extract isovalue of the transmission eigenstates

[baizq]

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

[Anders Blom]

No, and I may be wrong but I don't actually think that has ever been possible. Producing an isosurface is pretty difficult, and extracting data for the isosurface itself is probably never likely to work in another software.

I believe you are thinking of extracting the data grid itself, and then use another software than like VNL can do isosurfaces based on the data points. That's trivial - you can export CUBE files by using "Export" in the Result Viewer.

[baizq]

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

[Anders Blom]

It means you are trying to export a complex grid. So far, this export is only supported for real grids. But I have a Python script that can do complex grids too. It can even include the configuration too.

[baizq]

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

[Anders Blom]

We had a very nice summer, not Singapore-hot, but nice enough, dry and sunny. 

See attached file. I think you can understand the code regarding the choices for exporting complex data using either 'real', 'imag', 'abs', or (default) 'abs2', i.e. |psi|^2.

This file contains a bonus too - the possibility to make the post-scf analysis at a higher (or lower) mesh cut-off than used in the calculation, for higher level of detail in the plots.

[baizq]

Hi Anders，

Thank you very much for your help! 

baizq

[baizq]

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

[Anders Blom]

Tricky to say without further information, but a typical thing that can go wrong is that coordinates (or grid) are in Bohr and not Angstrom.

[baizq]

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.

[Anders Blom]

I only need to see the top of the CUBE file, the part with the coordinates and the "cell", along with the system in Python format.

[baizq]

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

[baizq]

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.

[Anders Blom]

Well, no The first few lines are not coordinates, that's the cell vectors, and the number of grid points in each direction. You can see the cube file format at http://paulbourke.net/dataformats/cube/. So, perhaps all is ok?

[baizq]

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)...