Dear Shanyi, just a quick question: have you considered the Basis Set Superposition Error (BSSE) in your SIESTA calculations?
----- Original Message ----- From: "shangy" <[email protected]> To: [email protected] Sent: Wednesday, April 24, 2013 3:20:16 PM Subject: [SIESTA-L] The noticeable discrepancies between SIESTA and VASP calculations Dear Siesta developers and users : (I am sorry for the same mail again. The last one was rejected by the mail server. And the pseudopotentails were not attached in last mail) I found there are noticeable discrepancies between SIESTA and VASP calculations when I calculated the formation energies of binary compounds in Mg-Y-Zn system, such as MgZn 2 , Mg 2 Zn 11 , Mg 24 Y 5 , Mg 2 Y , MgY , Zn 12 Y , Zn 17 Y 2 , Zn 3 Y and ZnY. The VASP calculations are consistent with the published results obtained by VASP. However, the formation energies calculated by SIESTA for these compounds are not comparable to these available results, as showed in following table 1. The formation energies (per atom) of various compounds with composition of Mg x Zn y Y z are calculated by: Delta_E f = E(Mg x Zn y Y z ) - E(Mg)*x/(x+y+x) - E(Zn)*y/(x+y+x) - E(Y)*z/(x+y+x), where E(Mg x Zn y Y z ) is the total energy of per atom of Mg x Zn y Y z , and E( i , i =Mg, Zn, Y) is the energy of per i atom in bulk. Table 1. The formation energies calculated by SIESTA and VASP for various binary compounds Formular Delta_E f (meV/atom) VASP SIESTA Scripta Mater., 67 (2012) 798 (with VASP) MgZn 2 -140.8 -84.8 -138 Mg 2 Zn 11 -71.7 -42.3 -68 Mg 24 Y 5 -59.3 -90.0 -59 Mg 2 Y -93.5 -129.4 -93 MgY -109.8 -140.6 -109 Zn 12 Y -187.8 -196.5 -184 Zn 17 Y 2 -244.5 -259.9 -241 Zn 3 Y -373.6 -462.1 -370 ZnY -366.2 -473.6 -363 The PAW-PBE pseudopotentials supplied by VASP and an energy cutoff of 300 eV were used in all VASP calculations. The attached Troullier-Martins PBE pseudopotentials of Mg, Zn and Y were used in SIESTA calculations. The pseudopotentials of Mg, Zn and Y were validated via the their lattices and cohesive energies, as showed in following table, which all are comparable to experimental data (the values within the bracket in table 2). Table 2. The lattices and cohesive energies calculated by SIESTA for Mg, Zn and Y bulk, the experimental data are given in the bracket. Pseudopotentials a (angstrom) c (angstrom) Cohesive (eV) Mg 3.234 (3.209) 5.158 (5.211) 1.447 (1.51) Zn 2.697 (2.665) 5.184 (4.947) 1.434 (1.35) Y 3.661 (3.648) 5.729 (5.732) 4.543 (4.37) The k-point meshes and convergence criteria of SIESTA calculations are identical to that of VASP calculations. The SIESTA input files for all calculations are similar except the k-points meshes and their atom coordinates. The optimzed structures and energies of various compounds are obtained with MD.VariableCell method and by restarting from previous calculations at least two times. Taking input file of MgZn 2 as an example, its input file is following: ------------------siesta-input-file-for-MgZn 2 --------------------- SystemName MgZn2-vc-opt-re2 SystemLabel MgZn2 NumberOfSpecies 2 NumberOfAtoms 12 XC.functional GGA XC.authors PBE MaxSCFIterations 150 #DM.UseSaveDM T #MD.UseSaveXV T #MD.UseSaveCG T #DM.MixSCF1 T DM.MixingWeight 0.01 DM.NumberPulay 5 DM.Tolerance 1.0E-4 DM.Require.Energy.Convergence T DM.Energy.Tolerance 1.0E-5 eV NumberOfEigenStates 400 Use.New.Diagk T MeshCutoff 400 Ry MeshSubDivision 6 SolutionMethod diagon OccupationFunction MP #OccupationMPOrder 3 ElectronicTemperature 1000 K Diag.ParallelOverK F MD.TypeOfRun CG MD.VariableCell T MD.NumCGsteps 500 MD.MaxForceTol 0.01 eV/Ang MD.MaxStressTol 0.05 Gpa MD.TargetPressure 0.0 Gpa WriteForces T WriteMDxmol T WriteCoorXmol T WriteCoorStep T PAO.BasisSize DZP PAO.EnergyShift 80 meV %block PAO.Basis Zn 2 n=4 0 2 P 0.0 0.0 n=3 2 2 0.0 0.0 %endblock PAO.Basis %block ChemicalSpeciesLabel 1 12 Mg 2 30 Zn %endblock ChemicalSpeciesLabel LatticeConstant 1 Ang %block LatticeVectors 5.2512841225 0.0000000000 0.0000000000 -2.6256420612 4.5477454525 0.0000000000 0.0000000000 0.0000000000 8.4452314377 %endblock LatticeVectors %block kgrid_Monkhorst_Pack 8 0 0 0.5 0 8 0 0.5 0 0 5 0 %endblock kgrid_Monkhorst_Pack AtomicCoordinatesFormat Fractional %block AtomicCoordinatesAndAtomicSpecies 0.33333299 0.66666698 0.06241800 1 0.66666698 0.33333299 0.56241798 1 0.66666698 0.33333299 0.93758202 1 0.33333299 0.66666698 0.43758199 1 0.00000000 0.00000000 0.00000000 2 0.00000000 0.00000000 0.50000000 2 0.17036100 0.34072199 0.75000000 2 0.82963902 0.17036100 0.25000000 2 0.34072199 0.17036100 0.25000000 2 0.65927798 0.82963902 0.75000000 2 0.17036100 0.82963902 0.75000000 2 0.82963902 0.65927798 0.25000000 2 %endblock AtomicCoordinatesAndAtomicSpecies And for Mg 2 Y, its input file is following: ------------------siesta-input-file-for-Mg 2 Y--------------------- SystemName Mg2Y-vc-opt-re2 SystemLabel Mg2Y NumberOfSpecies 2 NumberOfAtoms 12 XC.functional GGA XC.authors PBE MaxSCFIterations 150 #DM.UseSaveDM T #MD.UseSaveXV T #MD.UseSaveCG T #DM.MixSCF1 T DM.MixingWeight 0.01 DM.NumberPulay 5 DM.Tolerance 1.0E-4 DM.Require.Energy.Convergence T DM.Energy.Tolerance 1.0E-5 eV NumberOfEigenStates 400 Use.New.Diagk T MeshCutoff 400 Ry MeshSubDivision 6 SolutionMethod diagon OccupationFunction MP #OccupationMPOrder 3 ElectronicTemperature 1000 K Diag.ParallelOverK F MD.TypeOfRun CG MD.VariableCell T MD.NumCGsteps 500 MD.MaxForceTol 0.01 eV/Ang MD.MaxStressTol 0.05 Gpa MD.TargetPressure 0.0 Gpa WriteForces T WriteMDxmol T WriteCoorXmol T WriteCoorStep T PAO.BasisSize DZP PAO.EnergyShift 80 meV %block ChemicalSpeciesLabel 1 12 Mg 2 39 Y %endblock ChemicalSpeciesLabel LatticeConstant 1 Ang %block LatticeVectors 6.0594434738 0.0000000000 0.0000000000 -3.0297217369 5.2476319811 0.0000000000 0.0000000000 0.0000000000 9.8398962021 %endblock LatticeVectors %block kgrid_Monkhorst_Pack 7 0 0 0 0 7 0 0 0 0 5 0 %endblock kgrid_Monkhorst_Pack AtomicCoordinatesFormat Fractional %block AtomicCoordinatesAndAtomicSpecies 0.00000000 0.00000000 0.00000000 1 0.00000000 0.00000000 0.50000000 1 0.82894897 0.65789801 0.25000000 1 0.17105100 0.82894897 0.75000000 1 0.65789801 0.82894897 0.75000000 1 0.34210199 0.17105100 0.25000000 1 0.82894897 0.17105100 0.25000000 1 0.17105100 0.34210199 0.75000000 1 0.33333299 0.66666698 0.06474100 2 0.66666698 0.33333299 0.56474101 2 0.66666698 0.33333299 0.93525899 2 0.33333299 0.66666698 0.43525901 2 %endblock AtomicCoordinatesAndAtomicSpecies -------------------------------------------------------------------------------------------- I want to know why there are such noticeable discrepancies between SIESTA and VASP calculations on formation energies for these compounds. Did I miss some important settings or assign some unreasonable parameters in the input files? Or do these discrepancies arise from the description of interactions among Mg, Zn and Y atoms, which are different that of VASP. Any ideas and suggestions are highly appreciated! Thanks in advance! Shanyi Ma Institute of Metal Research, CAS
