def setUp(self):
nmin = 10
natoms = 13
sys = LJCluster(natoms)
pot = sys.get_potential()
mindist = sys.get_mindist()
db = create_random_database(nmin=nmin,
natoms=natoms,
nts=old_div(nmin, 2))
min1, min2 = list(db.minima())[:2]
self.db = db
self.natoms = natoms
self.connect = DoubleEndedConnect(min1,
min2,
pot,
mindist,
db,
merge_minima=True,
max_dist_merge=1e100)
# for ts in db.transition_states():
# self.add_ts(ts.energy, ts.coords,
# ts.minimum1.energy, ts.minimum1.coords,
# ts.minimum2.energy, ts.minimum2.coords)
for m in db.minima():
self.connect.dist_graph.addMinimum(m)
def get_double_ended_connect(self, min1, min2, database, **kwargs):
"""return a DoubleEndedConnect object
See Also
--------
pele.landscape
"""
kwargs = dict_copy_update(self.params["double_ended_connect"], kwargs)
pot = self.get_potential()
mindist = self.get_mindist()
# attach the function which orthogonalizes to known zero eigenvectors.
# This is amazingly ugly
# vr: yea, we should polish this parameters stuff and give create policies instead!
try:
kwargs["local_connect_params"]["tsSearchParams"]["orthogZeroEigs"]
except KeyError:
if "local_connect_params" in kwargs:
lcp = kwargs["local_connect_params"]
else:
lcp = kwargs["local_connect_params"] = BaseParameters()
if "tsSearchParams" in lcp:
tssp = lcp["tsSearchParams"]
else:
tssp = lcp["tsSearchParams"] = BaseParameters()
if not "orthogZeroEigs" in tssp:
tssp[
"orthogZeroEigs"] = self.get_orthogonalize_to_zero_eigenvectors(
)
try:
kwargs["local_connect_params"]["pushoff_params"]["quench"]
except Exception:
if not "pushoff_params" in kwargs["local_connect_params"]:
kwargs["local_connect_params"][
"pushoff_params"] = BaseParameters()
kwargs["local_connect_params"]["pushoff_params"][
"quench"] = self.get_minimizer()
return DoubleEndedConnect(min1, min2, pot, mindist, database, **kwargs)
def test2(self):
from pele.storage import Database
from pele.systems import LJCluster
np.random.seed(0)
natoms = 13
system = LJCluster(natoms)
pot = system.get_potential()
mindist = system.get_mindist(niter=1)
db = Database()
db.addMinimum(pot.getEnergy(_x1), _x1)
db.addMinimum(pot.getEnergy(_x2), _x2)
m1, m2 = db.minima()
connect = DoubleEndedConnect(m1, m2, pot, mindist, db, verbosity=10)
connect.connect()
self.assertTrue(connect.success())
path = connect.returnPath()
tsSearchParams["nfail_max"] = 200
NEBquenchParams = dict()
NEBquenchParams["iprint"] = 100
NEBparams = dict()
NEBparams["k"] = 5.
NEBparams["image_density"] = 15
NEBparams["NEBquenchParams"] = NEBquenchParams
local_connect_params = dict()
local_connect_params["tsSearchParams"] = tsSearchParams
local_connect_params["NEBparams"] = NEBparams
myconnect = DoubleEndedConnect(min1, min2, pot, mindist, database,
local_connect_params=local_connect_params,
)
if (myconnect.graph.areConnected(min1, min2)):
print "ALERT: The minima are already connected in the database file", dbfile
print " Delete it for a fresh run."
myconnect.connect()
print ""
print "found a path!"
# the path is now saved in the database. Lets retrieve it and
# print it in a more visual format
# now retrieve the path for printing
