def read_hdf5(fid,
variables=[
'geo_info', 'geo_spec_all', 'ao_spec', 'ao_spherical',
'mo_coeff_all', 'mo_energy_all', 'mo_occ_all', 'sym',
'index_list'
]):
'''Reads all variables specified in :literal:`variables` from an HDF5 file
created with :literal:`write_hdf5` and appends this data to the globals() of
this module.
'''
from orbkit.output import hdf5_open, hdf52dict
# Read HDF5 File
display('Reading Hierarchical Data Format file (HDF5) File from %s' % fid)
data_stored = []
for HDF5_file in hdf5_open(fid, mode='r'):
for i in variables:
try:
globals()[i] = hdf52dict(i, HDF5_file)
data_stored.append(i)
if i == 'sym':
s = dict(globals()[i])
globals()[i] = {}
for k, l in s.items():
globals()[i][k] = int(l)
except KeyError:
pass
if not data_stored:
raise IOError(
'Could not find any data in `%s` for the selected `variables`.' %
fid)
display('\tFound: ' + ', '.join(data_stored))
def hdf5_read(self,fid='out.h5',group='/ci:0'):
from orbkit.output import hdf5_open,hdf52dict
for hdf5_file in hdf5_open(fid,mode='r'):
for key in self.__dict__.keys():
try:
self.__dict__[key] = hdf52dict('%s/%s' % (group,key),hdf5_file)
except KeyError:
self.__dict__[key] = hdf5_file['%s' % group].attrs[key]
self.__dict__['info'] = dict(self.__dict__['info'])