Thank you Javier Junquera Sir. On 27 December 2017 at 17:00, Javier Junquera <javier.junqu...@unican.es> wrote:
> > Dear Sunetra: > > Take look at: > > http://personales.unican.es/junqueraj/JavierJunquera_ > files/Metodos/Hands-on-session.html > > And then follow the links to: > > 5. Converging the simulations > > Exercise 4. Convergence of the simulation with respect the MeshCutoff. > The egg box effect. > > Hope this helps, > > Best regards, > > Javier > > > El 26 dic 2017, a las 4:32, Sunetra Das <sunetra.das...@gmail.com> > escribió: > > Dear Andrei Postnikov Sir, > > Can you please guide me in how to do the 'eggbox test' ? I have gone > through the tutorials and examples but am still unclear on how to do that > test for a system. Will be very much thankful if you let me know the steps > on testing the eggbox effect and eliminating it. I have seen the term > 'eggbox energy' in siesta output file after completion of a run, but > confused what to decipher from it. > Thanking you and awaiting a reply. > > Warm regards and wishing you a happy new year in advance, > Sunetra Das. > > On 25 December 2017 at 19:52, Andrei Postnikov <andrei.postnikov@univ- > lorraine.fr> wrote: > >> Dear Najmeh, >> >> you are worrying about z-components of forces >> and try to help it by increasing the k(xy) mesh. It means that your >> bands dispersion becomes ever better in the plane, >> however, I don't think this would have an important effect on the >> z-force! >> >> Three observations: >> >> 1) >> Do you really have a problem? >> Your z-forces on atoms 1 and 2 do nicely sum up to zero within 0.001 - >> that is fine, - >> and the fact that they (individually) fluctuate with k simply reveals the >> fact >> that your structure is not at equilibrium. Try to get a better >> equilibrium - see 2). >> If you ultimate goal is phonons, why don't you calculate just Gamma >> and check if you get the acoustic modes close enough to zero? >> >> 2) >> In order to suppress fluctuations of forces / energy, >> the MeshCutoff is probably much more important that k-mesh. >> Apparently you tried 300 Ry and did not increase it any further. >> It might be not sufficient, depending on pseudos / basis. >> (However, it might well be OK in your case, see 1). >> In order to understand what's going on, the eggbox test >> (rigidly moving all the atoms... along Z, your "problematic" direction) >> for different values of MeshCutoff would help. >> With insufficient MeshCutoff, the increase of the k-mesh alone won't >> help you. >> (and... do you really need 20 Ang in the z-direction? You only need >> so much that the basis functions won't overlap). >> >> 3) >> The k-mesh is not a variational parameter, >> so you cannot expect a systematic lowering of the total energy >> (although it usually happens, albeit with fluctuations). >> For the phonon calculations, the total energy as such (i.e., >> its absolute value) is irrelevant anyway. >> >> Best regards >> >> Andrei Postnikov >> >> >> ----- Najmeh Honari <najmeh.honari...@gmail.com> a écrit : >> > >> Dear >> > Siesta users, >> >> > >> > >> >> I’m >> > trying to simulate 2D borophene δ*6*, in order to calculate phonon >> dispersion of the material. I did convergence >> > test for mesh-cut-off and k-points. I selected mesh cutoff=300Ry and >> started >> > k-grid from 12x12x1 and increased it to 40x40x1. The issue is that >> neither “total >> > energy” nor the “forces on atoms” are converged in other words >> fluctuations of >> > energies and forces are obsereved. Here are a table of some energy and >> forces >> > for different k-grid meshes of borophene >> > structure: >> >> > >> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> >> > >> >> K-grid >> >> > >> > >> >> Total >> > Energy (eV) >> >> > >> > >> >> Atomic >> > forces (eV/A) >> >> > >> >> > >> >> 15x15 >> >> > >> > >> >> -206.414196 >> >> > >> > >> >> 1 -0.000001 -0.000005 >> > -0.131499 >> >> > >> >> 2 -0.000002 -0.000004 0.131227 >> >> > >> >> > >> >> 17x17 >> >> > >> > >> >> -206.410794 >> >> > >> > >> >> 1 0.000000 -0.000003 >> > -0.423281 >> >> > >> >> 2 0.000004 -0.000001 0.423056 >> >> > >> >> > >> >> 20x20 >> >> > >> > >> >> -206.413284 >> >> > >> > >> >> 1 0.000001 -0.000006 >> > -0.287325 >> >> > >> >> 2 -0.000002 0.000002 0.287087 >> >> > >> >> > >> >> 23x23 >> >> > >> > >> >> -206.414429 >> >> > >> > >> >> 1 0.000000 -0.000000 >> > -0.355986 >> >> > >> >> 2 -0.000002 -0.000005 0.355733 >> >> > >> >> > >> >> 25x25 >> >> > >> > >> >> -206.423565 >> >> > >> > >> >> 1 -0.000001 -0.000000 >> > -0.416997 >> >> > >> >> 2 -0.000002 -0.000003 0.416772 >> >> > >> >> > >> >> 27x27 >> >> > >> > >> >> -206.424037 >> >> > >> > >> >> 1 -0.000002 -0.000006 >> > -0.308230 >> >> > >> >> 2 -0.000001 0.000000 0.307990 >> >> > >> >> > >> >> 30x30 >> >> > >> > >> >> -206.422290 >> >> > >> > >> >> 1 -0.000001 -0.000004 >> > -0.313348 >> >> > >> >> 2 -0.000000 -0.000002 0.313111 >> >> > >> >> > >> >> 33x33 >> >> > >> > >> >> -206.423341 >> >> > >> > >> >> 1 -0.000002 -0.000008 >> > -0.368439 >> >> > >> >> 2 -0.000001 -0.000005 0.368198 >> >> > >> >> > >> >> 35x35 >> >> > >> > >> >> -206.422301 >> >> > >> > >> >> 1 0.000002 -0.000004 >> > -0.275519 >> >> > >> >> 2 -0.000002 0.000001 0.275263 >> >> > >> >> > >> >> 38x38 >> >> > >> > >> >> -206.420742 >> >> > >> > >> >> 1 0.000002 0.000000 >> > -0.288896 >> >> > >> >> 2 -0.000000 0.000001 0.288655 >> >> > >> >> > >> >> 40x40 >> >> > >> > >> >> -206.420015 >> >> > >> > >> >> 1 -0.000001 -0.000005 >> > -0.357026 >> >> > >> >> 2 -0.000000 0.000000 0.356782 >> >> > >> > >> > >> >> >> > >> > >> >> The >> > input.fdf file that is used in simulations is as follow: >> >> > >> > >> >> >> > >> >>>>> >> >> > >> >> SystemName B >> >> > >> >> SystemLabel Borophene >> >> > >> >> NumberOfAtoms 2 >> >> > >> >> NumberOfSpecies 1 >> >> > >> >> ################## >> >> > >> >> #Basis# >> >> > >> >> ################## >> >> > >> >> PAO.BasisSize DZP >> >> > >> >> ################## >> >> > >> >> #ChemicalSpecies# >> >> > >> >> ################## >> >> > >> >> %block >> > ChemicalSpeciesLabel >> >> > >> >> 1 >> > 5 B >> >> > >> >> %endblock >> > ChemicalSpeciesLabel >> >> > >> >> ################################## >> >> > >> >> LatticeConstant 1.00 Ang >> >> > >> >> >> > >> >> %block LatticeVectors >> >> > >> >> 1.60000 0.0000 >> > 0.0000 >> >> > >> >> 0.00000 2.8200 >> > 0.0000 >> >> > >> >> 0.00000 0.0000 >> > 20.000 >> >> > >> >> %endblock >> > LatticeVectors >> >> > >> >> >> > >> >> AtomicCoordinatesFormat >> > Ang >> >> > >> >> >> >> > >> >> %block >> > AtomicCoordinatesAndAtomicSpecies >> >> > >> >> 0.00000 0.00000 >> 0.00000 1 >> >> > >> >> 0.80000 1.41000 >> > 0.91000 1 >> >> > >> >> %endblock AtomicCoordinatesAndAtomicSpecies >> >> > >> >> >> >> > >> >> BandLinesScale >> ReciprocalLatticeVectors >> >> > >> >> >> >> > >> >> %block BandLines >> >> > >> >> 1 0.0000000000 0.0000000000 0.0000000000 Gamma >> >> > >> >> 200 0.5000000000 0.0000000000 0.0000000000 X >> >> > >> >> 200 0.5000000000 0.5000000000 0.0000000000 S >> >> > >> >> 200 0.0000000000 0.5000000000 0.0000000000 Y >> >> > >> >> 200 0.0000000000 0.0000000000 0.0000000000 Gamma >> >> > >> >> %endblock BandLines >> >> > >> >> >> >> > >> >> %block kgrid_Monkhorst_Pack >> >> > >> >> 15 >> > 0 0 0.0 >> >> > >> >> 0 >> > 15 0 0.0 >> >> > >> >> 0 >> > 0 1 0.0 >> >> > >> >> %endblock >> > kgrid_Monkhorst_pack >> >> > >> >> ################ >> >> > >> >> #DFT, Grid, SCF# >> >> > >> >> ################ >> >> > >> >> SolutionMethod diagon >> >> > >> >> XC.Functional GGA >> >> > >> >> XC.authors PBE >> >> > >> >> SpinPolarized F >> >> > >> >> NonCollinearSpin F >> >> >> > >> >> FixSpin F >> >> > >> >> TotalSpin 0.0 >> >> >> > >> >> SingleExcitation F >> >> > >> >> MeshCutoff 300 Ry >> >> > >> >> MaxSCFIterations 100 >> >> > >> >> DM.MixingWeight 0.3 >> >> > >> >> DM.NumberPulay 6 >> >> > >> >> DM.NumberKick 5 >> >> > >> >> DM.KickMixingWeight 0.2 >> >> > >> >> DM.MixSCF1 F >> >> > >> >> DM.Tolerance 0.0001 >> >> > >> >> DM.InitSpinAF F >> >> >> > >> >> EggboxScale 1 eV >> >> > >> >> ##################### >> >> > >> >> #Eigenvalue problems# >> >> > >> >> ##################### >> >> > >> >> MD.TypeOfRun CG >> >> > >> >> MD.VariableCell F >> >> > >> >> MD.NumCGsteps 0 >> >> > >> >> MD.MaxCGDispl 0.2 Bohr >> >> > >> >> MD.PreconditionVariableCell 5.0 Ang >> >> > >> >> MD.MaxForceTol 0.001 eV/Ang >> >> > >> >> ################## >> >> > >> >> #Parallel options# >> >> > >> >> ################## >> >> > >> >> BlockSize 8 >> >> > >> >> DiagMemory 2.00 # Default value >> >> > >> >> DiagScale 1.25 >> >> > >> >> TryMemoryIncrease T # Default value >> >> > >> >> ################ >> >> > >> > >> > >> >> >> > >> > >> >> It’s >> > worth to say that I simulated BlackP by same INPUT.fdf file, and there >> were not >> > any fluctuation in energy and forces. Here are a table of some energy >> > and forces for different k-grid meshes of Black phosphorene structure. >> >> >> >> > >> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> >> > >> >> K-grid >> >> > >> > >> >> Total >> > Energy (eV) >> >> > >> > >> >> Atomic >> > forces (eV/A) >> >> > >> >> > >> >> 12x12 >> >> > >> > >> >> -834.239365 >> >> > >> > >> >> 1 1.028242 0.000000 0.123389 >> >> > >> >> 2 -1.168924 -0.000003 >> > -0.124082 >> >> > >> >> 3 1.182128 0.000001 >> > -0.130042 >> >> > >> >> 4 -1.021002 0.000000 0.123803 >> >> > >> >> > >> >> 15x15 >> >> > >> > >> >> -834.239563 >> >> > >> > >> >> 1 1.026970 -0.000001 0.121664 >> >> > >> >> 2 -1.167701 -0.000001 >> > -0.122354 >> >> > >> >> 3 1.180904 0.000003 >> > -0.128320 >> >> > >> >> 4 -1.019726 -0.000000 0.122082 >> >> > >> >> > >> >> 18x18 >> >> > >> > >> >> -834.239611 >> >> > >> > >> >> 1 1.026466 -0.000001 0.121037 >> >> > >> >> 2 -1.167212 -0.000000 >> > -0.121726 >> >> > >> >> 3 1.180422 0.000002 >> > -0.127694 >> >> > >> >> 4 -1.019227 -0.000001 0.121454 >> >> > >> >> > >> >> 21x21 >> >> > >> > >> >> -834.239629 >> >> > >> > >> >> 1 1.026270 -0.000002 0.120792 >> >> > >> >> 2 -1.167025 -0.000001 >> > -0.121484 >> >> > >> >> 3 1.180231 0.000001 >> > -0.127446 >> >> > >> >> 4 -1.019028 -0.000001 0.121212 >> >> > >> >> > >> >> 24x24 >> >> > >> > >> >> -834.239634 >> >> > >> > >> >> 1 1.026188 -0.000001 0.120697 >> >> > >> >> 2 -1.166949 0.000000 >> > -0.121387 >> >> > >> >> 3 1.180158 0.000002 >> > -0.127350 >> >> > >> >> 4 -1.018948 -0.000001 0.121115 >> >> > >> >> > >> >> 27x27 >> >> > >> > >> >> -834.239638 >> >> > >> > >> >> 1 1.026157 -0.000000 0.120657 >> >> > >> >> 2 -1.166919 -0.000001 >> > -0.121349 >> >> > >> >> 3 1.180126 0.000002 >> > -0.127309 >> >> > >> >> 4 -1.018913 0.000000 0.121076 >> >> > >> >> > >> >> 30x30 >> >> > >> > >> >> -834.239638 >> >> > >> > >> >> 1 1.026142 -0.000002 0.120640 >> >> > >> >> 2 -1.166907 -0.000000 >> > -0.121333 >> >> > >> >> 3 1.180114 0.000002 >> > -0.127294 >> >> > >> >> 4 -1.018900 -0.000001 0.121060 >> >> > >> > >> > >> >> >> > >> > >> >> Could >> > you let me know If I did something wrong with .fdf file in the first >> case? >> >> > >> >> Regards, >> Najmeh Honari >> >> >> > >
