I have performed a calculation of Electrostatic Potential using flag SaveElectrostaticPotential .true. and obtained the results with extension like .VH, .VT, .TOCH etc.,. I don’t know how to process this file further. Anyone having idea, please reply.
Dear Bhanu,
To analyse electrostatic potential you may convert first the SIESTA output file *VH into cube format. This can be done using SIESTA Utility Denchar. The folder with this utility contains examples and detailed user manual.
The obtained cube file contains volumetric information about variation of the potential in your system. This can be visualised using common atomic viewers as Vesta or VMD.
For analysis of polar hetero-structures, or interfaces you may also use planar and macro-avaeraged potential to understand the variation potential across your system. For this you may use another SIESTA Utility Macroave. The folder with this utility also contains examples and detailed user manual.
I hope these tips will help your to analyse the SIESTA output files.
Thank you for replying.
From my previous calculations after DENCHAR run, I have obtained files with extension RHO.cube and DRHO.cube which are basically charge density files. Kindly correct me if I’m wrong.
I have gone through the DENCHAR manual and nowhere it is mentioned about the file extensions *VH.
Dear AK1,
If you have performed the calculations for electrostatic potential, I would be grateful if you can share the files.
Dear Bhanu,
you can post process the .VH file using rho2xsf utility. This will generate a xsf file that you can open with xcrysden or Vesta.
Is there any way to visualize 1D electrostatic potential data from *.VH files?
One can also use sisl to convert any of the grid files to cube/xsf files:
sgrid siesta.VH siesta.VH.cube
done
Dear Zerothi,
Presently, I’m using SIESTA with Fortran compiler. I tried to install sisl through command line on my Ubuntu 16.04 LTS and received the following error :
Collecting sisl
Using cached https://files.pythonhosted.org/packages/c4/f2/5aef13a39df2851e616630c7082785851b334b9e84a03c909d7f3bf22314/sisl-0.11.0.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File “”, line 1, in
File “/tmp/pip-build-gsf7ksmq/sisl/setup.py”, line 187
pyx = ext_d.get(“pyxfile”, f"{ext}.pyx")
^
SyntaxError: invalid syntax
----------------------------------------
Command “python setup.py egg_info” failed with error code 1 in /tmp/pip-build-gsf7ksmq/sisl/
I dont know how to resolve this. Any help would be appreciated.
Could you see here: Installation — sisl latest documentation
Please note that you may need the Cython package as well, depending on the setup.