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. If you have some advise, please mail me! 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]> 2014-12-22 14:10 GMT+08:00 joyce79928cc . <[email protected]>: > > 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]> >> >>>>> > >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> > >> >
