I have worked with the SIESTA code last 2 years. Recently, I faced some errors Error in Cholesky factorisation in cdiag during graphene-BC3 heterostructure optimisation. I checked the SIESTA mailing list and tried to perform the calculation with a more accurate bond length and angle. Still, I am facing the same problem.

It would be of great help if you could suggest where I am doing wrong and how I can overcome this problem.

Output displaying cholesky error

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    $\begingroup$ Welcome to our site! This error is usually due to the Scalapack library. $\endgroup$
    – Camps
    Feb 8, 2022 at 12:02
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    $\begingroup$ Generally this may happen if the overlap matrix is close to singular. So first try to figure out if your atoms are almost on top of each other. That would be my first guess. $\endgroup$
    – nickpapior
    Feb 8, 2022 at 13:57
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    $\begingroup$ If the output file isn't too long, you can include it as a code block rather than an image. $\endgroup$
    – Tyberius
    Feb 8, 2022 at 15:59
  • $\begingroup$ You might simply have 2 atoms that are directly on top of each other so it becomes almost impossible to actually "see" the mistake. Recheck your coordinates for some duplicates ! $\endgroup$
    – Elie H
    Feb 8, 2022 at 17:27

1 Answer 1


Generally a failure in the Cholesky factorization happens when two orbitals are extremely similar and thus the overlap matrix $\mathbf S$ becomes singular. If you get this error first check the coordinates of atoms and ensure they are not on top of each other.


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