Dear Guotao,
I am not sure if this is the problem of the siesta version but I
would recommend the using of the newer version. The siesta-v4.1-b4
is two years old beta version, and there has been a lot of
improvements since then.
There are some information on this page about the siesta versions
to use:
https://gitlab.com/siesta-project/siesta/-/wikis/Guide-to-Siesta-versions
Personally I suggest using the Max or psml version, with which a
high quality pseuodopotential dataset (http://www.pseudo-dojo.org/)
in the psml format can be used. And the automatically generated
basis set will ease the work a lot (although the basis set are not
always optimal and still need to be tested.).
Best regards,
HeXu
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