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« on: March 25, 2019, 13:17 »
Hello! I am trying to find the spin transfer torque of my system. I am a new user of ATK and am following the procedure as mentioned in the tutorial. I've been able to obtain the output of the first part of the process. In the second part there is this program I have to execute which is available on the tutorial. I've slightly modified the codes as per my requirements and tried to execute the job. But in this part only the calculations for the left electrode is performed after which I get the following text on the logs
+------------------------------------------------------------------------------+
| |
| Left Electrode Calculation [Finished Mon Mar 25 16:17:55 2019] |
| |
+------------------------------------------------------------------------------+
|--------------------------------------------------|
Calculating Kinetic Matrix : ==================================================
|--------------------------------------------------|
Calculating Nonlocal Part : ==================================================
+------------------------------------------------------------------------------+
| |
| Device DFT Calculation [Finished Mon Mar 25 16:17:55 2019] |
| |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
File "device2dsys90.py", line 31, in <module>
device_configuration.update()
File "zipdir/NL/CommonConcepts/Configurations/DeviceConfiguration.py", line 653, in update
File "zipdir/NL/CommonConcepts/Configurations/AtomicConfiguration.py", line 1675, in update
File "zipdir/NL/Calculators/Interfaces/DeviceCalculatorInterface.py", line 420, in _update
File "zipdir/NL/Calculators/Interfaces/DeviceCalculatorInterface.py", line 282, in _updateElectrodes
File "zipdir/NL/Calculators/DensityFunctionalTheory/LCAOCalculator/BaseLCAOCalculator.py", line 343, in _checkOrbitalsMatch
NL.ComputerScienceUtilities.Exceptions.NLValueError: The number of orbitals must match for initializing the system. 210 != 150 (expected)
Please let me know what I can do to solve this issue. I need to find the spin transfer torque of this device.
I'll put the python file for my device down here as well.
# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Two-probe Configuration
# -------------------------------------------------------------
# -------------------------------------------------------------
# Left Electrode
# -------------------------------------------------------------
# Set up lattice
vector_a = [28.02575, 0.0, 0.0]*Angstrom
vector_b = [0.0, 28.02575, 0.0]*Angstrom
vector_c = [0.0, 0.0, 15.0]*Angstrom
left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
left_electrode_elements = [Nitrogen, Carbon, Carbon, Nitrogen, Carbon, Carbon, Nitrogen,
Carbon, Carbon, Nitrogen]
# Define coordinates
left_electrode_coordinates = [[ 10.89175 , 17.333092901836, 14.225787552286],
[ 10. , 16.071986558453, 14.232637054308],
[ 10.89175 , 14.810880215069, 14.239486556329],
[ 10. , 13.549773871686, 14.246336058351],
[ 10.89175 , 12.288667528302, 14.253185560372],
[ 10. , 11.027561184919, 14.260035062394],
[ 10.89175 , 9.766454841535, 14.266884564415],
[ 10. , 8.505348498152, 14.273734066437],
[ 10.89175 , 7.244242154768, 14.280583568459],
[ 10. , 5.983135811385, 14.28743307048 ]]*Angstrom
# Set up configuration
left_electrode = BulkConfiguration(
bravais_lattice=left_electrode_lattice,
elements=left_electrode_elements,
cartesian_coordinates=left_electrode_coordinates
)
# -------------------------------------------------------------
# Right Electrode
# -------------------------------------------------------------
# Set up lattice
vector_a = [28.02575, 0.0, 0.0]*Angstrom
vector_b = [0.0, 28.02575, 0.0]*Angstrom
vector_c = [0.0, 0.0, 16.0]*Angstrom
right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
right_electrode_elements = [Nickel, Nickel, Nickel, Nickel, Nickel, Nickel, Nickel, Nickel,
Nickel, Nickel]
# Define coordinates
right_electrode_coordinates = [[ 18.02575 , 22.404916283456, 0.083064917734],
[ 17.134 , 21.143809940073, 0.089914419755],
[ 18.02575 , 19.88270359669 , 0.096763921777],
[ 17.134 , 18.621597253306, 0.103613423798],
[ 18.02575 , 17.360490909923, 0.11046292582 ],
[ 17.134 , 16.099384566539, 0.117312427842],
[ 18.02575 , 14.838278223156, 0.124161929863],
[ 17.134 , 13.577171879772, 0.131011431885],
[ 18.02575 , 12.316065536389, 0.137860933906],
[ 17.134 , 11.054959193005, 0.144710435928]]*Angstrom
# Set up configuration
right_electrode = BulkConfiguration(
bravais_lattice=right_electrode_lattice,
elements=right_electrode_elements,
cartesian_coordinates=right_electrode_coordinates
)
# -------------------------------------------------------------
# Central Region
# -------------------------------------------------------------
# Set up lattice
vector_a = [28.02575, 0.0, 0.0]*Angstrom
vector_b = [0.0, 28.02575, 0.0]*Angstrom
vector_c = [0.0, 0.0, 35.15975]*Angstrom
central_region_lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
central_region_elements = [Nitrogen, Carbon, Carbon, Nitrogen, Carbon, Carbon, Nitrogen,
Carbon, Carbon, Nitrogen, Carbon, Carbon, Nitrogen, Carbon, Carbon,
Nitrogen, Carbon, Carbon, Nitrogen, Carbon, Carbon, Carbon, Carbon,
Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Nitrogen,
Carbon, Carbon, Nitrogen, Carbon, Carbon, Nitrogen, Carbon, Carbon,
Nitrogen, Nickel, Nickel, Nickel, Nickel, Nickel, Nickel, Nickel,
Nickel, Nickel, Nickel]
# Define coordinates
central_region_coordinates = [[ 10.89175 , 17.333092901836, 14.225787552286],
[ 10. , 16.071986558453, 14.232637054308],
[ 10.89175 , 14.810880215069, 14.239486556329],
[ 10. , 13.549773871686, 14.246336058351],
[ 10.89175 , 12.288667528302, 14.253185560372],
[ 10. , 11.027561184919, 14.260035062394],
[ 10.89175 , 9.766454841535, 14.266884564415],
[ 10. , 8.505348498152, 14.273734066437],
[ 10.89175 , 7.244242154768, 14.280583568459],
[ 10. , 5.983135811385, 14.28743307048 ],
[ 12.67525 , 18.601048747241, 15.480044393648],
[ 11.7835 , 17.339942403858, 15.48689389567 ],
[ 12.67525 , 16.078836060474, 15.493743397691],
[ 11.7835 , 14.817729717091, 15.500592899713],
[ 12.67525 , 13.556623373707, 15.507442401734],
[ 11.7835 , 12.295517030324, 15.514291903756],
[ 12.67525 , 11.03441068694 , 15.521141405777],
[ 11.7835 , 9.773304343557, 15.527990907799],
[ 12.67525 , 8.512198000174, 15.53484040982 ],
[ 11.7835 , 7.25109165679 , 15.541689911842],
[ 14.45875 , 19.869004592646, 16.73430123501 ],
[ 13.567 , 18.607898249263, 16.741150737032],
[ 14.45875 , 17.346791905879, 16.748000239053],
[ 13.567 , 16.085685562496, 16.754849741075],
[ 14.45875 , 14.824579219112, 16.761699243096],
[ 13.567 , 13.563472875729, 16.768548745118],
[ 14.45875 , 12.302366532346, 16.775398247139],
[ 13.567 , 11.041260188962, 16.782247749161],
[ 14.45875 , 9.780153845579, 16.789097251182],
[ 13.567 , 8.519047502195, 16.795946753204],
[ 16.24225 , 21.136960438051, 17.988558076372],
[ 15.3505 , 19.875854094668, 17.995407578393],
[ 16.24225 , 18.614747751284, 18.002257080415],
[ 15.3505 , 17.353641407901, 18.009106582437],
[ 16.24225 , 16.092535064518, 18.015956084458],
[ 15.3505 , 14.831428721134, 18.02280558648 ],
[ 16.24225 , 13.570322377751, 18.029655088501],
[ 15.3505 , 12.309216034367, 18.036504590523],
[ 16.24225 , 11.048109690984, 18.043354092544],
[ 15.3505 , 9.7870033476 , 18.050203594566],
[ 18.02575 , 22.404916283456, 19.242814917734],
[ 17.134 , 21.143809940073, 19.249664419755],
[ 18.02575 , 19.88270359669 , 19.256513921777],
[ 17.134 , 18.621597253306, 19.263363423798],
[ 18.02575 , 17.360490909923, 19.27021292582 ],
[ 17.134 , 16.099384566539, 19.277062427842],
[ 18.02575 , 14.838278223156, 19.283911929863],
[ 17.134 , 13.577171879772, 19.290761431885],
[ 18.02575 , 12.316065536389, 19.297610933906],
[ 17.134 , 11.054959193005, 19.304460435928]]*Angstrom
# Set up configuration
central_region = BulkConfiguration(
bravais_lattice=central_region_lattice,
elements=central_region_elements,
cartesian_coordinates=central_region_coordinates
)
device_configuration = DeviceConfiguration(
central_region,
[left_electrode, right_electrode]
)
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = NCGGA.PBE
#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
left_electrode_k_point_sampling = MonkhorstPackGrid(
na=3,
nb=3,
nc=3,
force_timereversal=False,
)
left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling=left_electrode_k_point_sampling,
density_mesh_cutoff=185.0*Hartree,
)
right_electrode_k_point_sampling = MonkhorstPackGrid(
na=3,
nb=3,
nc=3,
force_timereversal=False,
)
right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling=right_electrode_k_point_sampling,
density_mesh_cutoff=185.0*Hartree,
)
device_k_point_sampling = MonkhorstPackGrid(
na=3,
nb=3,
nc=3,
force_timereversal=False,
)
device_numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling=device_k_point_sampling,
density_mesh_cutoff=185.0*Hartree,
)
#----------------------------------------
# Poisson Solver Settings
#----------------------------------------
left_electrode_poisson_solver = FastFourier2DSolver(
boundary_conditions=[[PeriodicBoundaryCondition(),PeriodicBoundaryCondition()],
[PeriodicBoundaryCondition(),PeriodicBoundaryCondition()],
[PeriodicBoundaryCondition(),PeriodicBoundaryCondition()]]
)
right_electrode_poisson_solver = FastFourier2DSolver(
boundary_conditions=[[PeriodicBoundaryCondition(),PeriodicBoundaryCondition()],
[PeriodicBoundaryCondition(),PeriodicBoundaryCondition()],
[PeriodicBoundaryCondition(),PeriodicBoundaryCondition()]]
)
#----------------------------------------
# Contour Integral Settings
#----------------------------------------
equilibrium_contour = SemiCircleContour(
integral_lower_bound=4.95748378543*Hartree,
)
contour_parameters = ContourParameters(
equilibrium_contour=equilibrium_contour,
)
#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = LCAOCalculator(
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters,
poisson_solver=left_electrode_poisson_solver,
)
right_electrode_calculator = LCAOCalculator(
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters,
poisson_solver=right_electrode_poisson_solver,
)
#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=device_numerical_accuracy_parameters,
contour_parameters=contour_parameters,
electrode_calculators=
[left_electrode_calculator, right_electrode_calculator],
electrode_voltages=( 0.001*Volt, -0.001*Volt),
)
device_configuration.setCalculator(calculator)
# -------------------------------------------------------------
# Initial State
# -------------------------------------------------------------
initial_spin = InitialSpin(scaled_spins=[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0])
device_configuration.setCalculator(
calculator,
initial_spin=initial_spin,
)
device_configuration.update()
nlsave('Device 2d sys.hdf5', device_configuration)
nlprint(device_configuration)
Also the program I tried to execute is this.
# Read in the collinear calculation
device_configuration = nlread('/root/Documents/ayesha/march19/Device 2d sys.hdf5', DeviceConfiguration)[0]
# Use the special noncollinear mixing scheme
iteration_control_parameters = IterationControlParameters(
algorithm=PulayMixer(noncollinear_mixing=True),
)
# Get the calculator and modify it for noncollinear LDA
calculator = device_configuration.calculator()
calculator = calculator(
exchange_correlation=NCLDA.PZ,
iteration_control_parameters=iteration_control_parameters,
)
# Define the spin rotation in polar coordinates
theta = 90*Degrees
left_spins = [(i, 1, 0*Degrees, 0*Degrees) for i in range(29)]
right_spins = [(i, 1, theta, 0*Degrees) for i in range(30,49)]
spin_list = left_spins + right_spins
initial_spin = InitialSpin(scaled_spins=spin_list)
# Setup the initial state as a rotated collinear state
device_configuration.setCalculator(
calculator,
initial_spin=initial_spin,
initial_state=device_configuration,
)
# Calculate and save
device_configuration.update()
nlsave('device2dsys90.hdf5', device_configuration)
# -------------------------------------------------------------
# Mulliken Population
# -------------------------------------------------------------
mulliken_population = MullikenPopulation(device_configuration)
nlsave('device2dsys90.hdf5', mulliken_population)
nlprint(mulliken_population)
# -------------------------------------------------------------
# Electrostatic Difference Potential
# -------------------------------------------------------------
electrostatic_difference_potential = ElectrostaticDifferencePotential(device_configuration)
nlsave('device2dsys90.hdf5', electrostatic_difference_potential)
# -------------------------------------------------------------
# Transmission Spectrum
# -------------------------------------------------------------
kpoint_grid = MonkhorstPackGrid(
force_timereversal=False
)
transmission_spectrum = TransmissionSpectrum(
configuration=device_configuration,
energies=numpy.linspace(-2,2,101)*eV,
kpoints=kpoint_grid,
energy_zero_parameter=AverageFermiLevel,
infinitesimal=1e-06*eV,
self_energy_calculator=RecursionSelfEnergy(),
)
nlsave('device2dsys90.hdf5', transmission_spectrum)
This is very important for the project that I am doing right now. Please help me.
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