You are right, but the criteria will not effect the convergence test. Then in my experience, force often converges togenther with the total energy.
2014-12-22 8:08 GMT+08:00 joyce79928cc . <[email protected]>: > But I think siesta have default value for force and stress criterion. > Optimization will stop until force and stress reach the criterion, right? > Here I mean the criteria for convergence test in the str opt should be > stress and force. > > 2014-12-18 21:24 GMT+08:00 joyce79928cc . <[email protected]>: > >> 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]> >>>>>>> >>>>> > >>>>>>> >>>>> >>>>>>> >>>>> >>>>>>> >>>>> >>>>>>> >>>>> >>>>>>> >>>>> >>>>>>> > >>>>>>> >>>>>> >
