Dear 邵德喜: Thanks for your reply. you mean...I need to trace the force on the atom for every 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]> 2014-12-18 12:37 GMT+08:00 邵德喜 <[email protected]>: > > Maybe you should use Force and stress while not Free energy for the test. > > 2014-12-18 11:30 GMT+08:00 joyce79928cc . <[email protected]>: >> >> 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]> >>>>> >>>>> > >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> > >>>>> >>>>
