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replace full output info in __str__ by chemical formula #439

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Nov 29, 2021
Merged

replace full output info in __str__ by chemical formula #439

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2e8b493
replace full output info in __str__ by chemical formula
samwaseda Nov 25, 2021
20ba797
add test
samwaseda Nov 29, 2021
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6 changes: 3 additions & 3 deletions pyiron_atomistics/atomistics/structure/atoms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2031,9 +2031,6 @@ def __dir__(self):
# return len(self.indices)

def __repr__(self):
return self.__str__()

def __str__(self):
if len(self) == 0:
return "[]"
out_str = ""
Expand All @@ -2052,6 +2049,9 @@ def __str__(self):
out_str += str(self.cell) + "\n"
return out_str

def __str__(self):
return self.get_chemical_formula()

def __setitem__(self, key, value):
if isinstance(key, (int, np.integer)):
old_el = self.species[self.indices[key]]
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8 changes: 8 additions & 0 deletions tests/atomistics/structure/test_atoms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1558,6 +1558,14 @@ def test_set_dihedral():
structure = ase_to_pyiron(molecule('H2COH'))
structure.set_dihedral(4, 0, 1, 2, angle=90)

def test_str_repr(self):
H2 = Atoms(positions=[3*[0], 3*[0.5]], cell=np.eye(3), elements=2*['H'], pbc=True)
self.assertEqual(
repr(H2),
'H: [0. 0. 0.]\nH: [0.5 0.5 0.5]\npbc: [ True True True]\ncell: \nCell([1.0, 1.0, 1.0])\n'
)
self.assertEqual(str(H2), 'H2')

def test_cached_speed(self):
"""
Creating atoms should be faster after the first time, due to caches in periodictable/mendeleev.
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