I have tried to get the most stable (lowest of the energy) structure and do the calculation. but the distance between atoms and the results are just not the value that I want. because I want to repeat the result of the article 'Density functional method for nonequilibrium electron transport' just like I mentioned in the other letter.
I have built a 111 direction bulk of Au and test the kpoints, PAO.energyshift, meshcutoff, and got kpoints 12 12 6 0.0 0.0 0.0 can make the system converge. (value of energy/atom difference between kpoint 10 10 5 0.0 0.0 0.0 is less than 0.01 eV) PAO.energyshift is converge at 0.005 (pic attached) meshcutoff are almost the same between the value 50~500 Ry (pic attached) but I got the similar atom's distance at PAO.energyshift equals 0.04 but the result is still not match the article... -- 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 15:31 GMT+08:00 <[email protected]>: > > Dear Chiu Fang Yu: > > The criterion of convergence varies from case to case. > It depends on which property you are after. > In the test I suggest, this is the minimum in the Etot(z-step) curve. > You want to get your chain step with a certain accuracy. > Each set of parameters will give you a different curve. > Enhance the parameters till the minimum of the curve > (also its curvature) gets stable. > The absolute value of energies in each curve is not important, > it may drift with parameters. > > Best regards > > Andrei > > [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]> > >>>> > > >>>> > >>>> > >>>> > >>>> > >>>> > > >
