def test_loadfn(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
obj = loadfn(os.path.join(test_dir, "Li2O.cif"))
self.assertIsInstance(obj, Structure)
obj = loadfn(os.path.join(test_dir, "POSCAR"))
self.assertIsInstance(obj, Structure)
obj = loadfn(os.path.join(test_dir, "vasprun.xml"))
self.assertIsInstance(obj, Vasprun)
def test_loadfn(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
obj = loadfn(os.path.join(test_dir, "Li2O.cif"))
self.assertIsInstance(obj, Structure)
obj = loadfn(os.path.join(test_dir, "POSCAR"))
self.assertIsInstance(obj, Structure)
obj = loadfn(os.path.join(test_dir, "LiFePO4.vasp"))
self.assertIsInstance(obj, Structure)
obj = loadfn(os.path.join(test_dir, "vasprun.xml"))
self.assertIsInstance(obj, Vasprun)
def test_loadfn(self):
with warnings.catch_warnings():
warnings.simplefilter("ignore")
obj = loadfn(os.path.join(PymatgenTest.TEST_FILES_DIR, "Li2O.cif"))
self.assertIsInstance(obj, Structure)
obj = loadfn(os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR"))
self.assertIsInstance(obj, Structure)
obj = loadfn(
os.path.join(PymatgenTest.TEST_FILES_DIR, "LiFePO4.vasp"))
self.assertIsInstance(obj, Structure)
obj = loadfn(
os.path.join(PymatgenTest.TEST_FILES_DIR, "vasprun.xml"))
self.assertIsInstance(obj, Vasprun)
def __init__(self,
use_online_pubchem: bool = True,
name_preference: Tuple[str] = name_sources):
"""Class to match molecule graphs to known molecule names.
Args:
use_online_pubchem: Whether to try using the Pubchem website for
matching molecules if a match is not found in the offline
database. Defaults to ``True``. Requires a working internet
connection and for the ``pubchempy`` package to be installed.
name_preference: The order of preference for determining compound
names. Options are "traditional", and "iupac". If the
first option is not available, the subsequent options will be
used. Should be provided as a tuple of options, from 1st choice
to last.
"""
db_file = resource_filename('robocrys.condense', 'molecule_db.json.gz')
self.molecule_db = loadfn(db_file)
self.matched_molecules = {}
self.use_online_pubchem = use_online_pubchem
# append the sources list to the end in case the user only supplies
# a single preference
self.name_preference = tuple(
list(name_preference) + list(self.name_sources))
def test_auto_repr(sample):
"""
Test that the symmetry group created with the automatic representation matrix
is the matches a reference.
"""
pos_In = (0, 0, 0) # pylint: disable=invalid-name
pos_As = (0.25, 0.25, 0.25) # pylint: disable=invalid-name
orbitals = []
for spin in (sr.SPIN_UP, sr.SPIN_DOWN):
orbitals.extend([
sr.Orbital(position=pos_In, function_string=fct, spin=spin)
for fct in sr.WANNIER_ORBITALS['s'] + sr.WANNIER_ORBITALS['p']
])
orbitals.extend([
sr.Orbital(position=pos_As, function_string=fct, spin=spin)
for fct in sr.WANNIER_ORBITALS['p']
])
symops, symops_cart = mg.loadfn(sample('InAs_symops.json'))
symmetry_group = sr.SymmetryGroup(symmetries=[
sr.SymmetryOperation.from_orbitals(
orbitals=orbitals,
real_space_operator=sr.RealSpaceOperator.from_pymatgen(
sym_reduced),
rotation_matrix_cartesian=sym_cart.rotation_matrix,
numeric=True)
for sym_reduced, sym_cart in zip(symops, symops_cart)
],
full_group=True)
reference = sr.io.load(sample('symmetries_InAs.hdf5'))
assert symmetry_group.full_group == reference.full_group
for sym1, sym2 in zip(symmetry_group.symmetries, reference.symmetries):
assert_allclose(sym1.real_space_operator.rotation_matrix,
sym2.real_space_operator.rotation_matrix,
atol=1e-12)
assert_allclose(sym1.real_space_operator.translation_vector,
sym2.real_space_operator.translation_vector,
atol=1e-12)
assert sym1.repr.has_cc == sym2.repr.has_cc
assert_allclose(sym1.repr.matrix, sym2.repr.matrix, atol=1e-12)
import crystal_toolkit.components as ctc
#
#def test_plotly_actual_plot(test_files):
# dos_data = loadfn(str(test_files / "KAlSi3O8_dos_data.json"))
# pploter = PlotlyDosPlotter(dos_data)
# fig = pploter.show({"O": [10, 11]})
# fig.show()
app = Dash(suppress_callback_exceptions=True,
assets_folder=SETTINGS.ASSETS_PATH)
ctc.register_app(app)
test_files = Path(__file__).parent / ".." / ".." / "tests" / "test_data_files"
band_plot_data = loadfn(str(test_files / "KAlSi3O8_band_plot_info.json"))
dos_plot_data = loadfn(str(test_files / "KAlSi3O8_dos_plot_data.json"))
band_dos_component = BandDosComponent(dos_plot_data, band_plot_data)
#dos_component = BandDosComponent(None, band_plot_info)
#dos_component = BandDosComponent(dos_plot_data, band_plot_info, band_plot_info_2)
# example layout to demonstrate capabilities of component
my_layout = html.Div([
html.H1("BandDosComponent Example"),
band_dos_component.layout(),
])
# {'K_i1': [0, 1],
# 'Al_i1': [2, 3],
# 'Si_i1': [4, 5],
# 'Si_i2': [6, 7],
# 'Si_i3': [8, 9],