def test_AtomsList_sort():
"""Tests the method AtomsList.sort
"""
from matdb.atoms import Atoms, AtomsList
at1 = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43],info={"rand":10})
at2 = Atoms("S6",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75]],
cell=[6.43,5.43,4.43],info={"rand":10})
at3 = Atoms("CNi",positions=[[0,0,0],[0.5,0.5,0.5]], info={"rand":8})
at4 = Atoms("CoV",positions=[[0,0,0],[0.25,0.5,0.25]], info={"rand":8})
at1.add_param("vasp_energy", 25361.504084423999)
at2.add_param("vasp_energy", 25362.504084423999)
at3.add_param("vasp_energy", 25363.504084423999)
at4.add_param("vasp_energy", 25364.504084423999)
al1 = AtomsList([at4,at2,at1,at3])
#This is to test __getitem__
al2 = al1[0:2]
assert len(al2) == 2
al1.sort(key=len)
assert al1[0].get_chemical_formula() == "CoV"
assert al1[1].get_chemical_formula() == "CNi"
assert al1[2].get_chemical_formula() == "S6"
assert al1[3].get_chemical_formula() == "Si8"
al1.sort(attr="vasp_energy")
assert al1[0].get_chemical_formula() == "Si8"
assert al1[1].get_chemical_formula() == "S6"
assert al1[2].get_chemical_formula() == "CNi"
assert al1[3].get_chemical_formula() == "CoV"
al1.sort(attr="vasp_energy", reverse=True)
assert al1[0].get_chemical_formula() == "CoV"
assert al1[1].get_chemical_formula() == "CNi"
assert al1[2].get_chemical_formula() == "S6"
assert al1[3].get_chemical_formula() == "Si8"
def test_AtomsList_attributes():
"""Tests the atoms lists attributes.
"""
from matdb.atoms import Atoms, AtomsList
at1 = Atoms("Si8",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75],[0,0.5,0.5],[0.25,0.75,0.75]],
cell=[5.43,5.43,5.43],info={"rand":10})
at2 = Atoms("S6",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[0.75,0.75,0.25],
[0.5,0,0.5],[0.75,0.25,0.75]],
cell=[6.43,5.43,4.43],info={"rand":10})
at3 = Atoms("CNi",positions=[[0,0,0],[0.5,0.5,0.5]], info={"rand":8})
at4 = Atoms(info={"rand":7})
at4.copy_from(at3)
al1 = AtomsList([at1,at2,at3,at4])
alpos = al1.positions
assert np.allclose(alpos[0],at1.positions)
assert np.allclose(alpos[1],at2.positions)
assert np.allclose(alpos[2],at3.positions)
assert np.allclose(alpos[3],at4.positions)
with pytest.raises(AttributeError):
al1.__getattr__('__dict__')
assert al1.energy is None
alslice = al1[0:2]
assert len(alslice) == 2
assert alslice[0] == at1
assert alslice[1] == at2
alitems = al1[[0,1,3]]
assert len(alitems) == 3
assert alitems[0] == at1
assert alitems[1] == at2
assert alitems[2] == at4
with pytest.raises(IndexError):
al1[[0,2.3]]
alitems = al1[[True,True,False,True]]
assert len(alitems) == 3
for i in al1.iterframes():
assert isinstance(i,Atoms)
for i in al1.iterframes(reverse=True):
assert isinstance(i,Atoms)
assert al1.random_access
def get_pos(atoms):
return atoms.positions
alpos=al1.apply(get_pos)
assert np.allclose(alpos[0],at1.positions)
assert np.allclose(alpos[1],at2.positions)
assert np.allclose(alpos[2],at3.positions)
assert np.allclose(alpos[3],at4.positions)
al1.sort(reverse=True)
al1.sort(attr='rand')
with pytest.raises(ValueError):
al1.sort(attr='positions',key=2)
