iupac_formula=True,
use_common_formulas=True,
)
self.assertEqual(formula, "(CH3)2NH2ZrCuCl6")
def test_get_structure_components(self):
# test components are returned correctly with the right keys
components = get_structure_components(self.tricky_structure)
self.assertEqual(len(components), 1)
self.assertEqual(components[0]["dimensionality"], 3)
self.assertTrue(isinstance(components[0]["structure_graph"], StructureGraph))
self.assertEqual(components[0]["structure_graph"].structure.num_sites, 10)
# test 2D structure and get orientation information
components = get_structure_components(self.graphite, inc_orientation=True)
self.assertEqual(len(components), 2)
self.assertEqual(components[0]["dimensionality"], 2)
self.assertTrue(isinstance(components[0]["structure_graph"], StructureGraph))
self.assertEqual(components[0]["structure_graph"].structure.num_sites, 2)
self.assertEqual(components[0]["orientation"], (0, 0, 1))
# test getting component graphs
self.assertEqual(list(components[0]["structure_graph"].graph.nodes()), [0, 1])
def test_get_structure_components(self):
# test components are returned correctly with the right keys
components = get_structure_components(self.tricky_structure)
self.assertEqual(len(components), 1)
self.assertEqual(components[0]['dimensionality'], 3)
self.assertTrue(
isinstance(components[0]['structure_graph'], StructureGraph))
self.assertEqual(components[0]['structure_graph'].structure.num_sites,
10)
# test 2D structure and get orientation information
components = get_structure_components(
self.graphite, inc_orientation=True)
self.assertEqual(len(components), 2)
self.assertEqual(components[0]['dimensionality'], 2)
self.assertTrue(
isinstance(components[0]['structure_graph'], StructureGraph))
self.assertEqual(components[0]['structure_graph'].structure.num_sites,
2)
self.assertEqual(components[0]['orientation'], (0, 0, 1))
# test getting component graphs
self.assertEqual(list(components[0]['structure_graph'].graph.nodes()),
[0, 1])
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