How to properly utilise sisl to extract information from potential

[el-abed]

Good day all,
I was wondering in the sisl manual it focuses on extracting the information from RHO.grid.nc files to produce cube files in the following format:

sgrid PG.DeltaRho.grid.nc --geometry zeroPG.XV --diff P.DeltaRho.grid.nc --diff G.DeltaRho.grid.nc diffn.cube

My questions are as follow:
1- Is there a similar format for Electrostatic.grid.nc, TotalPotential.grid.nc, and TotalCharge.grid.nc files?
2- If i am interested only in one direction such as z-axis, how command should I use?
3- What available output formats can be done and how?

Thank you and looking forward to your reply.
EL-abed

[zerothi]

Hi,

1. The sgrid command works for any grid files, the command is exactly the same.
2. Currently, I haven't interfaced the grid to write out tables for 1D data (e.g. if you average/sum over x, y directions). This is in the works.
3. As of now, only xsf and cube files are supported. The file-format is determined from the file-suffix

sgrid Rho.grid.nc rho.cube # write a cube file
sgrid Rho.grid.nc rho.xsf # write a xsf file

[zerothi]

Regarding 2., I have now added the possibility of writing the 1D data to a data file. It should work with the latest commit of sisl.

[el-abed]

Really looking forward Nick. May I ask when is the expected release?

[zerothi]

Really looking forward Nick. May I ask when is the expected release?

You can just download this repository and install it like the regular sisl version :) That would be the easiest.

You could follow these instructions: http://zerothi.github.io/sisl/installation.html#development-version to install the development version :)

[el-abed]

Oh ! I did not know that, i thought sisl like siesta we have to wait the later versions. Thank you very much!

[zerothi]

@el-abed could you confirm whether it is working now? If it does, please close this issue (otherwise I'll close in a week or so).

[el-abed]

Hello nick,
I finally downloaded using the following command
pip3 install -v --no-binary :all: --user git+https://github.com/zerothi/sisl.git

But it seems there are multiple folders: pip-5y0u06ab-build pip-si96evx4-build pip-build-i3a5hujh

1- May I ask what is the difference between them?
2- Also how can I make sure I have the latest update including the 1D data file siutation?
3- Speaking of 1 D data file, what is the command to extract for example the potential vs z ?

Thank you Nick and looking forward to your reply.
EL-abed

[zerothi]

1. The pip command should install in a folder, I guess these folders are just temporary folders. I have no clue what these folders are. But I don't think they are useful.
2. If you just did the above, then you are pretty sure it works, otherwise you'll just see an error.
3. You have to do sgrid Rho.grid.nc --average 0 --average 1 --out rho_z.dat, to average the density on the x, y plane.

[el-abed]

The installation is successful where the aforementioned folders have sisl.
Concerning 3 when you say average on x,y plane it is equivalent of density as a function of z right?

[zerothi]

3. Yes.

[el-abed]

Beautiful. Thank you very much Nick :)
Really appreciate the quick replies. Do you mind if I just keep it open just to do some tests? Hopefully by tomorrow i should be able to make sure everything is set.

[zerothi]

sure :)

[el-abed]

I can confirm after a long day fixing the installation that the command in the latest sisl version:

sgrid Rho.grid.nc --average 0 --average 1 --out rho_z.dat

IS WORKING
THANK YOU VERY MUCH NICK! I WILL CLOSE IT NOW

[el-abed]

Sorry to bother again Nick. I was wondering what can we extract from the elements files ion.nc ?
Just curious becayse in the latest siesta manual i saw only that basis, KB projector, and other information is read. So other information like what? PDOS? DOS? Potential? Thank you and looking forward to your reply