Dear all,
Thank you for your valuable advice. Shuttleworth’s publication indeed
seems very close to what I want to do.
Best regards,
Roland.
Le 17/01/2026 à 22:00, Francisco Garcia a écrit :
Hello Roland,
I believe this paper by I. G. Shutteworth contains valuable
information that can address most of your questions:
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0022369715001663__;!!D9dNQwwGXtA!Qka0VxNOMOZH8VxLDJ5j1Z4Ias1m_1JrwIw7f-yswD1OUkdvjfkqzBSsiLsJ9gDnhn2M4a0B_RSKqN5Q2U7aXc0J-g$
<https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0022369715001663__;!!D9dNQwwGXtA!QWSMgD_jSmHzoxT8j_dmZrR27JUoQhVhq3G91IQB1d1oCiP3OqQKMUgc4Tjf1POpfiwSHM5tn4y4w_1w6mVa6w$>
All the best,
F. G.
On Fri, Jan 16, 2026 at 2:00 PM I. Camps <[email protected]> wrote:
Besides prof. Postnikov advices, if you are trying to compare your
results with previous calculations, you need to check:
- the slab structure (check the plane/direction for the slab)
- the structure optimization and/or constraints (there are
different ways to use and define the slab behavior)
- the type of pseudopotentials
- the size of the basis set
- the convergence thresholds
- the cut-off values
- the initial position of the B atom
- parameters that can affect the calculated energy values
(electronic temperature, mixer method/weight/etc.)
[]'s,
Camps
On Thu, Jan 15, 2026 at 6:00 PM Andrei Postnikov
<[email protected]> wrote:
Dear Roland,
some suggestions:
1. Check the structure. It is difficult to judge from your
input file;
make a visualisation from working XV in order to see that
everything is correct.
From my experience, surprises due to structure input errors
are not uncommon.
2. The 3x3 lateral cell size seems rather small to simulate
adsorption
of an isolated atom. In principle this might be a factor
responsible for a difference from the expected value.
Ideally, a convergence with respect to supercell size has to
be tested.
3. As a reference energy for desorbed case, move the boron
atom away from the surface
within the same cell, retaining the Cu atoms at their
positions. This will minimize
systematic errors. Check the BSSE later on.
4. The relaxation at the surface
with and without the boron atom adsorbed might be different.
Again,
the lateral size might be too small for correctly
incorporating the relaxation
around the adsorbed atom. (This is just a guess; I don't know
the system).
Good luck
Andrei
to get the adsorption energy, the boron energy from boron
crystal is not
a good reference. I'd suggest
----- Le 14 Jan 26, à 9:59, Roland Coratger
[email protected] a écrit :
> Dear all,
>
> I am trying, as a training exercise, to recover the
adsorption energy of
> a boron atom on a Cu(111) slab, which according to the
literature should
> be around -2 eV. The energy is given by: E(ads) = E(slab+B)
- E(slab) -
> E(B). For E(B), if I use a B atom in the slab’s box, the
energy is very
> negative and unrealistic (around -4 eV). If I use the energy
of a B atom
> from the 3D boron crystal, the energy becomes positive
(around +2 eV),
> so there is no adsorption. Below you will find my input file
for the
> slab+B system. I use the same parameters for the other two
energies. The
> BSSE correction (a few tenths of an eV) does not change the
observed
> trend. Am I making a mistake somewhere and/or do you have any
> suggestions to help me recover the correct value?
>
> Thank you in advance for you help.
>
> Regards,
>
> Roland.
>
> _______________________________________
> SystemName CuB test
> SystemLabel cu_b
> NumberOfAtoms 46
> NumberOfSpecies 2
>
> XC.functional GGA
> XC.authors PBE
>
> MaxSCFIterations 200
>
> %block ChemicalSpeciesLabel
>
> 1 29 Cu # Species index, atomic number, species label
> 2 5 B # Species index, atomic number, species label
>
> %endblock ChemicalSpeciesLabel
>
> PAO.FixSplitTable T
> PAO.EnergyShift 20 meV
> PAO.SplitNorm 0.15
> MeshCutoff 300.000000 Ry
> ElectronicTemperature 50.000000 K
>
> #
> MD.TypeOfRun CG # Broyden also possible
> MD.NumCGsteps 200
>
> #
> SolutionMethod diagon
> SCF.DM.Converge true # Converge SCF step
wrt density
> matrix (default: 1e-4)
> SCF.H.Converge true
> DM.NumberPulay 3
> DM.History.Depth 3
>
> #SCF Mixer -> Density pour les systèmes difficiles
>
> SCF.Mix Hamiltonian
>
> # Mixer 0.5 reduit le nombre de pas pour des systèmes faciles
> # Mixer 0.001 augmente le nombre de pas pour des systèmes
difficiles
>
> SCF.Mixer.Weight 0.05
> SCF.Mixer.History 6
> SCF.Mixer.Method Pulay
> MaxSCFIterations 100
>
> SCF.DM.Tolerance 5.0E-5 eV
> SCF.H.Tolerance 0.0005 eV
>
>
> MD.MaxStressTol 0.0025 eV/Ang**3
>
> # Nouvelle ligne pour la force entre atomes
>
> MD.MaxForceTol 0.01 eV/Ang
>
>
> # Use old data to save time
> MD.UseSaveXV
> MD.UseSaveDM
>
> # Save atomic coordinates at each step
> WriteCoorStep .true.
> WriteMDHistory .true.
>
>
> PAO.BasisType split
> PAO.BasisSize DZP
>
> LatticeConstant 1.0000 Ang
>
> %block LatticeVectors
> 7.65797 0.00000 0.00000
> 3.82898 6.63199 0.00000
> 0.00000 0.00000 24.00000
> %endblock LatticeVectors
>
> AtomicCoordinatesFormat Ang
>
> %block AtomicCoordinatesAndAtomicSpecies
>
> 3.829 0.7369 1.80 2 # Atome
de B en site cfc
>
> 0.0 0.0 0.0 1
> 1.2763 2.2107 0.0 1
> 2.5527 4.4213 0.0 1
> 2.5527 0.0 0.0 1
> 3.829 2.2107 0.0 1
> 5.1053 4.4213 0.0 1
> 5.1053 0.0 0.0 1
> 6.3816 2.2107 0.0 1
> 7.658 4.4213 0.0 1
>
> 0.0 1.4738 -2.0842 1
> 1.2763 3.6844 -2.0842 1
> 2.5527 5.8951 -2.0842 1
> 2.5527 1.4738 -2.0842 1
> 3.829 3.6844 -2.0842 1
> 5.1053 5.8951 -2.0842 1
> 5.1053 1.4738 -2.0842 1
> 6.3816 3.6844 -2.0842 1
> 7.658 5.8951 -2.0842 1
>
> 1.2763 0.7369 -4.1685 1
> 2.5527 2.9476 -4.1685 1
> 3.829 5.1582 -4.1685 1
> 3.829 0.7369 -4.1685 1
> 5.1053 2.9476 -4.1685 1
> 6.3816 5.1582 -4.1685 1
> 6.3816 0.7369 -4.1685 1
> 7.658 2.9476 -4.1685 1
> 8.9343 5.1582 -4.1685 1
>
> 0.0 0.0 -6.2527 1
> 1.2763 2.2107 -6.2527 1
> 2.5527 4.4213 -6.2527 1
> 2.5527 0.0 -6.2527 1
> 3.829 2.2107 -6.2527 1
> 5.1053 4.4213 -6.2527 1
> 5.1053 0.0 -6.2527 1
> 6.3816 2.2107 -6.2527 1
> 7.658 4.4213 -6.2527 1
>
> 0.0 1.4738 -8.3369 1
> 1.2763 3.6844 -8.3369 1
> 2.5527 5.8951 -8.3369 1
> 2.5527 1.4738 -8.3369 1
> 3.829 3.6844 -8.3369 1
> 5.1053 5.8951 -8.3369 1
> 5.1053 1.4738 -8.3369 1
> 6.3816 3.6844 -8.3369 1
> 7.658 5.8951 -8.3369 1
>
> %endblock AtomicCoordinatesAndAtomicSpecies
>
> %block kgrid_Monkhorst_Pack
> 12 0 0 0.
> 0 12 0 0.
> 0 0 1 0.
> %endblock kgrid_Monkhorst_Pack
>
> SaveTotalPotential T
> SaveTotalCharge T
> SaveElectrostaticPotential T
--
SIESTA is supported by the Spanish Research Agency (AEI) and
by the European H2020 MaX Centre of Excellence
(https://urldefense.com/v3/__http://www.max-centre.eu/__;!!D9dNQwwGXtA!Qka0VxNOMOZH8VxLDJ5j1Z4Ias1m_1JrwIw7f-yswD1OUkdvjfkqzBSsiLsJ9gDnhn2M4a0B_RSKqN5Q2U4KynTlrg$
<https://urldefense.com/v3/__http://www.max-centre.eu/__;!!D9dNQwwGXtA!StckWOSOOjpmsvjRweSqVEWqzGdIdPNy3eQF6OMu8DaMBJ1iNwSlSTbn0KsoLz3n_tNZZs7qzsBH$>)
