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!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!QWSMgD_jSmHzoxT8j_dmZrR27JUoQhVhq3G91IQB1d1oCiP3OqQKMUgc4Tjf1POpfiwSHM5tn4y4w_0vcYV5ZQ$ >> >> <https://urldefense.com/v3/__http://www.max-centre.eu/__;!!D9dNQwwGXtA!StckWOSOOjpmsvjRweSqVEWqzGdIdPNy3eQF6OMu8DaMBJ1iNwSlSTbn0KsoLz3n_tNZZs7qzsBH$> >> ) >> >
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
