def _load(self, filename):
fn = context.get_fn(filename)
members = []
with open(fn) as f:
state = 0
for line in f:
line = line[:line.find('#')].strip()
if len(line) > 0:
if state == 0:
# read element number
words = line.split()
number = int(words[0])
if len(words) > 1:
pseudo_number = int(words[1])
else:
pseudo_number = number
state = 1
elif state == 1:
# read rtf string
rtf = RTransform.from_string(line)
state = 2
elif state == 2:
nlls = np.array([int(w) for w in line.split()])
state = 0
members.append(
(number, pseudo_number, RadialGrid(rtf), nlls))
self._init_members_from_list(members)
def from_hdf5(cls, grp, lf):
records = []
for ds in grp.itervalues():
rtransform = RTransform.from_string(ds.attrs['rtransform'])
records.append((ds.attrs['number'], ds.attrs['pseudo_number'],
RadialGrid(rtransform), ds[:]))
return AtomicGridSpec(records)
def _load(self, filename):
fn = context.get_fn(filename)
members = []
with open(fn) as f:
state = 0
for line in f:
line = line[:line.find('#')].strip()
if len(line) > 0:
if state == 0:
# read element number
words = line.split()
number = int(words[0])
if len(words) > 1:
pseudo_number = int(words[1])
else:
pseudo_number = number
state = 1
elif state == 1:
# read rtf string
rtf = RTransform.from_string(line)
state = 2
elif state == 2:
nlls = np.array([int(w) for w in line.split()])
state = 0
members.append((number, pseudo_number, RadialGrid(rtf), nlls))
self._init_members_from_list(members)
def from_hdf5(cls, grp):
records = []
for ds in grp.itervalues():
rtransform = RTransform.from_string(ds.attrs['rtransform'])
records.append((
ds.attrs['number'], ds.attrs['pseudo_number'],
RadialGrid(rtransform), ds[:]
))
return AtomicGridSpec(records)
def load_proatom_records_h5_group(f):
'''Load proatom records from the given HDF5 group'''
records = []
for grp in f.itervalues():
assert isinstance(grp, h5.Group)
if 'deriv' in grp:
deriv = grp['deriv'][:]
else:
deriv = None
records.append(ProAtomRecord(
number=grp.attrs['number'],
charge=grp.attrs['charge'],
energy=grp.attrs['energy'],
rgrid=RadialGrid(RTransform.from_string(grp.attrs['rtransform'])),
rho=grp['rho'][:],
deriv=deriv,
pseudo_number=grp.attrs.get('pseudo_number'),
ipot_energy=grp.attrs.get('ipot_energy'),
))
return records
