def __call__(self, parser, ns, value, option_string=None):
out = value[0]
try:
# We figure out if the user wants to write
# to a geometry
obj = get_sile(out, mode='w')
if hasattr(obj, 'write_geometry'):
with obj as fh:
fh.write_geometry(ns._geometry)
return
raise NotImplementedError
except:
pass
if len(ns._data) == 0:
ns._data.append(ns._E)
ns._data_header.append('Energy[eV]')
ns._data.append(ns._PDOS_filter(ns._PDOS).sum(0))
if ns._PDOS_filter_name is not None:
ns._data_header.append(
f"DOS[spin={ns._PDOS_filter_name}][1/eV]")
else:
ns._data_header.append("DOS[1/eV]")
from sisl.io import tableSile
tableSile(out, mode='w').write(*ns._data,
comment=comment,
header=ns._data_header)
# Clean all data
ns._data = []
ns._data_header = []
ns._PDOS_filter_name = None
ns._PDOS_filter = _sum_filter
ns._Erng = None
def __call__(self, parser, ns, value, option_string=None):
out = value[0]
try:
# We figure out if the user wants to write
# to a geometry
obj = get_sile(out, mode='w')
if hasattr(obj, 'write_geometry'):
with obj as fh:
fh.write_geometry(ns._geometry)
return
raise NotImplementedError
except:
pass
if len(ns._data) == 0:
orbs = parse_atom_range(ns._geometry, f"1-{len(geometry)}")
ns._data.append(ns._E)
ns._data.append(ns._PDOS_filter(ns._PDOS)[orbs].sum(0))
ns._data_header.append("DOS[1/eV]")
from sisl.io import tableSile
tableSile(out, mode='w').write(*ns._data,
comment=comment,
header=ns._data_header)
# Clean all data
ns._data = []
ns._data_header = []
ns._PDOS_filter = _sum_filter
ns._Erng = None
def write(self, sile, *args, **kwargs):
""" Writes k-points to a `~sisl.io.tableSile`.
This allows one to pass a `tableSile` or a file-name.
"""
from sisl.io import tableSile
kw = np.concatenate((self.k, self.weight.reshape(-1, 1)), axis=1)
if isinstance(sile, tableSile):
sile.write_data(kw.T, *args, **kwargs)
else:
with tableSile(sile, 'w') as fh:
fh.write_data(kw.T, *args, **kwargs)
def __enter__(self):
""" Open the file and fill with stuff """
_log.debug(f"__enter__ {self.__class__.__name__}")
# check if the file exists
if self.out.exists():
# read in previous data
# this will be "[variables, runs]"
data, header = tableSile(self.out).read_data(ret_header=True)
else:
data = np.array([])
# check if the file exists
if self.out.exists() and data.size > 0:
nvars = data.shape[0] - 1
if nvars != len(self):
raise ValueError(
f"Found old file {self.out} which contains previous data for another number of parameters, please delete or move file"
)
# now parse header
*header, _ = header[1:].split()
idx = []
for name in self.names:
# find index in header
for i, head in enumerate(header):
if head == name:
idx.append(i)
break
if nvars != len(idx):
print(header)
print(self.names)
print(idx)
raise ValueError(
f"Found old file {self.out} which contains previous data with some variables being renamed, please correct header or move file"
)
# add functional value, no pivot
idx.append(len(self))
# re-arrange data (in case user swapped order of variables)
data = np.ascontiguousarray(data[idx].T)
x, y = data[:, :-1], data[:, -1]
# We populate with hashes without the functional
# That would mean we can't compare hashes between input arguments
# only make the first index a list (x.tolist() makes everything a list)
self.data.x = [xi for xi in x]
self.data.y = [yi for yi in y]
self.data.hash = list(map(self.get_hash, self.data.x))
# Re-open file (overwriting it)
# First output a few things in this file
comment = f"Created by sisl '{self.__class__.__name__}'."
header = self.names + ["metric"]
if len(self.data.x) == 0:
self._fh = tableSile(self.out, 'w').__enter__()
self._fh.write_data(comment=comment, header=header)
else:
comment += f" The first {len(self.data)} lines contains prior content."
data = np.column_stack((self.data.x, self.data.y))
self._fh = tableSile(self.out, 'w').__enter__()
self._fh.write_data(data.T,
comment=comment,
header=header,
fmt='20.17e')
self._fh.flush()
return self