def test_write_paths_task(self):
exafs = MPEXAFSSet(0, self.struct, edge="K", radius=10)
t = WriteEXAFSPaths(feff_input_set=exafs, paths=[[249, 0], [85, 0]])
paths = Paths(exafs.atoms, [[249, 0], [85, 0]])
paths.write_file("paths_ans.dat")
t.run_task({})
with open("paths_ans.dat") as ans, open("paths.dat") as tmp:
self.assertEqual(ans.readlines(), tmp.readlines())
def test_write_paths_task(self):
exafs = MPEXAFSSet(0, self.struct, edge='K', radius=10)
t = WriteEXAFSPaths(feff_input_set=exafs, paths=[[249, 0], [85, 0]])
paths = Paths(exafs.atoms, [[249, 0], [85, 0]])
paths.write_file("paths_ans.dat")
t.run_task({})
with open("paths_ans.dat", "r") as ans, open("paths.dat", "r") as tmp:
self.assertEqual(ans.readlines(), tmp.readlines())
def setUp(self):
feo = Structure.from_dict(
{'lattice': {'a': 3.3960486211791285,
'alpha': 91.45136142952781,
'b': 3.410591877060444,
'beta': 89.27127081348024,
'c': 10.71766796897646,
'gamma': 120.14175587658389,
'matrix': [[3.39597035, -0.00828486, 0.02151698],
[-1.70515997, 2.9534242, -0.04303398],
[0.06812465, -0.11799566, 10.71680189]],
'volume': 107.31813123502585},
'sites': [{'abc': [0.33497754, 0.66579918, 0.97174225],
'label': 'Fe',
'properties': {'coordination_no': 4,
'forces': [-0.01537896, -0.08731049, 0.04884326]},
'species': [{'element': 'Fe', 'occu': 1}],
'xyz': [0.06847928463257683, 1.8489508003914767, 10.392524897825345]},
{'abc': [0.99661905, 0.00734083, 0.22366433],
'label': 'Fe',
'properties': {'coordination_no': 4,
'forces': [-0.01685376, -0.01008504, 0.05451912]},
'species': [{'element': 'Fe', 'occu': 1}],
'xyz': [3.387208508781326, -0.0129676845693048, 2.4180946415046494]},
{'abc': [0.00338095, 0.01072178, 0.72366433],
'label': 'Fe',
'properties': {'coordination_no': 4,
'forces': [0.01716078, 0.00955327, 0.05451912]},
'species': [{'element': 'Fe', 'occu': 1}],
'xyz': [0.04249863509042039, -0.053751296415148794, 7.754978606437029]},
{'abc': [0.66502246, 0.33082164, 0.47174225],
'label': 'Fe',
'properties': {'coordination_no': 4,
'forces': [0.08330257, -0.03033668, 0.04884326]},
'species': [{'element': 'Fe', 'occu': 1}],
'xyz': [1.7264300141777726, 0.9158834813430974, 5.055640939524896]},
{'abc': [0.33062914, 0.66733572, 0.77744897],
'label': 'O',
'properties': {'coordination_no': 4,
'forces': [-0.07726687, -0.00523346, -0.05206924]},
'species': [{'element': 'O', 'occu': 1}],
'xyz': [0.03785603896498114, 1.8764506445041333, 8.310162619639584]},
{'abc': [0.00312189, 0.99229908, 0.52714445],
'label': 'O',
'properties': {'coordination_no': 4,
'forces': [-0.06744419, 0.00047044, -0.05129314]},
'species': [{'element': 'O', 'occu': 1}],
'xyz': [-1.6455152924521734, 2.8684534947950637, 5.606667232944964]},
{'abc': [0.99687811, 0.98917618, 0.02714445],
'label': 'O',
'properties': {'coordination_no': 4,
'forces': [0.03331469, 0.05864361, -0.05129314]},
'species': [{'element': 'O', 'occu': 1}],
'xyz': [1.7005140848662161, 2.9099949452040543, 0.2697833114717219]},
{'abc': [0.66937086, 0.33670658, 0.27744897],
'label': 'O',
'properties': {'coordination_no': 4,
'forces': [0.04316575, 0.06429835, -0.05206924]},
'species': [{'element': 'O', 'occu': 1}],
'xyz': [1.7179261258365088, 0.9561539434765862, 2.9732786612521678]}]})
atoms = Atoms(feo, 0, 10.0)
self.paths = Paths(atoms, [[22, 16, 0], [250, 282, 250, 0]])
def run_task(self, fw_spec):
atoms = self["feff_input_set"].atoms
paths = Paths(atoms, self["paths"], degeneracies=self.get("degeneracies", []))
paths.write_file()
def run_task(self, fw_spec):
atoms = self['feff_input_set'].atoms
paths = Paths(atoms, self["paths"], degeneracies=self.get("degeneracies", []))
paths.write_file()