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Messages - karolcia

Pages: [1]
1
General Questions and Answers / Re: neumann condiotion in gated device
« on: June 18, 2014, 13:55 »
I have just tried to change only for device the conditions like that:
----------------------
device_poisson_solver = MultigridSolver(
    boundary_conditions=[[NeumannBoundaryCondition,NeumannBoundaryCondition],
                         [NeumannBoundaryCondition,NeumannBoundaryCondition],
                         [DirichletBoundaryCondition,DirichletBoundaryCondition]]
    )
-----------------------------------------------
and it seems it works.

2
General Questions and Answers / Re: neumann condiotion in gated device
« on: June 18, 2014, 12:17 »
My trying to use version 12.2 (I know is little old)

The Script Generator only put device_poisson_solver into script, but the last pair of condition was not Periodic, but Dirichlet.

Therefore I tried to just copy from your post poisson_solver, but it did not work.
So I tried like this:

#----------------------------------------
# Poisson Solver Settings
#----------------------------------------
device_poisson_solver = MultigridSolver(
    boundary_conditions=[[NeumannBoundaryCondition,NeumannBoundaryCondition],
                                         [NeumannBoundaryCondition,NeumannBoundaryCondition],
                                         [PeriodicBoundaryCondition,PeriodicBoundaryCondition]]
    )

left_electrode_poisson_solver = MultigridSolver(
    boundary_conditions=[[NeumannBoundaryCondition,NeumannBoundaryCondition],
                         [NeumannBoundaryCondition,NeumannBoundaryCondition],
                         [PeriodicBoundaryCondition,PeriodicBoundaryCondition]]
    )

right_electrode_poisson_solver = MultigridSolver(
    boundary_conditions=[[NeumannBoundaryCondition,NeumannBoundaryCondition],
                         [NeumannBoundaryCondition,NeumannBoundaryCondition],
                         [PeriodicBoundaryCondition,PeriodicBoundaryCondition]]
   )

#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    poisson_solver=left_electrode_poisson_solver,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters,
    )

right_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    poisson_solver=right_electrode_poisson_solver,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters,
    )

#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    poisson_solver=device_poisson_solver,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    electrode_voltages=( 0.5*Volt, 0.0*Volt)
    )

device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration.update()
nlsave('n5s1.nc', device_configuration)

And I got another error message:
--------------------------------------------
Traceback (most recent call last):
  File "/tmp/9241002929559588.py", line 311, in <module>
    electrode_voltages=( 0.5*Volt, 0.0*Volt)
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 168, in __init__
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 1494, in setAndCheckPoissonSolver
NL.ComputerScienceUtilities.Exceptions.NLValueError:  The parameter, poisson_solver, must have DirichletBoundaryCondition in direction of the z-axis (2,0)
----------------------------------------------

How should I change my script?
Probably this is sth really simple, but I do not know...

3
General Questions and Answers / neumann condiotion in gated device
« on: June 17, 2014, 16:21 »
Dear all,

I have problem with applying Neumann conditions to my system: nanotube with gate.

Below I placed two files. First (1), with periodic boundary conditions works,
another (2), with Neumann condition does not. I tried to add Neumann conditions by Script builder, it seems that they are added, but it does not work.
The error message is:
-----------------------------------------------
Traceback (most recent call last):
  File "/tmp/9514443501104607.py", line 297, in <module>
    electrode_voltages=( 0.1*Volt, 0.0*Volt)
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 178, in __init__
  File "./zipdir/NL/Calculators/LCAOCalculator/DeviceLCAOCalculator.py", line 1576, in checkAndSetElectrodeCalculators
NL.ComputerScienceUtilities.Exceptions.NLValueError: The electrode_calculators poisson solver  must have same boundary condition in direction x as the poisson solver of the DeviceCalculator
----------------------------------------------
How can I add those conditions to electrodes? What should I change/add to my script file?


System 1: with periodic conditions (works):
-------------------------------------------------------------------------
# Set up configuration
central_region = BulkConfiguration(
    bravais_lattice=central_region_lattice,
    elements=central_region_elements,
    cartesian_coordinates=central_region_coordinates
    )

# Add metallic region
metallic_region_0 = BoxRegion(
    1*Volt,
    xmin = 0*Angstrom, xmax = 13.9168*Angstrom,
    ymin = 0*Angstrom, ymax = 0.5*Angstrom,
    zmin = 4.26258*Angstrom, zmax = 12.6253*Angstrom
)

metallic_regions = [metallic_region_0]
central_region.setMetallicRegions(metallic_regions)

# Add dielectric region
dielectric_region_0 = BoxRegion(
    4,
    xmin = 0*Angstrom, xmax = 13.9168*Angstrom,
    ymin = 0.5*Angstrom, ymax = 4.07914*Angstrom,
    zmin = 4.26258*Angstrom, zmax = 12.6253*Angstrom
)

dielectric_regions = [dielectric_region_0]
central_region.setDielectricRegions(dielectric_regions)

device_configuration = DeviceConfiguration(
    central_region,
    [left_electrode, right_electrode]
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
    GGABasis.Carbon_DoubleZetaPolarized,
    ]

#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = GGA.PBE

#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=(1, 1, 100),
    )

right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=(1, 1, 100),
    )

device_algorithm_parameters = DeviceAlgorithmParameters(
    self_energy_calculator_real=KrylovSelfEnergy(save_self_energies=True, lambda_min=0.1),
    )

#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters,
    )

right_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters,
    )

#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    device_algorithm_parameters=device_algorithm_parameters,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    electrode_voltages=( 0.1*Volt, 0.0*Volt)
    )

device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration.update()
nlsave('n5s1.nc', device_configuration)



System 2, with Neumann conditions (does not work):
# -------------------------------------------------------------
# TwoProbe configuration
# -------------------------------------------------------------
(...)
# Set up configuration
central_region = BulkConfiguration(
    bravais_lattice=central_region_lattice,
    elements=central_region_elements,
    cartesian_coordinates=central_region_coordinates
    )

# Add metallic region
metallic_region_0 = BoxRegion(
    1*Volt,
    xmin = 0*Angstrom, xmax = 13.9168*Angstrom,
    ymin = 0*Angstrom, ymax = 0.5*Angstrom,
    zmin = 4.26258*Angstrom, zmax = 12.6253*Angstrom
)

metallic_regions = [metallic_region_0]
central_region.setMetallicRegions(metallic_regions)

# Add dielectric region
dielectric_region_0 = BoxRegion(
    4,
    xmin = 0*Angstrom, xmax = 13.9168*Angstrom,
    ymin = 0.5*Angstrom, ymax = 4.07914*Angstrom,
    zmin = 4.26258*Angstrom, zmax = 12.6253*Angstrom
)

dielectric_regions = [dielectric_region_0]
central_region.setDielectricRegions(dielectric_regions)

device_configuration = DeviceConfiguration(
    central_region,
    [left_electrode, right_electrode]
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
    GGABasis.Carbon_DoubleZetaPolarized,
    ]

#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = GGA.PBE

#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=(1, 1, 100),
    )

right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    k_point_sampling=(1, 1, 100),
    )

#----------------------------------------
# Poisson Solver Settings
#----------------------------------------
device_poisson_solver = MultigridSolver(
    boundary_conditions=[[NeumannBoundaryCondition,NeumannBoundaryCondition],
                         [NeumannBoundaryCondition,NeumannBoundaryCondition],
                         [DirichletBoundaryCondition,DirichletBoundaryCondition]]
    )

device_algorithm_parameters = DeviceAlgorithmParameters(
    self_energy_calculator_real=KrylovSelfEnergy(save_self_energies=True, lambda_min=0.1),
    )

#----------------------------------------
# Electrode Calculators
#----------------------------------------
left_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=left_electrode_numerical_accuracy_parameters,
    )

right_electrode_calculator = LCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters,
    )

#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    exchange_correlation=exchange_correlation,
    poisson_solver=device_poisson_solver,
    device_algorithm_parameters=device_algorithm_parameters,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    electrode_voltages=( 0.1*Volt, 0.0*Volt)
    )

device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration.update()
nlsave('neumann.nc', device_configuration)



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