niter1 = calc.get_number_of_iterations()
calc.write('lead.gpw')
dump_lead_hs(calc, 'lead')
# Tip calculation
tip = atoms.copy()
tip.positions[:] += (atoms.cell / 2.0)[0, :] + (atoms.cell / 2.0)[1, :]
del tip[:4]
tip.translate([0, 0, 10])
tip.cell[2, 2] += 10
calc.set(kpts=(1, 1, 1))
tip.set_calculator(calc)
e2 = tip.get_potential_energy()
niter2 = calc.get_number_of_iterations()
calc.write('tip.gpw')
dump_hs(calc, 'tip', region='tip', cvl=2)
# Surface calculation
srf = atoms.copy()
del srf[8:]
srf.cell[2, 2] += 10
srf.set_calculator(calc)
e3 = srf.get_potential_energy()
niter3 = calc.get_number_of_iterations()
calc.write('srf.gpw', region='surface', cvl=2)
dump_hs(calc, 'srf', region='surface', cvl=2)
#STM simulation
tip = GPAW('tip')
srf = GPAW('srf')
# surface calculation
a = 4.0
srf = fcc100('Al', size=(2, 2, 10), vacuum=8.0)
srf.translate([0, 0, -4])
srf.pbc = (1, 1, 0)
srf += Atom('H', (a / 2**.5, a / 2**.5, srf.positions[-1][2] + 1.55))
srf.set_calculator(calc)
srf.get_potential_energy()
calc.write('srf')
# Dump the overlap matrix and the Hamiltonian matrix to the local directory.
# Here the keyword 'cvl' refers to the number of basis functions in the
# in the convergence layer, i.e. for the present system four atomic layers are used.
dump_hs(calc, 'srf', region='surface', cvl=4 * 4 * 9)
# tip calculation
a = 0.75 # lattice constant
tip = Atoms('H12', pbc=(1, 1, 0), cell=[5, 5, 12 * a + 7])
tip.positions[:, 2] = [i * a for i in range(12)]
tip.positions[:] += (tip.cell / 2.0)[0, :] + (tip.cell / 2.0)[1, :]
tip.translate([0, 0, 6])
tip.set_calculator(calc)
tip.get_potential_energy()
calc.write('tip')
dump_hs(calc, 'tip', region='tip',
cvl=4) # dump overlap and hamiltonian matrix
calc.set(
niter1 = calc.get_number_of_iterations()
calc.write('lead.gpw')
dump_lead_hs(calc, 'lead')
# Tip calculation
tip = atoms.copy()
tip.positions[:] += (atoms.cell / 2.0)[0, :] + (atoms.cell / 2.0)[1, :]
del tip[:4]
tip.translate([0, 0, 10])
tip.cell[2, 2] += 10
calc.set(kpts=(1, 1, 1))
tip.set_calculator(calc)
e2 = tip.get_potential_energy()
niter2 = calc.get_number_of_iterations()
calc.write('tip.gpw')
dump_hs(calc, 'tip', region='tip', cvl=2)
# Surface calculation
srf = atoms.copy()
del srf[8:]
srf.cell[2, 2] += 10
srf.set_calculator(calc)
e3 = srf.get_potential_energy()
niter3 = calc.get_number_of_iterations()
calc.write('srf.gpw', region='surface', cvl=2)
dump_hs(calc, 'srf', region='surface', cvl=2)
#STM simulation
tip = GPAW('tip')
srf = GPAW('srf')
niter1 = calc.get_number_of_iterations()
calc.write("lead.gpw")
dump_lead_hs(calc, "lead")
# Tip calculation
tip = atoms.copy()
tip.positions[:] += (atoms.cell / 2.0)[0, :] + (atoms.cell / 2.0)[1, :]
del tip[:4]
tip.translate([0, 0, 10])
tip.cell[2, 2] += 10
calc.set(kpts=(1, 1, 1))
tip.set_calculator(calc)
e2 = tip.get_potential_energy()
niter2 = calc.get_number_of_iterations()
calc.write("tip.gpw")
dump_hs(calc, "tip", region="tip", cvl=2)
# Surface calculation
srf = atoms.copy()
del srf[8:]
srf.cell[2, 2] += 10
srf.set_calculator(calc)
e3 = srf.get_potential_energy()
niter3 = calc.get_number_of_iterations()
calc.write("srf.gpw", region="surface", cvl=2)
dump_hs(calc, "srf", region="surface", cvl=2)
# STM simulation
tip = GPAW("tip")
srf = GPAW("srf")
# surface calculation
a = 4.0
srf = fcc100('Al', size=(2, 2, 10), vacuum=8.0)
srf.translate([0, 0, -4])
srf.pbc= (1, 1, 0)
srf += Atom('H', (a / 2**.5, a / 2**.5, srf.positions[-1][2] + 1.55))
srf.set_calculator(calc)
srf.get_potential_energy()
calc.write('srf')
# Dump the overlap matrix and the Hamiltonian matrix to the local directory.
# Here the keyword 'cvl' refers to the number of basis functions in the
# in the convergence layer, i.e. for the present system four atomic layers are used.
dump_hs(calc, 'srf', region='surface', cvl=4*4*9)
# tip calculation
a = 0.75 # lattice constant
tip = Atoms('H12', pbc=(1, 1, 0), cell=[5, 5, 12 * a + 7])
tip.positions[:,2] = [i * a for i in range(12)]
tip.positions[:] += (tip.cell / 2.0)[0, :] + (tip.cell / 2.0)[1, :]
tip.translate([0, 0, 6])
tip.set_calculator(calc)
tip.get_potential_energy()
calc.write('tip')
dump_hs(calc, 'tip', region='tip', cvl=4) # dump overlap and hamiltonian matrix
calc.set(kpts=(1, 1, 7)) # for the lead calculations we use kpoints in the z-direction
