def setUp(self):
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"),
"r",
encoding="utf-8") as f:
d = json.loads(f.read())
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotter(self.bs)
self.assertEqual(len(self.plotter._bs), 1,
"wrong number of band objects")
with open(os.path.join(test_dir, "N2_12103_bandstructure.json"),
"r",
encoding="utf-8") as f:
d = json.loads(f.read())
self.sbs_sc = BandStructureSymmLine.from_dict(d)
with open(os.path.join(test_dir, "C_48_bandstructure.json"),
"r",
encoding="utf-8") as f:
d = json.loads(f.read())
self.sbs_met = BandStructureSymmLine.from_dict(d)
self.plotter_multi = BSPlotter([self.sbs_sc, self.sbs_met])
self.assertEqual(len(self.plotter_multi._bs), 2,
"wrong number of band objects")
self.assertEqual(self.plotter_multi._nb_bands, [96, 96],
"wrong number of bands")
warnings.simplefilter("ignore")
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"),
"r",
encoding='utf-8') as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.assertListEqual(
self.bs._projections[Spin.up][10][12][Orbital.s],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "wrong projections")
self.assertListEqual(
self.bs._projections[Spin.up][25][0][Orbital.dyz],
[0.0, 0.0, 0.0011, 0.0219, 0.0219, 0.069], "wrong projections")
self.assertAlmostEqual(
self.bs.get_projection_on_elements()[Spin.up][25][10]['O'],
0.0328)
self.assertAlmostEqual(
self.bs.get_projection_on_elements()[Spin.up][22][25]['Cu'],
0.8327)
self.assertAlmostEqual(
self.bs.get_projections_on_elts_and_orbitals(
{'Cu': ['s', 'd']})[Spin.up][25][0]['Cu']['s'], 0.0027)
self.assertAlmostEqual(
self.bs.get_projections_on_elts_and_orbitals(
{'Cu': ['s', 'd']})[Spin.up][25][0]['Cu']['d'],
0.8495999999999999)
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"),
"r",
encoding='utf-8') as f:
d = json.load(f)
#print d.keys()
self.bs = BandStructureSymmLine.from_dict(d)
#print self.bs.as_dict().keys()
#this doesn't really test as_dict() -> from_dict very well
#self.assertEqual(self.bs.as_dict().keys(), d.keys())
self.one_kpoint = self.bs.kpoints[31]
self.assertEqual(self.bs._nb_bands, 16)
self.assertAlmostEqual(self.bs._bands[Spin.up][5][10], 0.5608)
self.assertAlmostEqual(self.bs._bands[Spin.up][5][10], 0.5608)
self.assertEqual(self.bs._branches[5]['name'], "L-U")
self.assertEqual(self.bs._branches[5]['start_index'], 80)
self.assertEqual(self.bs._branches[5]['end_index'], 95)
self.assertAlmostEqual(self.bs._distance[70], 4.2335127528765737)
with open(os.path.join(test_dir, "NiO_19009_bandstructure.json"),
"r",
encoding='utf-8') as f:
d = json.load(f)
self.bs_spin = BandStructureSymmLine.from_dict(d)
#this doesn't really test as_dict() -> from_dict very well
#self.assertEqual(self.bs_spin.as_dict().keys(), d.keys())
self.assertEqual(self.bs_spin._nb_bands, 27)
self.assertAlmostEqual(self.bs_spin._bands[Spin.up][5][10], 0.262)
self.assertAlmostEqual(self.bs_spin._bands[Spin.down][5][10],
1.6156)
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"), "r", encoding="utf-8") as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"), "r", encoding="utf-8") as f:
d = json.load(f)
self.bs2 = BandStructureSymmLine.from_dict(d)
with open(os.path.join(test_dir, "NiO_19009_bandstructure.json"), "r", encoding="utf-8") as f:
d = json.load(f)
self.bs_spin = BandStructureSymmLine.from_dict(d)
def setUp(self):
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"),
"r",
encoding='utf-8') as f:
d = json.loads(f.read())
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotter(self.bs)
def setUp(self):
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"),
"r", encoding='utf-8') as f:
d = json.loads(f.read())
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotter(self.bs)
warnings.simplefilter("ignore")
def test_old_format_load(self):
with open(os.path.join(test_dir, "bs_ZnS_old.json"),
"r", encoding='utf-8') as f:
d = json.load(f)
bs_old = BandStructureSymmLine.from_dict(d)
self.assertEqual(bs_old.get_projection_on_elements()[
Spin.up][0][0]['Zn'], 0.0971)
def setUp(self):
with open(os.path.join(test_dir, 'si_structure.json'), 'r') as sth:
si_str = Structure.from_dict(json.load(sth))
with open(os.path.join(test_dir, 'si_bandstructure_line.json'),
'r') as bsh:
si_bs_line = BandStructureSymmLine.from_dict(json.load(bsh))
si_bs_line.structure = si_str
with open(os.path.join(test_dir, 'si_bandstructure_uniform.json'),
'r') as bsh:
si_bs_uniform = BandStructure.from_dict(json.load(bsh))
si_bs_uniform.structure = si_str
self.si_kpts = list(HighSymmKpath(si_str).kpath['kpoints'].values())
self.df = pd.DataFrame({
'bs_line': [si_bs_line],
'bs_uniform': [si_bs_uniform]
})
with open(os.path.join(test_dir, 'VBr2_971787_bandstructure.json'),
'r') as bsh:
vbr2_uniform = BandStructure.from_dict(json.load(bsh))
self.vbr2kpts = [
k.frac_coords for k in vbr2_uniform.labels_dict.values()
]
self.vbr2kpts = [
[0.0, 0.0, 0.0], # \\Gamma
[0.2, 0.0, 0.0], # between \\Gamma and M
[0.5, 0.0, 0.0], # M
[0.5, 0.0, 0.5]
] # L
self.df2 = pd.DataFrame({'bs_line': [vbr2_uniform]})
def extract_bs(mat):
bs = None
# Process the bandstructure for information
if "bs" in mat["bandstructure"]:
bs_dict = mat["bandstructure"]["bs"]
# Add in structure if not already there
if "structure" not in bs_dict:
bs_dict["structure"] = mat["structure"]
# Add in High Symm K Path if not already there
if len(bs_dict.get("labels_dict", {})) == 0:
labels = get(mat, "inputs.nscf_line.kpoints.labels", None)
kpts = get(mat, "inputs.nscf_line.kpoints.kpoints", None)
if labels and kpts:
labels_dict = dict(zip(labels, kpts))
labels_dict.pop(None, None)
else:
struc = Structure.from_dict(mat["structure"])
labels_dict = HighSymmKpath(struc)._kpath["kpoints"]
bs_dict["labels_dict"] = labels_dict
bs = BandStructureSymmLine.from_dict(
BandStructure.from_dict(bs_dict).as_dict())
return bs
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"),
"r", encoding='utf-8') as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotterProjected(self.bs)
warnings.simplefilter("ignore")
def test_old_format_load(self):
with open(os.path.join(PymatgenTest.TEST_FILES_DIR, "bs_ZnS_old.json"),
encoding="utf-8") as f:
d = json.load(f)
bs_old = BandStructureSymmLine.from_dict(d)
self.assertEqual(
bs_old.get_projection_on_elements()[Spin.up][0][0]["Zn"],
0.0971)
def setUp(self):
with open(os.path.join(PymatgenTest.TEST_FILES_DIR,
"Cu2O_361_bandstructure.json"),
encoding="utf-8") as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotterProjected(self.bs)
warnings.simplefilter("ignore")
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"),
"r",
encoding='utf-8') as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"),
"r",
encoding='utf-8') as f:
d = json.load(f)
self.bs2 = BandStructureSymmLine.from_dict(d)
with open(os.path.join(test_dir, "NiO_19009_bandstructure.json"),
"r",
encoding='utf-8') as f:
d = json.load(f)
self.bs_spin = BandStructureSymmLine.from_dict(d)
def get_bs(db_file):
""" return bandstructure object from the database """
d1, d2, d3, d4 = get_collections(db_file)
db = get_db(db_file)
fs = gridfs.GridFS(db, 'bandstructure_fs')
bs_fs_id = d3["calcs_reversed"][0]["bandstructure_fs_id"]
bs_json = zlib.decompress(fs.get(bs_fs_id).read())
bs_dict = json.loads(bs_json.decode())
return BandStructureSymmLine.from_dict(bs_dict)
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 get_band_structure(self, task_id, line_mode=False):
m_task = self.collection.find_one({"task_id": task_id},
{"calcs_reversed": 1})
fs_id = m_task['calcs_reversed'][0]['bandstructure_fs_id']
fs = gridfs.GridFS(self.db, 'bandstructure_fs')
bs_json = zlib.decompress(fs.get(fs_id).read())
bs_dict = json.loads(bs_json)
if line_mode:
return BandStructureSymmLine.from_dict(bs_dict)
else:
return BandStructure.from_dict(bs_dict)
def get_band_structure(self, task_id, line_mode=False):
m_task = self.collection.find_one({"task_id": task_id},
{"calcs_reversed": 1})
fs_id = m_task['calcs_reversed'][0]['bandstructure_fs_id']
fs = gridfs.GridFS(self.db, 'bandstructure_fs')
bs_json = zlib.decompress(fs.get(fs_id).read())
bs_dict = json.loads(bs_json)
if line_mode:
return BandStructureSymmLine.from_dict(bs_dict)
else:
return BandStructure.from_dict(bs_dict)
def get_band_structure(self, task_id):
m_task = self.collection.find_one({"task_id": task_id}, {"calcs_reversed": 1})
fs_id = m_task['calcs_reversed'][0]['bandstructure_fs_id']
fs = gridfs.GridFS(self.db, 'bandstructure_fs')
bs_json = zlib.decompress(fs.get(fs_id).read())
bs_dict = json.loads(bs_json.decode())
if bs_dict["@class"] == "BandStructure":
return BandStructure.from_dict(bs_dict)
elif bs_dict["@class"] == "BandStructureSymmLine":
return BandStructureSymmLine.from_dict(bs_dict)
else:
raise ValueError("Unknown class for band structure! {}".format(bs_dict["@class"]))
def get_band_structure(self, task_id):
m_task = self.collection.find_one({"task_id": task_id}, {"calcs_reversed": 1})
fs_id = m_task['calcs_reversed'][0]['bandstructure_fs_id']
fs = gridfs.GridFS(self.db, 'bandstructure_fs')
bs_json = zlib.decompress(fs.get(fs_id).read())
bs_dict = json.loads(bs_json.decode())
if bs_dict["@class"] == "BandStructure":
return BandStructure.from_dict(bs_dict)
elif bs_dict["@class"] == "BandStructureSymmLine":
return BandStructureSymmLine.from_dict(bs_dict)
else:
raise ValueError("Unknown class for band structure! {}".format(bs_dict["@class"]))
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"),
"r", encoding='utf-8') as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.assertListEqual(self.bs._projections[Spin.up][10][12][Orbital.s], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "wrong projections")
self.assertListEqual(self.bs._projections[Spin.up][25][0][Orbital.dyz], [0.0, 0.0, 0.0011, 0.0219, 0.0219, 0.069], "wrong projections")
self.assertAlmostEqual(self.bs.get_projection_on_elements()[Spin.up][25][10]['O'], 0.0328)
self.assertAlmostEqual(self.bs.get_projection_on_elements()[Spin.up][22][25]['Cu'], 0.8327)
self.assertAlmostEqual(self.bs.get_projections_on_elts_and_orbitals({'Cu':['s','d']})[Spin.up][25][0]['Cu']['s'], 0.0027)
self.assertAlmostEqual(self.bs.get_projections_on_elts_and_orbitals({'Cu':['s','d']})[Spin.up][25][0]['Cu']['d'], 0.8495999999999999)
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"), "r",
encoding='utf-8') as f:
d = json.load(f)
#print d.keys()
self.bs = BandStructureSymmLine.from_dict(d)
#print self.bs.as_dict().keys()
#this doesn't really test as_dict() -> from_dict very well
#self.assertEqual(self.bs.as_dict().keys(), d.keys())
self.one_kpoint = self.bs.kpoints[31]
self.assertEqual(self.bs._nb_bands, 16)
self.assertAlmostEqual(self.bs._bands[Spin.up][5][10], 0.5608)
self.assertAlmostEqual(self.bs._bands[Spin.up][5][10], 0.5608)
self.assertEqual(self.bs._branches[5]['name'], "L-U")
self.assertEqual(self.bs._branches[5]['start_index'], 80)
self.assertEqual(self.bs._branches[5]['end_index'], 95)
self.assertAlmostEqual(self.bs._distance[70], 4.2335127528765737)
with open(os.path.join(test_dir, "NiO_19009_bandstructure.json"),
"r", encoding='utf-8') as f:
d = json.load(f)
self.bs_spin = BandStructureSymmLine.from_dict(d)
#this doesn't really test as_dict() -> from_dict very well
#self.assertEqual(self.bs_spin.as_dict().keys(), d.keys())
self.assertEqual(self.bs_spin._nb_bands, 27)
self.assertAlmostEqual(self.bs_spin._bands[Spin.up][5][10], 0.262)
self.assertAlmostEqual(self.bs_spin._bands[Spin.down][5][10],
1.6156)
def setUp(self):
with open(os.path.join(test_dir, 'si_structure.json'), 'r') as sth:
si_str = Structure.from_dict(json.load(sth))
with open(os.path.join(test_dir, 'si_bandstructure_line.json'),
'r') as bsh:
si_bs_line = BandStructureSymmLine.from_dict(json.load(bsh))
si_bs_line.structure = si_str
with open(os.path.join(test_dir, 'si_bandstructure_uniform.json'),
'r') as bsh:
si_bs_uniform = BandStructure.from_dict(json.load(bsh))
si_bs_uniform.structure = si_str
self.si_kpts = list(HighSymmKpath(si_str).kpath['kpoints'].values())
self.df = pd.DataFrame({
'bs_line': [si_bs_line],
'bs_uniform': [si_bs_uniform]
})
def get_band_structure(self, task_id):
"""
Read the BS data into a PMG BandStructure or BandStructureSymmLine object
Args:
task_id(int or str): the task_id containing the data
Returns:
BandStructure or BandStructureSymmLine
"""
obj_dict = self.get_data_from_maggma_or_gridfs(task_id,
key="bandstructure")
if obj_dict["@class"] == "BandStructure":
return BandStructure.from_dict(obj_dict)
elif obj_dict["@class"] == "BandStructureSymmLine":
return BandStructureSymmLine.from_dict(obj_dict)
else:
raise ValueError("Unknown class for band structure! {}".format(
obj_dict["@class"]))
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 build_bs(bs_dict, mat):
bs_dict["structure"] = mat["structure"]
# Add in High Symm K Path if not already there
if len(bs_dict.get("labels_dict", {})) == 0:
labels = get(mat, "inputs.nscf_line.kpoints.labels", None)
kpts = get(mat, "inputs.nscf_line.kpoints.kpoints", None)
if labels and kpts:
labels_dict = dict(zip(labels, kpts))
labels_dict.pop(None, None)
else:
struc = Structure.from_dict(bs_dict["structure"])
labels_dict = HighSymmKpath(struc)._kpath["kpoints"]
bs_dict["labels_dict"] = labels_dict
# This is somethign to do with BandStructureSymmLine's from dict being problematic
bs = BandStructureSymmLine.from_dict(bs_dict)
return bs
def setUp(self):
with open(os.path.join(test_dir, 'si_structure.json'),'r') as sth:
si_str = Structure.from_dict(json.load(sth))
with open(os.path.join(test_dir, 'si_bandstructure_line.json'),'r') as bsh:
si_bs_line = BandStructureSymmLine.from_dict(json.load(bsh))
si_bs_line.structure = si_str
with open(os.path.join(test_dir, 'si_bandstructure_uniform.json'),'r') as bsh:
si_bs_uniform = BandStructure.from_dict(json.load(bsh))
si_bs_uniform.structure = si_str
self.si_kpts = list(HighSymmKpath(si_str).kpath['kpoints'].values())
self.df = pd.DataFrame({'bs_line': [si_bs_line], 'bs_uniform': [si_bs_uniform]})
with open(os.path.join(test_dir, 'VBr2_971787_bandstructure.json'), 'r') as bsh:
vbr2_uniform = BandStructure.from_dict(json.load(bsh))
self.vbr2kpts = [k.frac_coords for k in vbr2_uniform.labels_dict.values()]
self.vbr2kpts = [[0.0, 0.0, 0.0], # \\Gamma
[0.2, 0.0, 0.0], # between \\Gamma and M
[0.5, 0.0, 0.0], # M
[0.5, 0.0, 0.5]] # L
self.df2 = pd.DataFrame({'bs_line': [vbr2_uniform]})
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 bs_dos_traces(bandStructureSymmLine, densityOfStates):
if bandStructureSymmLine == "error" or densityOfStates == "error":
return "error"
if bandStructureSymmLine == None or densityOfStates == None:
raise PreventUpdate
# - BS Data
bstraces = []
bs_reg_plot = BSPlotter(BSML.from_dict(bandStructureSymmLine))
bs_data = bs_reg_plot.bs_plot_data()
# -- Strip latex math wrapping
str_replace = {
"$": "",
"\\mid": "|",
"\\Gamma": "Γ",
"\\Sigma": "Σ",
"_1": "₁",
"_2": "₂",
"_3": "₃",
"_4": "₄",
}
for entry_num in range(len(bs_data["ticks"]["label"])):
for key in str_replace.keys():
if key in bs_data["ticks"]["label"][entry_num]:
bs_data["ticks"]["label"][entry_num] = bs_data[
"ticks"]["label"][entry_num].replace(
key, str_replace[key])
for d in range(len(bs_data["distances"])):
for i in range(bs_reg_plot._nb_bands):
bstraces.append(
go.Scatter(
x=bs_data["distances"][d],
y=[
bs_data["energy"][d][str(Spin.up)][i][j]
for j in range(len(bs_data["distances"][d]))
],
mode="lines",
line=dict(color=("#666666"), width=2),
hoverinfo="skip",
showlegend=False,
))
if bs_reg_plot._bs.is_spin_polarized:
bstraces.append(
go.Scatter(
x=bs_data["distances"][d],
y=[
bs_data["energy"][d][str(Spin.down)][i][j]
for j in range(len(bs_data["distances"]
[d]))
],
mode="lines",
line=dict(color=("#666666"),
width=2,
dash="dash"),
hoverinfo="skip",
showlegend=False,
))
# -- DOS Data
dostraces = []
dos = CompleteDos.from_dict(densityOfStates)
if Spin.down in dos.densities:
# Add second spin data if available
trace_tdos = go.Scatter(
x=dos.densities[Spin.down],
y=dos.energies - dos.efermi,
mode="lines",
name="Total DOS (spin ↓)",
line=go.scatter.Line(color="#444444", dash="dash"),
fill="tozeroy",
)
dostraces.append(trace_tdos)
tdos_label = "Total DOS (spin ↑)"
else:
tdos_label = "Total DOS"
# Total DOS
trace_tdos = go.Scatter(
x=dos.densities[Spin.up],
y=dos.energies - dos.efermi,
mode="lines",
name=tdos_label,
line=go.scatter.Line(color="#444444"),
fill="tozeroy",
legendgroup="spinup",
)
dostraces.append(trace_tdos)
p_ele_dos = dos.get_element_dos()
# Projected DOS
count = 0
colors = [
"#1f77b4", # muted blue
"#ff7f0e", # safety orange
"#2ca02c", # cooked asparagus green
"#d62728", # brick red
"#9467bd", # muted purple
"#8c564b", # chestnut brown
"#e377c2", # raspberry yogurt pink
"#bcbd22", # curry yellow-green
"#17becf", # blue-teal
]
for ele in p_ele_dos.keys():
if bs_reg_plot._bs.is_spin_polarized:
trace = go.Scatter(
x=p_ele_dos[ele].densities[Spin.down],
y=dos.energies - dos.efermi,
mode="lines",
name=ele.symbol + " (spin ↓)",
line=dict(width=3, color=colors[count], dash="dash"),
)
dostraces.append(trace)
spin_up_label = ele.symbol + " (spin ↑)"
else:
spin_up_label = ele.symbol
trace = go.Scatter(
x=p_ele_dos[ele].densities[Spin.up],
y=dos.energies - dos.efermi,
mode="lines",
name=spin_up_label,
line=dict(width=3, color=colors[count]),
)
dostraces.append(trace)
count += 1
traces = [bstraces, dostraces, bs_data]
return traces
def bs_dos_data(
mpid,
path_convention,
dos_select,
label_select,
bandstructure_symm_line,
density_of_states,
):
if not mpid and (bandstructure_symm_line is None
or density_of_states is None):
raise PreventUpdate
elif bandstructure_symm_line is None or density_of_states is None:
if label_select == "":
raise PreventUpdate
# --
# -- BS and DOS from API or DB
# --
bs_data = {"ticks": {}}
bs_store = GridFSStore(
database="fw_bs_prod",
collection_name="bandstructure_fs",
host="mongodb03.nersc.gov",
port=27017,
username="******",
password="",
)
dos_store = GridFSStore(
database="fw_bs_prod",
collection_name="dos_fs",
host="mongodb03.nersc.gov",
port=27017,
username="******",
password="",
)
es_store = MongoStore(
database="fw_bs_prod",
collection_name="electronic_structure",
host="mongodb03.nersc.gov",
port=27017,
username="******",
password="",
key="task_id",
)
# - BS traces from DB using task_id
es_store.connect()
bs_query = es_store.query_one(
criteria={"task_id": int(mpid)},
properties=[
"bandstructure.{}.task_id".format(path_convention),
"bandstructure.{}.total.equiv_labels".format(
path_convention),
],
)
es_store.close()
bs_store.connect()
bandstructure_symm_line = bs_store.query_one(criteria={
"metadata.task_id":
int(bs_query["bandstructure"][path_convention]["task_id"])
}, )
# If LM convention, get equivalent labels
if path_convention != label_select:
bs_equiv_labels = bs_query["bandstructure"][
path_convention]["total"]["equiv_labels"]
new_labels_dict = {}
for label in bandstructure_symm_line["labels_dict"].keys():
label_formatted = label.replace("$", "")
if "|" in label_formatted:
f_label = label_formatted.split("|")
new_labels.append(
"$" +
bs_equiv_labels[label_select][f_label[0]] +
"|" +
bs_equiv_labels[label_select][f_label[1]] +
"$")
else:
new_labels_dict["$" + bs_equiv_labels[label_select]
[label_formatted] +
"$"] = bandstructure_symm_line[
"labels_dict"][label]
bandstructure_symm_line["labels_dict"] = new_labels_dict
# - DOS traces from DB using task_id
es_store.connect()
dos_query = es_store.query_one(
criteria={"task_id": int(mpid)},
properties=["dos.task_id"],
)
es_store.close()
dos_store.connect()
density_of_states = dos_store.query_one(
criteria={"task_id": int(dos_query["dos"]["task_id"])}, )
# - BS Data
if (type(bandstructure_symm_line) != dict
and bandstructure_symm_line is not None):
bandstructure_symm_line = bandstructure_symm_line.to_dict()
if type(density_of_states
) != dict and density_of_states is not None:
density_of_states = density_of_states.to_dict()
bsml = BSML.from_dict(bandstructure_symm_line)
bs_reg_plot = BSPlotter(bsml)
bs_data = bs_reg_plot.bs_plot_data()
# Make plot continous for lm
if path_convention == "lm":
distance_map, kpath_euler = HSKP(
bsml.structure).get_continuous_path(bsml)
kpath_labels = [pair[0] for pair in kpath_euler]
kpath_labels.append(kpath_euler[-1][1])
else:
distance_map = [(i, False)
for i in range(len(bs_data["distances"]))]
kpath_labels = []
for label_ind in range(len(bs_data["ticks"]["label"]) - 1):
if (bs_data["ticks"]["label"][label_ind] !=
bs_data["ticks"]["label"][label_ind + 1]):
kpath_labels.append(
bs_data["ticks"]["label"][label_ind])
kpath_labels.append(bs_data["ticks"]["label"][-1])
bs_data["ticks"]["label"] = kpath_labels
# Obtain bands to plot over and generate traces for bs data:
energy_window = (-6.0, 10.0)
bands = []
for band_num in range(bs_reg_plot._nb_bands):
if (bs_data["energy"][0][str(Spin.up)][band_num][0] <=
energy_window[1]) and (bs_data["energy"][0][str(
Spin.up)][band_num][0] >= energy_window[0]):
bands.append(band_num)
bstraces = []
pmin = 0.0
tick_vals = [0.0]
cbm = bsml.get_cbm()
vbm = bsml.get_vbm()
cbm_new = bs_data["cbm"]
vbm_new = bs_data["vbm"]
for dnum, (d, rev) in enumerate(distance_map):
x_dat = [
dval - bs_data["distances"][d][0] + pmin
for dval in bs_data["distances"][d]
]
pmin = x_dat[-1]
tick_vals.append(pmin)
if not rev:
traces_for_segment = [{
"x":
x_dat,
"y": [
bs_data["energy"][d][str(Spin.up)][i][j]
for j in range(len(bs_data["distances"][d]))
],
"mode":
"lines",
"line": {
"color": "#1f77b4"
},
"hoverinfo":
"skip",
"name":
"spin ↑"
if bs_reg_plot._bs.is_spin_polarized else "Total",
"hovertemplate":
"%{y:.2f} eV",
"showlegend":
False,
"xaxis":
"x",
"yaxis":
"y",
} for i in bands]
elif rev:
traces_for_segment = [{
"x":
x_dat,
"y": [
bs_data["energy"][d][str(Spin.up)][i][j]
for j in reversed(
range(len(bs_data["distances"][d])))
],
"mode":
"lines",
"line": {
"color": "#1f77b4"
},
"hoverinfo":
"skip",
"name":
"spin ↑"
if bs_reg_plot._bs.is_spin_polarized else "Total",
"hovertemplate":
"%{y:.2f} eV",
"showlegend":
False,
"xaxis":
"x",
"yaxis":
"y",
} for i in bands]
if bs_reg_plot._bs.is_spin_polarized:
if not rev:
traces_for_segment += [{
"x":
x_dat,
"y": [
bs_data["energy"][d][str(Spin.down)][i][j]
for j in range(len(bs_data["distances"][d]))
],
"mode":
"lines",
"line": {
"color": "#ff7f0e",
"dash": "dot"
},
"hoverinfo":
"skip",
"showlegend":
False,
"name":
"spin ↓",
"hovertemplate":
"%{y:.2f} eV",
"xaxis":
"x",
"yaxis":
"y",
} for i in bands]
elif rev:
traces_for_segment += [{
"x":
x_dat,
"y": [
bs_data["energy"][d][str(Spin.down)][i][j]
for j in reversed(
range(len(bs_data["distances"][d])))
],
"mode":
"lines",
"line": {
"color": "#ff7f0e",
"dash": "dot"
},
"hoverinfo":
"skip",
"showlegend":
False,
"name":
"spin ↓",
"hovertemplate":
"%{y:.2f} eV",
"xaxis":
"x",
"yaxis":
"y",
} for i in bands]
bstraces += traces_for_segment
# - Get proper cbm and vbm coords for lm
if path_convention == "lm":
for (x_point, y_point) in bs_data["cbm"]:
if x_point in bs_data["distances"][d]:
xind = bs_data["distances"][d].index(x_point)
if not rev:
x_point_new = x_dat[xind]
else:
x_point_new = x_dat[len(x_dat) - xind - 1]
new_label = bs_data["ticks"]["label"][
tick_vals.index(x_point_new)]
if (cbm["kpoint"].label is None
or cbm["kpoint"].label in new_label):
cbm_new.append((x_point_new, y_point))
for (x_point, y_point) in bs_data["vbm"]:
if x_point in bs_data["distances"][d]:
xind = bs_data["distances"][d].index(x_point)
if not rev:
x_point_new = x_dat[xind]
else:
x_point_new = x_dat[len(x_dat) - xind - 1]
new_label = bs_data["ticks"]["label"][
tick_vals.index(x_point_new)]
if (vbm["kpoint"].label is None
or vbm["kpoint"].label in new_label):
vbm_new.append((x_point_new, y_point))
bs_data["ticks"]["distance"] = tick_vals
# - Strip latex math wrapping for labels
str_replace = {
"$": "",
"\\mid": "|",
"\\Gamma": "Γ",
"\\Sigma": "Σ",
"GAMMA": "Γ",
"_1": "₁",
"_2": "₂",
"_3": "₃",
"_4": "₄",
"_{1}": "₁",
"_{2}": "₂",
"_{3}": "₃",
"_{4}": "₄",
"^{*}": "*",
}
bar_loc = []
for entry_num in range(len(bs_data["ticks"]["label"])):
for key in str_replace.keys():
if key in bs_data["ticks"]["label"][entry_num]:
bs_data["ticks"]["label"][entry_num] = bs_data[
"ticks"]["label"][entry_num].replace(
key, str_replace[key])
if key == "\\mid":
bar_loc.append(
bs_data["ticks"]["distance"][entry_num])
# Vertical lines for disjointed segments
vert_traces = [{
"x": [x_point, x_point],
"y": energy_window,
"mode": "lines",
"marker": {
"color": "white"
},
"hoverinfo": "skip",
"showlegend": False,
"xaxis": "x",
"yaxis": "y",
} for x_point in bar_loc]
bstraces += vert_traces
# Dots for cbm and vbm
dot_traces = [{
"x": [x_point],
"y": [y_point],
"mode":
"markers",
"marker": {
"color": "#7E259B",
"size": 16,
"line": {
"color": "white",
"width": 2
},
},
"showlegend":
False,
"hoverinfo":
"text",
"name":
"",
"hovertemplate":
"CBM: k = {}, {} eV".format(list(cbm["kpoint"].frac_coords),
cbm["energy"]),
"xaxis":
"x",
"yaxis":
"y",
} for (x_point, y_point) in set(cbm_new)] + [{
"x": [x_point],
"y": [y_point],
"mode":
"marker",
"marker": {
"color": "#7E259B",
"size": 16,
"line": {
"color": "white",
"width": 2
},
},
"showlegend":
False,
"hoverinfo":
"text",
"name":
"",
"hovertemplate":
"VBM: k = {}, {} eV".format(list(vbm["kpoint"].frac_coords),
vbm["energy"]),
"xaxis":
"x",
"yaxis":
"y",
} for (x_point, y_point) in set(vbm_new)]
bstraces += dot_traces
# - DOS Data
dostraces = []
dos = CompleteDos.from_dict(density_of_states)
dos_max = np.abs(
(dos.energies - dos.efermi - energy_window[1])).argmin()
dos_min = np.abs(
(dos.energies - dos.efermi - energy_window[0])).argmin()
if bs_reg_plot._bs.is_spin_polarized:
# Add second spin data if available
trace_tdos = {
"x": -1.0 * dos.densities[Spin.down][dos_min:dos_max],
"y": dos.energies[dos_min:dos_max] - dos.efermi,
"mode": "lines",
"name": "Total DOS (spin ↓)",
"line": go.scatter.Line(color="#444444", dash="dot"),
"fill": "tozerox",
"fillcolor": "#C4C4C4",
"xaxis": "x2",
"yaxis": "y2",
}
dostraces.append(trace_tdos)
tdos_label = "Total DOS (spin ↑)"
else:
tdos_label = "Total DOS"
# Total DOS
trace_tdos = {
"x": dos.densities[Spin.up][dos_min:dos_max],
"y": dos.energies[dos_min:dos_max] - dos.efermi,
"mode": "lines",
"name": tdos_label,
"line": go.scatter.Line(color="#444444"),
"fill": "tozerox",
"fillcolor": "#C4C4C4",
"legendgroup": "spinup",
"xaxis": "x2",
"yaxis": "y2",
}
dostraces.append(trace_tdos)
ele_dos = dos.get_element_dos()
elements = [str(entry) for entry in ele_dos.keys()]
if dos_select == "ap":
proj_data = ele_dos
elif dos_select == "op":
proj_data = dos.get_spd_dos()
elif "orb" in dos_select:
proj_data = dos.get_element_spd_dos(
Element(dos_select.replace("orb", "")))
else:
raise PreventUpdate
# Projected DOS
count = 0
colors = [
"#d62728", # brick red
"#2ca02c", # cooked asparagus green
"#17becf", # blue-teal
"#bcbd22", # curry yellow-green
"#9467bd", # muted purple
"#8c564b", # chestnut brown
"#e377c2", # raspberry yogurt pink
]
for label in proj_data.keys():
if bs_reg_plot._bs.is_spin_polarized:
trace = {
"x":
-1.0 *
proj_data[label].densities[Spin.down][dos_min:dos_max],
"y":
dos.energies[dos_min:dos_max] - dos.efermi,
"mode":
"lines",
"name":
str(label) + " (spin ↓)",
"line":
dict(width=3, color=colors[count], dash="dot"),
"xaxis":
"x2",
"yaxis":
"y2",
}
dostraces.append(trace)
spin_up_label = str(label) + " (spin ↑)"
else:
spin_up_label = str(label)
trace = {
"x": proj_data[label].densities[Spin.up][dos_min:dos_max],
"y": dos.energies[dos_min:dos_max] - dos.efermi,
"mode": "lines",
"name": spin_up_label,
"line": dict(width=2, color=colors[count]),
"xaxis": "x2",
"yaxis": "y2",
}
dostraces.append(trace)
count += 1
traces = [bstraces, dostraces, bs_data]
return (traces, elements)
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 = BandStructureSymmLine.from_dict(mat["bandstructure"]["bs"])
dos = CompleteDos.from_dict(mat["bandstructure"]["dos"])
# Plot Band structure
if bs:
try:
plotter = WebBSPlotter(bs)
plot = plotter.get_plot()
ylim = plot.ylim()
d["bs_plot"] = image_from_plot(plot)
plot.close()
except Exception:
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 = 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()))
# Plot DOS
if dos:
try:
plotter = WebDosVertPlotter()
plotter.add_dos_dict(dos.get_element_dos())
plot = plotter.get_plot(ylim=ylim)
d["dos_plot"] = image_from_plot(plot)
plot.close()
except Exception:
self.logger.warning(
"Caught error in dos plotting for {}: {}".format(
mat[self.materials.key], traceback.format_exc()))
# Get basic bandgap properties
if bs:
try:
d["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"]
}
except Exception:
self.logger.warning(
"Caught error in calculating bandgap {}: {}".format(
mat[self.materials.key], traceback.format_exc()))
return d
def setUp(self):
with open(os.path.join(test_dir, "Cu2O_361_bandstructure.json"),
"r", encoding='utf-8') as f:
d = json.load(f)
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotterProjected(self.bs)
def bs_dos_data(
mpid,
path_convention,
dos_select,
label_select,
bandstructure_symm_line,
density_of_states,
):
if (not mpid
or "mpid" not in mpid) and (bandstructure_symm_line is None
or density_of_states is None):
raise PreventUpdate
elif mpid:
raise PreventUpdate
elif bandstructure_symm_line is None or density_of_states is None:
# --
# -- BS and DOS from API
# --
mpid = mpid["mpid"]
bs_data = {"ticks": {}}
# client = MongoClient(
# "mongodb03.nersc.gov", username="******", password="", authSource="fw_bs_prod",
# )
db = client.fw_bs_prod
# - BS traces from DB using task_id
bs_query = list(
db.electronic_structure.find(
{"task_id": int(mpid)},
[
"bandstructure.{}.total.traces".format(
path_convention)
],
))[0]
is_sp = (len(bs_query["bandstructure"][path_convention]
["total"]["traces"]) == 2)
if is_sp:
bstraces = (bs_query["bandstructure"][path_convention]
["total"]["traces"]["1"] +
bs_query["bandstructure"][path_convention]
["total"]["traces"]["-1"])
else:
bstraces = bs_query["bandstructure"][path_convention][
"total"]["traces"]["1"]
bs_data["ticks"]["distance"] = bs_query["bandstructure"][
path_convention]["total"]["traces"]["ticks"]
bs_data["ticks"]["label"] = bs_query["bandstructure"][
path_convention]["total"]["traces"]["labels"]
# If LM convention, get equivalent labels
if path_convention == "lm" and label_select != "lm":
bs_equiv_labels = bs_query["bandstructure"][
path_convention]["total"]["traces"]["equiv_labels"]
alt_choice = label_select
if label_select == "hin":
alt_choice = "h"
new_labels = []
for label in bs_data["ticks"]["label"]:
label_formatted = label.replace("$", "")
if "|" in label_formatted:
f_label = label_formatted.split("|")
new_labels.append(
"$" + bs_equiv_labels[alt_choice][f_label[0]] +
"|" + bs_equiv_labels[alt_choice][f_label[1]] +
"$")
else:
new_labels.append(
"$" +
bs_equiv_labels[alt_choice][label_formatted] +
"$")
bs_data["ticks"]["label"] = new_labels
# Strip latex math wrapping
str_replace = {
"$": "",
"\\mid": "|",
"\\Gamma": "Γ",
"\\Sigma": "Σ",
"GAMMA": "Γ",
"_1": "₁",
"_2": "₂",
"_3": "₃",
"_4": "₄",
}
for entry_num in range(len(bs_data["ticks"]["label"])):
for key in str_replace.keys():
if key in bs_data["ticks"]["label"][entry_num]:
bs_data["ticks"]["label"][entry_num] = bs_data[
"ticks"]["label"][entry_num].replace(
key, str_replace[key])
# - DOS traces from DB using task_id
dostraces = []
dos_tot_ele_traces = list(
db.electronic_structure.find(
{"task_id": int(mpid)},
["dos.total.traces", "dos.elements"]))[0]
dostraces = [
dos_tot_ele_traces["dos"]["total"]["traces"][spin] for spin
in dos_tot_ele_traces["dos"]["total"]["traces"].keys()
]
elements = [
ele
for ele in dos_tot_ele_traces["dos"]["elements"].keys()
]
if dos_select == "ap":
for ele_label in elements:
dostraces += [
dos_tot_ele_traces["dos"]["elements"][ele_label]
["total"]["traces"][spin]
for spin in dos_tot_ele_traces["dos"]["elements"]
[ele_label]["total"]["traces"].keys()
]
elif dos_select == "op":
orb_tot_traces = list(
db.electronic_structure.find({"task_id": int(mpid)},
["dos.orbitals"]))[0]
for orbital in ["s", "p", "d"]:
dostraces += [
orb_tot_traces["dos"]["orbitals"][orbital]
["traces"][spin] for spin in orb_tot_traces["dos"]
["orbitals"]["s"]["traces"].keys()
]
elif "orb" in dos_select:
ele_label = dos_select.replace("orb", "")
for orbital in ["s", "p", "d"]:
dostraces += [
dos_tot_ele_traces["dos"]["elements"][ele_label]
[orbital]["traces"][spin]
for spin in dos_tot_ele_traces["dos"]["elements"]
[ele_label][orbital]["traces"].keys()
]
traces = [bstraces, dostraces, bs_data]
return (traces, elements)
else:
# --
# -- BS and DOS passed manually
# --
# - BS Data
if type(bandstructure_symm_line) != dict:
bandstructure_symm_line = bandstructure_symm_line.to_dict()
if type(density_of_states) != dict:
density_of_states = density_of_states.to_dict()
bs_reg_plot = BSPlotter(
BSML.from_dict(bandstructure_symm_line))
bs_data = bs_reg_plot.bs_plot_data()
# - Strip latex math wrapping
str_replace = {
"$": "",
"\\mid": "|",
"\\Gamma": "Γ",
"\\Sigma": "Σ",
"GAMMA": "Γ",
"_1": "₁",
"_2": "₂",
"_3": "₃",
"_4": "₄",
}
for entry_num in range(len(bs_data["ticks"]["label"])):
for key in str_replace.keys():
if key in bs_data["ticks"]["label"][entry_num]:
bs_data["ticks"]["label"][entry_num] = bs_data[
"ticks"]["label"][entry_num].replace(
key, str_replace[key])
# Obtain bands to plot over:
energy_window = (-6.0, 10.0)
bands = []
for band_num in range(bs_reg_plot._nb_bands):
if (bs_data["energy"][0][str(Spin.up)][band_num][0] <=
energy_window[1]) and (bs_data["energy"][0][str(
Spin.up)][band_num][0] >= energy_window[0]):
bands.append(band_num)
bstraces = []
# Generate traces for total BS data
for d in range(len(bs_data["distances"])):
dist_dat = bs_data["distances"][d]
energy_ind = [
i for i in range(len(bs_data["distances"][d]))
]
traces_for_segment = [{
"x":
dist_dat,
"y":
[bs_data["energy"][d]["1"][i][j] for j in energy_ind],
"mode":
"lines",
"line": {
"color": "#666666"
},
"hoverinfo":
"skip",
"showlegend":
False,
} for i in bands]
if bs_reg_plot._bs.is_spin_polarized:
traces_for_segment += [{
"x":
dist_dat,
"y": [
bs_data["energy"][d]["-1"][i][j]
for j in energy_ind
],
"mode":
"lines",
"line": {
"color": "#666666"
},
"hoverinfo":
"skip",
"showlegend":
False,
} for i in bands]
bstraces += traces_for_segment
# - DOS Data
dostraces = []
dos = CompleteDos.from_dict(density_of_states)
dos_max = np.abs(
(dos.energies - dos.efermi - energy_window[1])).argmin()
dos_min = np.abs(
(dos.energies - dos.efermi - energy_window[0])).argmin()
if bs_reg_plot._bs.is_spin_polarized:
# Add second spin data if available
trace_tdos = go.Scatter(
x=dos.densities[Spin.down][dos_min:dos_max],
y=dos.energies[dos_min:dos_max] - dos.efermi,
mode="lines",
name="Total DOS (spin ↓)",
line=go.scatter.Line(color="#444444", dash="dash"),
fill="tozerox",
)
dostraces.append(trace_tdos)
tdos_label = "Total DOS (spin ↑)"
else:
tdos_label = "Total DOS"
# Total DOS
trace_tdos = go.Scatter(
x=dos.densities[Spin.up][dos_min:dos_max],
y=dos.energies[dos_min:dos_max] - dos.efermi,
mode="lines",
name=tdos_label,
line=go.scatter.Line(color="#444444"),
fill="tozerox",
legendgroup="spinup",
)
dostraces.append(trace_tdos)
ele_dos = dos.get_element_dos()
elements = [str(entry) for entry in ele_dos.keys()]
if dos_select == "ap":
proj_data = ele_dos
elif dos_select == "op":
proj_data = dos.get_spd_dos()
elif "orb" in dos_select:
proj_data = dos.get_element_spd_dos(
Element(dos_select.replace("orb", "")))
else:
raise PreventUpdate
# Projected DOS
count = 0
colors = [
"#1f77b4", # muted blue
"#ff7f0e", # safety orange
"#2ca02c", # cooked asparagus green
"#9467bd", # muted purple
"#e377c2", # raspberry yogurt pink
"#d62728", # brick red
"#8c564b", # chestnut brown
"#bcbd22", # curry yellow-green
"#17becf", # blue-teal
]
for label in proj_data.keys():
if bs_reg_plot._bs.is_spin_polarized:
trace = go.Scatter(
x=proj_data[label].densities[Spin.down]
[dos_min:dos_max],
y=dos.energies[dos_min:dos_max] - dos.efermi,
mode="lines",
name=str(label) + " (spin ↓)",
line=dict(width=3,
color=colors[count],
dash="dash"),
)
dostraces.append(trace)
spin_up_label = str(label) + " (spin ↑)"
else:
spin_up_label = str(label)
trace = go.Scatter(
x=proj_data[label].densities[Spin.up][dos_min:dos_max],
y=dos.energies[dos_min:dos_max] - dos.efermi,
mode="lines",
name=spin_up_label,
line=dict(width=3, color=colors[count]),
)
dostraces.append(trace)
count += 1
traces = [bstraces, dostraces, bs_data]
return (traces, elements)
def HSE_Gap_with_Vasp_from_icsd_data(file, vasp_cmd):
fws = []
all = json.load(open(file))
njobs = 0
g = open('/SCRATCH/acad/htbase/yugd/fw_workplace/hse_gaps_icsd/ids')
ids = g.read().split()
f = open('wrong_list.dat', 'a+')
for task in all:
icsd_id = 'icsd-' + str(task['icsd_ids'][0])
if icsd_id not in ids:
continue
try:
struct = Structure.from_dict(task['structure'])
pbe_bs = BandStructureSymmLine.from_dict(
task['band_structures']['line'])
is_spin_polarized = pbe_bs.is_spin_polarized
k_vbm = pbe_bs.get_vbm()['kpoint']._fcoords
k_cbm = pbe_bs.get_cbm()['kpoint']._fcoords
except:
f.write('all[' + str(all.index(task)) + ']')
continue
##########################################################
njobs = njobs + 1
queue_hse = {}
queue_pbesol = {}
queue_hse['job_name'] = icsd_id + '_HSE'
queue_pbesol['job_name'] = icsd_id + '_PBEsol'
nsites = struct.num_sites
if nsites <= 5:
queue_pbesol['ntasks'] = 6
queue_pbesol['walltime'] = '6:00:00'
queue_hse['ntasks'] = 12
queue_hse['walltime'] = '24:00:00'
elif 5 < nsites <= 10:
queue_pbesol['ntasks'] = 12
queue_pbesol['walltime'] = '6:00:00'
queue_hse['ntasks'] = 24
queue_hse['walltime'] = '48:00:00'
elif 10 < nsites <= 20:
queue_pbesol['ntasks'] = 12
queue_pbesol['walltime'] = '24:00:00'
queue_hse['ntasks'] = 48
queue_hse['walltime'] = '48:00:00'
elif 20 < nsites <= 50:
queue_pbesol['ntasks'] = 24
queue_pbesol['walltime'] = '48:00:00'
queue_hse['ntasks'] = 60
queue_hse['walltime'] = '72:00:00'
else:
queue_pbesol['ntasks'] = 36
queue_pbesol['walltime'] = '48:00:00'
queue_hse['ntasks'] = 96
queue_hse['walltime'] = '72:00:00'
queue_insert = {}
queue_insert['ntasks'] = 1
queue_insert['walltime'] = '01:00:00'
queue_insert['vmem'] = '1024mb'
queue_insert['job_name'] = icsd_id + '_Insert'
##########################################################
if pbe_bs.get_band_gap()['direct']:
ks_add = [k_vbm]
else:
ks_add = [k_vbm, k_cbm]
ftask00 = Generate_VaspInputFiles_for_Relax_with_PBEsol_icsd()
ftask01 = VaspRun()
fw0 = Firework(
[ftask00, ftask01],
spec={
'_pass_job_info': True,
'_preserve_fworker': True,
'_fworker': fworker,
'vasp_cmd': vasp_cmd,
'workdir': './',
'structure': struct,
'icsd_id': icsd_id,
'is_spin_polarized': is_spin_polarized,
'_queueadapter': queue_pbesol
},
name=icsd_id + '_pbesol')
ftask10 = Generate_VaspInputFiles_for_HSE_scf_icsd()
ftask11 = VaspRun()
fw1 = Firework(
[ftask10, ftask11],
parents=[fw0],
spec={
'_pass_job_info': True,
'_preserve_fworker': True,
'_fworker': fworker,
'vasp_cmd': vasp_cmd,
'workdir': './',
'icsd_id': icsd_id,
'ks_add': ks_add,
'is_spin_polarized': is_spin_polarized,
'_queueadapter': queue_hse
},
name=icsd_id + '_HSE')
finsert = Insert_Gap_into_monogdb_icsd()
fw2 = Firework([finsert],
parents=[fw1],
spec={
'icsd_id': icsd_id,
'_queueadapter': queue_insert,
'pbe_bs': pbe_bs
},
name=icsd_id + '_Insert')
fws.append(fw0)
fws.append(fw1)
fws.append(fw2)
wf = Workflow(fws, name='HSE_Gap_for_icsds')
launchpad.add_wf(wf)
f.close()
return njobs
def setUp(self):
with open(os.path.join(test_dir, "CaO_2605_bandstructure.json"),
"rb") as f:
d = json.loads(f.read())
self.bs = BandStructureSymmLine.from_dict(d)
self.plotter = BSPlotter(self.bs)
