Topics

1

General Questions and Answers / charge transfer

« on: August 5, 2013, 02:06 »

Hi,professor:
 we always calculate the charge transfer by ATK , in my paper, i calculate the scattering region charge transfer with the increase of bias voltage,but the reviewer refuse to accept my paper for the reason that "ATK uses the NEGF-DFT framework originally developed in McGill University, which assumes always keeping the charge neutrality of the whole central scattering region, at even non-equilibrium, i.e. there is no charge transfer at the boundary between lead and central region and the Hartree potential at the boundary should be continuous."  which means ATK can not calculate the charge transfer and without any meaning?
thank you!

2

General Questions and Answers / what is the physical meaning of electrostatic potential contour

« on: November 28, 2012, 03:21 »

I plot the electrostatic potential contour, but I don’t know what is the physical meaning of the picture. Anders Blom told the electrostatic difference potential is the solution to the Poisson equation where on the right-hand side you have the electron difference density, which is the (total) electron density minus the density of the neutral atoms on this forum.
In my picture, why the region is yellow on left side while red on the right side around the molecular, however it is opposite on the molecular. Can anybody tell me the physical meaning of the picture?

3

General Questions and Answers / About the bond length of Carbon and Gold in a chain

« on: October 28, 2012, 03:39 »

in atk tutorials, the bond length of C-C  is 2.9A in a carbon chain, but the actual length is 1.4A. so, i want to know how to set the length in a chain(such as gold(2.88) ) .

4

General Questions and Answers / how to achieve self-consistent

« on: September 17, 2012, 14:26 »

it can be well self-consistent below 0.4 voltage, however it cann't be self-consistent  above 0.6 voltage in my system(tolerance=0.00008). i have change some parameters, such as:grid_mesh_cutoff, circle_points=50,real_axis_infinitesimal=0.0005*Hartree, integral_lower_bound=5.0*Hartree, Maybe it is wrong.so i need you help me!. thank you!
i provide the export file.log under 1.2 voltage,if you want the input file, i can provide by E-mail.

5

General Questions and Answers / urgent problem

« on: June 7, 2012, 07:54 »

i want to know this script can be use  the former calculation result. such as we can use 0.2V self-consistent result to calculate the 0.3V properties? i found this script just using the zero bias  self-consistent result or just DeviceConfiguration. thank you!


#read in the old configuration
device_configuration = nlread("li-h2.nc",DeviceConfiguration)[0]
calculator = device_configuration.calculator()

# Define bias voltages
voltage_list=[0.1,0.2, 0.3, 0.4]*Volt
#make loop
for voltage in voltage_list:
    # Set new calculator with modified electrode voltages on the configuration
    # use the self consistent state of  the old calculation as starting input.
    device_configuration.setCalculator(
          calculator(electrode_voltages=(0*Volt, voltage)),
          initial_state=device_configuration)

    # Calculate the transmission spectrum
    transmission_spectrum = TransmissionSpectrum(
        configuration=device_configuration,
        energies=numpy.linspace(-5,5,100)*eV,
        )

    nlsave('li-h2.nc', transmission_spectrum)

6

General Questions and Answers / how to change the parameter

« on: June 4, 2012, 16:27 »

how to change the parameter  when it can not self-consistent under high bias, however, it can well self-consistent under small bias(atk12.2).thank you!

7

General Questions and Answers / how to print the current of spin up and spin down in ATk11.2

« on: May 19, 2012, 03:34 »

i have the self-consistent file.nc which contain the spin up and spin down transmissions  under different bias. but when i drag the file.nc to the Analysics-I-V curve, it just print a current under the same bias. how can i print the two current of the spin up and spin down

8

General Questions and Answers / how to calculate the sweep current

« on: May 16, 2012, 02:50 »

  hello, i want to calculate the sweep current using atk11.2. but i donot know how to calculate the sweep current for two probe spin systems. the script have modify according to forum support information. but
when i run it  an error occurred. the error message as follows:
Traceback (most recent call last):
        'File "c:\users\ysl\appdata\local\temp\9865068142889943.py", line 12, in <module>
        [left_electrode_calculator, right_electrode_calculator],
         NameError: name 'left_electrode_calculator' is not defined
         NanoLanguageScript execution failure'
can you help me to solve this problem, or edit a new script using calculating the spin current for two probe electrode systems(such as i want to calculate the (0,0.1,0.2,0.3,0.4,0.5,0.6)bias).
the iv.py script as follow:


# read in the 0 V configuration
device_configuration=nlread('D:/G/calculate materials/pentence.nc',DeviceConfiguration)[0]
calculator=device_configuration.calculator()

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

########### this is added by guohuazhong for bias loop calculations, begin
for bias in numpy.linspace(0.5,1.2,8)*Volt: 
#    device_configuration.setCalculator(calculator) 
    device_configuration.setCalculator(
        calculator(electrode_voltages=(0.5*bias,-0.5*bias)),
        initial_state=device_configuration
    )
    nlprint(device_configuration)
    device_configuration.update()
#  ('D:/G/calculate materials/pentence3iv_scf_%g.nc' % bias.inUnitsOf(Volt), device_configuration)
    nlsave('D:/G/calculate materials/pentence3.nc', device_configuration)

# -------------------------------------------------------------
# Transmission spectrum
# -------------------------------------------------------------

    transmission_spectrum = TransmissionSpectrum(
        configuration=device_configuration,
   energies=numpy.linspace(-5,5,401)*eV,
   kpoints=MonkhorstPackGrid(3,3),
   energy_zero_parameter=AverageFermiLevel,
   infinitesimal=1e-06*eV,
   self_energy_calculator=KrylovSelfEnergy(),
    )
    nlsave('D:/G/calculate materials/pentence3-transmission.nc', transmission_spectrum)
    nlprint(transmission_spectrum)

9

General Questions and Answers / how to build different electrode in molecular junction in 11.2.0 ATK

« on: April 10, 2012, 07:34 »

in 11.2.0 ATK,i build a molecular junction(Au-M-Au) in custom build block. if i want to build a different electrode such as (Au-M-Fe), how can i realize?

10

General Questions and Answers / ATK2008.10 about energy spectrum

« on: March 8, 2011, 05:58 »

Dear everyone,
I have performed a calculation of MPSH(Energy spectrum) for two probe spin injection system? I have some confusion about setting the quantum number to calculate the HOMO and LUMO. for my system’s molecule, there are 108 outer-shell electrons, usually based on that two electrons occupy one orbit, so the 108 outer-shell electrons will occupy 54 orbits, and the quantum number of HOMO should be 53 ,for LUMO is that 54. however, it seems not like that through calculating the energy spectrum, as following,
# Energy Spectrum
# -----------------------------------------------------------------------------
#     Spin-Up Energy (eV)  Spin-Down Energy (eV)
0         -18.77                 -18.77
   1         -18.52                 -18.51
   2         -18.18                 -18.18
   3         -17.90                 -17.90
   4         -16.04                 -16.03
   5         -15.67                 -15.65
   6         -15.29                 -15.26
   7         -14.99                 -14.99
   8         -14.83                 -14.82
   9         -14.78                 -14.78
  -----------------------------------------------------------------------------
   410       -0.73                  -0.03
   411       -0.69                  -0.03
   412       -0.69                  -0.03
   413       -0.69                  -0.02
   414       -0.69                  -0.02
   415       -0.69                  -0.01
   416       -0.68                  -0.01
   417       -0.68                   0.04
   418       -0.68                   0.05
   419       -0.68                   0.06
   420       -0.67                   0.07
   421       -0.67                   0.07
   422       -0.67                   0.07
   423       -0.67                   0.08
   424       -0.66                   0.08
   446       -0.55                   0.27
   447       -0.46                   0.27
   448       -0.46                   0.28
   449       -0.21                   0.31
   450       -0.15                   0.35
   451       -0.13                   0.42
   452       -0.12                   0.47
   453       -0.02                   0.49
   454       -0.01                   0.50
   455        0.43                   0.72
   456        0.44                   0.99
   457        0.49                   0.99
   458        0.50                   0.99
   459        0.53                   1.00
   460        0.66                   1.11
   461        0.67                   1.18
 -----------------------------------------------------------------------------
   872       80.93                  80.94
   873       81.46                  81.47
   874       84.84                  84.84
   875       85.24                  85.24
   876       87.08                  87.08
   877       88.39                  88.39
question:
      should I set the quantum number of HOMO to 454(-0.01eV)  and the LUMO to 455 for spin up, and HOMO to 416, LUMO to 417 for spin dowm?? I do not think so! Because we can find the energy orbit was degenerated from the output dat. So I want to know which is the quantum number for HOMO and LUMO ?
Attached is the calculated log out file.
Thanks!

11

General Questions and Answers / ATKError: hard to convergence

« on: December 22, 2010, 16:51 »

these days, I face to a problem as the following:
I want to calculate the spin two-probe systerms(use the version atk 2008.10) when I calculate scf , it always display on ATK command :

#Pulay mixing inversion failed.Using only last step.
#Pulay mixing inversion failed.Using only last step.
#Pulay mixing inversion failed.Using only last step.
...       

And the output file .log as:
# ----------------------------------------------------------------
# TwoProbe Calculation
# ----------------------------------------------------------------
# sc  0 : q =  648.06000 e
# sc  1 : q =  681.84046 e  dRho = 4.8957E-001
# sc  2 : q =   -4.94032 e  dRho = 6.3687E+000
# sc  3 : q =   -4.94032 e  dRho = 0.0000E+000
# sc  4 : q =   -0.03471 e  Etot =   -1.#IND0 Ry  dRho = 6.6863E+000
# sc  5 : q =   -0.03471 e  Etot =   -1.#IND0 Ry  dRho = 0.0000E+000  dEtot = -1.#INDE+000 Ry
Traceback<most recent call last>:
File"PNi0.3-.py",line 351, in?
runtime_parameters=runtime_parameters
ATKError:inverse<DZMatrix const &>: Could not LU factorize!

or when i change paramters according to the "ATK_TutorialSession_Part1_SCF.pdf".but it still display on ATK command
 TwoProbe Calculation. i find the value of q sharp change

# ----------------------------------------------------------------
# sc  0 : q =  648.98428 e
# sc  1 : q =   34.29715 e  dRho = 7.2077E+000
# sc  2 : q =   -0.03585 e  dRho = 7.5408E+000
# sc  3 : q =   -0.03585 e  dRho = 0.0000E+000

#Pulay mixing inversion failed. Using only last step.
#Pulay mixing inversion failed. Using only last step.
Traceback<most recent call last>:
File "PNi0.3-2.py",line 351,in?
runtime_parameters=runtime_parameters
ATKError:inverse<DZMatrix const &>:Could not LU factorize!

my module is (ni(initial spin 0.3)-molecular(0)-ni(0.3))why? how to solve it? Thank you very much!!!