atoms.center() pl_atoms1 = range(4) pl_atoms2 = range(8, 12) pl_cell1 = (L, L, 4 * a) pl_cell2 = pl_cell1 t = Transport(h=0.3, xc='LDA', basis={'Na': basis}, kpts=(1,1,1), occupations=FermiDirac(0.1), mode='lcao', poissonsolver=PoissonSolver(nn=2, relax='GS'), txt='Na_lcao.txt', mixer=Mixer(0.1, 5, weight=100.0), guess_steps=10, fix_contour=True, pl_atoms=[pl_atoms1, pl_atoms2], pl_cells=[pl_cell1, pl_cell2], pl_kpts=(1,1,16), fixed_boundary=False, analysis_data_list=['tc'], edge_atoms=[[0, 3], [0, 11]], mol_atoms=range(4, 8)) atoms.set_calculator(t) t.calculate_to_bias(0.0, 1) qn=QuasiNewton(atoms, trajectory='transport.traj') qn.run(fmax=0.05)
atoms.positions[:, :2] = L / 2. atoms.center() pl_atoms1 = range(4) pl_atoms2 = range(8, 12) pl_cell1 = (L, L, 4 * a) pl_cell2 = pl_cell1 t = Transport(h=0.3, xc='LDA', basis={'Na': basis}, kpts=(1, 1, 1), occupations=FermiDirac(0.1), mode='lcao', poissonsolver=PoissonSolver(nn=2, relax='GS'), txt='Na_lcao.txt', mixer=Mixer(0.1, 5, weight=100.0), guess_steps=10, fix_contour=True, pl_atoms=[pl_atoms1, pl_atoms2], pl_cells=[pl_cell1, pl_cell2], pl_kpts=(1, 1, 16), fixed_boundary=False, analysis_data_list=['tc'], edge_atoms=[[0, 3], [0, 11]], mol_atoms=range(4, 8)) atoms.set_calculator(t) t.calculate_to_bias(0.0, 1) qn = QuasiNewton(atoms, trajectory='transport.traj') qn.run(fmax=0.05)