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Messages - Yu Hailin

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1
Dear all,

 What is the meaning of different colors used to draw iso-surfaces representing the
transmission eigenstates? Thanks in advance!

Best Regards!

   Yu Hailin

2
Thank you very much!

4
Dear all,

I want to know the formulisms to calculate the transmission coefficient and conductance in ATK.  In some refernces, the conductance is equal to e*e*T(Ef)/h, where T(Ef) is the transmission coefficient at Fermi level. But in ATK, the units of transmission coefficient is 2*e/h, so I want to know the formulism to calulate the transmission coefficient and conductance. Thanks in advance.

Best Rgards!

Yu Hailin 

5
Dear all,

I have one basic question about transmission eigenstate. In the 3D view, the shape of eigenstate is changing according to the isovalue. With lower isovalue (such as 0.1), the shape of eigenstate include the d orbital and s orbital components, while with larger isovalue (such as 0.35), the shape only contain the d orbital component, it means the d robit has more contribution than s orbit? Thanks in advance.

Best Regards!



Hailin Yu

6
Indeed, with increase the tolerance of SCF loop, such as 10e-6, the attained transmission spectrum picture (attained by plot-show) is agreement with the tutorial. Thank you for your advance.

I have another question. For the transmission eigenstate calculation, the quantum number 0, 1, 2 is corresponding the s,p and d robit, respectively?

7
This is the full input file.

# -------------------------------------------------------------
# TwoProbe configuration
# -------------------------------------------------------------

# -------------------------------------------------------------
# Left electrode
# -------------------------------------------------------------

# Set up lattice
vector_a = [6.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 6.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 6.22841]*Angstrom
left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
left_electrode_elements = [Lithium, Lithium]

# Define coordinates
left_electrode_coordinates = [[ 3.       ,  3.       ,  1.5571025],
                              [ 3.       ,  3.       ,  4.6713075]]*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 = [6.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 6.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 6.22841]*Angstrom
right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
right_electrode_elements = [Lithium, Lithium]

# Define coordinates
right_electrode_coordinates = [[ 3.      ,  3.      ,  1.557102],
                               [ 3.      ,  3.      ,  4.671308]]*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 = [6.0, 0.0, 0.0]*Angstrom
vector_b = [0.0, 6.0, 0.0]*Angstrom
vector_c = [0.0, 0.0, 33.1418095157]*Angstrom
central_region_lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
central_region_elements = [Lithium, Lithium, Lithium, Lithium, Lithium, Hydrogen, Hydrogen,
                           Lithium, Lithium, Lithium, Lithium, Lithium]

# Define coordinates
central_region_coordinates = [[  3.        ,   3.        ,   1.5571025 ],
                              [  3.        ,   3.        ,   4.6713075 ],
                              [  3.        ,   3.        ,   7.76171051],
                              [  3.        ,   3.        ,  10.91847415],
                              [  3.        ,   3.        ,  13.93149176],
                              [  3.        ,   3.        ,  16.15851591],
                              [  3.        ,   3.        ,  16.98337712],
                              [  3.        ,   3.        ,  19.21030765],
                              [  3.        ,   3.        ,  22.2234055 ],
                              [  3.        ,   3.        ,  25.38002278],
                              [  3.        ,   3.        ,  28.47050152],
                              [  3.        ,   3.        ,  31.58470752]]*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
# -------------------------------------------------------------
#----------------------------------------
# Numerical Accuracy Settings
#----------------------------------------
left_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    grid_mesh_cutoff=50.0*Hartree,
    k_point_sampling=(1, 1, 100),
    )

right_electrode_numerical_accuracy_parameters = NumericalAccuracyParameters(
    grid_mesh_cutoff=50.0*Hartree,
    k_point_sampling=(1, 1, 100),
    )

device_numerical_accuracy_parameters = NumericalAccuracyParameters(
    grid_mesh_cutoff=50.0*Hartree,
    )

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

right_electrode_calculator = LCAOCalculator(
    numerical_accuracy_parameters=right_electrode_numerical_accuracy_parameters,
    )

#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    numerical_accuracy_parameters=device_numerical_accuracy_parameters,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    )

device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration.update()
nlsave('li_h2.nc', device_configuration)

# -------------------------------------------------------------
# Transmission spectrum
# -------------------------------------------------------------
transmission_spectrum = TransmissionSpectrum(
    configuration=device_configuration,
    energies=numpy.linspace(-5,5,101)*eV,
    kpoints=MonkhorstPackGrid(1,1),
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=KrylovSelfEnergy(),
    )
nlsave('li_h2.nc', transmission_spectrum)
nlprint(transmission_spectrum)

8
Dear all,
    I have performed the transmission spectrum of Li_H2_Li device system following " ATK Tutorial for Device Configuration". The tutorial result shown in fig_1. My results shown in fig_2. We can find there is a large difference at the fermi level. For the tutorial results, the transmission sepctrum is about 0.7, while for my result, the value of transmission sepctrum at fermi level is nearly 0.0. Further inspect the .log file, the transmission spectrum is shown the follow:
 -5.000000e+00   0.000000e+00
 -4.900000e+00   0.000000e+00
 -4.800000e+00   0.000000e+00
 -4.700000e+00   0.000000e+00
 -4.600000e+00   0.000000e+00
 -4.500000e+00   0.000000e+00
 -4.400000e+00   0.000000e+00
 -4.300000e+00   0.000000e+00
 -4.200000e+00   0.000000e+00
 -4.100000e+00   0.000000e+00
 -4.000000e+00   0.000000e+00
 -3.900000e+00   0.000000e+00
 -3.800000e+00   0.000000e+00
 -3.700000e+00   0.000000e+00
 -3.600000e+00   0.000000e+00
 -3.500000e+00   0.000000e+00
 -3.400000e+00   0.000000e+00
 -3.300000e+00   0.000000e+00
 -3.200000e+00   0.000000e+00
 -3.100000e+00   0.000000e+00
 -3.000000e+00   0.000000e+00
 -2.900000e+00   0.000000e+00
 -2.800000e+00   0.000000e+00
 -2.700000e+00   0.000000e+00
 -2.600000e+00   0.000000e+00
 -2.500000e+00   0.000000e+00
 -2.400000e+00   0.000000e+00
 -2.300000e+00   0.000000e+00
 -2.200000e+00   0.000000e+00
 -2.100000e+00   0.000000e+00
 -2.000000e+00   0.000000e+00
 -1.900000e+00   0.000000e+00
 -1.800000e+00   0.000000e+00
 -1.700000e+00   0.000000e+00
 -1.600000e+00   0.000000e+00
 -1.500000e+00   0.000000e+00
 -1.400000e+00   0.000000e+00
 -1.300000e+00   0.000000e+00
 -1.200000e+00   0.000000e+00
 -1.100000e+00   0.000000e+00
 -1.000000e+00   5.905583e-20
 -9.000000e-01  -4.175721e-21
 -8.000000e-01   3.975305e-19
 -7.000000e-01  -5.536259e-17
 -6.000000e-01   1.574674e-01
 -5.000000e-01   3.851957e-01
 -4.000000e-01   4.313864e-01
 -3.000000e-01   4.899291e-01
 -2.000000e-01   5.992184e-01
 -1.000000e-01   6.841177e-01
  0.000000e+00  -1.653292e-12
  1.000000e-01   6.847447e-01
  2.000000e-01   6.657173e-01
  3.000000e-01   6.713786e-01
  4.000000e-01   7.062737e-01
  5.000000e-01   7.637366e-01
  6.000000e-01   8.317686e-01
  7.000000e-01   8.970986e-01
  8.000000e-01   9.495191e-01
  9.000000e-01   9.845091e-01
  1.000000e+00   9.998768e-01
  1.100000e+00   9.772056e-01
  1.200000e+00   7.899830e-01
  1.300000e+00   2.396745e-12
  1.400000e+00   7.980452e-13
  1.500000e+00   2.459474e-13
  1.600000e+00   8.799147e-14
  1.700000e+00   3.948111e-14
  1.800000e+00   2.195293e-14
  1.900000e+00   1.478200e-14
  2.000000e+00   1.177868e-14
  2.100000e+00   1.100614e-14
  2.200000e+00   1.201965e-14
  2.300000e+00   1.566187e-14
  2.400000e+00   2.586120e-14
  2.500000e+00   2.949732e-01
  2.600000e+00   4.069243e-01
  2.700000e+00   3.886785e-01
  2.800000e+00   3.074267e-01
  2.900000e+00   2.423854e-01
  3.000000e+00   1.977910e-01
  3.100000e+00   1.645642e-01
  3.200000e+00   1.378944e-01
  3.300000e+00   1.166107e-01
  3.400000e+00   1.005860e-01
  3.500000e+00   1.684294e-01
  3.600000e+00   2.600974e-01
  3.700000e+00   3.407868e-01
  3.800000e+00   4.166005e-01
  3.900000e+00   4.881575e-01
  4.000000e+00   5.534211e-01
  4.100000e+00   6.095733e-01
  4.200000e+00   6.543246e-01
  4.300000e+00   6.866777e-01
  4.400000e+00   7.072491e-01
  4.500000e+00   7.181975e-01
  4.600000e+00   7.227375e-01
  4.700000e+00   7.243725e-01
  4.800000e+00   7.261865e-01
  4.900000e+00   7.304457e-01
  5.000000e+00   7.385041e-01

I find the above transmission spectrum don't agreement with my attained fig_2(which attained by plot-show). Anyone can tell me ? Thanks in advance!
Sorry, I don't know how to post picture.

10
Thank you very much!

11
Dear all,
     I have some questions about transmission eigenvalue and transmission eigenstat.
1. The transmission eigenvalue equal to the transmission coefficient, while transmission coefficient dependes on K (kx, ky), it means the transmission eigenvalue is also K-point dependent? Or the transmission coefficient here refer to the sum of T(K)?

2. How to set the K-points when calcualte the transmission eigenvalue and transmission eigenstat for Fe/MgO/Fe MTJ? As question 1 refered, if the transmission eigenvalue is K-point depened, it need to supply a k-points list? Or if not, how large a k-point (such as 9x9, 16x16) is enough? what is the criterion?

3. Is it possible to perform transmission eigenstat calculation with more than one quantum number? How to set the K-points?

Thanks in advance!

12
Dear all,
    I have performed the transmission eigenstates calculation and attained the .nc file. But how to visualize the transmission eigenstates in a 3D view? Thanks in advance!

Best Regards!

13
Dear all,
       I have performed the transmission sectrum calculation and attained the .nc file. Now, I want to calculate the transmission eigenstates. How to do to calculate the transmission eigenstates without to perform self-consistent again? Thanks in advance.

Best Regards!
   


Hailin Yu

14
General Questions and Answers / The calculation of conductance.
« on: January 22, 2011, 15:35 »
Dear all, the follow method to calculate the conductance  for two-electrode system is reasonable?

The method include:
i. calculate the transmission spectrum at zero bias.
ii. using the calculated transmission spectrum to calculate the conductance at different electrode_voltages, such as:

conductance = TransmissionSpectrum.conductance(electrode_voltages=[0,0.1]*Volt)
print conductance

conductance = TransmissionSpectrum.conductance(electrode_voltages=[0,0.2]*Volt)
print conductance

......

Or it is necessially to calculate the transmission spectrum at different bias before calcualte the conductance?

Thanks in advance!

15
Dear all,
     I have read a document about ATK (ATK_TutorialSession_Part2_Analysis.pdf, This document is easily downloaded by google search) and I am interesting for the calculation of TMR value (shown on page 26 of the document). But I am confused on the calculation of TMR when the bias voltage is zero. For zero bias voltage, there is no current. So it is hard to undertand.
Anyone can give me some advices? If you have the script, please give me (my e-mail: yuhailin@student.sysu.edu.cn).Thanks in advance!
Sincerely!
Yu Hailin

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