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Scripts, Tutorials and Applications / Re: How could I modify the script to get its' I-V curve?
« on: April 1, 2009, 14:46 »
I have compute successfully with your script, then I create a script through the Nanolanguage Scripter, and I try my best to modify the script to get its' I-V curve as mentioned above ,but I couldn't get it.Could you helpe me ?Give me a simple demonstration with my script.
from ATK.TwoProbe import *
from ATK.MPI import processIsMaster
# Generate time stamp
if processIsMaster():
import platform, time
print '#',time.ctime()
print '#',platform.node(),platform.platform()+'\n'
# Opening vnlfile
if processIsMaster(): file = VNLFile('D:/fe-mgo-fe.vnl')
# Scattering elements and coordinates
scattering_elements = [Iron, Iron, Iron, Iron,
Oxygen, Oxygen, Oxygen, Oxygen,
Magnesium, Magnesium, Magnesium, Magnesium,
Iron, Iron, Iron, Iron]
scattering_coordinates = [[ 0.7165 , 0.7165 , 1.433 ],
[ 2.1495 , 2.1495 , 2.866 ],
[ 0.7165 , 0.7165 , 4.299 ],
[ 2.1495 , 2.1495 , 5.732 ],
[ 2.1495 , 2.1495 , 7.932 ],
[ 0.7165 , 0.7165 , 10.12735],
[ 2.1495 , 2.1495 , 12.3227 ],
[ 0.7165 , 0.7165 , 14.51805],
[ 0.7165 , 0.7165 , 7.932 ],
[ 2.1495 , 2.1495 , 10.12735],
[ 0.7165 , 0.7165 , 12.3227 ],
[ 2.1495 , 2.1495 , 14.51805],
[ 0.7165 , 0.7165 , 16.71805],
[ 2.1495 , 2.1495 , 18.15105],
[ 0.7165 , 0.7165 , 19.58405],
[ 2.1495 , 2.1495 , 21.01705]]*Angstrom
# Set up left electrode
left_electrode_elements = [Iron, Iron, Iron, Iron]
left_electrode_coordinates = [[ 0.7165, 0.7165, 0.7165],
[ 2.1495, 2.1495, 2.1495],
[ 0.7165, 0.7165, 3.5825],
[ 2.1495, 2.1495, 5.0155]]*Angstrom
left_electrode_cell = [[ 2.866, 0. , 0. ],
[ 0. , 2.866, 0. ],
[ 0. , 0. , 5.732]]*Angstrom
# Set up right electrode
right_electrode_elements = [Iron, Iron, Iron, Iron]
right_electrode_coordinates = [[ 0.7165, 0.7165, 0.7165],
[ 2.1495, 2.1495, 2.1495],
[ 0.7165, 0.7165, 3.5825],
[ 2.1495, 2.1495, 5.0155]]*Angstrom
right_electrode_cell = [[ 2.866, 0. , 0. ],
[ 0. , 2.866, 0. ],
[ 0. , 0. , 5.732]]*Angstrom
# Set up electrodes
left_electrode_configuration = PeriodicAtomConfiguration(
left_electrode_cell,
left_electrode_elements,
left_electrode_coordinates
)
right_electrode_configuration = PeriodicAtomConfiguration(
right_electrode_cell,
right_electrode_elements,
right_electrode_coordinates
)
# Set up two-probe configuration
twoprobe_configuration = TwoProbeConfiguration(
(left_electrode_configuration,right_electrode_configuration),
scattering_elements,
scattering_coordinates,
electrode_repetitions=[[1,1],[1,1]],
equivalent_atoms=([0,0],[3,15])
)
if processIsMaster(): nlPrint(twoprobe_configuration)
if processIsMaster(): file.addToSample(twoprobe_configuration, 'twoprobe_configuration')
######################################################################
# Central region parameters
######################################################################
exchange_correlation_type = LDA.PZ
iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)
electron_density_parameters = electronDensityParameters(
mesh_cutoff = 100.0*Rydberg
)
basis_set_parameters = basisSetParameters(
type = DoubleZetaPolarized,
radial_sampling_dr = 0.001*Bohr,
energy_shift = 0.01*Rydberg,
delta_rinn = 0.8,
v0 = 40.0*Rydberg,
charge = 0.0,
split_norm = 0.15
)
iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)
electrode_voltages = (0.0,0.0)*Volt
two_probe_algorithm_parameters = twoProbeAlgorithmParameters(
electrode_constraint = ElectrodeConstraints.Off,
initial_density_type = InitialDensityType.EquivalentBulk
)
energy_contour_integral_parameters = energyContourIntegralParameters(
circle_points = 50,
integral_lower_bound = 7.0*Rydberg,
fermi_line_points = 10,
fermi_function_poles = 4,
real_axis_infinitesimal = 0.01*electronVolt,
real_axis_point_density = 0.02*electronVolt
)
two_center_integral_parameters = twoCenterIntegralParameters(
cutoff = 2500.0*Rydberg,
points = 1024
)
######################################################################
# Left electrode parameters
######################################################################
left_electrode_electron_density_parameters = electronDensityParameters(
mesh_cutoff = 100.0*Rydberg
)
left_electrode_iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)
left_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
monkhorst_pack_parameters = (5, 5, 100)
)
left_electrode_iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)
left_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
temperature = 1300.0*Kelvin
)
######################################################################
# Collect left electrode parameters
######################################################################
left_electrode_parameters = ElectrodeParameters(
brillouin_zone_integration_parameters = left_electrode_brillouin_zone_integration_parameters,
electron_density_parameters = left_electrode_electron_density_parameters,
eigenstate_occupation_parameters = left_electrode_eigenstate_occupation_parameters,
iteration_mixing_parameters = left_electrode_iteration_mixing_parameters,
iteration_control_parameters = left_electrode_iteration_control_parameters
)
######################################################################
# Right electrode parameters
######################################################################
right_electrode_electron_density_parameters = electronDensityParameters(
mesh_cutoff = 100.0*Rydberg
)
right_electrode_iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)
right_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
monkhorst_pack_parameters = (5, 5, 100)
)
right_electrode_iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)
right_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
temperature = 1300.0*Kelvin
)
######################################################################
# Collect right electrode parameters
######################################################################
right_electrode_parameters = ElectrodeParameters(
brillouin_zone_integration_parameters = right_electrode_brillouin_zone_integration_parameters,
electron_density_parameters = right_electrode_electron_density_parameters,
eigenstate_occupation_parameters = right_electrode_eigenstate_occupation_parameters,
iteration_mixing_parameters = right_electrode_iteration_mixing_parameters,
iteration_control_parameters = right_electrode_iteration_control_parameters
)
######################################################################
# Initialize self-consistent field calculation
######################################################################
two_probe_method = TwoProbeMethod(
electrode_parameters = (left_electrode_parameters,right_electrode_parameters),
exchange_correlation_type = exchange_correlation_type,
iteration_mixing_parameters = iteration_mixing_parameters,
electron_density_parameters = electron_density_parameters,
basis_set_parameters = basis_set_parameters,
iteration_control_parameters = iteration_control_parameters,
energy_contour_integral_parameters = energy_contour_integral_parameters,
two_center_integral_parameters = two_center_integral_parameters,
electrode_voltages = electrode_voltages,
algorithm_parameters = two_probe_algorithm_parameters
)
if processIsMaster(): nlPrint(two_probe_method)
runtime_parameters = runtimeParameters(
verbosity_level = 10,
checkpoint_filename = 'D:/fe-mgo-fe.nc'
)
# Perform self-consistent field calculation
scf = executeSelfConsistentCalculation(
twoprobe_configuration,
two_probe_method,
runtime_parameters = runtime_parameters
)
######################################################################
# Calculate physical properties
######################################################################
current = calculateCurrent(
self_consistent_calculation = scf,
brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters((1, 1)),
green_function_infinitesimal = 1.0e-5*electronVolt,
number_of_points = 100
)
if processIsMaster(): nlPrint(current)
if processIsMaster(): file.addToSample(current, 'twoprobe_configuration', 'Current')
from ATK.TwoProbe import *
from ATK.MPI import processIsMaster
# Generate time stamp
if processIsMaster():
import platform, time
print '#',time.ctime()
print '#',platform.node(),platform.platform()+'\n'
# Opening vnlfile
if processIsMaster(): file = VNLFile('D:/fe-mgo-fe.vnl')
# Scattering elements and coordinates
scattering_elements = [Iron, Iron, Iron, Iron,
Oxygen, Oxygen, Oxygen, Oxygen,
Magnesium, Magnesium, Magnesium, Magnesium,
Iron, Iron, Iron, Iron]
scattering_coordinates = [[ 0.7165 , 0.7165 , 1.433 ],
[ 2.1495 , 2.1495 , 2.866 ],
[ 0.7165 , 0.7165 , 4.299 ],
[ 2.1495 , 2.1495 , 5.732 ],
[ 2.1495 , 2.1495 , 7.932 ],
[ 0.7165 , 0.7165 , 10.12735],
[ 2.1495 , 2.1495 , 12.3227 ],
[ 0.7165 , 0.7165 , 14.51805],
[ 0.7165 , 0.7165 , 7.932 ],
[ 2.1495 , 2.1495 , 10.12735],
[ 0.7165 , 0.7165 , 12.3227 ],
[ 2.1495 , 2.1495 , 14.51805],
[ 0.7165 , 0.7165 , 16.71805],
[ 2.1495 , 2.1495 , 18.15105],
[ 0.7165 , 0.7165 , 19.58405],
[ 2.1495 , 2.1495 , 21.01705]]*Angstrom
# Set up left electrode
left_electrode_elements = [Iron, Iron, Iron, Iron]
left_electrode_coordinates = [[ 0.7165, 0.7165, 0.7165],
[ 2.1495, 2.1495, 2.1495],
[ 0.7165, 0.7165, 3.5825],
[ 2.1495, 2.1495, 5.0155]]*Angstrom
left_electrode_cell = [[ 2.866, 0. , 0. ],
[ 0. , 2.866, 0. ],
[ 0. , 0. , 5.732]]*Angstrom
# Set up right electrode
right_electrode_elements = [Iron, Iron, Iron, Iron]
right_electrode_coordinates = [[ 0.7165, 0.7165, 0.7165],
[ 2.1495, 2.1495, 2.1495],
[ 0.7165, 0.7165, 3.5825],
[ 2.1495, 2.1495, 5.0155]]*Angstrom
right_electrode_cell = [[ 2.866, 0. , 0. ],
[ 0. , 2.866, 0. ],
[ 0. , 0. , 5.732]]*Angstrom
# Set up electrodes
left_electrode_configuration = PeriodicAtomConfiguration(
left_electrode_cell,
left_electrode_elements,
left_electrode_coordinates
)
right_electrode_configuration = PeriodicAtomConfiguration(
right_electrode_cell,
right_electrode_elements,
right_electrode_coordinates
)
# Set up two-probe configuration
twoprobe_configuration = TwoProbeConfiguration(
(left_electrode_configuration,right_electrode_configuration),
scattering_elements,
scattering_coordinates,
electrode_repetitions=[[1,1],[1,1]],
equivalent_atoms=([0,0],[3,15])
)
if processIsMaster(): nlPrint(twoprobe_configuration)
if processIsMaster(): file.addToSample(twoprobe_configuration, 'twoprobe_configuration')
######################################################################
# Central region parameters
######################################################################
exchange_correlation_type = LDA.PZ
iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)
electron_density_parameters = electronDensityParameters(
mesh_cutoff = 100.0*Rydberg
)
basis_set_parameters = basisSetParameters(
type = DoubleZetaPolarized,
radial_sampling_dr = 0.001*Bohr,
energy_shift = 0.01*Rydberg,
delta_rinn = 0.8,
v0 = 40.0*Rydberg,
charge = 0.0,
split_norm = 0.15
)
iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)
electrode_voltages = (0.0,0.0)*Volt
two_probe_algorithm_parameters = twoProbeAlgorithmParameters(
electrode_constraint = ElectrodeConstraints.Off,
initial_density_type = InitialDensityType.EquivalentBulk
)
energy_contour_integral_parameters = energyContourIntegralParameters(
circle_points = 50,
integral_lower_bound = 7.0*Rydberg,
fermi_line_points = 10,
fermi_function_poles = 4,
real_axis_infinitesimal = 0.01*electronVolt,
real_axis_point_density = 0.02*electronVolt
)
two_center_integral_parameters = twoCenterIntegralParameters(
cutoff = 2500.0*Rydberg,
points = 1024
)
######################################################################
# Left electrode parameters
######################################################################
left_electrode_electron_density_parameters = electronDensityParameters(
mesh_cutoff = 100.0*Rydberg
)
left_electrode_iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)
left_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
monkhorst_pack_parameters = (5, 5, 100)
)
left_electrode_iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)
left_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
temperature = 1300.0*Kelvin
)
######################################################################
# Collect left electrode parameters
######################################################################
left_electrode_parameters = ElectrodeParameters(
brillouin_zone_integration_parameters = left_electrode_brillouin_zone_integration_parameters,
electron_density_parameters = left_electrode_electron_density_parameters,
eigenstate_occupation_parameters = left_electrode_eigenstate_occupation_parameters,
iteration_mixing_parameters = left_electrode_iteration_mixing_parameters,
iteration_control_parameters = left_electrode_iteration_control_parameters
)
######################################################################
# Right electrode parameters
######################################################################
right_electrode_electron_density_parameters = electronDensityParameters(
mesh_cutoff = 100.0*Rydberg
)
right_electrode_iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)
right_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
monkhorst_pack_parameters = (5, 5, 100)
)
right_electrode_iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)
right_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
temperature = 1300.0*Kelvin
)
######################################################################
# Collect right electrode parameters
######################################################################
right_electrode_parameters = ElectrodeParameters(
brillouin_zone_integration_parameters = right_electrode_brillouin_zone_integration_parameters,
electron_density_parameters = right_electrode_electron_density_parameters,
eigenstate_occupation_parameters = right_electrode_eigenstate_occupation_parameters,
iteration_mixing_parameters = right_electrode_iteration_mixing_parameters,
iteration_control_parameters = right_electrode_iteration_control_parameters
)
######################################################################
# Initialize self-consistent field calculation
######################################################################
two_probe_method = TwoProbeMethod(
electrode_parameters = (left_electrode_parameters,right_electrode_parameters),
exchange_correlation_type = exchange_correlation_type,
iteration_mixing_parameters = iteration_mixing_parameters,
electron_density_parameters = electron_density_parameters,
basis_set_parameters = basis_set_parameters,
iteration_control_parameters = iteration_control_parameters,
energy_contour_integral_parameters = energy_contour_integral_parameters,
two_center_integral_parameters = two_center_integral_parameters,
electrode_voltages = electrode_voltages,
algorithm_parameters = two_probe_algorithm_parameters
)
if processIsMaster(): nlPrint(two_probe_method)
runtime_parameters = runtimeParameters(
verbosity_level = 10,
checkpoint_filename = 'D:/fe-mgo-fe.nc'
)
# Perform self-consistent field calculation
scf = executeSelfConsistentCalculation(
twoprobe_configuration,
two_probe_method,
runtime_parameters = runtime_parameters
)
######################################################################
# Calculate physical properties
######################################################################
current = calculateCurrent(
self_consistent_calculation = scf,
brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters((1, 1)),
green_function_infinitesimal = 1.0e-5*electronVolt,
number_of_points = 100
)
if processIsMaster(): nlPrint(current)
if processIsMaster(): file.addToSample(current, 'twoprobe_configuration', 'Current')