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 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 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)