def do_mindist(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
mindist = system.get_mindist()
m0 = db.minima()[0]
for m1 in db.minima()[1:6]:
d, x1, x2 = mindist(m0.coords, m1.coords)
print d
def setUp(self):
np.random.seed(0)
self.nmol = 4
self.system = OTPCluster(self.nmol)
pot = self.system.get_potential()
self.db = self.system.create_database()
self.m1 = self.db.addMinimum(pot.getEnergy(_x1), _x1)
self.m2 = self.db.addMinimum(pot.getEnergy(_x2), _x2)
def do_NEB(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
mindist = system.get_mindist()
pot = system.get_potential()
m1 = db.minima()[0]
for m2 in db.minima()[1:3]:
neb = NEBDriver(pot, m1.coords, m2.coords)
neb.run()
def do_connect(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
m1 = db.minima()[0]
for m2 in db.minima()[1:5]:
connect = system.get_double_ended_connect(m1,
m2,
db,
fresh_connect=True)
connect.connect()
def do_ts_search(nmol=20):
from pele.transition_states import findTransitionState
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
orthogopt = system.get_orthogonalize_to_zero_eigenvectors()
for ts in db.transition_states():
coords = db.transition_states()[0].coords.copy()
coords += np.random.uniform(-.5, .5, coords.size)
print system.params.double_ended_connect.local_connect_params.tsSearchParams
findTransitionState(coords,
system.get_potential(),
orthogZeroEigs=orthogopt,
**system.params.double_ended_connect.
local_connect_params.tsSearchParams)
def setUp(self):
np.random.seed(0)
self.nmol = 3
self.system = OTPCluster(self.nmol)
# pot = self.system.get_potential()
# self.db = self.system.create_database()
# self.m1 = self.db.addMinimum(pot.getEnergy(_x1), _x1)
# self.m2 = self.db.addMinimum(pot.getEnergy(_x2), _x2)
self.x0 = np.array([
0, 1, 2, 3, 4, 5, 6, 7, 8, 0.517892, 0.575435, 0.632979, 0.531891,
0.576215, 0.620539, 0.540562, 0.5766, 0.612637
])
from pele.angleaxis.aamindist import TransformAngleAxisCluster
self.topology = self.system.aatopology
self.transform = TransformAngleAxisCluster(self.topology)
self.p0 = np.array(list(range(1, 4)), dtype=float)
self.p0 /= np.linalg.norm(self.p0)
def get_random_rbcoords(self):
otp = OTPCluster(self.nrigid)
ret = otp.get_random_minimized_configuration(tol=100.)
return ret.coords
def getdb(nmol=20):
system = OTPCluster(nmol)
db = system.create_database("test.sqlte")
bh = system.get_basinhopping(db)
bh.run(20)