def from_dict(cls, d):
"""
Args:
A dict with all data for a band structure symm line object.
Returns:
A BandStructureSymmLine object
"""
labels_dict = d['labels_dict']
projections = {}
structure = None
if 'projections' in d and len(d['projections']) != 0:
structure = Structure.from_dict(d['structure'])
projections = {
Spin.from_int(int(spin)):
[[{
Orbital.from_string(orb): [
d['projections'][spin][i][j][orb][k]
for k in range(len(d['projections'][spin][i][j][orb]))
]
for orb in d['projections'][spin][i][j]
} for j in range(len(d['projections'][spin][i]))]
for i in range(len(d['projections'][spin]))]
for spin in d['projections']
}
return BandStructureSymmLine(
d['kpoints'],
{Spin.from_int(int(k)): d['bands'][k]
for k in d['bands']},
Lattice(d['lattice_rec']['matrix']),
d['efermi'],
labels_dict,
structure=structure,
projections=projections)
def from_dict(d):
"""
Args:
A dict with all data for a band structure symm line object.
Returns:
A BandStructureSymmLine object
"""
labels_dict = d['labels_dict']
projections = {}
structure = None
if 'projections' in d and len(d['projections']) != 0:
structure = Structure.from_dict(d['structure'])
projections = {
Spin.from_int(int(spin)): [
[{Orbital.from_string(orb): [
d['projections'][spin][i][j][orb][k]
for k in range(len(d['projections'][spin][i][j][orb]))]
for orb in d['projections'][spin][i][j]}
for j in range(len(d['projections'][spin][i]))]
for i in range(len(d['projections'][spin]))]
for spin in d['projections']}
return BandStructureSymmLine(
d['kpoints'], {Spin.from_int(int(k)): d['bands'][k]
for k in d['bands']},
Lattice(d['lattice_rec']['matrix']), d['efermi'],
labels_dict, structure=structure, projections=projections)
def from_dict(cls, d):
"""
Args:
A dict with all data for a band structure symm line object.
Returns:
A BandStructureSymmLine object
"""
# Strip the label to recover initial string (see trick used in as_dict to handle $ chars)
labels_dict = {k.strip(): v for k, v in d['labels_dict'].items()}
projections = {}
structure = None
if 'projections' in d and len(d['projections']) != 0:
structure = Structure.from_dict(d['structure'])
projections = {
Spin.from_int(int(spin)): [
[{Orbital.from_string(orb): [
d['projections'][spin][i][j][orb][k]
for k in range(len(d['projections'][spin][i][j][orb]))]
for orb in d['projections'][spin][i][j]}
for j in range(len(d['projections'][spin][i]))]
for i in range(len(d['projections'][spin]))]
for spin in d['projections']}
return BandStructureSymmLine(
d['kpoints'], {Spin.from_int(int(k)): d['bands'][k]
for k in d['bands']},
Lattice(d['lattice_rec']['matrix']), d['efermi'],
labels_dict, structure=structure, projections=projections)
def get_dos_from_id(self, task_id):
"""
Overrides the get_dos_from_id for the MIT gridfs format.
"""
args = {'task_id': task_id}
fields = ['calculations']
structure = self.get_structure_from_id(task_id)
dosid = None
for r in self.query(fields, args):
dosid = r['calculations'][-1]['dos_fs_id']
if dosid != None:
self._fs = gridfs.GridFS(self.db, 'dos_fs')
with self._fs.get(dosid) as dosfile:
s = dosfile.read()
try:
d = json.loads(s)
except:
s = zlib.decompress(s)
d = json.loads(s)
tdos = Dos.from_dict(d)
pdoss = {}
for i in range(len(d['pdos'])):
ados = d['pdos'][i]
all_ados = {}
for j in range(len(ados)):
orb = Orbital.from_vasp_index(j)
odos = ados[str(orb)]
all_ados[orb] = {Spin.from_int(int(k)): v
for k, v
in odos['densities'].items()}
pdoss[structure[i]] = all_ados
return CompleteDos(structure, tdos, pdoss)
return None
def from_dict(cls, d):
"""
Returns Dos object from dict representation of Dos.
"""
return Dos(d["efermi"], d["energies"],
{Spin.from_int(int(k)): v
for k, v in d["densities"].items()})
def get_dos_from_id(self, task_id):
"""
Overrides the get_dos_from_id for the MIT gridfs format.
"""
args = {'task_id': task_id}
fields = ['calculations']
structure = self.get_structure_from_id(task_id)
dosid = None
for r in self.query(fields, args):
dosid = r['calculations'][-1]['dos_fs_id']
if dosid != None:
self._fs = gridfs.GridFS(self.db, 'dos_fs')
with self._fs.get(dosid) as dosfile:
s = dosfile.read()
try:
d = json.loads(s)
except:
s = zlib.decompress(s)
d = json.loads(s)
tdos = Dos.from_dict(d)
pdoss = {}
for i in range(len(d['pdos'])):
ados = d['pdos'][i]
all_ados = {}
for j in range(len(ados)):
orb = Orbital.from_vasp_index(j)
odos = ados[str(orb)]
all_ados[orb] = {
Spin.from_int(int(k)): v
for k, v in odos['densities'].items()
}
pdoss[structure[i]] = all_ados
return CompleteDos(structure, tdos, pdoss)
return None
def from_dict(cls, d):
"""
Returns Dos object from dict representation of Dos.
"""
return Dos(d["efermi"], d["energies"],
{Spin.from_int(int(k)): v
for k, v in d["densities"].items()})
def from_dict(d):
"""
Returns PDos object from dict representation.
"""
return PDos(
d["efermi"],
d["energies"],
{Spin.from_int(int(k)): v for k, v in d["densities"].items()},
Orbital.from_string(d["orbital"]),
)
def from_dict(cls, d):
"""
Args:
A dict with all data for a band structure symm line object.
Returns:
A BandStructureSymmLine object
"""
labels_dict = d["labels_dict"]
projections = {}
structure = None
if "projections" in d and len(d["projections"]) != 0:
structure = Structure.from_dict(d["structure"])
projections = {
Spin.from_int(int(spin)): [
[
{
Orbital.from_string(orb): [
d["projections"][spin][i][j][orb][k]
for k in range(len(d["projections"][spin][i][j][orb]))
]
for orb in d["projections"][spin][i][j]
}
for j in range(len(d["projections"][spin][i]))
]
for i in range(len(d["projections"][spin]))
]
for spin in d["projections"]
}
return BandStructureSymmLine(
d["kpoints"],
{Spin.from_int(int(k)): d["bands"][k] for k in d["bands"]},
Lattice(d["lattice_rec"]["matrix"]),
d["efermi"],
labels_dict,
structure=structure,
projections=projections,
)
def from_dict(cls, d):
"""
Args:
A dict with all data for a band structure symm line object.
Returns:
A BandStructureSymmLine object
"""
# Strip the label to recover initial string (see trick used in as_dict to handle $ chars)
labels_dict = {k.strip(): v for k, v in d['labels_dict'].items()}
projections = {}
structure = None
if 'projections' in d and len(d['projections']) != 0:
structure = Structure.from_dict(d['structure'])
projections = {
Spin.from_int(int(spin)):
[[{
Orbital.from_string(orb): [
d['projections'][spin][i][j][orb][k]
for k in range(len(d['projections'][spin][i][j][orb]))
]
for orb in d['projections'][spin][i][j]
} for j in range(len(d['projections'][spin][i]))]
for i in range(len(d['projections'][spin]))]
for spin in d['projections']
}
return BandStructureSymmLine(
d['kpoints'],
{Spin.from_int(int(k)): d['bands'][k]
for k in d['bands']},
Lattice(d['lattice_rec']['matrix']),
d['efermi'],
labels_dict,
structure=structure,
projections=projections)
def from_dict(cls, d):
"""
Returns CompleteDos object from dict representation.
"""
tdos = Dos.from_dict(d)
struct = Structure.from_dict(d["structure"])
pdoss = {}
for i in range(len(d["pdos"])):
at = struct[i]
orb_dos = {}
for orb_str, odos in d["pdos"][i].items():
orb = Orbital.from_string(orb_str)
orb_dos[orb] = {Spin.from_int(int(k)): v
for k, v in odos["densities"].items()}
pdoss[at] = orb_dos
return CompleteDos(struct, tdos, pdoss)
def from_dict(cls, d):
"""
Returns CompleteDos object from dict representation.
"""
tdos = Dos.from_dict(d)
struct = Structure.from_dict(d["structure"])
pdoss = {}
for i in range(len(d["pdos"])):
at = struct[i]
orb_dos = {}
for orb_str, odos in d["pdos"][i].items():
orb = Orbital.from_string(orb_str)
orb_dos[orb] = {Spin.from_int(int(k)): v
for k, v in odos["densities"].items()}
pdoss[at] = orb_dos
return CompleteDos(struct, tdos, pdoss)
def test_cached(self):
self.assertEqual(id(Spin.from_int(1)), id(Spin.up))
def test_from_int(self):
self.assertEqual(Spin.from_int(1), Spin.up)
self.assertEqual(Spin.from_int(-1), Spin.down)
self.assertRaises(ValueError, Spin.from_int, 0)
def test_cached(self):
self.assertEquals(id(Spin.from_int(1)), id(Spin.up))
def test_from_int(self):
self.assertEquals(Spin.from_int(1), Spin.up)
self.assertEquals(Spin.from_int(-1), Spin.down)
self.assertRaises(ValueError, Spin.from_int, 0)
