def map_raw_data_onto_grid(self, unfold=False, filter_tol=1e-5):
vlog('\nMapping raw n(k) data onto regular grid')
data = self.get_raw_data()
structure = self.get_attribute('structure', assigned=unfold)
if structure is not None:
kaxes = structure.kaxes
else:
kaxes = self.get_attribute('kaxes')
#end if
if filter_tol is not None:
vlog.increment()
data = self.filter_raw_data(filter_tol, store=False)
vlog.decrement()
#end if
if not unfold:
for s, sdata in data.items():
vlog('Mapping {} data onto grid'.format(s), n=1, time=True)
self[s] = grid_function(
points=sdata.k,
values=sdata.nk,
axes=kaxes,
)
#end for
else:
rotations = structure.point_group_operations()
for s, sdata in data.items():
if s == 'd' and 'u' in data and id(sdata) == id(data.u):
continue
#end if
vlog('Unfolding {} data'.format(s), n=1, time=True)
k = []
nk = []
ks = sdata.k
nks = sdata.nk
for n, R in enumerate(rotations):
vlog('Processing rotation {:<3}'.format(n), n=2, mem=True)
k.extend(np.dot(ks, R))
nk.extend(nks)
#end for
k = np.array(k, dtype=float)
nk = np.array(nk, dtype=float)
vlog('Unfolding finished', n=2, time=True)
vlog('Mapping {} data onto grid'.format(s), n=1, time=True)
vlog.increment(2)
self[s] = grid_function(
points=k,
values=nk,
axes=kaxes,
average=True,
)
vlog.decrement(2)
#end for
#end if
if 'd' not in self and 'u' in self:
self.d = self.u
#end if
vlog('Mapping complete', n=1, time=True)
vlog('Current memory: ', n=1, mem=True)
def read_xsf(self, filepath, component=None):
component = self.process_component_name(component)
vlog('Reading density data from XSF file for component "{}"'.format(
component),
time=True)
if isinstance(filepath, XsfFile):
vlog('XSF file already loaded, reusing data.')
xsf = filepath
copy_values = True
else:
vlog('Loading data from file', n=1, time=True)
vlog('file location: {}'.format(filepath), n=2)
vlog('memory before: ', n=2, mem=True)
xsf = XsfFile(filepath)
vlog('load complete', n=2, time=True)
vlog('memory after: ', n=2, mem=True)
copy_values = False
#end if
# read structure
if not self.has_attribute('structure'):
vlog('Reading structure from XSF data', n=1, time=True)
s = Structure()
s.read_xsf(xsf)
self.set_attribute('structure', s)
#end if
# read grid
if not self.has_attribute('grid'):
vlog('Reading grid from XSF data', n=1, time=True)
g = read_grid(xsf)
self.set_attribute('grid', g)
self.set_attribute('distance_units', 'B')
#end if
# read values
xsf.remove_ghost()
d = xsf.get_density()
values = d.values_noghost.ravel()
if copy_values:
values = values.copy()
#end if
# create grid function for component
vlog('Constructing grid function from XSF data', n=1, time=True)
f = grid_function(
type='parallelotope',
grid=self.grid,
values=values,
copy=False,
)
self.set_attribute(component, f)
self.set_attribute('distance_units', 'A')
vlog('Read complete', n=1, time=True)
vlog('Current memory:', n=1, mem=True)