def test_Atoms_copy_from_aseAtoms():
"""Tests the mothed Atoms.copy_from() to copy from an ase.atoms
"""
from ase.atoms import Atoms as aseAtoms
from matdb.atoms import Atoms
from numpy import array_equal
at1 = aseAtoms("Co3W2V3",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[1.75,1.75,1.25],
[1.5,1,1.5],[2.75,2.25,2.75],[2,2.5,2.5],[2.25,2.75,2.75]],
cell=[5.43,5.43,5.43])
at1.info['nneightol'] = 1112
at1.info['cutoff'] = 521
at1.info['cutoff_break'] = 1042
at2 = Atoms()
at2.copy_from(at1)
assert at2.info["params"]['nneightol'] == at1.info['nneightol']
assert at2.info["params"]['cutoff'] == at1.info['cutoff']
assert at2.info["params"]['cutoff_break'] == at1.info['cutoff_break']
# make sure the symbols and positions are still match
assert at1.get_chemical_symbols() == at2.get_chemical_symbols()
assert array_equal(at1.positions, at2.positions)
assert array_equal(at1.cell, at2.cell)
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)])
def test_Atoms_copy_from():
"""Tests the mothed Atoms.copy_from to copy from an matdb.atoms
"""
from matdb.atoms import Atoms
from numpy import array_equal
at1 = Atoms("Co3W2V3",positions=[[0,0,0],[0.25,0.25,0.25],[0.5,0.5,0],[1.75,1.75,1.25],
[1.5,1,1.5],[2.75,2.25,2.75],[2,2.5,2.5],[2.25,2.75,2.75]],
cell=[5.43,5.43,5.43],info={"rand":10, "params":{"vasp_energy": 1234}, "properties":{}})
at1.__setattr__("magnetic_moments", [1.2,2.3,3.4,4.5,5.6,6.7,7.8,8.9])
at2 = Atoms()
at2.copy_from(at1)
assert at1.info["params"] == at2.info["params"]
assert at1.info["properties"] == at2.info["properties"]
# make sure the symbols and positions are still match
assert at1.get_chemical_symbols() == at2.get_chemical_symbols()
assert array_equal(at1.positions, at2.positions)
assert array_equal(at1.cell, at2.cell)
def _cfgd_to_atoms(cfgd, species=None):
"""Converts a CFG dictionary to an atoms object.
Args:
cfgd (dict): dict of a single config extracted by :func:`cfg_to_xyz`.
species (list): list of element names corresponding to the integer species in
the CFG dictionary.
"""
from matdb.atoms import Atoms
lattice = np.array(cfgd["Supercell"]["vals"])
natoms = cfgd["Size"]["vals"][0][0]
stressdict = cfgd["PlusStress"]
stress = {k: v for k, v in zip(stressdict["cols"], stressdict["vals"][0])}
energy = cfgd["Energy"]["vals"][0][0]
alabels = cfgd["AtomData"]["cols"]
positions = []
forces = []
types = []
for entry in cfgd["AtomData"]["vals"]:
vals = {k: v for k, v in zip(alabels, entry)}
pos = []
force = []
types.append(species[vals["type"]])
for poslabel in _cfg_pos:
pos.append(vals[poslabel])
positions.append(pos)
for flabel in _cfg_force:
force.append(vals[flabel])
forces.append(force)
aseatoms = ase.Atoms(symbols=types,
positions=np.array(positions),
cell=lattice)
aseatoms.calc = SinglePointCalculator(aseatoms,
energy=energy,
forces=np.array(forces),
stress=order_stress(**stress))
aseatoms.get_total_energy()
aseatoms.get_forces()
aseatoms.get_stress()
result = Atoms()
result.copy_from(aseatoms)
result.pbc = True
prefix = ""
if "EFS_by" in cfgd["features"]:
prefix = "{}_".format(cfgd["features"]["EFS_by"][0].lower())
force_name, energy_name, virial_name = [
"{}{}".format(prefix, l) for l in ["force", "energy", "virial"]
]
result.properties[force_name] = aseatoms.calc.results["forces"].T
result.params[energy_name] = energy
result.params[virial_name] = symmetrize(*aseatoms.calc.results["stress"])
assert result.n == natoms
return result
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)
