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huangyc

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专业: 理论和计算化学

[交流] 【求助】atk出错

试运行了vnl2008tutorial中的双电极体系(au-dabp45-au)，结果出错

Traceback (most recent call last):
File "c:/docume~1/huang/locals~1/temp/tmp39wpev.nl", line 295, in ?
mulliken_population = calculateMullikenPopulation(self_consistent_calculation = scf)
NLTypeError: The population must contain non-negative numbers only.
Terminated Abnormally

请问什么原因，谢谢

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1楼 2009-11-17 10:26:11

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zxzj05(金币+1,VIP+0):讨论奖励！ 11-17 21:53

LZ可以把整个py脚本传上来看一下吗？

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2楼2009-11-17 13:12:09

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huangyc

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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('audabp45au_20091116223048.vnl')

# Scattering elements and coordinates
scattering_elements = [Gold,    Gold,    Gold,    Gold,
                     Gold,    Gold,    Gold,    Gold,
                     Hydrogen, Hydrogen, Hydrogen, Nitrogen,
                     Hydrogen, Hydrogen, Carbon, Carbon,
                     Carbon, Carbon, Carbon, Carbon,
                     Nitrogen, Hydrogen, Hydrogen, Hydrogen,
                     Hydrogen, Hydrogen, Carbon, Carbon,
                     Carbon, Carbon, Carbon, Carbon,
                     Hydrogen, Hydrogen, Gold,    Gold,
                     Gold,    Gold,    Gold,    Gold,
                     Gold,    Gold]
scattering_coordinates = [[  0.00000000e+00, 0.00000000e+00, 6.11700010e+00],
                        [  0.00000000e+00, 2.88358140e+00, 6.11700010e+00],
                        [  2.88358140e+00, 0.00000000e+00, 6.11700010e+00],
                        [  2.88358140e+00, 2.88358140e+00, 6.11700010e+00],
                        [  1.44179070e+00, 4.32537222e+00, 8.15600014e+00],
                        [  1.44179070e+00, 1.44179070e+00, 8.15600014e+00],
                        [  4.32537222e+00, 4.32537222e+00, 8.15600014e+00],
                        [  4.32537222e+00, 1.44179070e+00, 8.15600014e+00],
                        [  1.60086274e-01,  -9.67610180e-01, 2.05394861e+01],
                        [  2.01193213e+00, 8.63351941e-01, 1.42820068e+01],
                        [  1.99148810e+00, 8.42127383e-01, 1.17814972e+01],
                        [ -1.89441778e-02,  -8.51594284e-03, 1.01856329e+01],
                        [ -2.00306058e+00,  -8.31739187e-01, 1.18283054e+01],
                        [ -1.98261642e+00,  -8.10514867e-01, 1.43288158e+01],
                        [  1.59706529e-02, 2.77248267e-02, 1.44547799e+01],
                        [  1.12803686e+00, 4.90180582e-01, 1.37419685e+01],
                        [  1.11672044e+00, 4.78353053e-01, 1.23422050e+01],
                        [ -7.09924707e-03, 3.88790248e-03, 1.16555326e+01],
                        [ -1.11916542e+00,  -4.58568066e-01, 1.23683443e+01],
                        [ -1.10784888e+00,  -4.46740210e-01, 1.37681078e+01],
                        [  2.89612487e-02,  -2.04552617e-02, 2.02142112e+01],
                        [ -1.98882377e+00, 8.17189336e-01, 1.86205718e+01],
                        [ -2.00961518e+00, 8.44308078e-01, 1.61201218e+01],
                        [ -8.49456787e-01, 3.36450189e-01, 2.05622060e+01],
                        [  1.99886203e+00,  -7.95792818e-01, 1.60689443e+01],
                        [  2.01965380e+00,  -8.22910905e-01, 1.85693950e+01],
                        [  1.65651944e-02,  -4.44326876e-03, 1.87443506e+01],
                        [ -1.11093760e+00, 4.62091446e-01, 1.80589754e+01],
                        [ -1.12270451e+00, 4.77325112e-01, 1.66592482e+01],
                        [ -6.52637938e-03, 2.58399248e-02, 1.59451657e+01],
                        [  1.12097657e+00,  -4.40694392e-01, 1.66305413e+01],
                        [  1.13274348e+00,  -4.55927581e-01, 1.80302686e+01],
                        [  7.36190081e-01,  -5.87917387e-01, 9.84774752e+00],
                        [ -8.99853408e-01,  -3.79354864e-01, 9.85917110e+00],
                        [  1.44179070e+00, 4.32537222e+00, 2.23060002e+01],
                        [  1.44179070e+00, 1.44179070e+00, 2.23060002e+01],
                        [  4.32537222e+00, 4.32537222e+00, 2.23060002e+01],
                        [  4.32537222e+00, 1.44179070e+00, 2.23060002e+01],
                        [  2.88358140e+00, 2.88358140e+00, 2.43450003e+01],
                        [  2.88358140e+00, 0.00000000e+00, 2.43450003e+01],
                        [  0.00000000e+00, 2.88358140e+00, 2.43450003e+01],
                        [  0.00000000e+00, 0.00000000e+00, 2.43450003e+01]]*Angstrom


electrode_elements = [Gold, Gold, Gold]
electrode_coordinates = [[ 0.       ,  0.       ,  0.       ],
                     [ 1.44179073,  1.44179073,  2.039    ],
                     [ 0.       ,  0.       ,  4.078    ]]*Angstrom

electrode_cell = [[ 2.88358145,  0.       ,  0.       ],
               [ 0.       ,  2.88358145,  0.       ],
               [ 0.       ,  0.       ,  6.117    ]]*Angstrom

# Set up electrodes
electrode_configuration = PeriodicAtomConfiguration(
electrode_cell,
electrode_elements,
electrode_coordinates
)

# Set up two-probe configuration
twoprobe_configuration = TwoProbeConfiguration(
(electrode_configuration,electrode_configuration),
scattering_elements,
scattering_coordinates,
electrode_repetitions=[[2,2],[2,2]],
equivalent_atoms=([0,0],[2,41])
)
if processIsMaster(): nlPrint(twoprobe_configuration)
if processIsMaster(): file.addToSample(twoprobe_configuration, 'audabp45au')

######################################################################
# 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 = 150.0*Rydberg
)

basis_set_parameters_Common = basisSetParameters(
type = SingleZeta,
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
)

basis_set_parameters_Carbon = basisSetParameters(
type = DoubleZetaPolarized,
energy_shift = 0.005*Rydberg,
delta_rinn = 0.8,
v0 = 40.0*Rydberg,
charge = 0.0,
split_norm = 0.15,
element = Carbon
)

basis_set_parameters = [
basis_set_parameters_Common,
basis_set_parameters_Carbon
]

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 = 30,
integral_lower_bound = 3*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 = 150.0*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 = (1, 1, 500)
)

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 = 300.0*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 = 150.0*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 = (1, 1, 500)
)

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 = 300.0*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 = 'audabp45au.nc'
)

# Perform self-consistent field calculation
scf = executeSelfConsistentCalculation(
twoprobe_configuration,
two_probe_method,
runtime_parameters = runtime_parameters
)

######################################################################
# Calculate physical properties
######################################################################
atomic_forces = calculateAtomicForces(self_consistent_calculation = scf)
if processIsMaster(): nlPrint(atomic_forces)
if processIsMaster(): file.addToSample(atomic_forces, 'audabp45au', 'Atomic Forces')

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, 'audabp45au', 'Current')

electron_density = calculateElectronDensity(self_consistent_calculation = scf)
if processIsMaster(): file.addToSample(electron_density, 'audabp45au', 'Electron Density')

mulliken_population = calculateMullikenPopulation(self_consistent_calculation = scf)
if processIsMaster(): nlPrint(mulliken_population)
if processIsMaster(): file.addToSample(mulliken_population, 'audabp45au', 'Mulliken Population')

# Set verbosity level so that all energy components are printed
import ATK
verbosity_level=ATK.verbosityLevel()
ATK.setVerbosityLevel(10)
total_energy = calculateTotalEnergy(self_consistent_calculation = scf)
ATK.setVerbosityLevel(verbosity_level)

if processIsMaster(): nlPrint(total_energy,'Total energy')
if processIsMaster(): file.addToSample(total_energy, 'audabp45au', 'Total energy')

transmission_spectrum = calculateTransmissionSpectrum(
self_consistent_calculation = scf,
energies = (0.0,)*electronVolt,
brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters((1, 1)),
green_function_infinitesimal = 1.0e-5*electronVolt
)
if processIsMaster(): nlPrint(transmission_spectrum)
if processIsMaster(): file.addToSample(transmission_spectrum, 'audabp45au', 'Transmission Spectrum')

лл

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3楼2009-11-17 19:22:40

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iamddba

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小木虫(金币+0.5):给个红包，谢谢回帖交流
yjmaxpayne(金币+3,VIP+0):谢谢 11-18 15:04

从你的模型来看，很明显出现了电极层堆叠错误（stacking fault），可以看出你的模型和tutorial中的例子不一样，是因为你将surface cell 中的layers设置为3的缘故。这和教程中说的是不一样的。

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4楼2009-11-17 23:12:29

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