def __init__(self, config):
setup = SubfolderHandle(config['folder'], config['subfolder'])
counter = 0
for file in setup.fileiter(config['dbfiles']):
if counter == 0:
copied = False
if not exists_and_isfile(config['mother_db']):
copy(file, config['mother_db'])
copied = True
info = PySurfDB.info_database(config['mother_db'])
if 'natoms' not in info['dimensions']:
model = True
else:
model = False
mother_db = PySurfDB.load_database(
config['mother_db'],
data=info['variables'],
dimensions=info['dimensions'],
model=model,
sp=False)
counter += 1
if copied is True:
continue
CombineDBs(mother_db, file, start=config['start_value'])
print(f"Added file {file} to DB")
def __init__(self, config):
dbin = PySurfDB.load_database(config['db_in'], read_only=True)
info = PySurfDB.info_database(config['db_in'])
self.thresh = config['energy_threshold']
self.trust_radius_general = config['trust_radius_general']
self.trust_radius_ci = config['trust_radius_ci']
self.crd_mode = config['crd_mode']
if 'natoms' in info['dimensions']:
model = False
else:
model = True
dbout = PySurfDB.generate_database(config['db_out'],
data=info['variables'],
dimensions=info['dimensions'],
model=model)
self.crds = None
for i, crd in enumerate(dbin['crd']):
if self.crd_mode == 'internal':
crd = internal(np.copy(crd))
else:
crd = np.copy(crd)
if i % 1000 == 0:
print(f"Processing point {i}")
crd_shape = crd.shape
crd.resize((1, crd.size))
if self.crds is None:
self.crds = crd.reshape((1, crd.size))
else:
diff = np.diff(dbin.get('energy', i))
_, (trust_general, trust_ci) = within_trust_radius(
crd,
self.crds,
radius=self.trust_radius_general,
radius_ci=self.trust_radius_ci,
metric='euclidean')
if np.min(diff) < self.thresh:
if trust_ci is True:
continue
else:
if trust_general is True:
continue
self.crds = np.concatenate((self.crds, crd))
crd.resize(crd_shape)
for prop in info['variables']:
dbout.append(prop, dbin.get(prop, i))
dbout.increase
def __init__(self, main_db, added_db, start=0):
if not isinstance(main_db, PySurfDB):
info = PySurfDB.info_database(main_db)
if 'natoms' in info['dimensions']:
model = False
else:
model = True
main_db = PySurfDB.load_database(main_db,
dimensions=info['dimensions'],
data=info['variables'],
model=model)
if not isinstance(added_db, PySurfDB):
added_db = PySurfDB.load_database(added_db, read_only=True)
keys_raw = main_db.get_keys()
keys = []
for key in keys_raw:
if main_db.get_dimension(key)[0].isunlimited() is True:
keys += [key]
#check whether dbs fit together
check = True
for key in keys:
if key in added_db.get_keys():
for dim1, dim2 in zip(
main_db.get_dimension(key)[1:],
added_db.get_dimension(key)[1:]):
if dim1.size != dim2.size:
check = False
else:
check = False
if check is False:
print('Error DBs do not fit together by dimensions')
exit()
# nn = NextNeighbor(db1)
for i in range(start, len(added_db)):
# min_dist = nn.get(crd)
# if min_dist[0] > 0.25:
for key in keys:
main_db.append(key, added_db[key][i])
main_db.increase