def test_to_dict(tmpdir):
"""Tests the conversion of atoms to dictionaries.
"""
from matdb.calculators import Vasp
from matdb.atoms import Atoms as Atoms
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("atoms_dict"))
globals_setup(target)
if not path.isdir(target):
mkdir(target)
atSi = 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])
kwargs = {"encut":400, "kpoints": {"rmin": 50},
"potcars":{"xc": "pbe", "directory": "./tests/vasp", "versions": {"Si": "05Jan2001"}}}
calc = Vasp(atSi, target, '.', 0, **kwargs)
atSi.set_calculator(calc)
atSi.group_uuid = "123456"
Sidict = atSi.to_dict()
assert "calc" in Sidict
assert "calc_kwargs" in Sidict
assert Sidict["calc_kwargs"]["encut"] == 400
assert Sidict["group_uuid"] == "123456"
assert "potcars" in Sidict["calc_kwargs"]
assert "kpoints" in Sidict["calc_kwargs"]
def test_read_atoms(tmpdir):
"""Tests the reading of atoms objects from files.
"""
from matdb.calculators import Vasp
from matdb.atoms import Atoms as Atoms
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("read_atoms"))
globals_setup(target)
if not path.isdir(target):
mkdir(target)
atSi = 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])
kwargs = {"encut":400, "kpoints": {"rmin": 50},
"potcars":{"xc": "pbe", "directory": "./tests/vasp", "versions": {"Si": "05Jan2001"}}}
calc = Vasp(atSi, target, '.', 0, **kwargs)
atSi.set_calculator(calc)
atSi.set_calculator(calc)
atSi.add_property("vasp_force", [[-18057.59589857, -18057.59589857, -18057.59589857],
[ -2997.55626529, -2997.55626529, -2997.55626529],
[ 3044.17916471, 3044.17916471, -34130.71583118],
[ 18969.1757571 , 18969.1757571 , 11159.15815145],
[ 3044.17916471, -34130.71583118, 3044.17916471],
[ 18969.1757571 , 11159.15815145, 18969.1757571 ],
[-34130.71583118, 3044.17916471, 3044.17916471],
[ 11159.15815145, 18969.1757571 , 18969.1757571 ]])
atSi.add_param("vasp_energy", 25360.504084423999)
atSi.add_param("vasp_virial", [[ 33538.34327189, 11045.88697112, 11045.88697112],
[ 11045.88697112, 33538.34327189, 11045.88697112],
[ 11045.88697112, 11045.88697112, 33538.34327189]])
atSi.group_uuid = "123456"
temp = path.join(target,"temp.h5")
atSi.write(temp)
atR = Atoms(temp)
assert atR.calc.name == "Vasp"
assert hasattr(atR.calc,"potcars")
assert atR.calc.kwargs["encut"] == 400
assert np.allclose(atR.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]])
