Dear Andrei: Can you tell me how to do a "egg box" test?
-- Best Regards 邱芳瑜 Chiu Fang Yu 國立成功大學 材料科學與工程學系碩二 MOBILE：0930287221(中華) GMAIL：[email protected] <[email protected]> 2014-12-17 14:38 GMT+08:00 <[email protected]>: > Dear joyce79928: > > just some ideas. > Your results may be noise due to insufficient basis and/or > insufficient k-mesh ans/or insufficient MeshCutoff > (probably all three). > Does your DOS have any resemblance with what is expected for a 1-dim. > chain? > Does your stress definition in the GeometryConstrains block > serve any purpose? > There is a number of works with Siesta on Au chains around, > maybe scroll through them first. > Anyway, you can systematically proceed in the following way: > > Take just one atom along the chain step, not three > (make the third lattice vector shorter :-). > Fix it. > For the k-mesh, you need just 1 point in the plane but more than 4 > along Z. > Run a sequence of calculations just varying the 3d lattice vector > (chain step) - single point, no relaxation. > Trace the total energy curve as function of chain step. > This will give you an approximation to "true Siesta" result. > Study how it depends on basis, k-mesh and MeshCutoff. > Find "good" values for all three. > Make the usual "egg box" test. > Then hopefully your forces will be OK so that > you can add more atoms to your unit, release them, let them relax etc. > > Good luck > > Andrei > > [email protected] > > > > Dear: > > > > I want to relax the chain with Siesta. > > but different atom position with same parameter will get different > > structure. > > for example, I set the distance between chain to 2.93 A and get a final > > structure of 2.569 A between chain. > > Then I change initial chain distance to 2.88 A and get a final structure > > of > > 2.758 A between chain. > > > > why this happened? > > > > Thanks for reading my mail and it is welcome to discuss with me. > > > > below's are my fdf input file. > > > > SystemName bulk_au > > SystemLabel bulk_au > > > > ================================================== > > ================================================== > > # SPECIES AND BASIS > > > > # Number of species > > NumberOfSpecies 1 > > %block ChemicalSpeciesLabel > > 1 79 Au > > %endblock ChemicalSpeciesLabel > > > > PAO.BasisSize SZP > > PAO.EnergyShift 0.04 Ry > > > > > > # K-points > > > > %block kgrid_Monkhorst_Pack > > 4 0 0 0.0 > > 0 4 0 0.0 > > 0 0 4 0.5 > > %endblock kgrid_Monkhorst_Pack > > > > > > # UNIT CELL AND ATOMIC POSITIONS > > > > # UNIT CELL > > LatticeConstant 1.0 Ang > > %block LatticeVectors > > 8.81553253 0.00000000 0.00000000 > > 4.40776625 7.63447409 0.00000000 > > 0.00000000 0.00000000 8.79434817 > > %endblock LatticeVectors > > > > # Atomic coordinates > > NumberOfAtoms 3 > > AtomicCoordinatesFormat ScaledCartesian > > %block AtomicCoordinatesAndAtomicSpecies > > 4.407766232 4.241374236 0.00000000 1 > > 4.407766232 4.241374236 2.93144939 1 > > 4.407766232 4.241374236 5.86289878 1 > > %endblock AtomicCoordinatesAndAtomicSpecies > > > > ================================================== > > ================================================== > > # General variables > > > > ElectronicTemperature 300 K > > MeshCutoff 200. Ry > > xc.functional LDA # Exchange-correlation functional > > xc.authors CA > > SpinPolarized .false. > > SolutionMethod Diagon > > > > > > # SCF variables > > > > DM.MixSCF1 T > > MaxSCFIterations 300 # Maximum number of SCF iter > > DM.MixingWeight 0.03 # New DM amount for next SCF cycle > > DM.Tolerance 1.d-4 # Tolerance in maximum difference > > DM.UseSaveDM true # to use continuation files > > DM.NumberPulay 5 > > #Diag.ParallelOverK yes > > > > # MD variables > > > > MD.FinalTimeStep 1 > > MD.TypeOfRun CG > > MD.NumCGsteps 50 > > MD.VariableCell T > > UseSaveData T > > > > # Output variables > > > > WriteMullikenPop 1 > > WriteBands .false. > > SaveRho .false. > > SaveDeltaRho .false. > > SaveHS .false. > > SaveElectrostaticPotential True > > SaveTotalPotential no > > WriteCoorXmol .true. > > WriteMDXmol .true. > > WriteMDhistory .false. > > WriteEigenvalues yes > > > > %block GeometryConstraints > > stress 4 5 6 > > position 1 > > %endblock GeometryConstraints > > > > > > > > -- > > Best Regards > > > > 邱芳瑜 Chiu Fang Yu > > 國立成功大學 材料科學與工程學系碩二 > > MOBILE：0930287221(中華) > > GMAIL：[email protected] <[email protected]> > > > > > > >
