Messages

31

General Questions and Answers / Re: extract isovalue of the transmission eigenstates

« on: August 30, 2013, 16:59 »

Ok...Ok...That might be where the problem lies...it is five column..."the first is the atom number, second (?), the last three are the x,y,z coordinates of the atom center".

Let me try to change the code first...

But... why do they make a space for such an extra meaningless column....

32

General Questions and Answers / Re: extract isovalue of the transmission eigenstates

« on: August 30, 2013, 16:53 »

Ok. I have checked the coordinates. If converting the unit from Bohr to Angstrom, they appear to be correct. Then the problem should lie in the importing of the cube file to VESTA...

Thank you for your help, Anders.

33

General Questions and Answers / Re: extract isovalue of the transmission eigenstates

« on: August 30, 2013, 16:37 »

Oh...sorry...I am less familiar with the Gaussian cube format... let me read it through first...

But I still don't think the problem is solved because when I drag and drop the CUBE file to VESTA, the atomic coordinates are all wrong... (see attached file extracted from VESTA and the one directly from VNL)...

34

General Questions and Answers / Re: extract isovalue of the transmission eigenstates

« on: August 30, 2013, 16:03 »

The system contains Ti (22), Mo (42), and S(16). Obviously the atomic numbers in the first a few lines are wrong.

Here I also attached the python file for your reference.

35

General Questions and Answers / Re: extract isovalue of the transmission eigenstates

« on: August 30, 2013, 15:58 »

OK. Here it is.

Code

CUBE FILE. DATA VALUES IN UNITS OF 1/Hartree**0.5/Bohr**1.5, LENGTHS IN BOHR
OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z
  213 0.000000e+00 0.000000e+00 0.000000e+00
  257 1.812844e-01 1.110047e-17 1.110047e-17
   58 0.000000e+00 1.783511e-01 1.092086e-17
  746 0.000000e+00 0.000000e+00 1.813732e-01
   22 2.777701e+00 2.586091e+00 7.464619e-01
   22 1.162003e+01 2.586091e+00 7.464619e-01
   22 2.777701e+00 7.758274e+00 7.464619e-01
   22 1.162003e+01 7.758274e+00 7.464619e-01
   42 1.821067e+01 1.724095e+00 2.239386e+00
   16 1.539942e+01 5.172182e+00 2.239386e+00
   16 2.102191e+01 5.172182e+00 2.239386e+00
   22 7.199100e+00 2.586091e+00 3.732310e+00
   22 7.199100e+00 7.758274e+00 3.732310e+00
   22 2.777701e+00 1.700851e-16 5.225234e+00
   22 1.162003e+01 7.115218e-16 5.225234e+00
   16 1.539942e+01 9.429425e-16 5.225234e+00
   16 2.102191e+01 1.287221e-15 5.225234e+00
   22 2.777701e+00 5.172182e+00 5.225234e+00
   22 1.162003e+01 5.172182e+00 5.225234e+00
   42 1.821067e+01 6.896278e+00 5.225234e+00
   22 7.199100e+00 4.408177e-16 8.212425e+00
   42 1.821067e+01 1.724095e+00 8.212425e+00
   22 7.199100e+00 5.172182e+00 8.212425e+00
   16 1.539942e+01 5.172182e+00 8.212425e+00
   16 2.102191e+01 5.172182e+00 8.212425e+00
   22 2.777701e+00 2.586091e+00 9.705349e+00
   22 1.162003e+01 2.586091e+00 9.705349e+00
   22 2.777701e+00 7.758274e+00 9.705349e+00
   22 1.162003e+01 7.758274e+00 9.705349e+00
   16 1.539942e+01 9.429425e-16 1.119827e+01
   16 2.102191e+01 1.287221e-15 1.119827e+01
   42 1.821067e+01 6.896278e+00 1.119827e+01
   22 7.199100e+00 2.586091e+00 1.269120e+01
   22 7.199100e+00 7.758274e+00 1.269120e+01
   22 2.777701e+00 1.700851e-16 1.418412e+01
   22 1.162003e+01 7.115218e-16 1.418412e+01
   42 1.821067e+01 1.724095e+00 1.418412e+01
   22 2.777701e+00 5.172182e+00 1.418412e+01
   22 1.162003e+01 5.172182e+00 1.418412e+01
   16 1.539942e+01 5.172182e+00 1.418412e+01
   16 2.102191e+01 5.172182e+00 1.418412e+01
   22 7.199100e+00 4.408177e-16 1.716997e+01
   16 1.539942e+01 9.429425e-16 1.716997e+01
   16 2.102191e+01 1.287221e-15 1.716997e+01
   22 7.199100e+00 5.172182e+00 1.716997e+01
   42 1.821067e+01 6.896278e+00 1.716997e+01
   22 2.777701e+00 2.586091e+00 1.866289e+01
   22 1.162003e+01 2.586091e+00 1.866289e+01
   22 2.777701e+00 7.758274e+00 1.866289e+01
   22 1.162003e+01 7.758274e+00 1.866289e+01
   42 1.821067e+01 1.724095e+00 2.015582e+01
   16 1.539942e+01 5.172182e+00 2.015582e+01
   16 2.102191e+01 5.172182e+00 2.015582e+01
   22 7.199100e+00 2.586091e+00 2.165008e+01
   22 7.199100e+00 7.758274e+00 2.165008e+01
   22 2.777701e+00 1.700851e-16 2.314301e+01
   22 1.162003e+01 7.115218e-16 2.314301e+01
   16 1.539942e+01 9.429425e-16 2.314301e+01
   16 2.102191e+01 1.287221e-15 2.314301e+01
   22 2.777701e+00 5.172182e+00 2.314301e+01
   22 1.162003e+01 5.172182e+00 2.314301e+01
   42 1.821067e+01 6.896278e+00 2.314301e+01
   22 7.199100e+00 4.408177e-16 2.612886e+01
   42 1.821067e+01 1.724095e+00 2.612886e+01
   22 7.199100e+00 5.172182e+00 2.612886e+01
   16 1.539942e+01 5.172182e+00 2.612886e+01
   16 2.102191e+01 5.172182e+00 2.612886e+01
   22 2.777701e+00 2.586091e+00 2.762178e+01
   22 1.162003e+01 2.586091e+00 2.762178e+01
   22 2.777701e+00 7.758274e+00 2.762178e+01
   22 1.162003e+01 7.758274e+00 2.762178e+01
   16 1.539942e+01 9.429425e-16 2.911470e+01
   16 2.102191e+01 1.287221e-15 2.911470e+01
   42 1.821067e+01 6.896278e+00 2.911470e+01
   22 7.199100e+00 2.586091e+00 3.060763e+01
   22 7.199100e+00 7.758274e+00 3.060763e+01
   22 2.777701e+00 1.700851e-16 3.210055e+01
   22 1.162003e+01 7.115218e-16 3.210055e+01
   42 1.821067e+01 1.724095e+00 3.210055e+01
   22 2.777701e+00 5.172182e+00 3.210055e+01
   22 1.162003e+01 5.172182e+00 3.210055e+01
   16 1.539942e+01 5.172182e+00 3.210055e+01
   16 2.102191e+01 5.172182e+00 3.210055e+01
   22 7.199100e+00 4.408177e-16 3.508774e+01
   16 1.539942e+01 9.429425e-16 3.508774e+01
   16 2.102191e+01 1.287221e-15 3.508774e+01
   22 7.199100e+00 5.172182e+00 3.508774e+01
   42 1.821067e+01 6.896278e+00 3.508774e+01
   22 2.777701e+00 2.586091e+00 3.658067e+01
   22 1.162003e+01 2.586091e+00 3.658067e+01
   22 2.777701e+00 7.758274e+00 3.658067e+01
   22 1.162003e+01 7.758274e+00 3.658067e+01
   42 1.821067e+01 1.724095e+00 3.807359e+01
   16 1.539942e+01 5.172182e+00 3.807359e+01
   16 2.102191e+01 5.172182e+00 3.807359e+01
   22 7.199100e+00 2.586091e+00 3.956651e+01
   22 7.199100e+00 7.758274e+00 3.956651e+01
   22 2.777701e+00 1.700851e-16 4.105944e+01
   22 1.162003e+01 7.115218e-16 4.105944e+01
   16 1.539942e+01 9.429425e-16 4.105944e+01
   16 2.102191e+01 1.287221e-15 4.105944e+01
   22 2.777701e+00 5.172182e+00 4.105944e+01
   22 1.162003e+01 5.172182e+00 4.105944e+01
   42 1.821067e+01 6.896278e+00 4.105944e+01
   22 7.199100e+00 4.408177e-16 4.404529e+01
   42 1.821067e+01 1.724095e+00 4.404529e+01
   22 7.199100e+00 5.172182e+00 4.404529e+01
   16 1.539942e+01 5.172182e+00 4.404529e+01
   16 2.102191e+01 5.172182e+00 4.404529e+01
   22 2.777701e+00 2.586091e+00 4.553821e+01
   22 1.162003e+01 2.586091e+00 4.553821e+01
   22 2.777701e+00 7.758274e+00 4.553821e+01
   22 1.162003e+01 7.758274e+00 4.553821e+01
   16 1.539942e+01 9.429425e-16 4.703113e+01
   16 2.102191e+01 1.287221e-15 4.703113e+01
   42 1.821067e+01 6.896278e+00 4.703113e+01
   22 7.199100e+00 2.586091e+00 4.852540e+01
   22 7.199100e+00 7.758274e+00 4.852540e+01
   22 2.777701e+00 1.700851e-16 5.001833e+01
   22 1.162003e+01 7.115218e-16 5.001833e+01
   42 1.821067e+01 1.724095e+00 5.001833e+01
   22 2.777701e+00 5.172182e+00 5.001833e+01
   22 1.162003e+01 5.172182e+00 5.001833e+01
   16 1.539942e+01 5.172182e+00 5.001833e+01
   16 2.102191e+01 5.172182e+00 5.001833e+01
   22 7.199100e+00 4.408177e-16 5.300417e+01
   16 1.539942e+01 9.429425e-16 5.300417e+01
   16 2.102191e+01 1.287221e-15 5.300417e+01
   22 7.199100e+00 5.172182e+00 5.300417e+01
   42 1.821067e+01 6.896278e+00 5.300417e+01
   22 2.777701e+00 2.586091e+00 5.449710e+01
   22 1.162003e+01 2.586091e+00 5.449710e+01
   22 2.777701e+00 7.758274e+00 5.449710e+01
   22 1.162003e+01 7.758274e+00 5.449710e+01
   42 1.821067e+01 1.724095e+00 5.599002e+01
   16 1.539942e+01 5.172182e+00 5.599002e+01
   16 2.102191e+01 5.172182e+00 5.599002e+01
   22 7.199100e+00 2.586091e+00 5.748295e+01
   22 7.199100e+00 7.758274e+00 5.748295e+01
   16 1.539942e+01 9.429425e-16 5.897587e+01
   16 2.102191e+01 1.287221e-15 5.897587e+01
   42 1.821067e+01 6.896278e+00 5.897587e+01
   42 1.821067e+01 1.724095e+00 6.196306e+01
   16 1.539942e+01 5.172182e+00 6.196306e+01
   16 2.102191e+01 5.172182e+00 6.196306e+01
   16 1.539942e+01 9.429425e-16 6.494891e+01
   16 2.102191e+01 1.287221e-15 6.494891e+01
   42 1.821067e+01 6.896278e+00 6.494891e+01
   42 1.821067e+01 1.724095e+00 6.793476e+01
   16 1.539942e+01 5.172182e+00 6.793476e+01
   16 2.102191e+01 5.172182e+00 6.793476e+01
   16 1.539942e+01 9.429425e-16 7.092060e+01
   16 2.102191e+01 1.287221e-15 7.092060e+01
   42 1.821067e+01 6.896278e+00 7.092060e+01
   42 1.821067e+01 1.724095e+00 7.390645e+01
   16 1.539942e+01 5.172182e+00 7.390645e+01
   16 2.102191e+01 5.172182e+00 7.390645e+01
   16 1.539942e+01 9.429425e-16 7.689364e+01
   16 2.102191e+01 1.287221e-15 7.689364e+01
   42 1.821067e+01 6.896278e+00 7.689364e+01
   42 1.821067e+01 1.724095e+00 7.987949e+01
   16 1.539942e+01 5.172182e+00 7.987949e+01
   16 2.102191e+01 5.172182e+00 7.987949e+01
   16 1.539942e+01 9.429425e-16 8.286534e+01
   16 2.102191e+01 1.287221e-15 8.286534e+01
   42 1.821067e+01 6.896278e+00 8.286534e+01
   42 1.821067e+01 1.724095e+00 8.585119e+01
   16 1.539942e+01 5.172182e+00 8.585119e+01
   16 2.102191e+01 5.172182e+00 8.585119e+01
   16 1.539942e+01 9.429425e-16 8.883838e+01
   16 2.102191e+01 1.287221e-15 8.883838e+01
   42 1.821067e+01 6.896278e+00 8.883838e+01
   42 1.821067e+01 1.724095e+00 9.182423e+01
   16 1.539942e+01 5.172182e+00 9.182423e+01
   16 2.102191e+01 5.172182e+00 9.182423e+01
   16 1.539942e+01 9.429425e-16 9.481007e+01
   16 2.102191e+01 1.287221e-15 9.481007e+01
   42 1.821067e+01 6.896278e+00 9.481007e+01
   42 1.821067e+01 1.724095e+00 9.779592e+01
   16 1.539942e+01 5.172182e+00 9.779592e+01
   16 2.102191e+01 5.172182e+00 9.779592e+01
   16 1.539942e+01 9.429425e-16 1.007818e+02
   16 2.102191e+01 1.287221e-15 1.007818e+02
   42 1.821067e+01 6.896278e+00 1.007818e+02
   42 1.821067e+01 1.724095e+00 1.037690e+02
   16 1.539942e+01 5.172182e+00 1.037690e+02
   16 2.102191e+01 5.172182e+00 1.037690e+02
   16 1.539942e+01 9.429425e-16 1.067548e+02
   16 2.102191e+01 1.287221e-15 1.067548e+02
   42 1.821067e+01 6.896278e+00 1.067548e+02
   42 1.821067e+01 1.724095e+00 1.097407e+02
   16 1.539942e+01 5.172182e+00 1.097407e+02
   16 2.102191e+01 5.172182e+00 1.097407e+02
   16 1.539942e+01 9.429425e-16 1.127265e+02
   16 2.102191e+01 1.287221e-15 1.127265e+02
   42 1.821067e+01 6.896278e+00 1.127265e+02
   42 1.821067e+01 1.724095e+00 1.157137e+02
   16 1.539942e+01 5.172182e+00 1.157137e+02
   16 2.102191e+01 5.172182e+00 1.157137e+02
   16 1.539942e+01 9.429425e-16 1.186995e+02
   16 2.102191e+01 1.287221e-15 1.186995e+02
   42 1.821067e+01 6.896278e+00 1.186995e+02
   42 1.821067e+01 1.724095e+00 1.216854e+02
   16 1.539942e+01 5.172182e+00 1.216854e+02
   16 2.102191e+01 5.172182e+00 1.216854e+02
   16 1.539942e+01 9.429425e-16 1.246712e+02
   16 2.102191e+01 1.287221e-15 1.246712e+02
   42 1.821067e+01 6.896278e+00 1.246712e+02
   42 1.821067e+01 1.724095e+00 1.276571e+02
   16 1.539942e+01 5.172182e+00 1.276571e+02
   16 2.102191e+01 5.172182e+00 1.276571e+02
   16 1.539942e+01 9.429425e-16 1.306443e+02
   16 2.102191e+01 1.287221e-15 1.306443e+02
   42 1.821067e+01 6.896278e+00 1.306443e+02
   42 1.821067e+01 1.724095e+00 1.336301e+02
   16 1.539942e+01 5.172182e+00 1.336301e+02
   16 2.102191e+01 5.172182e+00 1.336301e+02

36

General Questions and Answers / Re: extract isovalue of the transmission eigenstates

« on: August 30, 2013, 15:47 »

I have noticed the coordinates are in Bohr instead of Angstrom. But even taking this into account, the coordinates are also completely wrong. Since both the nc and cube files are huge, I cannot attach them to the forum. Let me try to share them in another way.

37

General Questions and Answers / Re: extract isovalue of the transmission eigenstates

« on: August 30, 2013, 14:50 »

Hi Anders,

I have got a problem with the script you passed to me: the extracted isovalue grid of transmission eigenstates is correct but the geometric configuration is not. The way I called the cubefile_with_configuration() function is as follows:

Code

    
import sys

# Complex grid
configuration = nlread('/home/z400/B1/MS/Ti-mos2/MoS2-Ti-singlecontact.nc', object_id='gID000')[0]
te = TransmissionEigenstate(
    configuration=configuration,
    energy=0.48*eV,
    k_point=[0, 0],
    quantum_number=0,
    spin=Spin.Up,
    contributions=Left,
    energy_zero_parameter=AverageFermiLevel,
    )

with open("transmission_eigenstates_Ti_long.cube","w") as cubefile:
    cubefile_with_configuration(te, stream=cubefile)

The program reads in the device configuration from the converged .nc file, makes a post-processing for transmission eigenstates, and dumps the configuration and isovalue grid to the .cube file. But output atomic coordinates, as well as some of the atomic numbers, are not correct. Do you have any suggestion about this?

Thanks&regards,
baizq

38

General Questions and Answers / Re: extract isovalue of the transmission eigenstates

« on: August 15, 2013, 14:05 »

Hi Anders，

Thank you very much for your help! 

baizq

39

General Questions and Answers / Re: extract isovalue of the transmission eigenstates

« on: August 15, 2013, 10:47 »

Thanks... I am waiting... what's the weather like in Copenhagen?

40

General Questions and Answers / Re: extract isovalue of the transmission eigenstates

« on: August 15, 2013, 10:13 »

Hi Anders,

Thanks. Yes, what I want is to extract the data grid. But when I follow your suggestion by "Export" to CUBE, the file contains the following information:

CUBE FILE.
OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z
    0 0.000000e+00 0.000000e+00 0.000000e+00
  264 1.811253e-01 1.109073e-17 1.109073e-17
   58 0.000000e+00 1.783511e-01 1.092086e-17
  738 0.000000e+00 0.000000e+00 1.813163e-01

Not supported - yet.

May I know what it means...?

baizq

41

General Questions and Answers / extract isovalue of the transmission eigenstates

« on: August 15, 2013, 05:50 »

Dear all,

I remember that, in some previous version (maybe ver 2008.x), it is possible to extract isovalues of transmission eigenstates using VNL for plotting with other software. Is the functionality still available in the current versions (ver. 12.x)? Or is there any other way for the extraction?

Thanks&regards,
baizq

42

General Questions and Answers / Re: Slater-Koster TB model for a self-defined system

« on: July 13, 2013, 04:22 »

Hi Anders,

Thanks! If no exsiting TB parameters, is it possible to exact from a preceding DFT calculation?

baizq

43

General Questions and Answers / Slater-Koster TB model for a self-defined system

« on: July 12, 2013, 16:38 »

Dear ATK developers,

I would like to make sure whether we can use the Slater-Koster method as implemented in ATK to model a somewhat complex system, e.g., the Ni/Graphene contact system in your paper PRB 85, 165442 (2012). The complexity may include the either contacted or freestanding regions of graphene, the metal edge, and the atomic position change due to relaxation, etc...

Best,
baizq

44

General Questions and Answers / Re: noncollinear-spin functionality

« on: April 25, 2013, 17:19 »

Thanks a lot for both of your replies.

I have read the references you recommended. I have a question here. For a magnetic tunnel junction, the Fe/MgO/Fe sandwich for example, is the global spin-quantization axis always confined in the transverse plane perpendicular to the transport direction? If I align all the spin pointing along z-axis (transport direction), would the calculated conduction the same as that obtained from collinear calculation (parallel)?

By the way, can we extract the k-dependent transmission spectrum from a noncollinear transport calculation(parallel, antiparallel), just as what we do for the collinear case (parallel majority/minority, antiparallel)?

45

General Questions and Answers / Re: magnetic tunnel junction

« on: April 25, 2013, 11:48 »

Hi,

We may never expect the calculated TMR ratio (for Fe/MgO/Fe, several thousand percent) to be comparable to that in experiment (typically several hundred percent for (Co)Fe/MgO/(Co)/Fe). There're also quite a lot of computational work trying to explain the deviation, say, PRL 105, 236801 (2008).

The calculated MR ratio also depends on the model you use, for instance, how many MgO layers there are. TMR would differ a lot w.r.t. different number of MgO layers.

baizq