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