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Higher Bond length of Arsenous acid Date: 2019/07/13 16:12 Name: Lovleen Kaur   <lovleenkaurkkr@gmail.com> Dear Developers Hello, I am optimizing the structure of Arsenous acid. I am getting a bond length (As-O) of 1.8454, 1.8457 and 1.8721 which is quite high in comparison to literature which is 1.82A and 1.84A. These values of bond length are with following PAO's As9.0-s2p2d2f1, O6.0-s2p2d1 and H6.0-s2p1 the input file for this calculation is as .. I have also tried with PAO As-7.0 and As11.0-s2p2d2f1 for arsenic and O7.0-s2p2d1 still the results are not likely with the reported literature. Please guide how can i reduce this bond length to required bond length to required length. System.CurrrentDirectory ./ System.Name as DATA.PATH ../../../../../../../../DFT_DATA13 level.of.stdout 1 level.of.fileout 1 Species.Number 3 <Definition.of.Atomic.Species H H6.0-s2p1 H_PBE13 As As9.0-s2p2d2f1 As_PBE13 O O6.0-s2p2d1 O_PBE13 Definition.of.Atomic.Species> Atoms.Number 7 Atoms.SpeciesAndCoordinates.Unit Ang <Atoms.SpeciesAndCoordinates 1 As -0.06241700 0.03192000 -0.43117500 7.5 7.5 2 O -1.56916200 0.33927500 0.54656000 3.0 3.0 3 H -1.40508400 0.02386800 1.46500100 0.5 0.5 4 O 0.47272000 -1.51669800 0.37303700 3.0 3.0 5 H 1.29607900 -1.29543700 0.86552500 0.5 0.5 6 O 1.20771500 0.96899300 0.54278600 3.0 3.0 7 H 1.27858300 1.88563700 0.19919500 0.5 0.5 Atoms.SpeciesAndCoordinates> Atoms.UnitVectors.Unit Ang <Atoms.UnitVectors 21.68805 0.00270 -0.00015 0.00194 30.23267 0.00024 -0.00011 0.00024 29.97246 Atoms.UnitVectors> scf.XcType GGA-PBE scf.SpinPolarization on scf.ElectronicTemperature 300.0 scf.energycutoff 250.0 scf.maxIter 100 scf.EigenvalueSolver Cluster scf.Kgrid 1 1 1 scf.Mixing.Type rmm-diisk scf.Init.Mixing.Weight 0.05 scf.Min.Mixing.Weight 0.01 scf.Max.Mixing.Weight 0.30 scf.Mixing.History 25 scf.Mixing.StartPulay 15 scf.criterion 1.0e-7 # # vdW # scf.dftD onDFT.scale8 0.7875 DFTD.a1 0.4289 DFT.a2 4.4407 # # MD or Geometry Optimization # MD.Type Opt # Opt|EF|BFGS|RF|DIIS MD.Opt.DIIS.History 3 # default=3 MD.Opt.StartDIIS 10 # default=5 #MD.Opt.EveryDIIS 10000 # default=10 MD.maxIter 200 # MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.) version.dftD 3 DFTD3.damp bj DFTD.IntDirection 0 0 0 DFT.scale6 1.0 Best regards, Lovleen Kaur

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Re: Higher Bond length of Arsenous acid ( No.1 ) Date: 2019/11/10 20:55 Name: Jhon W. Gonzalez You should try changing the type of approach to van der Waals interaction. Try changing version.dftD=3 to D2. Also, DFTD.IntDirection 0 0 0 means no vdW correction. REMOVE: scf.dftD onDFT.scale8 0.7875 DFTD.a1 0.4289 DFT.a2 4.4407 version.dftD 3 DFTD3.damp bj DFTD.IntDirection 0 0 0 DFT.scale6 1.0 ADD: scf.dftD on # on|off, default=off version.dftD 2 # 2|3, default=2 Re: Higher Bond length of Arsenous acid ( No.2 ) Date: 2019/12/18 18:20 Name: T. Ozaki Hi, I have found only a single paper reporting the optimized structure of arsenous acid in the C1-symmetry using SIESTA with the GGA-PBE functional that you also used: Marc Blanchard, Kate Wright, Julian D. Gale, and C. Richard A. Catlow, J. Phys. Chem. C 2007, 111, 30, 11390-11396. https://doi.org/10.1021/jp072468v In Table 6 in the paper above, we see the bond length you may have referred in your post. However, I do not see any information about the basis functions used for the calculations, although the comparison of basis functions is shown for the case of lattice parameter for pyritein in Table 2 in the same paper. So, it would be difficult to conclude the origin of the discrepancy between SIESTA and OpenMX, where the discrepancy might be attributed to pseudopotentials, basis functions, and/or numerical integrations. If you really want to fix the problem, more systematic calculations including all electron calculations might be needed. Regards, TO

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