def load_data_from_online(self, url, meta_data={}):
id_ = ID.new_ID()
new_orbital = OrbitalData.init_from_online(url,
ID=id_,
meta_data=meta_data)
self.orbitals.append(new_orbital)
return new_orbital
def test_file_initialization(self):
ID = 1
data = OrbitalData.init_from_file(
__directory__ / '../example/data/' / '5A_MO_73.cube', ID)
self.assertEqual(data.name, '5A_MO_73')
self.assertEqual(data.ID, ID)
self.assertEqual(data.meta_data, {
'origin': 'Cube file generated by NWChem',
'alias': 'pentacene_MO_73'
})
def test_default_initialization(self):
name = 'Test'
ID = 1
meta_data = {'origin': 'selfmade'}
with open(__directory__ / '../example/data/5A_MO_73.cube', 'r') as f:
file = f.read()
data = OrbitalData(file, ID, name=name, meta_data=meta_data)
self.assertEqual(data.name, name)
self.assertEqual(data.ID, ID)
self.assertEqual(data.meta_data, meta_data)
def test_online_initialization(self):
ID = 1
data = OrbitalData.init_from_online(
'http://143.50.77.12/' + 'OrganicMolecule/B3LYP/5A/' +
'charge0mult1/5A_MO_73', ID)
self.assertEqual(data.name, '5A_MO_73')
self.assertEqual(data.ID, ID)
self.assertEqual(data.meta_data, {
'origin': 'Cube file generated by NWChem',
'alias': 'pentacene_MO_73'
})
def load_data_from_path(self, path, ID=None):
if ID is None:
id_ = IDD.new_ID()
else:
id_ = ID
IDD.update(id_)
new_orbital = OrbitalData.init_from_file(path, ID=id_)
self.orbitals.append([new_orbital, 'path', path, None, id_])
return new_orbital
def load_data_from_online(self, url, meta_data={}, ID=None):
if ID is None:
id_ = IDD.new_ID()
else:
id_ = ID
IDD.update(id_)
new_orbital = OrbitalData.init_from_online(url,
ID=id_,
meta_data=meta_data)
self.orbitals.append([new_orbital, 'url', url, meta_data, id_])
return new_orbital
def setUpClass(cls):
file_path = os.path.dirname(os.path.realpath(__file__))
input_path = file_path + '/../../example/data/'
sliced_path = input_path + 'example5_6584.hdf5'
cls.sliced_data = SlicedData.init_from_hdf5(sliced_path)
orbital_paths = [
'PTCDA_C.cube', 'PTCDA_D.cube', 'PTCDA_E.cube', 'PTCDA_F.cube'
]
cls.orbitals = [
OrbitalData.init_from_file(input_path + path, ID)
for ID, path in enumerate(orbital_paths)
]
cls.expected = np.loadtxt(file_path + '/output/weights_PTCDA')
cls.background_expected = np.loadtxt(file_path +
'/output/background_expected')
from kmap.library.orbitaldata import OrbitalData
from kmap.model.lmfit_model import LMFitModel
# Path to data folder; replace with your own; use '/' instead of '+'
# when concatenating with strings
data_path = Path(__file__).parent / Path('../data/')
# Load experimental data as SlicedData object
exp_data = SlicedData.init_from_hdf5(data_path / 'example5_6584.hdf5')
# Load orbitals for fitting as OrbitalData objects
orbital_paths = [
'PTCDA_C.cube', 'PTCDA_D.cube', 'PTCDA_E.cube', 'PTCDA_F.cube'
]
orbitals = [
OrbitalData.init_from_file(data_path / path, ID)
for ID, path in enumerate(orbital_paths)
]
# Initialize fit as LMFitModel object
lmfit = LMFitModel(exp_data, orbitals)
# Set common range and delta-k-grid for exp. and sim. kmaps
range_, dk = [-3.0, 3.0], 0.04
lmfit.set_axis_by_step_size(range_, dk)
lmfit.set_polarization('toroid', 'p')
lmfit.set_background_equation('c')
# Set parameters not intended for fitting to desired value
lmfit.edit_parameter('E_kin', value=27.2, vary=False)
lmfit.edit_parameter('alpha', value=40, vary=False)
# kMap.py Imports
from kmap.library.sliceddata import SlicedData
from kmap.library.orbitaldata import OrbitalData
from kmap.model.lmfit_model import LMFitModel
# Path to data folder; replace with your own; use '/' instead of '+'
# when concatenating with strings
data_path = Path(__file__).parent / Path('../data/')
# Load experimental data as SlicedData object
exp_data = SlicedData.init_from_hdf5(data_path / 'example4_3271.hdf5')
# Load orbital for fitting as OrbitalData objects
orbital_paths = ['pentacene_HOMO.cube']
orbitals = [OrbitalData.init_from_file(
data_path / path, ID) for ID, path in enumerate(orbital_paths)]
# Initialize fit as LMFitModel object
lmfit = LMFitModel(exp_data, orbitals)
# Set common range and delta-k-grid for exp. and sim. kmaps
range_, dk = [-3.0, 3.0], 0.04
lmfit.set_axis_by_step_size(range_, dk)
lmfit.set_polarization('toroid', 'p')
lmfit.set_symmetrization('2-fold')
# Set parameters not intended for fitting to desired value
lmfit.edit_parameter('E_kin', value=28, vary=False)
lmfit.edit_parameter('alpha', value=40, vary=False)
lmfit.set_background_equation('c')
def load_data_from_path(self, path):
id_ = ID.new_ID()
new_orbital = OrbitalData.init_from_file(path, ID=id_)
self.orbitals.append([new_orbital, 'path', path, None, id_])
return new_orbital