def setUp(self):
self.Al2O3_xane_1 = XANES(Al2O3_spect['x'], Al2O3_spect['y'], Al2O3_stru, Element('Al'), 'K')
self.Al2O3_xane_2 = deepcopy(self.Al2O3_xane_1)
self.Al2O3_xane_2.x = self.Al2O3_xane_2.x - 40
self.Al2O3_xane_left_shift5 = deepcopy(self.Al2O3_xane_1)
self.Al2O3_xane_left_shift5.x = self.Al2O3_xane_left_shift5.x - 5
self.Al2O3_xane_right_shift5 = deepcopy(self.Al2O3_xane_1)
self.Al2O3_xane_right_shift5.x = self.Al2O3_xane_right_shift5.x + 5
self.LiCoO2_xane = XANES(LiCoO2_spect['x'], LiCoO2_spect['y'], LiCoO2_stru, Element('Co'), 'K')
def msonify_xas(item):
energy = py_.pluck(item['spectrum'], 0) # (eV)
intensity = py_.pluck(item['spectrum'], 3) # (mu)
structure = Structure.from_dict(item['structure'])
absorption_specie = structure[item['absorbing_atom']].species_string
mid_and_el = ",".join([item["mp_id"], absorption_specie])
edge = "K"
structure.add_site_property(
'absorbing_atom',
[i == item['absorbing_atom'] for i, _ in enumerate(structure.sites)])
if len(energy) == 0:
return {
"spectrum": None,
"mid_and_el": mid_and_el,
"error": "Empty spectrum"
}
try:
out = {
"spectrum":
XANES(
x=energy,
y=intensity,
structure=structure,
absorption_specie=absorption_specie,
edge=edge,
).as_dict(),
"mid_and_el":
mid_and_el,
}
except ValueError as e:
out = {"spectrum": None, "mid_and_el": mid_and_el, "error": str(e)}
return out
def data_missing(xas_docs):
"""
Do some sites have no spectra recorded?
Checks symmetrically equivalent sites.
"""
xas_docs = [d for d in xas_docs if "error" not in d]
if len(xas_docs) == 0:
return "No docs at all"
spectra = [XANES.from_dict(d['spectrum']) for d in xas_docs]
absorption_specie = spectra[0].absorption_specie
ss = SymmSites(spectra[0].structure)
absorbing_atoms = set([
next(i for i, yes in enumerate(
s.structure.site_properties['absorbing_atom']) if yes)
for s in spectra
])
site_indices_with_absorption_specie = [
i for i, site in enumerate(spectra[0].structure.sites)
if site.species_and_occu.reduced_formula == absorption_specie
]
some_sites_absent = any(
len(set(ss.get_equivalent_site_indices(i)) & absorbing_atoms) == 0
for i in site_indices_with_absorption_specie)
some_spectra_empty = any(len(s.energy) == 0 for s in spectra)
return ((some_sites_absent and ("absent sites", absorbing_atoms))
or (some_spectra_empty and "empty spectra"))
def site_weighted_spectrum(xas_docs, num_samples=200):
"""
Equivalent-site-weighted spectrum for a specie in a structure.
Args:
xas_docs (list): MongoDB docs for all XAS XANES K-edge spectra
for a specie for a structure.
num_samples (int): Number of samples for interpolation.
Original data has 100 data points.
Returns:
tuple: a plottable (x, y) pair for the spectrum
"""
maxes, mins = [], []
fs = []
multiplicities = []
absorbing_atoms = set()
spectra = [XANES.from_dict(d['spectrum']) for d in xas_docs]
for spectrum in spectra:
# Checking the multiplicities of sites
structure = spectrum.structure
sa = SpacegroupAnalyzer(structure)
ss = sa.get_symmetrized_structure()
absorbing_atom = next(i for i, yes in enumerate(
structure.site_properties['absorbing_atom']) if yes)
multiplicity = len(ss.find_equivalent_sites(structure[absorbing_atom]))
multiplicities.append(multiplicity)
# Getting axis limits for each spectrum for the sites corresponding to
# K-edge is a bit tricky, because the x-axis data points don't align
# among different spectra for the same structure. So, prepare for
# interpolation within the intersection of x-axis ranges.
mins.append(spectrum.energy[0])
maxes.append(spectrum.energy[-1])
# 3rd-order spline interpolation
f = interp1d(spectrum.energy,
spectrum.intensity,
kind='cubic',
bounds_error=False,
fill_value=0)
fs.append(f)
absorbing_atoms |= set(
SymmSites(structure).get_equivalent_site_indices(absorbing_atom))
energy = np.linspace(max(mins), min(maxes), num=num_samples)
weighted_intensity = np.zeros(num_samples)
sum_multiplicities = sum(multiplicities)
for i in range(len(multiplicities)):
weighted_intensity += (multiplicities[i] *
fs[i](energy)) / sum_multiplicities
structure = spectra[0].structure
structure.remove_site_property('absorbing_atom')
structure.add_site_property(
'absorbing_atom',
[i in absorbing_atoms for i, _ in enumerate(structure.sites)])
return XANES(
x=energy,
y=weighted_intensity,
structure=structure,
absorption_specie=spectra[0].absorption_specie,
edge=spectra[0].edge,
)
def setUp(self):
self.xanes = XANES.from_dict(spect_data_dict)
def test_to_from_dict(self):
s = XANES.from_dict(self.xanes.as_dict())
self.assertArrayAlmostEqual(s.y, self.xanes.y)
def setUp(self):
self.xanes = XANES.from_dict(spect_data_dict)
def test_to_from_dict(self):
s = XANES.from_dict(self.xanes.as_dict())
self.assertArrayAlmostEqual(s.y, self.xanes.y)
def compare_my_unknown(fname,
mpid,
absorbing_atom,
data_dir=None,
dbroot=None,
xsrange=None,
ysrange=None):
here = os.getcwd()
if data_dir is None:
data_dir = global_cache['data_dir']
os.chdir(data_dir)
if not os.path.isfile(fname):
print(
fname +
' is not found in unknowns folder.\n Please put it here as two-column text data.\n Exitting....'
)
os.chdir(here)
return
if dbroot is None:
dbroot = t4iss_defaults['t4iss_data']
if not os.path.isdir(dbroot):
os.mkdir(dbroot)
os.chdir(dbroot)
if not os.path.isdir(mpid):
print('XANES for ' + mpid +
' is NOT available in local database\n Exitting....')
os.chdir(here)
return
else:
os.chdir(mpid)
ux, uy = np.loadtxt(join(data_dir, fname),
unpack=True,
comments='#',
usecols=(0, 1),
skiprows=0)
uy = uy - uy[0]
uy = uy / max(uy)
structure = mg.Structure.from_file("CONTCAR")
finder = SpacegroupAnalyzer(structure)
symmetrized_structure = finder.get_symmetrized_structure()
[
sites, indices
] = symmetrized_structure.equivalent_sites, symmetrized_structure.equivalent_indices
spectra = []
for i, s in enumerate(sites):
if s[0].species_string is absorbing_atom:
f = 'feff_{:03d}_{}'.format(indices[i][0] + 1, absorbing_atom)
if os.path.isdir(f):
os.chdir(f)
if os.path.isfile('xanes.pkl'):
xanes = pickle.load(open('xanes.pkl', 'rb'))
elif os.path.isfile('xmu.dat'):
abs_specie = absorbing_atom
x, y = np.loadtxt('xmu.dat',
unpack=True,
comments='#',
usecols=(0, 3),
skiprows=0)
xanes = XANES(x, y, structure, Element(abs_specie), 'K')
pickle.dump(xanes, open('xanes.pkl', 'wb'))
else:
xanes = []
s_weight = len(indices[i])
local_environment = symmetrized_structure.get_sites_in_sphere(
symmetrized_structure[indices[i][0]].coords, 10.1)
spectra.append([s_weight, xanes, local_environment])
os.chdir('..')
else:
xanes = []
s_weight = len(indices[i])
local_environment = symmetrized_structure.get_sites_in_sphere(
symmetrized_structure[indices[i][0]].coords, 10.1)
spectra.append([s_weight, xanes, local_environment])
unknown_spectra = [ux, uy]
try:
os.chdir(here)
if xsrange is None:
xsrange = [-6.0, 6.0]
if ysrange is None:
ysrange = [-2.0, 2.0]
plot_XANES_with_unknown(spectra, mpid, unknown_spectra, xsrange,
ysrange)
except Exception as exc:
os.chdir(here)
print('Error: \n Unable to plot. Something is wrong...')
print(exc)
#os.chdir(here)
#plot_XANES_with_unknown(spectra,mpid,unknown_spectra,xsrange,ysrange)
return
def compare_two(mpid1, mpid2, absorbing_atom, dbroot=None):
here = os.getcwd()
if dbroot is None:
dbroot = t4iss_defaults['t4iss_data']
if not os.path.isdir(dbroot):
os.mkdir(dbroot)
os.chdir(dbroot)
if not os.path.isdir(mpid1):
print(
'XANES for ' + mpid1 +
' is NOT available in local database\n Try get_XANES function first \n Exitting....'
)
os.chdir(here)
return
if not os.path.isdir(mpid2):
print(
'XANES for ' + mpid2 +
' is NOT available in local database\n Try get_XANES function first \n Exitting....'
)
os.chdir(here)
return
os.chdir(mpid1)
structure = mg.Structure.from_file("CONTCAR")
finder = SpacegroupAnalyzer(structure)
symmetrized_structure = finder.get_symmetrized_structure()
[
sites, indices
] = symmetrized_structure.equivalent_sites, symmetrized_structure.equivalent_indices
spectra = []
for i, s in enumerate(sites):
if s[0].species_string is absorbing_atom:
f = 'feff_{:03d}_{}'.format(indices[i][0] + 1, absorbing_atom)
if os.path.isdir(f):
os.chdir(f)
if os.path.isfile('xanes.pkl'):
xanes = pickle.load(open('xanes.pkl', 'rb'))
elif os.path.isfile('xmu.dat'):
abs_specie = absorbing_atom
x, y = np.loadtxt('xmu.dat',
unpack=True,
comments='#',
usecols=(0, 3),
skiprows=0)
xanes = XANES(x, y, structure, Element(abs_specie), 'K')
pickle.dump(xanes, open('xanes.pkl', 'wb'))
else:
xanes = []
s_weight = len(indices[i])
local_environment = symmetrized_structure.get_sites_in_sphere(
symmetrized_structure[indices[i][0]].coords, 10.1)
spectra.append([s_weight, xanes, local_environment])
os.chdir('..')
else:
xanes = []
s_weight = len(indices[i])
local_environment = symmetrized_structure.get_sites_in_sphere(
symmetrized_structure[indices[i][0]].coords, 10.1)
spectra.append([s_weight, xanes, local_environment])
os.chdir('..')
spectra1 = spectra
os.chdir(mpid2)
structure = mg.Structure.from_file("CONTCAR")
finder = SpacegroupAnalyzer(structure)
symmetrized_structure = finder.get_symmetrized_structure()
[
sites, indices
] = symmetrized_structure.equivalent_sites, symmetrized_structure.equivalent_indices
spectra = []
for i, s in enumerate(sites):
if s[0].species_string is absorbing_atom:
f = 'feff_{:03d}_{}'.format(indices[i][0] + 1, absorbing_atom)
if os.path.isdir(f):
os.chdir(f)
if os.path.isfile('xanes.pkl'):
xanes = pickle.load(open('xanes.pkl', 'rb'))
elif os.path.isfile('xmu.dat'):
abs_specie = absorbing_atom
x, y = np.loadtxt('xmu.dat',
unpack=True,
comments='#',
usecols=(0, 3),
skiprows=0)
xanes = XANES(x, y, structure, Element(abs_specie), 'K')
pickle.dump(xanes, open('xanes.pkl', 'wb'))
else:
xanes = []
s_weight = len(indices[i])
local_environment = symmetrized_structure.get_sites_in_sphere(
symmetrized_structure[indices[i][0]].coords, 10.1)
spectra.append([s_weight, xanes, local_environment])
os.chdir('..')
else:
xanes = []
s_weight = len(indices[i])
local_environment = symmetrized_structure.get_sites_in_sphere(
symmetrized_structure[indices[i][0]].coords, 10.1)
spectra.append([s_weight, xanes, local_environment])
os.chdir('..')
spectra2 = spectra
try:
os.chdir(here)
plot_XANES_two_together(spectra1, mpid1, spectra2, mpid2)
except Exception as exc:
os.chdir(here)
print('Error: \n Unable to plot. Something is wrong...')
print(exc)
return
def get_XANES(mpr,
mpid,
absorbing_atom,
run_feff=None,
dbroot=None,
plot=None,
n_cpu=None,
export_figure=None):
here = os.getcwd()
# this is the package current directory
#here = os.path.dirname(os.path.realpath(__file__)) + "/.."
if dbroot is None:
dbroot = t4iss_defaults['t4iss_data']
if not os.path.isdir(dbroot):
os.mkdir(dbroot)
if run_feff is None:
run_feff = False
elif run_feff:
if os.name == 'nt':
print(
'Windows OS is not supported for run_feff=True \nSorry......')
run_feff = False
else:
rFMS = 8.1
rSCF = 6.1
corehole = 'RPA'
feff_cmd = global_cache['feff_cmd']
if plot is None:
plot = True
if n_cpu is None:
n_cpu = 2
if export_figure is None:
export_figure = False
os.chdir(dbroot)
if not os.path.isdir(mpid):
data = mpr._make_request(
'/xas/spectra_for', {
"material_ids": json.dumps([mpid]),
"elements": json.dumps([absorbing_atom])
})
if not data:
mp_xas_avail = False
if run_feff:
os.makedirs(mpid, exist_ok=True)
os.chdir(mpid)
else:
#print('XANES is not available in MP or local database.')
try:
structure = mpr.get_structure_by_material_id(mpid,
final=True)
os.makedirs(mpid, exist_ok=True)
os.chdir(mpid)
except:
print('structure for ' + mpid +
' is not available in MP.\nExitting....')
os.chdir(here)
return
else:
mp_xas_avail = True
data = mpr.get_data(mpid, data_type="feff", prop="xas")
os.makedirs(mpid, exist_ok=True)
os.chdir(mpid)
else:
os.chdir(mpid)
if not os.path.isfile('CONTCAR'):
structure = mpr.get_structure_by_material_id(mpid, final=True)
structure.to(fmt='poscar', filename='CONTCAR')
structure = mg.Structure.from_file("CONTCAR")
finder = SpacegroupAnalyzer(structure)
symmetrized_structure = finder.get_symmetrized_structure()
[
sites, indices
] = symmetrized_structure.equivalent_sites, symmetrized_structure.equivalent_indices
feff_todos = []
for i, s in enumerate(sites):
if s[0].species_string is absorbing_atom:
f = 'feff_{:03d}_{}'.format(indices[i][0] + 1, absorbing_atom)
if os.path.isdir(f):
os.chdir(f)
if not os.path.isfile('xanes.pkl'):
data = mpr._make_request(
'/xas/spectra_for', {
"material_ids": json.dumps([mpid]),
"elements": json.dumps([absorbing_atom])
})
if not data:
mp_xas_avail = False
else:
mp_xas_avail = True
if mp_xas_avail:
data = mpr.get_data(mpid, data_type="feff", prop="xas")
for xas_doc in data[0]['xas']:
abs_atom = xas_doc['absorbing_atom']
if abs_atom is indices[i][0]:
x, y = xas_doc['spectrum']
struct = xas_doc["structure"]
edge = xas_doc["edge"]
xanes = XANES(x,
y,
struct,
Element(absorbing_atom),
edge='K')
pickle.dump(xanes, open('xanes.pkl', 'wb'))
#out = np.column_stack( (x,y) )
#np.savetxt('xanes.dat', out, fmt="%10.3f %6.4e")
os.chdir('..')
elif os.path.isfile('xmu.dat'):
x, y = np.loadtxt('xmu.dat',
unpack=True,
comments='#',
usecols=(0, 3),
skiprows=0)
xanes = XANES(x, y, structure, Element(absorbing_atom),
'K')
pickle.dump(xanes, open('xanes.pkl', 'wb'))
os.chdir('..')
#out = np.column_stack( (x,y) )
#np.savetxt('xanes.dat', out, fmt="%10.3f %6.4e")
elif run_feff:
write_feffinp('../CONTCAR',
cai=indices[i][0],
dmax=rFMS + 2,
rFMS=rFMS,
rSCF=rSCF,
corehole=corehole)
feff_todos.append(os.getcwd())
os.chdir('..')
else:
os.chdir('..')
else:
data = mpr._make_request(
'/xas/spectra_for', {
"material_ids": json.dumps([mpid]),
"elements": json.dumps([absorbing_atom])
})
if data:
os.makedirs(f, exist_ok=True)
os.chdir(f)
data = mpr._make_request(
'/xas/spectra_for', {
"material_ids": json.dumps([mpid]),
"elements": json.dumps([absorbing_atom])
})
if not data:
mp_xas_avail = False
else:
mp_xas_avail = True
if mp_xas_avail:
data = mpr.get_data(mpid, data_type="feff", prop="xas")
for xas_doc in data[0]['xas']:
abs_atom = xas_doc['absorbing_atom']
if abs_atom is indices[i][0]:
x, y = xas_doc['spectrum']
struct = xas_doc["structure"]
edge = xas_doc["edge"]
xanes = XANES(x,
y,
struct,
Element(absorbing_atom),
edge='K')
pickle.dump(xanes, open('xanes.pkl', 'wb'))
#out = np.column_stack( (x,y) )
#np.savetxt('xanes.dat', out, fmt="%10.3f %6.4e")
os.chdir('..')
elif run_feff:
os.makedirs(f, exist_ok=True)
os.chdir(f)
write_feffinp('../CONTCAR',
cai=indices[i][0],
dmax=rFMS + 2,
rFMS=rFMS,
rSCF=rSCF,
corehole=corehole)
feff_todos.append(os.getcwd())
os.chdir('..')
else:
break
if run_feff:
chunks = [
feff_todos[i:i + n_cpu] for i in range(0, len(feff_todos), n_cpu)
]
for c in chunks:
f = open('feff.sh', "w+")
for i in c:
f.write('cd ' + i + '\n')
f.write(feff_cmd + ' &\n')
print('running feff at ' + i)
f.write('wait')
f.close()
subprocess.call(' chmod +x feff.sh ', shell=True)
subprocess.call(' ./feff.sh ', shell=True)
if os.path.exists('feff.sh'): os.remove('feff.sh')
spectra = []
for i, s in enumerate(sites):
if s[0].species_string is absorbing_atom:
f = 'feff_{:03d}_{}'.format(indices[i][0] + 1, absorbing_atom)
if os.path.isdir(f):
os.chdir(f)
if os.path.isfile('xanes.pkl'):
xanes = pickle.load(open('xanes.pkl', 'rb'))
elif os.path.isfile('xmu.dat'):
abs_specie = absorbing_atom
x, y = np.loadtxt('xmu.dat',
unpack=True,
comments='#',
usecols=(0, 3),
skiprows=0)
xanes = XANES(x, y, structure, Element(abs_specie), 'K')
pickle.dump(xanes, open('xanes.pkl', 'wb'))
#out = np.column_stack( (x,y) )
#np.savetxt('xanes.dat', out, fmt="%10.3f %6.4f")
else:
xanes = []
s_weight = len(indices[i])
local_environment = symmetrized_structure.get_sites_in_sphere(
symmetrized_structure[indices[i][0]].coords, 10.1)
spectra.append([s_weight, xanes, local_environment])
os.chdir('..')
else:
xanes = []
s_weight = len(indices[i])
local_environment = symmetrized_structure.get_sites_in_sphere(
symmetrized_structure[indices[i][0]].coords, 10.1)
spectra.append([s_weight, xanes, local_environment])
if plot:
try:
os.chdir(here)
plot_XANES(spectra, mpid, export_figure)
except Exception as exc:
print('Error: \n Unable to plot. Something is wrong...')
print(exc)
os.chdir(here)
return
os.chdir(here)
return