I want atom 1 as a reference position -- 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]> 2014-12-18 11:14 GMT+08:00 邵德喜 <[email protected]>: > > Fix the stress here just will control the distortion in you str opt. your > setting seems all right. But I can not understand that the constraints > "position > 1" in the INPUT. > > 2014-12-17 22:34 GMT+08:00 joyce79928cc . <[email protected]>: >> >> Thanks for replying. >> >> I think fixed the stress is fit the calculation of bulk periodic system, >> right? >> >> >> -- >> 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]> >>> >>>>> > >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> > >>> >>
