Messages

31

General Questions and Answers / question on admittance code tutorial

« on: August 27, 2015, 07:49 »

Hi everyone,
I have a question on the admittance code tutorial.
In that code the Hamiltonian is calculated from calculateHamiltonianAndOverlap. But with what bases? tight binding as mentioned in the reference paper at gamma point? In addition, what should i do to improve it for DFT ?
thanks in advanced,
Rose

32

General Questions and Answers / Re: Convergence Problem in IV for 1V bias

« on: June 21, 2015, 18:01 »

Hi
thanks.
I used 1*10*100 points for k sampling but it did not converged for 1V
any other ideas?
rose

33

General Questions and Answers / Re: Convergence Problem in IV for 1V bias

« on: June 11, 2015, 12:47 »

Hi
Thanks. I check it with 15unitcell in z direction and larger supercell as electrodes, but still i have problem in bias voltage 1V.
Should I do it with larger channel?
yours
Rose

34

General Questions and Answers / Convergence Problem in IV for 1V bias

« on: June 10, 2015, 18:19 »

Hi,
I have structure as attached and I check all the techniques that mentioned in the forum and tutorials to get convergence but i did not success. For short I check following options: increasing  k points in x y and z, mesh cut off, electron temperature, history steps,circle points, Integral lower boundary and reduce damping factor. I use both DZP, SZP, LSDA, sGGA but i not get any divergence while bias is 1V. I got divergence with zero and 0.5V bias.
any idea how can i fix it?
thanks
rose

35

General Questions and Answers / Re: admittance code tutorial

« on: March 13, 2015, 16:03 »

thanks...i am running it and till now no problem...Nice Work...

36

General Questions and Answers / Re: admittance code tutorial

« on: March 13, 2015, 12:42 »

thanks for the response, as i mentioned i overcome that problem by adding up to individual code to single one. Now i can not understand why Gamma_L is asking for unit or something like that???!!!
___________________________________________________________________________________
 YD = displacementAdmittance(average_fermi_level, omega, T, N, H, S, Sigma_L, Sigma_R)
  File "c:\users\utabco\appdata\local\temp\2897894476902862.py", line 75, in displacementAdmittance
    Gamma_L = 1j*(Sigma_L-numpy.conj(Sigma_L.transpose()))
  File ".\zipdir\NL\CommonConcepts\PhysicalQuantity.py", line 425, in __sub__
  File ".\zipdir\NL\CommonConcepts\PhysicalQuantity.py", line 753, in inUnitsOf
  File ".\zipdir\NL\CommonConcepts\PhysicalQuantity.py", line 249, in unit
AttributeError: 'PhysicalQuantity' object has no attribute '_PhysicalQuantity__unit'
___________________________________________________________________________________
what it means? and how can i overcome this error?
thanks,

37

General Questions and Answers / Re: admittance code tutorial

« on: March 13, 2015, 11:46 »

I add all two files togeather now a new error:

   YD = displacementAdmittance(average_fermi_level, omega, T, N, H, S, Sigma_L, Sigma_R)
  File "c:\users\utabco\appdata\local\temp\2897894476902862.py", line 75, in displacementAdmittance
    Gamma_L = 1j*(Sigma_L-numpy.conj(Sigma_L.transpose()))
  File ".\zipdir\NL\CommonConcepts\PhysicalQuantity.py", line 425, in __sub__
  File ".\zipdir\NL\CommonConcepts\PhysicalQuantity.py", line 753, in inUnitsOf
  File ".\zipdir\NL\CommonConcepts\PhysicalQuantity.py", line 249, in unit
AttributeError: 'PhysicalQuantity' object has no attribute '_PhysicalQuantity__unit'

now what??

38

General Questions and Answers / admittance code tutorial

« on: March 12, 2015, 22:46 »

Hi
In the short tutorial admittance, i add the path to the system and then run the code (CNT_admittance.py). unfortunetly i got error as follow:

eps = 1e-5*eV
NameError: name 'eV' is not defined


by removing eV from the admittance... the code is running and then error as follow:

    TE = boltzmann_constant*T
NameError: global name 'boltzmann_constant' is not defined

and by defining boltzmann_constant in admitance and then running following error appear:

0 = Ef-omega-8*TE
  File ".\zipdir\NL\CommonConcepts\PhysicalQuantity.py", line 425, in __sub__
  File ".\zipdir\NL\CommonConcepts\PhysicalQuantity.py", line 754, in inUnitsOf

NL.ComputerScienceUtilities.Exceptions.NLValueError: Unable to convert unit value 0.2064 K to an incompatible unit Hartree.

which apper to be happen due to not defining proper unit in previous parts.
How can i correct the CNT_admitance.py or admitance.py
?
thanks

39

General Questions and Answers / question on transport above surface

« on: March 7, 2015, 10:03 »

Hi,
I would wonder how i can investigate transmission pathway or similar characteristic to see the transport above the surface of nano-structures such as benzene. I read somewhere that the transport properties of these structures are above surface of atoms (almost 0.6A above surface for benzene).
yours

40

General Questions and Answers / Run Time Error on phonon

« on: December 27, 2014, 06:56 »

To all
i use atk 2014.1 trial license. I run phonon band-structure for 72 carbon atoms. However, i got "terminate rum time error". can it be problem in my structure or ATK??! I use Windows version with i7-8G RAM,

thanks

41

General Questions and Answers / change in extended huckel parameters

« on: December 2, 2014, 08:09 »

hi
i would wonder how can i change the intrinsic parameters of extended huckel (i.e. Eion,W1,W2,etc) for new usage of them?
I can not find any option in VNL for that or in the editor.
thanks

42

General Questions and Answers / Lithium niobate LiNbO3

« on: January 29, 2014, 12:26 »

Hi everyone,
i can not find the structure of Lithium niobate in the database of ATK. I would wonder if anyone known the exact places of atoms in the primitive unit cell.....
thanks

43

General Questions and Answers / Electron localization function

« on: January 18, 2014, 09:28 »

Hi everyone,
I try to use Electron localization function in ATK 11.8.2 but i got error even using the example of
http://quantumwise.com/documents/manuals/latest/ReferenceManual/index.html/ref.electronlocalizationfunction.html

I got following error:
elf = ElectronLocalizationFunction(molecule_configuration)
NameError: name 'ElectronLocalizationFunction' is not defined

how can i solve it?

thanks

44

General Questions and Answers / abinit error in ATK 13.8

« on: October 26, 2013, 17:51 »

Hi,
i want to run very simple calculation using Abinit in ATK 13.8
unfortunately i got following error
what is the problem? and how i can solve it?
+------------------------------------------------------------------------------+
| NanoLanguageScript execution started                                         |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 13.8.0 [Demo][Build e8e7427]                               |
|                                                                              |
+------------------------------------------------------------------------------+
+----------------------------------------------------------+
| Bulk Bravais lattice                                     |
+----------------------------------------------------------+
Type:
UnitCell

Lattice constants:

Primitive vectors:
u_1 =     10.000000      0.000000      0.000000 Ang
u_2 =      0.000000     17.104300      0.000000 Ang
u_3 =      0.000000      0.000000      2.461002 Ang

+----------------------------------------------------------+
| Bulk: Cartesian (Angstrom) / fractional                  |
+----------------------------------------------------------+
10
Bulk
C     5.000000e+00  1.210430e+01  0.000000e+00    0.50000  0.70768  0.00000
C     5.000000e+00  5.000000e+00  0.000000e+00    0.50000  0.29232  0.00000
C     5.000000e+00  5.710430e+00  1.230501e+00    0.50000  0.33386  0.50000
C     5.000000e+00  7.131290e+00  1.230501e+00    0.50000  0.41693  0.50000
C     5.000000e+00  7.841720e+00  0.000000e+00    0.50000  0.45846  0.00000
C     5.000000e+00  9.262580e+00  0.000000e+00    0.50000  0.54154  0.00000
C     5.000000e+00  9.973010e+00  1.230501e+00    0.50000  0.58307  0.50000
C     5.000000e+00  1.139387e+01  1.230501e+00    0.50000  0.66614  0.50000
H     5.000000e+00  1.319430e+01  0.000000e+00    0.50000  0.77140  0.00000
H     5.000000e+00  3.910001e+00  0.000000e+00    0.50000  0.22860  0.00000
+------------------------------------------------------------------------------+
|                                                                              |
| Abinit Calculation  [Started Sat Oct 26 12:05:39 2013]                       |
|                                                                              |
+------------------------------------------------------------------------------+
################################################################################
#                                                                              #
# INFO                                                                         #
#                                                                              #
# ============================================================================ #
#                                                                              #
# Running "C:\Program Files\QuantumWise\atk-13.8.0\atkpython\bin\abinit.exe" < #
# "c:\docume~1\apaclu~1\locals~1\temp\tmpiu01f8\files.files"                   #
#                                                                              #
################################################################################
+------------------------------------------------------------------------------+
| Abinit log                                                                   |
+------------------------------------------------------------------------------+
| Abinit PID = 1628                                                            |
| Path to files: c:\docume~1\apaclu~1\locals~1\temp\tmpiu01f8                  |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
Traceback (most recent call last):
  File ".\zipdir\NL\Calculators\AbinitCalculator\AbinitCalculator.py", line 510, in _results
  File ".\zipdir\NL\Calculators\AbinitCalculator\AbinitRun.py", line 739, in readResults
NLIOError: ERROR while reading c:\docume~1\apaclu~1\locals~1\temp\tmpiu01f8\output_OUT.nc

45

General Questions and Answers / Re: Joint DOS in optic

« on: October 26, 2013, 17:47 »

Would it be possible to guide me about the algorithm that i should do in order to define JDOS in atk?
thanks