def fill_db(filename, npoints):
if exists_and_isfile(filename) is True:
os.remove(filename)
ho = HarmonicOscillator()
model = PyrazineSala({'n_states': 3})
nmodes = len(model.crd)
nstates = 3
db = PySurfDB.generate_database(filename,
data=['crd', 'energy'],
dimensions={
'nmodes': nmodes,
'nstates': nstates
},
model=True)
x = (np.random.random((npoints, nmodes)) - 0.5) * 20
y = []
for r in x:
db.append('crd', r)
y += [
model.get(Request(r, ['energy'],
[i for i in range(nstates)]))['energy']
]
db.append(
'energy',
model.get(Request(r, ['energy'],
[i for i in range(nstates)]))['energy'])
db.increase
return 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