Bug with siesta-sisl-tb2j

[Dorye Esteras]

Hello,

I just wanted to report what I believe is a bug, please forgive me if I am wrong.

Before, in the siesta input atomic coordinates could be written like this:

0.000 0.000 0.000 1

or like this:

0.000 0.000 0.000 1 Cr

However in the recent versions you could also write them like this:

Cr 0.000 0.000 0.000 1

Which indeed is more consistent with other DFT packages. Then, when you run tb2j, there is a crash:     species = _a.fromiteri(map(lambda x: x.split()[3], species[:na])) - 1
ValueError: invalid literal for int() with base 10: '0.000' Which it comes from sisl trying to extract the species type (1) from the number in the 4th position which is the z coordinate in this format (0.000). In my case, I will just change to the old format my coordinates, but I wanted to report this issue. Thanks a lot, Dorye

[Xu He]

Hi, 

Thanks for reporting this issue. Could you send me an example input file in the new format so I can try with it? 

TB2J does not actually parse the siesta input, but calls sisl as a library to do that. So I cannot modify TB2J to fix this. But indeed we can try if updating to the most recent version of sisl works. Otherwise I will have a look at the sisl code. 

Best regards, 

HeXu

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[D]

Hi,

I send you an input of siesta that crashes and one with the old convention that does not crash. Also the command of tb2j and the crash.

Thanks for your answer!

Dorye

siesta2J.py --fdf_fname I_crash.fdf --elements Cr --kmesh 1 1 1 --np 1

 species = _a.fromiteri(map(lambda x: x.split()[3], species[:na])) - 1

ValueError: invalid literal for int() with base 10: '6.872000000'