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 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 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_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()