I fix the stress to prevent it become the non-symmetry structure. since siesta is a software using localized basis sets not plane wave basis set, if I didn't stress the angle, it will become a non-symmetry structure.
-- 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 14:56 GMT+08:00 joyce79928cc . <[email protected]>: > > sorry, it is > 'change the kpoint until the energy/atom (eV) change is less than 0.01eV > ?' > > -- > 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 14:55 GMT+08:00 joyce79928cc . <[email protected]>: >> >> I was wondering how to decide whether it is converge? >> change the kpoint until the energy(eV) change is less than 0.01eV or...? >> Thanks! >> >> -- >> 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 14:51 GMT+08:00 joyce79928cc . <[email protected]>: >>> >>> Thanks for reply. I will try to fix it! >>> >>> -- >>> 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]> >>>> > >>>> >>>> >>>> >>>> >>>>
