def write(self, target="atoms.h5", **kwargs):
"""Writes an atoms object to file.
Args:
target (str): The path to the target file. Default is "atoms.h5".
"""
frmt = target.split('.')[-1]
if frmt == "h5" or frmt == "hdf5":
from matdb.io import save_dict_to_h5
with h5py.File(target, "w") as hf:
data = self.to_dict()
save_dict_to_h5(hf, data, '/')
else:
io.write(target, self, **kwargs)
def write(self, target, **kwargs):
"""Writes an atoms object to file.
Args:
target (str): The path to the target file.
kwargs (dict): A dictionary of key word args to pass to the ase write function.
"""
frmt = target.split('.')[-1]
if frmt == "h5" or frmt == "hdf5":
from matdb.io import save_dict_to_h5
with h5py.File(target, "w") as hf:
for atom in self:
data = atom.to_dict()
hf.create_group("atom_{}".format(data["uuid"]))
save_dict_to_h5(hf, data, "/atom_{}/".format(data["uuid"]))
else:
io.write(target, self)
def _fix_precomp(db, purge=False):
"""Reconstitutes the `pre_comp_atoms.h5` file by copying the existing
`atoms.h5`, and applying some modifications to the atoms object.
Args:
db (matdb.database.Group): a group to create pre_comp files for.
purge (bool): when True, remove the `atoms.h5` files after the pre-comp
file is created.
"""
for aid, apath in db.configs.items():
target = path.join(apath, "atoms.h5")
with h5py.File(target, "r") as hf:
data = load_dict_from_h5(hf)
data["pbc"] = np.array([1, 1, 1], dtype=bool)
newtarg = path.join(apath, "pre_comp_atoms.h5")
with h5py.File(newtarg, "w") as hf:
save_dict_to_h5(hf, data, '/')
if path.isfile(newtarg) and purge:
remove(target)
def test_hdf5_in_out():
"""Tests the writing of dictionaries to hdf5 and reading back out.
"""
import h5py
from matdb.io import load_dict_from_h5, save_dict_to_h5
from os import remove
dict_1_in = {
"a": {
"B": np.int64(1),
"C": np.int64(3),
"D": {
"temp": np.array([10, 11, 12])
}
},
"n": np.array([3, 2]),
"t": np.int64(5)
}
dict_2_in = {"a": np.int64(10), "b": np.array([1, 2, 10])}
hf = h5py.File("temp.h5", "w")
save_dict_to_h5(hf, dict_1_in, "/")
hf.close()
hf = h5py.File("temp.h5", "r")
out = load_dict_from_h5(hf)
hf.close()
assert compare_nested_dicts(dict_1_in, out)
remove("temp.h5")
hf = h5py.File("temp.h5", "w")
save_dict_to_h5(hf, dict_2_in, "/")
hf.close()
hf = h5py.File("temp.h5", "r")
out = load_dict_from_h5(hf)
hf.close()
assert compare_dicts(dict_2_in, out)
remove("temp.h5")
hf = h5py.File("temp.h5", "w")
with pytest.raises(ValueError):
save_dict_to_h5(hf, {"a": remove}, "/")
hf.close()
remove("temp.h5")
def test_reading_multiple_files(tmpdir):
"""Tests the reading in of multiple atoms objects to an AtomsList.
"""
from matdb.calculators import Vasp
from matdb.atoms import Atoms as Atoms, AtomsList
from matdb.io import save_dict_to_h5
import h5py
from matdb.utility import _set_config_paths
_set_config_paths("AgPd_Enumerated", str(tmpdir))
target = str(tmpdir.join("read_atoms2"))
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)
temp = path.join(target,"temp.h5")
atSi.write(temp)
atSi2 = 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=[6.43,6.43,6.43])
kwargs = {"encut":600, "kpoints": {"rmin": 50},
"potcars":{"xc": "pbe", "directory": "./tests/vasp", "versions": {"Si": "05Jan2001"}}}
calc = Vasp(atSi2, target, '.', 0, **kwargs)
atSi2.set_calculator(calc)
temp2 = path.join(target,"temp2.h5")
atSi2.write(temp2)
atRL = AtomsList([temp,temp2])
assert len(atRL) == 2
assert atRL[0].calc.kwargs["encut"] != atRL[1].calc.kwargs["encut"]
assert atRL[1].calc.kwargs["encut"] in [400,600]
assert atRL[0].calc.kwargs["encut"] in [400,600]
atom_dict = {"atom_1":temp, "atom_2": temp2}
temp3 = path.join(target,"temp3.h5")
with h5py.File(temp3,"w") as hf:
save_dict_to_h5(hf,atom_dict,'/')
atRL = AtomsList(temp3)
assert len(atRL) == 2
assert atRL[0].calc.kwargs["encut"] != atRL[1].calc.kwargs["encut"]
assert atRL[1].calc.kwargs["encut"] in [400,600]
assert atRL[0].calc.kwargs["encut"] in [400,600]