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Topics - kaypu

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16
General Questions and Answers / Question about zero charge at 0 bias
« on: December 16, 2013, 07:35 »
Dear QuantumWise staff:

    i want to test the polarization transport of the two-probe system of Ni-benzene-Ni.  but all the charges in the center scattering area are zero, as shown in the following:

+------------------------------------------------------------------------------+
| Density Matrix Report                         DM     DM[D]      DD        |
+------------------------------------------------------------------------------+
|   0  Ni   [   0.623 ,   0.622 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   1  Ni   [   3.115 ,   0.622 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   2  Ni   [   5.608 ,   0.622 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   3  Ni   [   0.623 ,   3.115 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   4  Ni   [   3.115 ,   3.115 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   5  Ni   [   5.608 ,   3.115 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   6  Ni   [   0.623 ,   5.607 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   7  Ni   [   3.115 ,   5.607 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   8  Ni   [   5.608 ,   5.607 ,   0.881 ]   -0.00000  -0.00000 -10.00000     |
|   9  Ni   [   1.869 ,   1.869 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  10  Ni   [   4.361 ,   1.869 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  11  Ni   [   6.854 ,   1.869 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  12  Ni   [   1.869 ,   4.361 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  13  Ni   [   4.361 ,   4.361 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  14  Ni   [   6.854 ,   4.361 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  15  Ni   [   1.869 ,   6.854 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  16  Ni   [   4.361 ,   6.854 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  17  Ni   [   6.854 ,   6.854 ,   2.644 ]   -0.00000  -0.00000 -10.00000     |
|  18  Ni   [   0.623 ,   0.622 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  19  Ni   [   3.115 ,   0.622 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  20  Ni   [   5.608 ,   0.622 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  21  Ni   [   0.623 ,   3.115 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  22  Ni   [   3.115 ,   3.115 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  23  Ni   [   5.608 ,   3.115 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  24  Ni   [   0.623 ,   5.607 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  25  Ni   [   3.115 ,   5.607 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  26  Ni   [   5.608 ,   5.607 ,   4.406 ]   -0.00000  -0.00000 -10.00000     |
|  27  Ni   [   1.869 ,   1.869 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  28  Ni   [   4.361 ,   1.869 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  29  Ni   [   6.854 ,   1.869 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  30  Ni   [   1.869 ,   4.361 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  31  Ni   [   4.361 ,   4.361 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  32  Ni   [   6.854 ,   4.361 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  33  Ni   [   1.869 ,   6.854 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  34  Ni   [   4.361 ,   6.854 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  35  Ni   [   6.854 ,   6.854 ,   6.169 ]   -0.00000  -0.00000 -10.00000     |
|  36  Ni   [   0.623 ,   0.622 ,   7.977 ]   -0.00000  -0.00000 -10.00000     |
|  37  Ni   [   3.125 ,   0.623 ,   7.977 ]   -0.00000  -0.00000 -10.00000     |
|  38  Ni   [   5.598 ,   0.623 ,   7.977 ]   -0.00000  -0.00000 -10.00000     |
|  39  Ni   [   0.623 ,   3.123 ,   7.971 ]   -0.00000  -0.00000 -10.00000     |
|  40  Ni   [   3.084 ,   3.081 ,   8.044 ]   -0.00000  -0.00000 -10.00000     |
|  41  Ni   [   5.640 ,   3.081 ,   8.044 ]   -0.00000  -0.00000 -10.00000     |
|  42  Ni   [   0.623 ,   5.599 ,   7.971 ]   -0.00000  -0.00000 -10.00000     |
|  43  Ni   [   3.083 ,   5.642 ,   8.043 ]   -0.00000  -0.00000 -10.00000     |
|  44  Ni   [   5.641 ,   5.643 ,   8.043 ]   -0.00000  -0.00000 -10.00000     |
|  45   S   [   4.364 ,   4.366 ,   9.313 ]   -0.00000  -0.00000  -6.00000     |
|  46   C   [   4.364 ,   4.368 ,  11.106 ]   -0.00000  -0.00000  -4.00000     |
|  47   H   [   4.367 ,   6.532 ,  11.228 ]   -0.00000  -0.00000  -1.00000     |
|  48   H   [   4.367 ,   2.204 ,  11.228 ]   -0.00000  -0.00000  -1.00000     |
|  49   C   [   4.367 ,   3.145 ,  11.808 ]   -0.00000  -0.00000  -4.00000     |
|  50   C   [   4.366 ,   5.592 ,  11.807 ]   -0.00000  -0.00000  -4.00000     |
|  51   C   [   4.369 ,   5.591 ,  13.208 ]   -0.00000  -0.00000  -4.00000     |
|  52   C   [   4.369 ,   3.145 ,  13.208 ]   -0.00000  -0.00000  -4.00000     |
|  53   H   [   4.374 ,   2.203 ,  13.783 ]   -0.00000  -0.00000  -1.00000     |
|  54   H   [   4.374 ,   6.534 ,  13.783 ]   -0.00000  -0.00000  -1.00000     |
|  55   C   [   4.369 ,   4.368 ,  13.913 ]   -0.00000  -0.00000  -4.00000     |
|  56   S   [   4.368 ,   4.368 ,  15.711 ]   -0.00000  -0.00000  -6.00000     |
|  57  Ni   [   0.624 ,   0.624 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  58  Ni   [   3.116 ,   0.624 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  59  Ni   [   5.609 ,   0.624 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  60  Ni   [   0.624 ,   3.116 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  61  Ni   [   3.116 ,   3.116 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  62  Ni   [   5.609 ,   3.116 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  63  Ni   [   0.624 ,   5.609 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  64  Ni   [   3.116 ,   5.609 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  65  Ni   [   5.609 ,   5.609 ,  17.080 ]   -0.00000  -0.00000 -10.00000     |
|  66  Ni   [   1.870 ,   1.870 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  67  Ni   [   4.362 ,   1.870 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  68  Ni   [   6.855 ,   1.870 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  69  Ni   [   1.870 ,   4.362 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  70  Ni   [   4.362 ,   4.362 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  71  Ni   [   6.855 ,   4.362 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  72  Ni   [   1.870 ,   6.855 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  73  Ni   [   4.362 ,   6.855 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  74  Ni   [   6.855 ,   6.855 ,  18.842 ]   -0.00000  -0.00000 -10.00000     |
|  75  Ni   [   0.624 ,   0.624 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  76  Ni   [   3.116 ,   0.624 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  77  Ni   [   5.609 ,   0.624 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  78  Ni   [   0.624 ,   3.116 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  79  Ni   [   3.116 ,   3.116 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  80  Ni   [   5.609 ,   3.116 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  81  Ni   [   0.624 ,   5.609 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  82  Ni   [   3.116 ,   5.609 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  83  Ni   [   5.609 ,   5.609 ,  20.605 ]   -0.00000  -0.00000 -10.00000     |
|  84  Ni   [   1.870 ,   1.870 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  85  Ni   [   4.362 ,   1.870 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  86  Ni   [   6.855 ,   1.870 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  87  Ni   [   1.870 ,   4.362 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  88  Ni   [   4.362 ,   4.362 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  89  Ni   [   6.855 ,   4.362 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  90  Ni   [   1.870 ,   6.855 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  91  Ni   [   4.362 ,   6.855 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
|  92  Ni   [   6.855 ,   6.855 ,  22.367 ]   -0.00000  -0.00000 -10.00000     |
+------------------------------------------------------------------------------+
|  15 E =  0.000508546 dE =  7.311566e-08 dH =  7.445477e-05  

          
The script is in the attachment

whar's wrong with it? should i increase the integral lower bound?

17
General Questions and Answers / Question about stacking
« on: December 9, 2013, 08:50 »
Dear QuantumWise staff

i made a two-probe system as shown in the attachment, it is stacking fault(i mean in the Z-direction the periodicity is broken)

left electrode: ABAB...
right electrode: BABA...

is it right to use this type of two-probe system? or can it lead to wrong electronic transport properties
?

18
General Questions and Answers / Does the phase of electron change in the coherence transport ?
« on: November 12, 2013, 02:44 »
Dear QuantumWise staff:
    Does the phase of electron change in the coherence transport ? 

19
General Questions and Answers / How to obtain DOS from a subband
« on: May 6, 2013, 04:36 »
Dear QuantumWise staff:

     The bandstructure of zigzag graphene nanoribbons(n=12)is shown in the attachment. there are three subbands in the  energy region of [0eV, 2eV].
      i want to get the DOS of a specified subband in the energy region of [0eV, 2eV](red arrow or blue arrow )
how to compile the script in atk 2012.8.2?

20
General Questions and Answers / Questions on script of TE
« on: March 2, 2013, 14:41 »
Dear QuantumWise staff:
       i use the script to calculate TE, the script is as follow:
*****************************************************************
# Define input and output NetCDF files here 
scf_filename = "/home/zwk/New/SY12C/SY12C-scf%g.nc"
analysis_filename = "/home/zwk/New/SY12C/SY12C-TE.nc" 
 
biases = [0., 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2]
# Read configurations from NetCDF files
configurations = [ ]
for bias in biases:
   
    configurations.append(nlread(scf_filename % bias, DeviceConfiguration)[0])

biases = [float(conf.calculator().electrodeVoltages()[0]-conf.calculator().electrodeVoltages()[1]) for conf in configurations]
configurations = [configurations[j] for j in numpy.argsort(biases)]


for configuration in configurations:

    # For each one, extract the bias,
    calculator = configuration.calculator()
    bias = calculator.electrodeVoltages()[0]-calculator.electrodeVoltages()[1]

    # ... calculate and save the transmission spectrum,
    transmission_spectrum = TransmissionSpectrum(
        configuration=configuration,
        energies=numpy.linspace(-2,2,201)*eV,
        kpoints=MonkhorstPackGrid(1,1),
        energy_zero_parameter=AverageFermiLevel,
        infinitesimal=1e-06*eV,
        self_energy_calculator=KrylovSelfEnergy(),
        )
    nlsave(analysis_filename, transmission_spectrum, object_id="Transmission %s" % bias)
    nlprint(transmission_spectrum)
************************************************************************
but something wrong with it
*************************************************************
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 11.8.2 [Build 09819e5]                                     |
|                                                                              |
+------------------------------------------------------------------------------+
Traceback (most recent call last):
  File "SY12C-TE.py", line 10, in <module>
    configurations.append(nlread(scf_filename % bias, DeviceConfiguration)[0])
  File "./zipdir/NL/IO/NLSaveUtilities.py", line 256, in nlread
  File "./zipdir/NL/CommonConcepts/Configurations/ReadConfigurations.py", line 165, in nlreadDeviceConfiguration
  File "./zipdir/NL/NanoLanguage/ScopeExecuter.py", line 66, in execute
NL.ComputerScienceUtilities.Exceptions.NLScopeExecutionError: invalid syntax (<string>, line 2)
*********************************************************************************************************
how to modify the script?

21
General Questions and Answers / How to plot electrostatic potential?
« on: February 22, 2013, 14:30 »
Dear QuantumWise staff:

how to plot electrostatic potential (not electrostatic difference potential) using ATK2011.8?

22
General Questions and Answers / Questions on sequential tunneling
« on: December 28, 2012, 04:02 »
Dear QuantumWise staff:
     
      A few days ago, i was fortunate to read the paper by professor Anders and Kurt (IEEE,2011), it is very helpful. Sequential tunneling mentioned in the paper puzzle me a lot. 

i don't know what' the different between Sequential tunneling, incoherent tunneling, hopping, and Coulomb blockade regime?

in my view:
Ⅰ. ①(the length of central molecule is smaller than 2.5nm). if the molecule-electrode coupling is strong, the transport regime is coherent tunneling, the incident wave function tunnel through the electrostatic potential field  does not cause any change of the electrostatic potential field. it is to say that the incident electron need only one step from left electrode to right electrode. if the bias is low, there is no "molecule energy" in the bias window the tunneling is weak, if the bias is high, some molecule eneries in the bias window, the tunneling is orbital-mediated and it is strong. DFT-NEGF(ATK) can deal with it very powerful.
Am i right?

②(the length of central molecule is longer than 2.5nm). the incident electron will stay for a long time in a potential well of the central molecule, the phase of incident electron is changed due to the interaction. at this time, incoherent tunneling is the main transport regime, and it can be decompose into a series of coherent tunneling. is it means Sequential tunneling?  i only know hopping is temperature-dependent, tunneling is not, and hopping is over the barrier, tunneling is through the barrier.what' the different between Hopping and sequential tunneling?
 

Ⅱ. if the molecule-electrode coupling is weak, couloumb blockade effect between the molecule and electrode is established, the electron spend long enough time stay in the central region, so, electron(incident)-electron(molecule) exchange-correlation interaction and interaction between incident electron wave and molecule vibration can't be neglected. the interaction lead to Kondo effect(at Kondo temperture) and inelastic tunneling. DFT-NEGF(ATK) can not simulate.  Am i right?


Regards
kaypu





     

23
General Questions and Answers / Question on script of energy dependent LDOS
« on: December 26, 2012, 02:02 »
Dear QuantumWise staff:
   
      i've got a problem in calculating energy dependent LDOS using the script in "http://www.quantumwise.com/documents/tutorials/latest/MolecularDevice/index.html/chap.analysis.html#sect1.analysis.lddos", maybe the memory of my laptop is not enough. So i save the LDOS in separated NC(-1~-0.5eV: LDOS0.nc; -0.4~0eV: LDOS1.nc; 0.1~0.5eV: LDOS2.nc; 0.6~1eV: LDOS3.nc).
     
      how to plot all of these NC in one pic?

PS: the script in the website:

      # import list with lddos
lddos_list = nlread('lddos.nc', LocalDeviceDensityOfStates)            .............how to read all of the NC using nlread?

#Find the z-spacing
dX, dY, dZ = lddos_list[0].volumeElement().convertTo(Ang)
dz = dZ.norm()
shape = lddos_list[0].shape()
z = dz * numpy.arange(shape[2])

# calculate average lddos along z for each spectrum
energies = []
lddos_z = []
for lddos in lddos_list:
    energies = energies + [lddos.energy().inUnitsOf(eV)]
    avg_z = numpy.apply_over_axes(numpy.mean,lddos[:,:,:],[0,1]).flatten()
    lddos_z = lddos_z + [avg_z]

# plot as contour plot
# make variables
energies = numpy.array(energies)
X, Y = numpy.meshgrid(z, energies)
Z = numpy.array(lddos_z).reshape(numpy.shape(X))


import pylab
#plot the LDDOS(E, z)
pylab.xlabel('z (Angstrom)',fontsize=12,family='sans-serif')
pylab.ylabel('Energy (eV)',fontsize=12,family='sans-serif')
contour_values = numpy.linspace(0,0.02,21)
pylab.contourf(X, Y, Z, contour_values)
pylab.colorbar()
pylab.axis([6,16,-3, 3])

pylab.title('Au-DTB-Au : LDDOS(E, z)')
pylab.savefig('lddos.png',dpi=100)


pylab.show()   


Regards
kaypu

24
General Questions and Answers / Question on combining nc
« on: December 25, 2012, 02:22 »
Dear QuantumWise staff:

     i want to combine four separate NC into one NC, how to do it?

Merry Christmas


25
General Questions and Answers / Question on Van der Waals potential in DFT-NEGF
« on: December 14, 2012, 10:14 »
Dear QuantumWise staff:

       i want to study the transport properties fo Li absorption in a few layer graphene, and Van der Waals interaction is important in multilayer graphene, it will change interlayer spacing of the multilayer graphene. using DFT-D, i can opt the system, for transport of DFT-NEGF, can ATK suit for the job? or modify the EXC, maybe +empirical potential.

Regards

26
General Questions and Answers / Question on initial state under bias
« on: December 14, 2012, 03:20 »
Dear QuantumWise staff:
     
     i  use initial state of low bias to calculate the state of high bias.  if the initial state of low state i used is an unconverged state(bias= 1.5V, dH=1E-1), fortunately, i got converged state(bias=1.6, dH=1E-5). is it safe to use this converged state to get TE or DOS under 1.6V?

Regards

27
General Questions and Answers / Question about electrostatic difference potential
« on: December 2, 2012, 01:51 »
Dear QuamWise staff:

   professor Anders  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.

i don't know how to define density of the neutral atom? is it the summation of the Isolated atom?

another question, atk use electrostatic difference potential to calculate voltage drop,  it is to say that : Voltage drop= electrostatic difference potential(under bias)- electrostatic difference potential(zero bias), we can also get the voltage drop using electrostatic potential.  it means: Voltage drop= electrostatic potential(under bias)-electrostatic potential(zero bias)  am i right?

28
General Questions and Answers / Question about molecular energy spectrum in two-probe
« on: November 21, 2012, 08:47 »
Dear QuantumWise staff:

i calculate the  molecular energy spectrum in two-probe, the energy zero is Fermilevel, i will upload the energy spectrum in the attcherment.

the orbital of 109 is LUMO, but there are still almost one electron? why?

  Au electrode consists of a (5×5) supercell, T=300K, the K-point 3*3*100, it is enough to correctly describe  Fermilevel.


29
General Questions and Answers / how to use preconditioner Kerker for convergence?
« on: November 12, 2012, 01:33 »
Dear QuantumWise staff

my two-probe system is quasi-one-dimensional armchair-nanoribbon, and it is hard to converge for 0.4V,  the parameter: T=1000k, meshcutoff=75.0*Hartree, k-point=1*1*100, damping factor=0.01 history step=10
*************************************************
........
307 E = -365.631 dE =  1.123687e-03 dH =  6.392827e-03
308 E = -365.632 dE =  6.391485e-04 dH =  2.665628e-03
309 E = -365.632 dE =  5.746915e-06 dH =  2.754449e-03
310 E = -365.632 dE =  1.763446e-04 dH =  2.789024e-03
311 E = -365.632 dE =  2.103748e-04 dH =  1.979505e-03
312 E = -365.632 dE =  5.505047e-05 dH =  2.247296e-03
*************************************************
dE meets the needs of condition of convergence but dH, i don't know whether the parameter of preconditioner Kerker can help me. if this could be, can you tell me how to set the parameter of preconditioner Kerker.

30
General Questions and Answers / Another question about calculation error
« on: November 9, 2012, 01:26 »
Dear QuantumWise staff:

i got another problem when i calculation the two-probe system under 0.1V:
***************************************************************************
/opt/QuantumWise/atk-11.8.2/atkpython/bin/atkpython: line 3:  8058 Killed                  PSEUDOPOTENTIALS_PATH=$EXEC_DIR/../share/pseudopotentials GPAW_SETUP_PATH=$EXEC_DIR/../share/gpaw-setups/ PYTHONHOME=$EXEC_DIR/.. PYTHONPATH= LD_LIBRARY_PATH=$EXEC_DIR/../lib $EXEC_DIR/atkpython_exec $*
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what's wrong?  something wrong with PSEUDOPOTENTIALS PATH?

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