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 (http://www.max-centre.eu/)
