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]> >>>>>> >>>>> > >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> > >>>>>> >>>>>
