def update_system_details(self, h5f):
"""
Updates system element list, sources list, and entries
in hdf5.
Args:
h5f: h5py object.
"""
entries = np.asarray(self.entries)
energy_indices = np.asarray([float(x) for x in entries[:, -1]])
entries = entries[np.lexsort((energy_indices, entries[:, 3]))]
entries = np.asarray([b';'.join(line) for line in entries])
sources = np.string_(self.sources)
write_to_group(h5f,
'system',
{'sys_elements': np.string_(self.sys_elements)}, {
'collated_entries': entries,
'collated_sources': sources
},
dset_types={
'collated_entries': entries.dtype,
'collated_sources': sources.dtype
},
maxshape=(None, ))
self.summary()
def to_file(self, filename):
"""
Write preprocessed fingerprints to file.
Args:
filename (str): Output file (e.g. preprocessed.h5).
"""
assert self.standards # ensure preprocess_fingerprints() completed
libver = self.settings['libver']
with h5py.File(filename, 'w', libver=libver) as h5f:
energies = np.asarray(self.m_energies)
element_counts = np.asarray(self.m_element_counts)
m_names = np.string_(self.m_names.tolist())
write_to_group(h5f,
'preprocessed', {}, {
'energies': energies,
'element_counts': element_counts,
'all': self.all,
'm_names': m_names
},
dset_types={
'energies': energies.dtype,
'element_counts': element_counts.dtype,
'all': self.all.dtype,
'm_names': m_names.dtype
})
scaling_standards = {
'standard_{}'.format(j): standard
for j, standard in enumerate(self.standards)
}
write_to_group(h5f, 'system',
{'sys_elements': np.string_(self.sys_elements)},
scaling_standards)
def to_file(self, h5o, path):
"""
Save collated molecule to file.
Args:
h5o: h5py object for writing.
path (str): Path to molecule subgroup.
e.g. 'molecules/au55.1.2'
"""
write_to_group(h5o, path, self.attrs_dict, self.dsets_dict)
data = [
np.string_(path.split('/')[-1]),
np.string_(str(np.sum(self.element_counts))),
np.string_('-'.join([str(x) for x in self.element_counts])),
np.string_(str(self.periodic)),
np.string_(str(self.coords.shape).replace(',', '-')),
np.string_(self.energy_val)
]
return data
def update_system_details(self, h5f):
"""
Updates system element list, descriptor parameters, and entries
in hdf5.
Args:
h5f: h5py object.
"""
entries = np.asarray([b';'.join(entry) for entry in self.entries])
write_to_group(h5f, 'system',
{'sys_elements': np.string_(self.sys_elements)}, {
'pair_params': self.parameters[0],
'triplet_params': self.parameters[1]
})
write_to_group(h5f,
'system', {}, {'fingerprint_entries': entries},
dset_types={'fingerprint_entries': entries.dtype},
maxshape=(None, ))
self.summary()
def to_file(self, h5o, path):
"""
Save fingerprint to file.
Args:
h5o: h5py object for writing.
path (str): Path to molecule subgroup
e.g. 'fingerprints/Au55.1.2'
"""
write_to_group(h5o, path, self.attrs_dict, self.dsets_dict)
data = [
np.string_(path.split('/')[-1]),
np.string_(str(self.natoms)),
np.string_('-'.join(self.elements_set)),
np.string_('-'.join([str(x) for x in self.element_counts])),
self.fingerprint_shapes,
np.string_(self.energy_val)
]
return data