Topics

1

General Questions and Answers / How to create MPSH in new version

« on: August 11, 2010, 10:37 »

Dear all,
I am a little bit confuse with the new version. My aim is to project Hamiltonian in the scattering region.
In the old version I used this script:
######################################
from ATK.TwoProbe import *

# Restore initial density from old calculation
scf = restoreSelfConsistentCalculation("name.nc")

vnl_file = VNLFile('name.vnl')
atomic_configuration = vnl_file.readAtomicConfigurations()['name']

projected_hamiltonian_eigenstates = calculateProjectedHamiltonianEigenstates(
    self_consistent_calculation = scf,
    projection_atoms = (32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76),
   quantum_numbers = [(72,73,74,75),Spin.Up]
)


vnl_file = VNLFile("name-MPSH.vnl")
vnl_file.addToSample(atomic_configuration,'name-MPSH')
for projected_hamiltonian_eigenstates_index,state in enumerate(projected_hamiltonian_eigenstates):
    label = 'Projected Hamiltonian Eigenstates-0V'+' '+str(projected_hamiltonian_eigenstates_index)
    vnl_file.addToSample(state, 'name-MPSH', label)
#############################################################################

So now in the new Nanolenguage :
instead to used readAtomicConfiguration I should use nlread ('name-file', object_id="gID000")[0]

That is Ok.

Now, how I should replace restartSelfConsistentCoalculations?

How to save my output file because the new version is not using .vnl files anymore?

Or with one word can you just write a small script from the beginning to the end, please?

Few more points that I noticed :
When I have Transmission spectra  in old version was possible to place the mouse at some point of the screen and I will have X and Y coordinates. The same was valid for the Molecule Energy spectra. It was possible to see the number of Molecule orbital and the energy from the window. In the new version it is not possible. I believe that will be very useful and convenient to have these features back in the new version. 

2

General Questions and Answers / Error: 'function' object has no attribute 'isabs'

« on: July 30, 2010, 11:04 »

Hi all,
I am playing now with the new version. I am having small problem. After making my geometry and input file with VNL/ATK I saved my file such as "input.py". The file after this is executable-running without a problem but when I wanted to open the same file with VNL again I am having this error:

The following error message was generated when running the script:
'function' object has no attribute 'isabs'
Typically this is caused by a syntax error or a spelling mistake; the message above should be helpful in correcting the issue in such cases.

Traceback (most recent call last):
  File "./zipdir/NL/GUI/Tools/ScriptGenerator/ScriptGenerator.py", line 474, in dropReceiver
  File "./zipdir/NL/NanoLanguage/ScopeExecuter.py", line 58, in execute
NLScopeExecutionError: 'function' object has no attribute 'isabs'

I didn't change a single letter in the file. It is created only with VNL.

Thank you very much in advance.

3

General Questions and Answers / How to apply charge of the system in ATK 2008.10.0 ???

« on: May 24, 2010, 11:04 »

Dear All,
I would like to apply additional charge to my molecule in ATK version 2008.10.0.
Molecule -> Molecule 1-?
Can you tell me if it possible to do this at all in 2008.10.0 version?

From the information posted here in this forum, I found that this is possible in the new version ATK 2010.02 with the object LCAOCalculator. I found the tutorial as well : Properties of an isolated benzene molecule.

4

Scripts, Tutorials and Applications / Function for charge density difference

« on: December 13, 2009, 13:57 »

Dear all,
I just want to ask you if it is possible to be create a script for charge redistrubution.


What I mean:
The transfered charged and the induced change in the electrostatic potential are obtained  by taking the difference between the self-consistent charge/potential  distribution in the equilibrium metal-molecule-metal junction and the charge/potential distribution in the isolated molecule plus the bare bimetallic junction.(Phys.Rev. B 69,085403 (2004))

I know that here we have a function written by ipsecog which calculated density difference.  I successfully used this function to calculated the density difference in different bias.
I trued to make the same for the charged redistribution for the : (metal-molecule-metal) - (molecule) and the error is :

File "elec_density-diffrence.py", line 22, in ?
    diff_density = calculateDensityDifference(density1,density2)
  File "elec_density-diffrence.py", line 15, in calculateDensityDifference
    density._ElectronDensity__electron_density_data = (n1-n2)
ValueError: shape mismatch: objects cannot be broadcast to a single shape


I know that is something wrong with the formats of the input files and I suspect that the reason is that for the metal-molecule-metal file I used Atk.TwoProbe method to calculate while for the molecule I used  ATK.KohnSham and according to me the size of the two files doesn't match. After this I made them text files but they are massive and impossible to handle.

I will really appreciate your help and ideas how to get the charge density difference.


----------------------------- This is my script-----------------------------------

from ATK.TwoProbe import *


def calculateDensityDifference (d1,d2):

    import copy

    n1 = d1.toArray()
    n2 = d2.toArray()
    density = copy.copy(d1)
    density._ElectronDensity__electron_density_data = (n1-n2)
    return density

scf1 = restoreSelfConsistentCalculation ('metal-molecule-metal.nc')
scf2 = restoreSelfConsistentCalculation ('molecule-scf.nc')
density1 = calculateElectronDensity(scf1)   # Two-probe
density2 = calculateElectronDensity(scf2)   # molecule 0.0 V bias
diff_density = calculateDensityDifference(density1,density2)

f = VNLFile('elec_density-difference.vnl')
f.addToSample(atomic_configuration,'elec_density-difference')
f.addToSample(density1,'elec_density-difference','Two-probe')
f.addToSample(density2,'elec_density-difference','Molecule')
f.addToSample(diff_density,'elec_density-difference','Difference density')

5

Installation and License Questions / Error[88]: Operating in stand-alone mode using terminal client.

« on: September 10, 2009, 10:53 »

Dear all,
I just get the license but I have this error :

Sentinel RMS Development Kit: Error[88]: Operating in stand-alone mode using terminal client. This is not allowed by the vendor.
Unable to start license system (Error 88)
Connection to license server lost!
The process for monitoring the license has been killed or tampered by user - shutting down (1)



My system is 64 bit and atk-2009.06 is 64 bit.

Thank you in advance.

6

General Questions and Answers / Do we really have scattering in the "scattering " region ?

« on: July 3, 2009, 12:33 »

Hi Andres,
I looked for an answer of my question in the forum before I wrote this message because I don't want to waist your time .  So I didn't find it , therefore I decided to ask. I am 90 % sure for the answer, but I just want to be 110 % sure


My question is : When the Current and Transmission function are calculate for the scattering region, do we include real scattering between the electrons ?

I checked the papers and according to M. Brandbyge, J.-L. Mozos, P. Ordejón, J. Taylor, and K. Stokbro, Phys. Rev. B 65, 165401 (2002)   equation 42 , the current depend on only how the channel is connected with the contacts. There is no scattering at all. Is it correct?

If it is true in this case ATK works in "ballistic" transport regime ? Is it correct?

Thank you very much in advance and have a HAPPY SUMMER.
See you soon

Moderator edit: Fixed typo in subject to help searching

7

General Questions and Answers / Pseudopotential transfer between ATK and SIESTA

« on: April 22, 2009, 18:41 »

Dear all,
I would like to know if it is possible  to transfer psoudopotentials between ATK and SIESTA.

I made N-pseudopotential in SIESTA, the beginning of the file is :


SIESTA---------- NITROGEN.psf


  N ca nrl nc
 ATM 3.2.2 22-APR-09 Kerker                                   
 2s 2.00  r= 0.92/2p 3.00  r= 0.80/3d 0.00  r= 0.79/4f 0.00  r= 0.79/ 
   4  0 1018  0.354107453809E-03  0.125000000000E-01   5.00000000000   
 Radial grid follows
  0.445412344792E-05  0.896427287179E-05  0.135311529916E-04  0.181554773917E-04
  0.228379686322E-04  0.275793583619E-04  0.323803874325E-04  0.372418060146E-04
  0.421643737147E-04  0.471488596942E-04  0.521960427889E-04  0.573067116317E-04
  0.624816647748E-04  0.677217108153E-04  0.730276685210E-04  0.784003669585E-04
  0.838406456230E-04  0.893493545690E-04  0.949273545435E-04  0.100575517120E-03
  0.106294724837E-03  0.112085871330E-03  0.117949861479E-03  0.123887611544E-03
  0.129900049310E-03  0.135988114233E-03  0.142152757586E-03  0.148394942607E-03
  0.154715644649E-03  0.161115851336E-03  0.167596562712E-03  0.174158791402E-03
-----------------------------------------------------------------------------------------------------------------------

The ATK pseudopotential file with name - n_pz.upf  contain this information in the begining:

<PP_INFO>
 ATM3      no_date   Troullier-Martins
</PP_INFO>
<PP_HEADER>
    0                  Version Number
    N                  Element
   NC                  Norm - Conserving pseudopotential
    T                  Nonlinear Core Correction
 SLA  PZ   NOGX NOGC   PZ   Exchange-Correlation functional
                5      Z valence
                0      Total energy
  0.0000000  0.0000000 Suggested cutoff for wfc and rho
    3                  Max angular momentum component
 1018                  Number of points in mesh
    4    4             Number of Wavefunctions, Number of Projectors
 Wavefunctions         nl  l   occ
                       2S  0  2
                       2P  1  3
                       3D  2  0
                       4F  3  0
</PP_HEADER>
<PP_MESH>
<PP_R>
     4.45412344792e-06     8.96427287179e-06     1.35311529916e-05     1.81554773917e-05
     2.28379686322e-05     2.75793583619e-05     3.23803874325e-05     3.72418060146e-05
     4.21643737147e-05     4.71488596942e-05     5.21960427889e-05     5.73067116317e-05
     6.24816647748e-05     6.77217108153e-05      7.3027668521e-05     7.84003669585e-05
      8.3840645623e-05      8.9349354569e-05     9.49273545435e-05      0.00010057551712
     0.000106294724837      0.00011208587133     0.000117949861479     0.000123887611544
      0.00012990004931     0.000135988114233     0.000142152757586     0.000148394942607
     0.000154715644649     0.000161115851336     0.000167596562712     0.000174158791402
     0.000180803562768     0.000187531915069     0.000194344899623     0.000201243580973
     0.000208229037052     0.000215302359352     0.000222464653093       0.0002297170374
     0.000237060645471      0.00024449662476     0.000252026137154     0.000259650359155
------------------------------------------------------------------------------------------------------------------------------
The beginning of the radial grid is the same. I checked the file further and the numbers are almost match. Therefore my question is:
Can I use the redial grid from ATK program in my SIESTA calculation?
Obviously their is some relation.
One more question:
what is the difference between the files:
'chemical-element' _pz.upf and 'hemical-element' _pbe.upf
Thank you very much for your help.