def test1(self):
np.random.seed(0)
pot = LJ()
neb = NEBDriver(pot, _x1, _x2, adjustk_freq=10, adaptive_nimages=True, adaptive_niter=True, reinterpolate=10)
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()
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 test1(self):
from pele.storage import Database
from pele.systems import LJCluster
np.random.seed(0)
pot = LJ()
neb = NEBDriver(pot, _x1, _x2, adjustk_freq=10, adaptive_nimages=True, adaptive_niter=True, reinterpolate=10)
neb.run()
def test1(self):
np.random.seed(0)
pot = LJ()
neb = NEBDriver(pot,
_x1,
_x2,
adjustk_freq=10,
adaptive_nimages=True,
adaptive_niter=True,
reinterpolate=10)
neb.run()
def createNEB(self, coords1, coords2, **kwargs):
pot = self.get_potential()
NEBparams = self.params.double_ended_connect.local_connect_params.NEBparams.copy(
)
NEBparams.update(kwargs)
return NEBDriver(pot, coords1, coords2, verbose=True, **NEBparams)
def construct_neb_configs(base_path, coords_list):
potential = setup_inverse_power_from_folder(base_path)
x1 = coords_list[0].flatten()
x2 = coords_list[1].flatten()
x3 = coords_list[2].flatten()
neb1 = NEBDriver(
potential,
x1,
x2,
adjustk_freq=10,
adaptive_nimages=True,
adaptive_niter=True,
reinterpolate=10,
)
neb2 = NEBDriver(
potential,
x2,
x3,
adjustk_freq=10,
adaptive_nimages=True,
adaptive_niter=True,
reinterpolate=10,
)
neb3 = NEBDriver(
potential,
x3,
x1,
adjustk_freq=10,
adaptive_nimages=True,
adaptive_niter=True,
reinterpolate=10,
)
neb1.run()
neb2.run()
neb3.run()
print(neb1.path)
print(neb2.path)
print(neb3.path)
