I am trying to passivate the surface of $\ce{ZnO}$ quantum dot using siesta. I generated pseudo-hydrogens with fractional charges of 1.5e (to passivate Zn) and .5e (to passivate O) using the siesta utility code. To begin with, I tried to passivate each separately to see if it is working (eventually I want to passivate both Zn and O). My initial attempts give me the following error:

initatom: Reading input for the pseudopotentials and atomic orbitals ----------
Species number:   1 Atomic number:    8 Label: O
Species number:   2 Atomic number:   30 Label: Zn
Species number:   3 Atomic number:    1 Label: H-Fraction-0.50000
Ground state valence configuration:   2s02  2p04
Reading pseudopotential information in formatted form from O.psf

Valence configuration for pseudopotential generation:
2s( 2.00) rc: 1.47
2p( 4.00) rc: 1.47
3d( 0.00) rc: 1.47
4f( 0.00) rc: 1.47
Ground state valence configuration:   4s02  3d10
Reading pseudopotential information in formatted form from Zn.psf

Valence configuration for pseudopotential generation:
4s( 2.00) rc: 2.43
4p( 0.00) rc: 2.37
3d(10.00) rc: 2.09
4f( 0.00) rc: 2.82
Ground state valence configuration:   1s01
Reading pseudopotential information in formatted form from H-Fraction-0.50000.psf
ERROR expected valence charge for species H-Fraction-0.50000  
ERROR and the value read from the vps file
ERROR differ:  Zval(expected)=  1.000 Zval(vps)=  0.500

A similar error message for H-Fraction-1.50000, but with Zval(vps)=1.500.

My block for synthetic atoms for H-Fraction-0.500 is

%block SyntheticAtoms
 1 2 3 4
 0.50000 0.00000 0.00000 0.00000
%endblock SyntheticAtoms

Why do I get the error message? I used the siesta utility to generate the pseudo hydrogen psfs.

  • 1
    $\begingroup$ Which atomic number does your synthetic atom have? Your output seems to suggest atomic number 1, while in the Siesta documentation, I read "Atomic numbers over 200 are used to represent synthetic atoms (created for example as a “mixture” of two real ones for a “virtual crystal” (VCA) calculation)." I'm not a Siesta user though, so this may be the wrong lead. $\endgroup$ Oct 7, 2022 at 22:42

1 Answer 1


Leopold is right. According to the output you show, H is entered with an atomic number of 1, while it should have, say, an "atomic number" of 201. This is the mechanism used by Siesta to tag an species as "synthetic" and process the rest of the relevant information (i.e. the actual valence charge).


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