Siesta

How can I get the electrostatic difference potential-voltage profile using transiesta?

Asked by Jianjun Mao

Dear Nick,

I want to get the voltage profile to see if the screening region is long enough to ensure smooth transitions between the central region and the electrodes and if the potential is bulk like in my electrode regions. How can I get it using siesta or transiesta?

Many thanks~!

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Nick Papior
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Nick Papior (nickpapior) said : 		#1

I would highly recommend you to do the tutorial here https://github.com/zerothi/ts-tbt-sisl-tutorial

In TS_02 you will create a potential profile plot.

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Jianjun Mao (jjmao) said : 		#2

Thanks Nick Papior, that solved my question.

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Jianjun Mao (jjmao) said : 		#3

Dear Nick,

I have installed the sisl successfully~ When I try this command"sgrid scat.VT scat.VT.cube" after a calculation. It shows this following error:

 File "/home/jjmao/bin/sgrid", line 6, in <module>
    from sisl.grid import sgrid
  File "/home/jjmao/lib/python2.7/site-packages/sisl/__init__.py", line 93, in <module>
    from . import utils
  File "/home/jjmao/lib/python2.7/site-packages/sisl/utils/__init__.py", line 41, in <module>
    from . import mathematics as math
  File "/home/jjmao/lib/python2.7/site-packages/sisl/utils/mathematics.py", line 8, in <module>
    from sisl._indices import indices_le
ImportError: /home/jjmao/lib/python2.7/site-packages/sisl/_indices.so: undefined symbol: __intel_sse2_strlen

I can not find the detailed tutorial of sisl in the folder of "2018". I don't know "Jupyter notebook" and how to run run.ipynb.
Maybe some basics are needed.

Besides sisl, I also installed most of the post-process tools in /Util of Siesta. And I encountered some problems about analysing Siesta output:
1. How to use grid2cube to process .VH .VT.....Files. Does they need input files? Can I use these commands to get the potential profile plot?

2. How to visualize the .cube files? Any recommend softwares?

Many thanks Nick, for your patience ~!

Revision history for this message
Jianjun Mao (jjmao) said : 		#4

Dear Nick,

I have installed the sisl successfully~ When I try this command"sgrid scat.VT scat.VT.cube" after a calculation. It shows this following error:

 File "/home/jjmao/bin/sgrid", line 6, in <module>
    from sisl.grid import sgrid
  File "/home/jjmao/lib/python2.7/site-packages/sisl/__init__.py", line 93, in <module>
    from . import utils
  File "/home/jjmao/lib/python2.7/site-packages/sisl/utils/__init__.py", line 41, in <module>
    from . import mathematics as math
  File "/home/jjmao/lib/python2.7/site-packages/sisl/utils/mathematics.py", line 8, in <module>
    from sisl._indices import indices_le
ImportError: /home/jjmao/lib/python2.7/site-packages/sisl/_indices.so: undefined symbol: __intel_sse2_strlen

I can not find the detailed tutorial of sisl in the folder of "2018". I don't know "Jupyter notebook" and how to run run.ipynb.
Maybe some basics are needed.

Besides sisl, I also installed most of the post-process tools in /Util of Siesta. And I encountered some problems about analysing Siesta output:
1. How to use grid2cube to process .VH .VT.....Files. Does they need input files? Can I use these commands to get the potential profile plot?

2. How to visualize the .cube files? Any recommend softwares?

Many thanks Nick, for your patience ~!

Revision history for this message
Best Nick Papior (nickpapior) said : 		#5

You have a faulty Python installation. Please try and fix this.

1. The header of the grid2cube file contains information on how to use it.

2. Any volumetric software may be used, VMD, XCrySDen or others.

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Jianjun Mao (jjmao) said : 		#6

Thanks Nick Papior, that solved my question.