def test_AtomsList_empty_io(tmpdir):
from matdb.atoms import Atoms, AtomsList
from os import path
target = str(tmpdir.join("empty_AtomsList"))
globals_setup(target)
if not path.isdir(target):
mkdir(target)
empty_list = AtomsList([])
empty_list.write(path.join(target,"temp.h5"))
assert len(empty_list) == 0
assert path.isfile(path.join(target,"temp.h5"))
aR = AtomsList()
aR.read(path.join(target,"temp.h5"))
assert len(aR) == 0
def test_AtomsList_io(tmpdir):
"""Tests the AtomsList writing and reading from file.
"""
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]])
at4 = Atoms()
at4.copy_from(at3)
al1 = AtomsList([at1,at2,at3,at4])
target = str(tmpdir.join("atomList_to_hdf5"))
if not path.isdir(target):
mkdir(target)
al1.write(path.join(target,"temp.h5"))
aR = AtomsList()
aR.read(path.join(target,"temp.h5"))
assert len(aR) == len(al1)
alpos = aR.positions
assert any([np.allclose(alpos[i],at1.positions) for i in range(4) if
len(alpos[i])==len(at1.positions)])
assert any([np.allclose(alpos[i],at2.positions) for i in range(4) if
len(alpos[i])==len(at2.positions)])
assert any([np.allclose(alpos[i],at3.positions) for i in range(4) if
len(alpos[i])==len(at3.positions)])
assert any([np.allclose(alpos[i],at4.positions) for i in range(4) if
len(alpos[i])==len(at4.positions)])
al1.write(path.join(target,"temp.xyz"))
aR = AtomsList()
aR.read(path.join(target,"temp.xyz"))
assert len(aR) == len(al1)
aR.read(path.join(target,"temp.xyz"))
assert len(aR) == 2*len(al1)
# Test reading in of a single atoms object.
aR1 = Atoms(path.join(target,"temp.h5"))
assert isinstance(aR1,Atoms)
assert any([np.allclose(alpos[i],at1.positions) for i in range(4) if
len(alpos[i])==len(at1.positions)])
