Dear: I have tried using one atom and fixed the atom's position by varying the lattice vector. But I still got different output distance between chain when I set different input chain distance. and I have plot the figure of different input chain distance vs final energy. and there's no curve for the most stable chain distance.
I still can't understand why there's different output chain distance when I set different input chain distance. -- 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 15:38 GMT+08:00 <[email protected]>: > > The basis set a priori has nothing to do with symmetry. > You want to run a chain geometry; this means that the atoms > in the (x,y) plane are far enough from each other that > their basis functions do not overlap. Consequently, > there is no force nor stress in this direction; > whatever comes out is numerical noise. > Why don't you simply fix the lattice instead of > using variable cell. > However, fixing (correctly chosen) stress components > may effectively serve the same purpose. > It is too difficult for me to figure out which components > to fix... > > Good luck > > Andrei > > [email protected] > > > > 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]> > >>>>> > > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > > >
