Author Topic: c:/users/nano/appdata/local/temp/tmpuqo2g4.nl  (Read 3823 times)

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Offline abhishek_sharmacct

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c:/users/nano/appdata/local/temp/tmpuqo2g4.nl
« on: December 23, 2010, 16:31 »
I am getting following error : :-\


Traceback (most recent call last):
  File "c:/users/nano/appdata/local/temp/tmpuqo2g4.nl", line 487, in ?
    runtime_parameters = runtime_parameters
ATKError: bad allocation
Terminated Abnormally

I have checked my c drive but there is no such folder or file. Than what is meaning of line 487.

Also please tell me about mistake of my script


My script is:


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('C:/Users/Nano/Desktop/apt chrismas/apt1.vnl')

# Scattering elements and coordinates
scattering_elements = [Platinum, Platinum, Platinum, Platinum,
                       Platinum, Platinum, Platinum, Platinum,
                       Carbon,   Carbon,   Carbon,   Carbon,   
                       Carbon,   Carbon,   Carbon,   Carbon,   
                       Carbon,   Carbon,   Carbon,   Carbon,   
                       Carbon,   Carbon,   Carbon,   Carbon,   
                       Carbon,   Carbon,   Carbon,   Carbon,   
                       Platinum, Platinum, Platinum, Platinum,
                       Platinum, Platinum]
scattering_coordinates = [[  0.        ,   0.        ,   7.84800005],
                          [  0.        ,   2.77468705,   7.84800005],
                          [  2.77468705,   0.        ,   7.84800005],
                          [  2.77468705,   2.77468705,   7.84800005],
                          [  1.38734353,   4.1620307 ,   9.81000042],
                          [  1.38734353,   1.38734353,   9.81000042],
                          [  4.1620307 ,   4.1620307 ,   9.81000042],
                          [  4.1620307 ,   1.38734353,   9.81000042],
                          [  4.31650639,   2.95859623,  13.7       ],
                          [  4.31650639,   2.95859623,  16.16297622],
                          [  4.31650639,   2.95859623,  18.62595243],
                          [  2.95859623,   4.31650639,  14.93148811],
                          [  2.95859623,   4.31650639,  17.39446445],
                          [  1.60068655,   2.95859623,  13.7       ],
                          [  1.60068655,   2.95859623,  16.16297622],
                          [  1.60068655,   2.95859623,  18.62595243],
                          [  2.95859623,   1.60068655,  14.93148811],
                          [  2.95859623,   1.60068655,  17.39446445],
                          [  3.63755131,   4.13458109,  13.7       ],
                          [  3.63755131,   4.13458109,  16.16297622],
                          [  3.63755131,   4.13458109,  18.62595243],
                          [  1.78261185,   3.63755131,  14.93148811],
                          [  1.78261185,   3.63755131,  17.39446445],
                          [  2.27964163,   1.78261185,  13.7       ],
                          [  2.27964163,   1.78261185,  16.16297622],
                          [  2.27964163,   1.78261185,  18.62595243],
                          [  4.13458109,   2.27964163,  14.93148811],
                          [  4.13458109,   2.27964163,  17.39446445],
                          [  2.77468705,   2.77468705,  11.77200005],
                          [  2.77468705,   2.77468705,  20.59799979],
                          [  4.1620307 ,   1.38734353,  22.56000056],
                          [  4.1620307 ,   4.1620307 ,  22.56000056],
                          [  1.38734353,   1.38734353,  22.56000056],
                          [  1.38734353,   4.1620307 ,  22.56000056]]*Angstrom
       

electrode_elements = [Platinum, Platinum, Platinum, Platinum]
electrode_coordinates = [[ 0.       ,  0.       ,  0.       ],
                         [ 1.3873435,  1.3873435,  1.962    ],
                         [ 0.       ,  0.       ,  3.924    ],
                         [ 1.3873435,  1.3873435,  5.886    ]]*Angstrom

electrode_cell = [[ 2.77468701,  0.        ,  0.        ],
                  [ 0.        ,  2.77468701,  0.        ],
                  [ 0.        ,  0.        ,  7.848     ]]*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],[3,30])
    )
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 = 0.05,
    quantity = IterationMixing.Hamiltonian,
    history_steps = 6
)

electron_density_parameters = electronDensityParameters(
    mesh_cutoff = 200.0*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 = 110
)

electrode_voltages = (-0.1,0.1)*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 = 3.0*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 = 200.0*Rydberg
)

left_electrode_iteration_control_parameters = iterationControlParameters(
    tolerance = 1e-005,
    criterion = IterationControl.TotalEnergy,
    max_steps = 110
)

left_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
    monkhorst_pack_parameters = (5, 5, 500)
)

left_electrode_iteration_mixing_parameters = iterationMixingParameters(
    algorithm = IterationMixing.Pulay,
    diagonal_mixing_parameter = 0.05,
    quantity = IterationMixing.Hamiltonian,
    history_steps = 6
)

left_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
    temperature = 2000.0*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 = 200.0*Rydberg
)

right_electrode_iteration_control_parameters = iterationControlParameters(
    tolerance = 1e-005,
    criterion = IterationControl.TotalEnergy,
    max_steps = 110
)

right_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
    monkhorst_pack_parameters = (5, 5, 500)
)

right_electrode_iteration_mixing_parameters = iterationMixingParameters(
    algorithm = IterationMixing.Pulay,
    diagonal_mixing_parameter = 0.05,
    quantity = IterationMixing.Hamiltonian,
    history_steps = 6
)

right_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
    temperature = 2000.0*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 = 'C:/Users/Nano/Desktop/apt chrismas/apt1.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')

local_density_of_states = calculateLocalDensityOfStates(
    self_consistent_calculation = scf,
    energy = 0.0*electronVolt,
    quantum_number = (0.0,0.0),
    green_function_infinitesimal = 1.0e-5*electronVolt
)
if processIsMaster(): file.addToSample(local_density_of_states, 'twoprobe_configuration', 'Local Density Of States')

transmission_coefficients = calculateTransmissionCoefficients(
    self_consistent_calculation = scf,
    energy = 0.0*electronVolt,
    quantum_numbers = ((0.0,0.0),(0.5,0.5)),
    green_function_infinitesimal = 1.0e-5*electronVolt
)
if processIsMaster(): nlPrint(transmission_coefficients)
if processIsMaster(): file.addToSample(transmission_coefficients, 'twoprobe_configuration', 'Transmission Coefficients')

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, 'twoprobe_configuration', 'Transmission Spectrum')

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

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

transmission_eigenstates = calculateTransmissionEigenstates(
    self_consistent_calculation = scf,
    energy = 0.0*electronVolt,
    quantum_numbers = (0,((0.0,0.0),(0.5,0.5)))
)
for state_index,state in enumerate(transmission_eigenstates):
    label='Transmission Eigenstates'+' '+str(state_index)
    if processIsMaster(): file.addToSample(state, 'twoprobe_configuration', label)

transmission_eigenvalues = calculateTransmissionEigenvalues(
    self_consistent_calculation = scf,
    energy = 0.0*electronVolt,
    quantum_numbers = ((0.0,0.0),(0.5,0.5))
)
if processIsMaster(): nlPrint(transmission_eigenvalues)
for value_index,transmission_eigenvalue in enumerate(transmission_eigenvalues):
    label='Transmission Eigenvalues'+' '+str(value_index)
    if processIsMaster(): file.addToSample(transmission_eigenvalue, 'twoprobe_configuration', label)