Semicore States

I am new to Siesta.
I wish to optimize CNT+CFO (Cobalt ferrite) system but I have received error- " must be in PAO.Basis (it has semicore states)".
I am not able to short out. Please see the link and help me.
(rlx.fdf - Google Drive) -
(rlx.out - Google Drive)-

Thanking you


Because you are using pseudos with semicore electrons in the valente you have to add a basis set block in the input with the correct electronic configuration.
Please, check the manual for more info.

If you do not know how to do it you can post in here the pseudos you are using, we will pass you a basis set that work with your pseudos.

Thank you for your suggestion. But I am new to Siesta, so it would be difficult for me to adjust.
I am requesting to provide me basis set.

Could you also attach the other pseudopotential files?

Please find the attachments.
I am requesting to you that please turn on notification of this topic.

Thank You


The chemical species block is not properly set.
Try to use this,

%block ChemicalSpeciesLabel
1 6 C
2 26 Fe
3 27 Co
4 8 O
%endblock ChemicalSpeciesLabel

Basis set extension can be defined using the energyshift flag.

Basis set block (%block PAO.Basis) sometimes needs to be set manually if you have pseudos with semicore electrons in the valence or if you want to tune them for certain systems.

I have followed your suggestion and again I found some mistakes. Please find the attachment (output file) and help me further.
Block Chemical_species_label does not exist.
Block Chemical_species_label does not exist.
reinit: -----------------------------------------------------------------------
reinit: System Name:
reinit: -----------------------------------------------------------------------
reinit: System Label: siesta
reinit: -----------------------------------------------------------------------
Stopping Program from Node: 0

initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Block Chemical_species_label does not exist.
Stopping Program from Node: 0
reinit: Dumped input in INPUT_TMP.66628
************************** Dump of input data file ****************************

Thank you

Have you used the same input?
Could you send me the entire output file?

I am enable to upload the file nor type G drive link.
please give me your email id or I am copying paste o/p file in 2 parts.
Please find it

Please upload zip file, you should not have any problem.

Could you please delete the last posts containing the whole output file, it is too long to be put in a post.

Thanks. (12.0 KB)

Thank you please find input and output.

The last input you pass me gave problem because of “CRLF line terminators”.
I attach the same file with unix type of line endings, hopefully it will work.

I see in your output that you are running a parallel version in serial mode and there are multiple repetition of the expected output file, you should check the command you use to submit the calculation. (3.8 KB)

Thank you for back to back support.
Again I received error. I am attaching, please find it. (891 Bytes)

After rename systemlabel with rlx, I found following error;

initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Block Chemical_species_label does not exist.

What’s wrong with it?

Renaming the system should not affect the calculation.
If you get a new error please post the new fdf input file because I cannot reproduce your problem.

Thank You. I have successfully ran calculation.

I am using SIESTA for the first time and I don’t know how to use the PAO. I am working with Co, Mn and Ga, only the Ga pseudopotential has semicore state but I don’t know to define this. Could you please help me out with this? Thanks

Try to have a look at the manual, there you can find the explanation and an example of the basis set block.
If you have problems figuring out the basis set block for your pseudo you can post the pseudos in here with the fdf file.