Siesta

how can I read Hamiltonian Matrix from .HSX file?

Asked by Siddharth

I am working on my research work using SIESTA 4.0. I am trying to get Hamiltonian and overlap matrix. I am using "SaveHS .true." command to get Polyethelene.HSX file. HSX file is not readable so I am using hsx2hs from Util/HSX and converting to Polyethelene.HS file. This HS file doesn't show any matrix.

Can you please help me how can I get readable hamiltonian and overlap matrix? I would be grateful if I can get the proper way to find it.

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Nick Papior (nickpapior) said : 		#1

Both HS and HSX may be read to obtain the Hamiltonian and overlap matrices.

However, you should note that both stores the Hamiltonian and overlap in a sparse matrix.

If you want guidance of how the file formats are used, I would suggest you to read in the Util/HSX folder and the hsx_m.f90 file which is capable of reading and writing HS/HSX files.

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marc barbry (mbarbry) said : 		#2

The answer come a bit late, but for the people using python, there is now the possibility to read the HSX (and other siesta output) using the siesta calculator from the ase package (https://wiki.fysik.dtu.dk/ase/about.html).

This functionality is for the moment only in the development version, but the version 3.13 of ase should be out soon (and it will be included with it).

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