def setUp(self):
with open(os.path.join(test_dir, 'si_dos.json'), 'r') as sDOS:
si_dos = CompleteDos.from_dict(json.load(sDOS))
self.df = pd.DataFrame({'dos': [si_dos], 'site': [0]})
with open(os.path.join(test_dir, 'nb3sn_dos.json'), 'r') as sDOS:
nb3sn_dos = CompleteDos.from_dict(json.load(sDOS))
self.nb3sn_df = pd.DataFrame({'dos': [nb3sn_dos]})
def get_dos(self, task_id):
m_task = self.collection.find_one({"task_id": task_id}, {"calcs_reversed": 1})
fs_id = m_task['calcs_reversed'][0]['dos_fs_id']
fs = gridfs.GridFS(self.db, 'dos_fs')
dos_json = zlib.decompress(fs.get(fs_id).read())
dos_dict = json.loads(dos_json.decode())
return CompleteDos.from_dict(dos_dict)
def setUp(self):
self.vbm_val = 2.6682
self.gap = 1.5
self.entries = list(loadfn(os.path.join(os.path.dirname(__file__), "GaAs_test_defentries.json")).values())
for entry in self.entries:
entry.parameters.update( {'vbm': self.vbm_val})
self.pd = DefectPhaseDiagram(self.entries, self.vbm_val, self.gap)
self.mu_elts = {Element("As"): -4.658070555, Element("Ga"): -3.7317319750000006}
# make Vac_As (q= -2) only defect test single-stable-charge exceptions
self.extra_entry = DefectEntry(self.entries[5].defect.copy(), 100.)
sep_entries = [ent for ent in self.entries if not (ent.name == 'Vac_As_mult4' and
ent.charge in [-2,-1,0,1,2])]
sep_entries.append( self.extra_entry.copy())
self.sep_pd = DefectPhaseDiagram( sep_entries, self.vbm_val, self.gap)
# make Vac_As (q= -2) is incompatible for larger supercell
ls_entries = self.entries[:]
for entry in ls_entries:
if entry.name == 'Vac_As_mult4' and entry.charge == -2.:
entry.parameters['is_compatible'] = False
self.pd_ls_fcTrue = DefectPhaseDiagram(ls_entries, self.vbm_val, self.gap, filter_compatible=True)
self.pd_ls_fcFalse = DefectPhaseDiagram(ls_entries, self.vbm_val, self.gap, filter_compatible=False)
# load complete dos for fermi energy solving
with open(os.path.join(test_dir, "complete_dos.json"), "r") as f:
dos_dict = json.load(f)
self.dos = CompleteDos.from_dict(dos_dict)
def setUp(self):
with open(os.path.join(test_dir, "complete_dos.json"),
"r",
encoding='utf-8') as f:
self.dos = CompleteDos.from_dict(json.load(f))
self.plotter = DosPlotter(sigma=0.2, stack=True)
warnings.simplefilter("ignore")
def setUp(self):
with open(os.path.join(PymatgenTest.TEST_FILES_DIR,
"complete_dos.json"),
encoding="utf-8") as f:
self.dos = CompleteDos.from_dict(json.load(f))
self.plotter = DosPlotter(sigma=0.2, stack=True)
warnings.simplefilter("ignore")
def setUpClass(cls):
cls.vbm_val = 2.6682
cls.gap = 1.5
cls.entries = list(loadfn(os.path.join(os.path.dirname(__file__), "GaAs_test_defentries.json")).values())
for entry in cls.entries:
entry.parameters.update({"vbm": cls.vbm_val})
cls.pd = DefectPhaseDiagram(cls.entries, cls.vbm_val, cls.gap)
cls.mu_elts = {Element("As"): -4.658070555, Element("Ga"): -3.7317319750000006}
# make Vac_As (q= -2) only defect test single-stable-charge exceptions
cls.extra_entry = DefectEntry(cls.entries[5].defect.copy(), 100.0)
sep_entries = [
ent for ent in cls.entries if not (ent.name == "Vac_As_mult4" and ent.charge in [-2, -1, 0, 1, 2])
]
sep_entries.append(cls.extra_entry.copy())
cls.sep_pd = DefectPhaseDiagram(sep_entries, cls.vbm_val, cls.gap)
# make Vac_As (q= -2) is incompatible for larger supercell
ls_entries = cls.entries[:]
for entry in ls_entries:
if entry.name == "Vac_As_mult4" and entry.charge == -2.0:
entry.parameters["is_compatible"] = False
cls.pd_ls_fcTrue = DefectPhaseDiagram(ls_entries, cls.vbm_val, cls.gap, filter_compatible=True)
cls.pd_ls_fcFalse = DefectPhaseDiagram(ls_entries, cls.vbm_val, cls.gap, filter_compatible=False)
# load complete dos for fermi energy solving
with open(os.path.join(PymatgenTest.TEST_FILES_DIR, "complete_dos.json")) as f:
dos_dict = json.load(f)
cls.dos = CompleteDos.from_dict(dos_dict)
def _get_cdos(pdos_file, site_file):
if not (pdos_file and site_file):
raise ValueError('Both dos.ext and site.ext are needed for PDOS')
energies, data, efermi, nsp = _read_dos_data(pdos_file)
if nsp == 1:
fake_tdos = Dos(efermi, energies, {Spin.up: 0 * energies})
spins = (Spin.up, )
elif nsp == 2:
fake_tdos = Dos(efermi, energies, {
Spin.up: 0 * energies,
Spin.down: 0 * energies
})
spins = (Spin.up, Spin.down)
else:
raise ValueError('There can\'t be {} spin channels, that makes '
'no sense!'.format(nsp))
site_data = QuestaalSite.from_file(site_file)
structure = site_data.structure
pdoss = {}
for site, orbital, spin in product(
range(len(site_data.sites)),
range(16), # forget about g orbs
range(len(spins))):
if structure.sites[site] not in pdoss:
pdoss.update({structure.sites[site]: {}})
if Orbital(orbital) not in pdoss[structure.sites[site]]:
pdoss[structure.sites[site]].update({Orbital(orbital): {}})
pdoss[structure.sites[site]][Orbital(orbital)].update(
{spins[spin]: data[site * (25 * nsp) + orbital * nsp + spin]})
return CompleteDos(structure, fake_tdos, pdoss)
def merge_up_down_doses(dos_up, dos_dn):
"""
Merge the up and down DOSs.
Args:
dos_up: Up DOS.
dos_dn: Down DOS
Return:
CompleteDos object
"""
warnings.warn("This function is not useful anymore. VasprunBSLoader deals \
with spin case.")
cdos = Dos(
dos_up.efermi,
dos_up.energies,
{
Spin.up: dos_up.densities[Spin.up],
Spin.down: dos_dn.densities[Spin.down]
},
)
if hasattr(dos_up, "pdos") and hasattr(dos_dn, "pdos"):
pdoss = {}
for site in dos_up.pdos:
pdoss.setdefault(site, {})
for orb in dos_up.pdos[site]:
pdoss[site].setdefault(orb, {})
pdoss[site][orb][Spin.up] = dos_up.pdos[site][orb][Spin.up]
pdoss[site][orb][Spin.down] = dos_dn.pdos[site][orb][Spin.down]
cdos = CompleteDos(dos_up.structure, total_dos=cdos, pdoss=pdoss)
return cdos
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 is not 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.decode("utf-8"))
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(j)
odos = ados[str(orb)]
all_ados[orb] = {Spin(int(k)): v
for k, v
in odos['densities'].items()}
pdoss[structure[i]] = all_ados
return CompleteDos(structure, tdos, pdoss)
return None
def get_dos(self, task_id):
m_task = self.collection.find_one({"task_id": task_id}, {"calcs_reversed": 1})
fs_id = m_task['calcs_reversed'][0]['dos_fs_id']
fs = gridfs.GridFS(self.db, 'dos_fs')
dos_json = zlib.decompress(fs.get(fs_id).read())
dos_dict = json.loads(dos_json.decode())
return CompleteDos.from_dict(dos_dict)
def extract_dos(mat):
dos = None
if "dos" in mat["bandstructure"]:
dos_dict = mat["bandstructure"]["dos"]
dos = CompleteDos.from_dict(dos_dict)
return dos
def setUp(self):
try:
import scipy
except ImportError:
raise SkipTest("scipy not present. Skipping...")
with open(os.path.join(test_dir, "complete_dos.json"), "r") as f:
self.dos = CompleteDos.from_dict(json.load(f))
self.plotter = DosPlotter(sigma=0.2, stack=True)
def get_bs(dos, vasprun_bands, kpts_bands):
## get BandStructureSymmLine object and "save" in hidden div in json format
bands = Vasprun(vasprun_bands, parse_projected_eigen = True)
if dos:
dos = CompleteDos.from_dict(json.loads(dos))
bs = bands.get_band_structure(kpts_bands, line_mode=True, efermi=dos.efermi)
else:
bs = bands.get_band_structure(kpts_bands, line_mode=True)
return json.dumps(bs.as_dict(), cls=MyEncoder)
def from_dict(complete_dos_dict):
"""
Returns FeffLdos object from dict representation.
Args:
complete_dos_dict:
dict representation os complete_dos
"""
complete_dos = CompleteDos.from_dict(complete_dos_dict)
return FeffLdos(complete_dos)
def from_dict(d):
"""
Returns FeffLdos object from dict representation
Args:
complete_dos: dict representation of complete_dos
"""
complete_dos = CompleteDos.from_dict(d['complete_dos'])
charge_transfer = d['charge_transfer']
return FeffLdos(complete_dos, charge_transfer)
def update_dosbandsfig(n_clicks, dos, bs, projlist):
## figure updates when the inputs change or the button is clicked
## figure does NOT update when elements or orbitals are selected
## de-serialize dos and bs from json format to pymatgen objects
if dos:
dos = CompleteDos.from_dict(json.loads(dos))
if bs:
bs = BandStructureSymmLine.from_dict(json.loads(bs))
## update the band structure and dos figure
dosbandfig = BandsFig().generate_fig(dos, bs, projlist)
return dosbandfig
def from_dict(d):
"""
Returns FeffLdos object from dict representation
Args:
complete_dos: dict representation of complete_dos
"""
complete_dos = CompleteDos.from_dict(d['complete_dos'])
charge_transfer = d['charge_transfer']
return FeffLdos(complete_dos, charge_transfer)
def get_dos(self, task_id):
"""
Read the DOS data into a PMG DOS object
Args:
task_id(int or str): the task_id containing the data
Returns:
CompleteDos object
"""
obj_dict = self.get_data_from_maggma_or_gridfs(task_id, key="dos")
return CompleteDos.from_dict(obj_dict)
def featurize(self, dos):
"""
Args:
dos (pymatgen CompleteDos or their dict):
The density of states to featurize. Must be a complete DOS,
(i.e. contains PDOS and structure, in addition to total DOS)
and must contain the structure.
Returns:
xbm_score_i (float): fractions of ith contributor orbital
xbm_location_i (str): fractional coordinate of ith contributor.
For example, '0.0;0.0;0.0' if Gamma
xbm_specie_i: (str) elemental specie of ith contributor (ex: 'Ti')
xbm_character_i: (str) orbital character of ith contributor (s p d or f)
xbm_nsignificant: (int) the number of orbitals with contributions
above the significance_threshold
"""
if isinstance(dos, dict):
dos = CompleteDos.from_dict(dos)
if dos.structure is None:
raise ValueError('The input dos must contain the structure.')
orbscores = get_cbm_vbm_scores(dos, self.energy_cutoff,
self.sampling_resolution,
self.gaussian_smear)
self.feat = {}
for ex in ['cbm', 'vbm']:
orbscores.sort(key=lambda x: x['{}_score'.format(ex)],
reverse=True)
scores = np.array([s['{}_score'.format(ex)] for s in orbscores])
self.feat['{}_nsignificant'.format(ex)] = len(
scores[scores > self.significance_threshold])
i = 0
while i < self.contributors:
sd = orbscores[i]
if i < len(orbscores):
for p in ['character', 'specie']:
self.feat['{}_{}_{}'.format(ex, p, i + 1)] = sd[p]
self.feat['{}_location_{}'.format(
ex,
i + 1)] = '{};{};{}'.format(sd['location'][0],
sd['location'][1],
sd['location'][2])
self.feat['{}_score_{}'.format(ex, i + 1)] = float(
sd['{}_score'.format(ex)])
else:
for p in [
'{}_score'.format(ex), 'character', 'specie',
'location'
]:
self.feat['{}_{}_{}'.format(ex, p,
i + 1)] = float('NaN')
i += 1
return list(self.feat.values())
def get_partial_doses(self, tdos, eband_ud, spins, enr, npts_mu, T,
progress):
"""
Return a CompleteDos object interpolating the projections
tdos: total dos previously calculated
npts_mu: number of energy points of the Dos
T: parameter used to smooth the Dos
progress: Default False, If True a progress bar is shown.
"""
if not self.data.proj:
raise BoltztrapError("No projections loaded.")
bkp_data_ebands = np.copy(self.data.ebands)
pdoss = {}
if progress:
n_iter = np.prod(
np.sum(
[np.array(i.shape)[2:] for i in self.data.proj.values()]))
t = tqdm(total=n_iter * 2)
for spin, eb in zip(spins, eband_ud):
for isite, site in enumerate(self.data.structure.sites):
if site not in pdoss:
pdoss[site] = {}
for iorb, orb in enumerate(Orbital):
if progress:
t.update()
if iorb == self.data.proj[spin].shape[-1]:
break
if orb not in pdoss[site]:
pdoss[site][orb] = {}
self.data.ebands = self.data.proj[spin][:, :, isite,
iorb].T
coeffs = fite.fitde3D(self.data, self.equivalences)
proj, vvproj, cproj = fite.getBTPbands(
self.equivalences, coeffs, self.data.lattvec)
edos, pdos = BL.DOS(eb,
npts=npts_mu,
weights=np.abs(proj.real),
erange=enr)
if T:
pdos = BL.smoothen_DOS(edos, pdos, T)
pdoss[site][orb][spin] = pdos
self.data.ebands = bkp_data_ebands
return CompleteDos(self.data.structure, total_dos=tdos, pdoss=pdoss)
def featurize(self, dos, energy_cutoff=None):
"""
takes in the density of state and return the orbitals contributions
and hybridizations.
Args:
dos (pymatgen CompleteDos): note that dos.structure is required
energy_cutoff (float or None): if set, it overrides the instance
variable self.energy_cutoff.
Returns ([float]): features, see class doc for more info
"""
energy_cutoff = energy_cutoff or self.energy_cutoff
if isinstance(dos, dict):
dos = CompleteDos.from_dict(dos)
if dos.structure is None:
raise ValueError('The input dos must contain the structure.')
orbscores = get_cbm_vbm_scores(dos, energy_cutoff,
self.sampling_resolution,
self.gaussian_smear)
feat = OrderedDict()
for ex in ['cbm', 'vbm']:
for orbital in ['s', 'p', 'd', 'f']:
feat['{}_{}'.format(ex, orbital)] = 0.0
for specie in self.species:
feat['{}_{}_{}'.format(ex, specie, orbital)] = 0.0
for hybrid in ['sp', 'sd', 'sf', 'pd', 'pf', 'df']:
feat['{}_{}'.format(ex, hybrid)] = 0.0
for contrib in orbscores:
character = contrib['character']
feat['cbm_{}'.format(character)] += contrib['cbm_score']
feat['vbm_{}'.format(character)] += contrib['vbm_score']
for specie in self.species:
if contrib['specie'] == specie:
feat['cbm_{}_{}'.format(specie,
character)] += contrib['cbm_score']
feat['vbm_{}_{}'.format(specie,
character)] += contrib['vbm_score']
for ex in ['cbm', 'vbm']:
for hybrid in ['sp', 'sd', 'sf', 'pd', 'pf', 'df']:
orb1 = feat['{}_{}'.format(ex, hybrid[0])]
orb2 = feat['{}_{}'.format(ex, hybrid[1])]
feat['{}_{}'.format(
ex, hybrid)] = (orb1 * orb2) * 4.0 # 4x so max=1.0
return list(feat.values())
def featurize(self, dos, decay_length=None):
"""
takes in the density of state and return the orbitals contributions
and hybridizations.
Args:
dos (pymatgen CompleteDos): note that dos.structure is required
decay_length (float or None): if set, it overrides the instance
variable self.decay_length.
Returns ([float]): features, see class doc for more info
"""
decay_length = decay_length or self.decay_length
if isinstance(dos, dict):
dos = CompleteDos.from_dict(dos)
if dos.structure is None:
raise ValueError('The input dos must contain the structure.')
orbscores = get_cbm_vbm_scores(dos,
decay_length,
self.sampling_resolution,
self.gaussian_smear)
feat = OrderedDict()
for ex in ['cbm', 'vbm']:
for orbital in ['s', 'p', 'd', 'f']:
feat['{}_{}'.format(ex, orbital)] = 0.0
for specie in self.species:
feat['{}_{}_{}'.format(ex, specie, orbital)] = 0.0
for hybrid in ['sp', 'sd', 'sf', 'pd', 'pf', 'df']:
feat['{}_{}'.format(ex, hybrid)] = 0.0
for contrib in orbscores:
character = contrib['character']
feat['cbm_{}'.format(character)] += contrib['cbm_score']
feat['vbm_{}'.format(character)] += contrib['vbm_score']
for specie in self.species:
if contrib['specie'] == specie:
feat['cbm_{}_{}'.format(specie, character)] += contrib[
'cbm_score']
feat['vbm_{}_{}'.format(specie, character)] += contrib[
'vbm_score']
for ex in ['cbm', 'vbm']:
for hybrid in ['sp', 'sd', 'sf', 'pd', 'pf', 'df']:
orb1 = feat['{}_{}'.format(ex, hybrid[0])]
orb2 = feat['{}_{}'.format(ex, hybrid[1])]
feat['{}_{}'.format(ex, hybrid)] = (orb1 * orb2) * 4.0 # 4x so max=1.0
return list(feat.values())
def from_dos(cls, dos: CompleteDos):
"""
:param dos: CompleteDos object with project element-orbital DOS. Can be obtained from Vasprun.get_complete_dos.
:param sigma: Smearing for Gaussian.
:return: XPS
"""
total = np.zeros(dos.energies.shape)
for el in dos.structure.composition.keys():
spd_dos = dos.get_element_spd_dos(el)
for orb, pdos in spd_dos.items():
weight = CROSS_SECTIONS[el.symbol].get(str(orb), None)
if weight is not None:
total += pdos.get_densities() * weight
else:
warnings.warn(f"No cross-section for {el}{orb}")
return XPS(-dos.energies, total / np.max(total))
def merge_up_down_doses(dos_up, dos_dn):
cdos = Dos(dos_up.efermi, dos_up.energies,
{Spin.up: dos_up.densities[Spin.up], Spin.down: dos_dn.densities[Spin.down]})
if hasattr(dos_up, 'pdos') and hasattr(dos_dn, 'pdos'):
pdoss = {}
for site in dos_up.pdos:
pdoss.setdefault(site, {})
for orb in dos_up.pdos[site]:
pdoss[site].setdefault(orb, {})
pdoss[site][orb][Spin.up] = dos_up.pdos[site][orb][Spin.up]
pdoss[site][orb][Spin.down] = dos_dn.pdos[site][orb][Spin.down]
cdos = CompleteDos(dos_up.structure, total_dos=cdos, pdoss=pdoss)
return cdos
def test_to_from_dict(self):
d = self.dos.as_dict()
dos = CompleteDos.from_dict(d)
el_dos = dos.get_element_dos()
self.assertEqual(len(el_dos), 4)
spd_dos = dos.get_spd_dos()
sum_spd = spd_dos[OrbitalType.s] + spd_dos[OrbitalType.p] + spd_dos[OrbitalType.d]
sum_element = None
for pdos in el_dos.values():
if sum_element is None:
sum_element = pdos
else:
sum_element += pdos
# The sums of the SPD or the element doses should be the same.
self.assertTrue((abs(sum_spd.energies - sum_element.energies) < 0.0001).all())
def test_to_from_dict(self):
d = self.dos.as_dict()
dos = CompleteDos.from_dict(d)
el_dos = dos.get_element_dos()
self.assertEqual(len(el_dos), 4)
spd_dos = dos.get_spd_dos()
sum_spd = spd_dos[OrbitalType.s] + spd_dos[OrbitalType.p] + spd_dos[OrbitalType.d]
sum_element = None
for pdos in el_dos.values():
if sum_element is None:
sum_element = pdos
else:
sum_element += pdos
# The sums of the SPD or the element doses should be the same.
self.assertTrue((abs(sum_spd.energies - sum_element.energies) < 0.0001).all())
def process_item(self, mat):
"""
Process the tasks and materials into just a list of materials
Args:
mat (dict): material document
Returns:
(dict): electronic_structure document
"""
d = {self.electronic_structure.key: mat[self.materials.key]}
self.logger.info("Processing: {}".format(mat[self.materials.key]))
bs = build_bs(mat["bandstructure"]["bs"], mat)
dos = CompleteDos.from_dict(mat["bandstructure"]["dos"])
if bs and dos:
try:
pdos = get_pdos(dos)
dos_plotter = SDOSPlotter(dos, pdos)
bs_plotter = SBSPlotter(bs)
plt = bs_plotter.get_plot(dos_plotter=dos_plotter,
**self.plot_options)
d["plot"] = image_from_plot(plt)
plt.close()
except Exception:
traceback.print_exc()
self.logger.warning(
"Caught error in bandstructure plotting for {}: {}".format(
mat[self.materials.key], traceback.format_exc()))
# Reduced Band structure plot
try:
gap = bs.get_band_gap()["energy"]
plot_data = bs_plotter.bs_plot_data()
d["bs_plot_small"] = get_small_plot(plot_data, gap)
except Exception:
self.logger.warning(
"Caught error in generating reduced bandstructure plot for {}: {}"
.format(mat[self.materials.key], traceback.format_exc()))
# Store task_ids
for k in ["bs_task", "dos_task", "uniform_task"]:
if k in mat["bandstructure"]:
d[k] = mat["bandstructure"][k]
return d
def get_partial_doses(self, tdos, npts_mu, T):
"""
Return a CompleteDos object interpolating the projections
tdos: total dos previously calculated
npts_mu: number of energy points of the Dos
T: parameter used to smooth the Dos
"""
spin = self.data.spin if isinstance(self.data.spin, int) else 1
if not isinstance(self.data.proj, np.ndarray):
raise BoltztrapError("No projections loaded.")
bkp_data_ebands = np.copy(self.data.ebands)
pdoss = {}
# for spin in self.data.proj:
for isite, site in enumerate(self.data.structure.sites):
if site not in pdoss:
pdoss[site] = {}
for iorb, orb in enumerate(Orbital):
if iorb == self.data.proj.shape[-1]:
break
if orb not in pdoss[site]:
pdoss[site][orb] = {}
self.data.ebands = self.data.proj[:, :, isite, iorb].T
coeffs = fite.fitde3D(self.data, self.equivalences)
proj, vvproj, cproj = fite.getBTPbands(self.equivalences,
coeffs,
self.data.lattvec)
edos, pdos = BL.DOS(self.eband,
npts=npts_mu,
weights=np.abs(proj.real))
if T is not None:
pdos = BL.smoothen_DOS(edos, pdos, T)
pdoss[site][orb][Spin(spin)] = pdos
self.data.ebands = bkp_data_ebands
return CompleteDos(self.data.structure, total_dos=tdos, pdoss=pdoss)
def get_complete_dos(self, structure):
"""
Gives a CompleteDos object with the DOS from the interpolated projected band structure
Args:
the structure (necessary to identify sites for projection)
Returns:
a CompleteDos object
"""
pdoss = {}
for s in self._dos_partial:
if structure.sites[int(s)] not in pdoss:
pdoss[structure.sites[int(s)]] = {}
for o in self._dos_partial[s]:
if Orbital.from_string(o) not in pdoss[structure.sites[int(s)]]:
pdoss[structure.sites[int(s)]][Orbital.from_string(o)] = {}
pdoss[structure.sites[int(s)]][Orbital.from_string(o)][Spin.up] = self._dos_partial[s][o]
return CompleteDos(structure, total_dos=self.dos, pdoss=pdoss)
def featurize(self, dos):
"""
Args:
dos (pymatgen CompleteDos or their dict):
The density of states to featurize. Must be a complete DOS,
(i.e. contains PDOS and structure, in addition to total DOS)
and must contain the structure.
"""
if isinstance(dos, dict):
dos = CompleteDos.from_dict(dos)
if dos.structure is None:
raise ValueError('The input dos must contain the structure.')
orbscores = get_cbm_vbm_scores(dos, self.energy_cutoff,
self.sampling_resolution,
self.gaussian_smear)
feat = OrderedDict()
for ex in ['cbm', 'vbm']:
orbscores.sort(key=lambda x: x['{}_score'.format(ex)],
reverse=True)
scores = np.array([s['{}_score'.format(ex)] for s in orbscores])
feat['{}_nsignificant'.format(ex)] = len(
scores[scores > self.significance_threshold])
i = 0
while i < self.contributors:
sd = orbscores[i]
if i < len(orbscores):
for p in ['character', 'specie']:
feat['{}_{}_{}'.format(ex, p, i + 1)] = sd[p]
feat['{}_location_{}'.format(ex,
i + 1)] = '{};{};{}'.format(
sd['location'][0],
sd['location'][1],
sd['location'][2])
feat['{}_score_{}'.format(ex, i + 1)] = float(
sd['{}_score'.format(ex)])
else:
for p in ['character', 'specie', 'location', 'score']:
feat['{}_{}_{}'.format(ex, p, i + 1)] = float('NaN')
i += 1
return list(feat.values())
def _get_bs_dos(data):
data = data or {}
# this component can be loaded either from mpid or
# directly from BandStructureSymmLine or CompleteDos objects
# if mpid is supplied, this is preferred
mpid = data.get("mpid")
bandstructure_symm_line = data.get("bandstructure_symm_line")
density_of_states = data.get("density_of_states")
if not mpid and (bandstructure_symm_line is None
or density_of_states is None):
return None, None
if mpid:
with MPRester() as mpr:
try:
bandstructure_symm_line = mpr.get_bandstructure_by_material_id(
mpid)
except Exception as exc:
print(exc)
bandstructure_symm_line = None
try:
density_of_states = mpr.get_dos_by_material_id(mpid)
except Exception as exc:
print(exc)
density_of_states = None
else:
if bandstructure_symm_line and isinstance(bandstructure_symm_line,
dict):
bandstructure_symm_line = BandStructureSymmLine.from_dict(
bandstructure_symm_line)
if density_of_states and isinstance(density_of_states, dict):
density_of_states = CompleteDos.from_dict(density_of_states)
return bandstructure_symm_line, density_of_states
def featurize(self, dos):
"""
Args:
dos (pymatgen CompleteDos or their dict):
The density of states to featurize. Must be a complete DOS,
(i.e. contains PDOS and structure, in addition to total DOS)
and must contain the structure.
"""
if isinstance(dos, dict):
dos = CompleteDos.from_dict(dos)
if dos.structure is None:
raise ValueError('The input dos must contain the structure.')
orbscores = get_cbm_vbm_scores(dos, self.decay_length,
self.sampling_resolution,
self.gaussian_smear)
feat = OrderedDict()
for ex in ['cbm', 'vbm']:
orbscores.sort(key=lambda x: x['{}_score'.format(ex)],
reverse=True)
scores = np.array([s['{}_score'.format(ex)] for s in orbscores])
feat['{}_hybridization'.format(ex)] = - np.sum(
scores * np.log(scores + 1e-10)) # avoid log(0)
i = 0
while i < self.contributors:
sd = orbscores[i]
if i < len(orbscores):
for p in ['character', 'specie']:
feat['{}_{}_{}'.format(ex, p, i + 1)] = sd[p]
feat['{}_location_{}'.format(ex, i + 1)] =\
'{};{};{}'.format(sd['location'][0], sd['location'][1],
sd['location'][2])
feat['{}_score_{}'.format(ex, i + 1)] =\
float(sd['{}_score'.format(ex)])
else:
for p in ['character', 'specie', 'location', 'score']:
feat['{}_{}_{}'.format(ex, p, i + 1)] = float('NaN')
i += 1
return list(feat.values())
def setUp(self):
self.vbm_val = 2.6682
self.gap = 1.5
self.entries = list(
loadfn(
os.path.join(os.path.dirname(__file__),
"GaAs_test_defentries.json")).values())
for entry in self.entries:
entry.parameters.update({'vbm': self.vbm_val})
self.pd = DefectPhaseDiagram(self.entries, self.vbm_val, self.gap)
self.mu_elts = {
Element("As"): -4.658070555,
Element("Ga"): -3.7317319750000006
}
# make Vac_As (q= -2) only defect test single-stable-charge exceptions
self.extra_entry = DefectEntry(self.entries[5].defect.copy(), 100.)
sep_entries = [
ent for ent in self.entries if not (
ent.name == 'Vac_As_mult4' and ent.charge in [-2, -1, 0, 1, 2])
]
sep_entries.append(self.extra_entry.copy())
self.sep_pd = DefectPhaseDiagram(sep_entries, self.vbm_val, self.gap)
# make Vac_As (q= -2) is incompatible for larger supercell
ls_entries = self.entries[:]
for entry in ls_entries:
if entry.name == 'Vac_As_mult4' and entry.charge == -2.:
entry.parameters['is_compatible'] = False
self.pd_ls_fcTrue = DefectPhaseDiagram(ls_entries,
self.vbm_val,
self.gap,
filter_compatible=True)
self.pd_ls_fcFalse = DefectPhaseDiagram(ls_entries,
self.vbm_val,
self.gap,
filter_compatible=False)
# load complete dos for fermi energy solving
with open(os.path.join(test_dir, "complete_dos.json"), "r") as f:
dos_dict = json.load(f)
self.dos = CompleteDos.from_dict(dos_dict)
def featurize(self, dos, idx):
"""
get dos scores for given site index
Args:
dos (pymatgen CompleteDos or their dict):
dos to featurize, must contain pdos and structure
idx (int): index of target site in structure.
"""
if isinstance(dos, dict):
dos = CompleteDos.from_dict(dos)
if dos.structure is None:
raise ValueError('The input dos must contain the structure.')
orbscores = get_site_dos_scores(dos, idx, self.decay_length,
self.sampling_resolution,
self.gaussian_smear)
features = []
for edge in ['cbm', 'vbm']:
for score in ['s', 'p', 'd', 'f', 'total']:
features.append(orbscores[edge][score])
return features
def featurize(self, dos, idx):
"""
get dos scores for given site index
Args:
dos (pymatgen CompleteDos or their dict):
dos to featurize, must contain pdos and structure
idx (int): index of target site in structure.
"""
if isinstance(dos, dict):
dos = CompleteDos.from_dict(dos)
if dos.structure is None:
raise ValueError('The input dos must contain the structure.')
orbscores = get_site_dos_scores(dos, idx, self.fermi_temperature,
self.sampling_resolution,
self.gaussian_smear)
features = []
for edge in ['cbm', 'vbm']:
for score in ['s', 'p', 'd', 'f', 'total']:
features.append(orbscores[edge][score])
return features
def get_cdos():
for n in range(1, 74):
pdos = defaultdict(dict)
atom = ''
orb = ''
for a in atoms:
if os.path.exists(f'pwscf.pdos_atm#{n}({a})_wfc#{1}(s)'):
atom = Element(a)
if atom == '':
continue
for l, o in enumerate(orbital):
if os.path.exists(f'pwscf.pdos_atm#{n}({str(atom)})_wfc#{l + 1}({o})'):
orb = OrbitalType(l)
data = np.genfromtxt(f'pwscf.pdos_atm#{n}({str(atom)})_wfc#{l + 1}({orb.name})')
pdos[orb][Spin.up] = data[:, 1]
pdos[orb][Spin.down] = data[:, 2]
energies = data[:,0]
pdoss.append(pdos)
efermi = fermi_fromfile('report.scf')
total_density= six.moves.reduce(add_densities, [six.moves.reduce(add_densities, p.values()) for p in pdoss])
total_dos = Dos(efermi, energies, total_density)
s = Structure.from_file('123.cif')
return CompleteDos(s, total_dos, pdoss)
el: chempots_delta[el] + c.chempots_reference[el]
for el in chempots_delta
}
pressures.append(np.around(partial_pressure, decimals=4))
reservoirs.append(chempots_abs)
print('Reading defect calculation data...\n')
with open('vacancies_NN_HSE.json') as json_file:
data = json.load(json_file)
defects_analysis = DefectsAnalysis.from_dict(data)
print('Reading DOS...\n')
with open('dos_NN_HSE.json') as json_file:
data = json.load(json_file)
bulk_dos = CompleteDos.from_dict(data)
concentrations = []
for r in reservoirs:
fermi_energy = defects_analysis.equilibrium_fermi_level(r, bulk_dos)
cn = defects_analysis.defect_concentrations_stable_charges(
r, temperature=temperature, fermi_level=fermi_energy)
concentrations.append(cn)
data = {
'partial_pressures': pressures,
'defect_concentrations': concentrations
}
with open('defect_concentrations_NN_HSE.json', 'w') as json_file:
def setUp(self):
with open(os.path.join(test_dir, "complete_dos.json"), "r",
encoding='utf-8') as f:
self.dos = CompleteDos.from_dict(json.load(f))
self.plotter = DosPlotter(sigma=0.2, stack=True)
def from_file(feff_inp_file="feff.inp", ldos_file="ldos"):
"""
Creates LDos object from raw Feff ldos files by
by assuming they are numbered consecutively, i.e. ldos01.dat
ldos02.dat...
Args:
feff_inp_file (str): input file of run to obtain structure
ldos_file (str): output ldos file of run to obtain dos info, etc.
"""
header_str = Header.header_string_from_file(feff_inp_file)
header = Header.from_string(header_str)
structure = header.struct
nsites = structure.num_sites
parameters = Tags.from_file(feff_inp_file)
if "RECIPROCAL" in parameters:
pot_dict = {}
pot_readstart = re.compile(".*iz.*lmaxsc.*xnatph.*xion.*folp.*")
pot_readend = re.compile(".*ExternalPot.*switch.*")
pot_inp = re.sub(r"feff.inp", r"pot.inp", feff_inp_file)
dos_index = 1
begin = 0
with zopen(pot_inp, "r") as potfile:
for line in potfile:
if len(pot_readend.findall(line)) > 0:
break
if begin == 1:
begin += 1
continue
if begin == 2:
z_number = int(line.strip().split()[0])
ele_name = Element.from_Z(z_number).name
if ele_name not in pot_dict:
pot_dict[ele_name] = dos_index
else:
pot_dict[ele_name] = min(dos_index,
pot_dict[ele_name])
dos_index += 1
if len(pot_readstart.findall(line)) > 0:
begin = 1
else:
pot_string = Potential.pot_string_from_file(feff_inp_file)
dicts = Potential.pot_dict_from_string(pot_string)
pot_dict = dicts[0]
with zopen(ldos_file + "00.dat", "r") as fobject:
f = fobject.readlines()
efermi = float(f[0].split()[4])
dos_energies = []
ldos = {}
for i in range(1, len(pot_dict) + 1):
if len(str(i)) == 1:
ldos[i] = np.loadtxt(f"{ldos_file}0{i}.dat")
else:
ldos[i] = np.loadtxt(f"{ldos_file}{i}.dat")
for i in range(0, len(ldos[1])):
dos_energies.append(ldos[1][i][0])
all_pdos = []
vorb = {
"s": Orbital.s,
"p": Orbital.py,
"d": Orbital.dxy,
"f": Orbital.f0
}
forb = {"s": 0, "p": 1, "d": 2, "f": 3}
dlength = len(ldos[1])
for i in range(nsites):
pot_index = pot_dict[structure.species[i].symbol]
all_pdos.append(defaultdict(dict))
for k, v in vorb.items():
density = [
ldos[pot_index][j][forb[k] + 1] for j in range(dlength)
]
updos = density
downdos = None
if downdos:
all_pdos[-1][v] = {Spin.up: updos, Spin.down: downdos}
else:
all_pdos[-1][v] = {Spin.up: updos}
pdos = all_pdos
vorb2 = {0: Orbital.s, 1: Orbital.py, 2: Orbital.dxy, 3: Orbital.f0}
pdoss = {
structure[i]: {v: pdos[i][v]
for v in vorb2.values()}
for i in range(len(pdos))
}
forb = {"s": 0, "p": 1, "d": 2, "f": 3}
tdos = [0] * dlength
for i in range(nsites):
pot_index = pot_dict[structure.species[i].symbol]
for v in forb.values():
density = [ldos[pot_index][j][v + 1] for j in range(dlength)]
for j in range(dlength):
tdos[j] = tdos[j] + density[j]
tdos = {Spin.up: tdos}
dos = Dos(efermi, dos_energies, tdos)
complete_dos = CompleteDos(structure, dos, pdoss)
charge_transfer = LDos.charge_transfer_from_file(
feff_inp_file, ldos_file)
return LDos(complete_dos, charge_transfer)
def setUp(self):
with open(os.path.join(test_dir, "complete_dos.json"), "r") as f:
self.dos = CompleteDos.from_dict(json.load(f))
def process_item(self, mat):
"""
Process the tasks and materials into just a list of materials
Args:
mat (dict): material document
Returns:
(dict): electronic_structure document
"""
self.logger.info("Processing: {}".format(mat[self.materials.key]))
d = {self.electronic_structure.key: mat[
self.materials.key], "bandstructure": {}}
bs = None
dos = None
interpolated_dos = None
# Process the bandstructure for information
if "bs" in mat["bandstructure"]:
if "structure" not in mat["bandstructure"]["bs"]:
mat["bandstructure"]["bs"]["structure"] = mat["structure"]
if len(mat["bandstructure"]["bs"].get("labels_dict", {})) == 0:
struc = Structure.from_dict(mat["structure"])
kpath = HighSymmKpath(struc)._kpath["kpoints"]
mat["bandstructure"]["bs"]["labels_dict"] = kpath
# Somethign is wrong with the as_dict / from_dict encoding in the two band structure objects so have to use this hodge podge serialization
# TODO: Fix bandstructure objects in pymatgen
bs = BandStructureSymmLine.from_dict(
BandStructure.from_dict(mat["bandstructure"]["bs"]).as_dict())
d["bandstructure"]["band_gap"] = {"band_gap": bs.get_band_gap()["energy"],
"direct_gap": bs.get_direct_band_gap(),
"is_direct": bs.get_band_gap()["direct"],
"transition": bs.get_band_gap()["transition"]}
if self.small_plot:
d["bandstructure"]["plot_small"] = get_small_plot(bs)
if "dos" in mat["bandstructure"]:
dos = CompleteDos.from_dict(mat["bandstructure"]["dos"])
if self.interpolate_dos and "uniform_bs" in mat["bandstructure"]:
try:
interpolated_dos = self.get_interpolated_dos(mat)
except Exception:
self.logger.warning("Boltztrap interpolation failed for {}. Continuing with regular DOS".format(mat[self.materials.key]))
# Generate static images
if self.static_images:
try:
ylim = None
if bs:
plotter = WebBSPlotter(bs)
fig = plotter.get_plot()
ylim = fig.ylim() # Used by DOS plot
fig.close()
d["bandstructure"]["bs_plot"] = image_from_plotter(plotter)
if dos:
plotter = WebDosVertPlotter()
plotter.add_dos_dict(dos.get_element_dos())
if interpolated_dos:
plotter.add_dos("Total DOS", interpolated_dos)
d["bandstructure"]["dos_plot"] = image_from_plotter(plotter, ylim=ylim)
d["bandstructure"]["dos_plot"] = image_from_plotter(plotter, ylim=ylim)
except Exception:
self.logger.warning(
"Caught error in electronic structure plotting for {}: {}".format(mat[self.materials.key], traceback.format_exc()))
return None
return d
def setUp(self):
with open(os.path.join(test_dir, "complete_dos.json"), "r") as f:
self.dos = CompleteDos.from_dict(json.load(f))
