pseudo-hydrogen pseudopotential generated by fractional utility

Asked by Bruno on 2019-09-07

I'm trying to run calculations with pseudo-hydrogen for surface passivation.

I've generated a pseudo-hydrogen pseudopotential with 0.33 valence from H pseudopotential using the fractional utility as:
fractional H 0.33

Then I've added the fractional label and synthetic block as generated by the fractional utility to my input fdf file, and also copied the generated psf file to the calculation folder.

When reading the pseudopotential information, siesta correctly reads the pseudo info for the other atoms, but when it reaches the fractional H atom it stops with the following error:

Reading pseudopotential from: H-Fraction-0.33000.psf

Reading pseudopotential information in formatted form from H-Fraction-0.33000.psf

Pseudopotential generated from a relativistic atomic calculation

Valence configuration for pseudopotential generation:
Cannot get gen_zval
Stopping Program from Node: 0

My input looks like the following:

SystemName na3bi
SystemLabel na3bi
NumberOfSpecies 3
NumberOfAtoms 140
%block ChemicalSpeciesLabel
  1 11 Na
  2 83 Bi
  3 1 H-Fraction-0.33000
%endblock ChemicalSpeciesLabel

%block SyntheticAtoms
 3
  1 2 3 4
    0.330000 0.000000 0.000000 0.000000
%endblock SyntheticAtoms

LatticeConstant 1.00 Ang
%block LatticeVectors
      100.1870422363 0.0000000000 0.0000000000
        0.0000000000 9.2217702866 0.0000000000
        0.0000000000 0.0000000000 15.0000000000
%endblock LatticeVectors

AtomicCoordinatesFormat Fractional
%block AtomicCoordinatesAndAtomicSpecies
structure ....
%endblock AtomicCoordinatesAndAtomicSpecies

%block kgrid_Monkhorst_Pack
   1 0 0 0.
   0 11 0 0.
   0 0 1 0.
%endblock kgrid_Monkhorst_Pack

PAO.BasisType split
PAO.TailSplitNorm .true.

%block PAO.Basis
Na 4
 n=2 0 1 E 178.1680093 7.6936734
     3.4863815
     1.00000
 n=2 1 1 E 160.9169354 7.6903427
     4.1010247
     1.00000
 n=3 0 2 E 149.93 6.43
     7.999 6.430
     1.00000 1.00000
 n=3 1 1 E 149.99 6.10
     7.99600
     1.00000
Bi 4
 n=6 0 2 E 7.17410 3.93029
     5.23943 2.01196
     1.00000 1.00000
 n=6 1 2 E 32.62154 4.95495
     5.82774 2.77529
     1.00000 1.00000
 n=5 2 1 E 23.3492494 7.2763834
     5.3513410
     1.00000
 n=6 2 1 E 41.30975 3.74375
     4.30874
     1.00000
H-Fraction-0.33000 1
 n=1 0 1 E 2.07 0.00
   4.971
   1.000
%endblock PAO.Basis

XC.functional GGA
XC.authors PBE
MaxSCFIterations 2000
WriteDM .true.
DM.Require.Energy.Convergence .true.
DM.Energy.Tolerance 0.01 meV
MeshCutoff 500 Ry
SCF.H.Converge .true.
SCF.H.Tolerance 0.1 meV
SCF.MixAfterConvergence .false.

Spin spin-orbit+onsite

%block DM.InitSpin
%endblock DM.InitSpin

SCF.Mixer.Weight 0.05
SCF.MixAfterConvergence .false.

How can I fix that error ? What am I doing wrong ?

Question information

Language:
English Edit question
Status:
Answered
For:
Siesta Edit question
Assignee:
No assignee Edit question
Last query:
2019-09-07
Last reply:
2019-09-12
Alberto Garcia (albertog) said : #1

I have requested more information by direct email.

> On 7 Sep 2019, at 18:02, Bruno <email address hidden> wrote:
>
> New question #683730 on Siesta:
> https://answers.launchpad.net/siesta/+question/683730
>
> I'm trying to run calculations with pseudo-hydrogen for surface passivation.
>
> I've generated a pseudo-hydrogen pseudopotential with 0.33 valence from H pseudopotential using the fractional utility as:
> fractional H 0.33
>
> Then I've added the fractional label and synthetic block as generated by the fractional utility to my input fdf file, and also copied the generated psf file to the calculation folder.
>
> When reading the pseudopotential information, siesta correctly reads the pseudo info for the other atoms, but when it reaches the fractional H atom it stops with the following error:
>
> Reading pseudopotential from: H-Fraction-0.33000.psf
>
> Reading pseudopotential information in formatted form from H-Fraction-0.33000.psf
>
> Pseudopotential generated from a relativistic atomic calculation
>
> Valence configuration for pseudopotential generation:
> Cannot get gen_zval
> Stopping Program from Node: 0
>
> My input looks like the following:
>
> SystemName na3bi
> SystemLabel na3bi
> NumberOfSpecies 3
> NumberOfAtoms 140
> %block ChemicalSpeciesLabel
> 1 11 Na
> 2 83 Bi
> 3 1 H-Fraction-0.33000
> %endblock ChemicalSpeciesLabel
>
> %block SyntheticAtoms
> 3
> 1 2 3 4
> 0.330000 0.000000 0.000000 0.000000
> %endblock SyntheticAtoms
>
> LatticeConstant 1.00 Ang
> %block LatticeVectors
> 100.1870422363 0.0000000000 0.0000000000
> 0.0000000000 9.2217702866 0.0000000000
> 0.0000000000 0.0000000000 15.0000000000
> %endblock LatticeVectors
>
> AtomicCoordinatesFormat Fractional
> %block AtomicCoordinatesAndAtomicSpecies
> structure ....
> %endblock AtomicCoordinatesAndAtomicSpecies
>
> %block kgrid_Monkhorst_Pack
> 1 0 0 0.
> 0 11 0 0.
> 0 0 1 0.
> %endblock kgrid_Monkhorst_Pack
>
> PAO.BasisType split
> PAO.TailSplitNorm .true.
>
> %block PAO.Basis
> Na 4
> n=2 0 1 E 178.1680093 7.6936734
> 3.4863815
> 1.00000
> n=2 1 1 E 160.9169354 7.6903427
> 4.1010247
> 1.00000
> n=3 0 2 E 149.93 6.43
> 7.999 6.430
> 1.00000 1.00000
> n=3 1 1 E 149.99 6.10
> 7.99600
> 1.00000
> Bi 4
> n=6 0 2 E 7.17410 3.93029
> 5.23943 2.01196
> 1.00000 1.00000
> n=6 1 2 E 32.62154 4.95495
> 5.82774 2.77529
> 1.00000 1.00000
> n=5 2 1 E 23.3492494 7.2763834
> 5.3513410
> 1.00000
> n=6 2 1 E 41.30975 3.74375
> 4.30874
> 1.00000
> H-Fraction-0.33000 1
> n=1 0 1 E 2.07 0.00
> 4.971
> 1.000
> %endblock PAO.Basis
>
> XC.functional GGA
> XC.authors PBE
> MaxSCFIterations 2000
> WriteDM .true.
> DM.Require.Energy.Convergence .true.
> DM.Energy.Tolerance 0.01 meV
> MeshCutoff 500 Ry
> SCF.H.Converge .true.
> SCF.H.Tolerance 0.1 meV
> SCF.MixAfterConvergence .false.
>
> Spin spin-orbit+onsite
>
> %block DM.InitSpin
> %endblock DM.InitSpin
>
> SCF.Mixer.Weight 0.05
> SCF.MixAfterConvergence .false.
>
> How can I fix that error ? What am I doing wrong ?
>
> --
> You received this question notification because you are an answer
> contact for Siesta.

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