[DFTB-Plus-User] R: visualisation of potential profile

[Alessandro Pecchia]

Hi Aicha,

 

I think there is a source of confusion because there are two alternative codes for the same purpose.

One is a fortran code that should be found in the same place as buildwire.

This works as: 

makecube potential.dat [-r refpot] [-b boxfile xfile yfile zfile]

It is enough to run:

$ makecube potential.dat

 

Make sure all the files box3d.dat and Xvector.dat, … are present in the folder with potential.dat.

 

-r refpot is useful to subtract an equilibrium potential. E.g., first run an equilibrium calculation then copy potential.dat into –say- potential0.dat and then

 

$makecube potential.dat –r potential0.dat

 

This should give the difference V-V0, useful to see relative changes due to the applied bias.

 

The other makecube is a python code that should do the same job but it has a different user interface. 

This is the executable invoked in your case. It does work in a similar way:

 

$makecube potential.dat potential.cube

 

If you use something like paraview or visit to visualize, you can also output to vtk format.

 

I used to display the cube files with jmol.

For this also look in tools/misc/transport/README.jmol

 

This shows how to import a colormap and plot the potential on a plane cutting the box.

Look also at jmol script reference page for this: 

https://chemapps.stolaf.edu/jmol/docs/?ver=14.29#isosurface

 

In fact I see that recent versions of jmol have many more plotting options than what I used.

 

I hope this helps.

 

 

Alex

 

Da: DFTB-Plus-User [mailto:dftb-plus-user-bounces at mailman.zfn.uni-bremen.de] Per conto di Khemissi Aicha
Inviato: sabato 28 novembre 2020 08:30
A: DFTB-Plus-User at mailman.zfn.uni-bremen.de
Oggetto: [DFTB-Plus-User] visualisation of potential profile

 

Dear DFTB+ users 

***i am trying to convert the potential.dat to the cube file  to be plotted in jmol , by using  this command (manual DFTB+)
makecube potential.dat [-r refpot] [-b boxfile xfile yfile zfile]
how can i use this command knowing that i have these files after running transport calculation !!!
box3d.dat,Xvector.dat,Yvector.dat,Zvector.dat
ps: When I tried to use it,  I got errors like this below.
usage: makecube [-h] [--xvec XVEC] [--yvec YVEC] [--zvec ZVEC]
                [--reference REFERENCE] [--format FORMAT] source dest
makecube: error: unrecognized arguments: box3d.dat Xvector.dat Yvector.dat Zvector.dat]
***also ,could you help me if you know,  how can I convert the vtk file to cube file to be viewed in xcrysden !!!

thanks 

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