Dear Marcos, Thank you once again. I recalculated the same jobs (systems) with MD relaxation parameters: MD.TypeOfRun CG MD.NumCGsteps 50 to compare the results. The results are the same no matter with or without relaxation steps (no changing in structural parameters at the end of calculations compared to the initial ones). As to forces and stresses, they were (and are) much below their respective tolerances. So the convergence is reached very fast (within 17 - 22 SCF iterations).
I was looking for answers to my questions in the SIESTA archive but still I am stuck at the same. I still need some help. Could you push me to the right direction? Thanks a lot, Artem Baskin, PhD student, University of Illinois at Chicago On Wed, April 28, 2010 2:25 am, Marcos Veríssimo Alves wrote: > Artem, > > Before proceeding to any other discussion: if this is indeed the complete > input, then the results will be the same, since you don't specify the > number > of relaxation steps; Siesta uses the default value, which is zero. So > nothing is moved, and all results are identical in what regards the > positions of the atoms and that of the Fermi level. However, how do the > forces and cell stresses look in each of the cases? Can you confirm that > Siesta is indeed performing a non-zero number of CG steps and that, by the > end of your calculation, all forces and stresses are below their > respective > tolerances? > > Marcos > > On Wed, Apr 28, 2010 at 3:46 AM, Artem Baskin <[email protected]> wrote: > >> Dear Marcos, >> >> Thank you for your elucidative response. I learned a lot. I also >> apologize >> for my not well defined questions and for that I did not provide my >> input >> file for graphene. >> Here it is. (that one that used initially) >> >> NumberOfAtoms 2 >> NumberOfSpecies 1 >> >> %block ChemicalSpeciesLabel >> 1 6 C # Species index, atomic number, species label >> %endblock ChemicalSpeciesLabel >> Meshcutoff 800.00 Ry >> LongOutput T >> WriteDenchar T >> AtomicCoordinatesFormat Ang >> %block AtomicCoordinatesAndAtomicSpecies >> 0.000 0.000 0.000 1 >> 1.42 0.00 0.000 1 >> >> %endblock AtomicCoordinatesAndAtomicSpecies >> >> %block PAO.BasisSizes >> C DZP >> %endblock PAO.BasisSizes >> >> LatticeConstant 2.459512147 Ang >> %block LatticeVectors >> 0.866025403 0.5 0.0 >> 0.866025403 -0.5 0.0 >> 0.0 0.0 60.0 >> >> %endblock LatticeVectors >> >> %block BandLines >> 1 0.0 -1.33333333 0.0 >> 30 0.0 0.0 0.0 >> 30 0.577350269 1.0 0.0 >> 20 0.0 1.33333333 0.0 >> %endblock BandLines >> >> I did what you suggested. I used the the content of STRUCT_NEXT_ITER >> files >> to see the difference in structural parameters and here they are : >> ---------------------------------------------------------------- >> 1) MD.VariableCell .false.; no k-point sampling; Meshcutoff=800 Ry >> >> 2.129999998 1.229756074 0.000000000 >> 2.129999998 -1.229756074 0.000000000 >> 0.000000000 0.000000000 147.570728820 >> 2 >> 1 6 0.000000000 -0.000000001 0.000000000 >> 1 6 0.333333333 0.333333334 0.000000000 >> >> FE=2.916573 >> ----------------------------------------------------------------- >> 2) MD.VariableCell .true.; no k-point sampling; Meshcutoff=800 Ry >> >> 2.129999998 1.229756074 0.000000000 >> 2.129999998 -1.229756074 0.000000000 >> 0.000000000 0.000000000 147.570728820 >> 2 >> 1 6 0.000000000 -0.000000001 0.000000000 >> 1 6 0.333333333 0.333333334 0.000000000 >> FE=2.916573 >> ------------------------------------------------------------------- >> 3) MD.VariableCell .true.;k-point sampling: >> %block kgrid_Monkhorst_Pack >> 21 0 0 0.0 >> 0 21 0 0.0 >> 0 0 1 0.0 >> %endblock kgrid_Monkhorst_Pack ; Meshcutoff=800 Ry >> 2.129999998 1.229756074 0.000000000 >> 2.129999998 -1.229756074 0.000000000 >> 0.000000000 0.000000000 147.570728820 >> 2 >> 1 6 0.000000001 -0.000000001 0.000000000 >> 1 6 0.333333334 0.333333335 0.000000000 >> FE=-3.788733 >> ------------------------------------------------------------------- >> 4) MD.VariableCell .true.;k-point sampling: >> %block kgrid_Monkhorst_Pack >> 6 0 0 0.0 >> 0 6 0 0.0 >> 0 0 1 0.0 >> %endblock kgrid_Monkhorst_Pack ; Meshcutoff=800 Ry >> 2.129999998 1.229756074 0.000000000 >> 2.129999998 -1.229756074 0.000000000 >> 0.000000000 0.000000000 147.570728820 >> 2 >> 1 6 0.000000001 0.000000000 0.000000000 >> 1 6 0.333333334 0.333333335 0.000000000 >> FE=-3.785969 >> >> Is it that info that you asked for? So, if it is that, you may easily >> see >> that there is no difference in cell vectors and atomic positions >> regardless of the presence of the options you indicated. The only >> significant difference is the Fermi Level (as it is expected). It is >> also >> interesting that the band structure looks very similarly in all these >> cases but the crossing points (at the K-points) are shifted and do not >> tally with the calculated level of FE (in case without k-point >> sampling). >> The fact that there is no difference in structure parameters may be the >> simple consequence of that I used the initial geometry very closed to >> equilibrium one. Is it so? >> >> Now I have more questions. >> 1) Why do you want to compare these results? Are they indicative for >> what? >> 2) How to specify (what reasons or ideas to follow) the k-point sampling >> in case of GNRs? >> 3) Why I got the more or less correct band structure (merely shifted >> with >> respect to correct FE) for Zigzag NR without sampling and can not get >> the >> same WITH k-point sampling along that ribbon? >> 4) Why I could not get the more or less reasoning BS for Armchair NR >> until >> I used >> %block kgrid_Monkhorst_Pack >> 45 0 0 0.0 >> 0 1 0 0.0 >> 0 0 1 0.0 >> %endblock kgrid_Monkhorst_Pack ? >> 5) How does k-point sampling influence the convergence of SCF loop? >> 6) Why the doubling of unit cell for Armchair NR (with the same or >> larger >> k-point sampling along the ribbon) does not lead to convergence and any >> reasonable results? >> 7) What should I do now to circumvent all these hurdles? >> >> I'm looking forward for you instructive (enlightening) advice. >> >> Artem Baskin, >> PhD student, >> University of Illinois at Chicago >> >> >> >> >> >> >> >> >> On Thu, April 22, 2010 7:35 pm, Marcos Veríssimo Alves wrote: >> > Artem, >> > >> > Let's go step by step. The fact that you get "good" results with >> graphene >> > only at the Gamma point seems extremely strange (weird might not sound >> so >> > good, I acknowledge that) for the following. >> > >> > Graphene has an extremely small Fermi surface - actually, a *single* >> > k-point, >> > which is located at the high-symmetry point K of the Brillouin zone. >> To >> > accurately sum over the bands of graphene, you need a specific k-point >> > sampling, which includes the coordinates of K in reciprocal space, as >> well >> > as a pretty dense k-point mesh in order to get the (linear, in the >> > vicinity >> > of K) dispersion of the bands in this region. >> > >> > Why is this important? Well, due to symmetry reasons, the Fermi level >> lies >> > * >> > exactly* at this point. Thus, it is important to accurately sample the >> > region of the BZ close to K, both including this particular point in >> your >> > sampling, *and* including enough k-points in order to accurately sum >> over >> > the occupied states and get a good total energy, which is the >> variational >> > quantity in DFT. Andf, as you may easily realize, Gamma-only sampling >> is >> > not >> > enough for that. >> > >> > You do not provide enough details on your graphene calculation, >> therefore >> > I >> > cannot know what you have done (this is the reason we always ask for >> the >> > input files. Repetitive? Yes, but... an image is worth a thousand >> words, >> > if >> > you catch my drift). So, I propose the following test for you, in your >> > graphene unit cell with two atoms. Start from ideal positions ((0,0,0) >> ; >> > (0.3333333333,0.3333333333,0.3333333333) in fractional coordinates) >> for >> > the >> > C atoms, and the following cell: >> > >> > LatticeConstant 2.44 Ang >> > %block LatticeParameters >> > 1.00 1.00 10.0 90.0 90.0 60.0 >> > %endblock LatticeParameters >> > >> > (check the convention for the angles between the lattice vectors in >> > crystallographic format in the manual, but I think this would be the >> > correct >> > setting). Now, do two calculations: >> > >> > 1) one with fixed cell, and only atomic coordinate relaxation >> > (MD.VariableCell .false.), and >> > 2) one with MD.VariableCell .true. . >> > >> > For those, check the cell parameters and angle between the cell >> vectors >> at >> > the end of the second calculation. >> > >> > After this, do a third calculation, starting from the same ideal >> > coordinates >> > and with MD. VariableCell set to .true., but now using >> > >> > %block kgrid_Monkhorst_Pack >> > 21 0 0 0.0 >> > 0 21 0 0.0 >> > 0 0 1 0.0 >> > %endblock kgrid_Monkhorst_Pack >> > >> > This is a sampling that, for the graphene cell described, includes the >> > high-symmetry point K in the sampling, and has a rather dense k-point >> > grid. >> > As a final calculation, lower the Monkhorst-Pack grid to >> > >> > %block kgrid_Monkhorst_Pack >> > 6 0 0 0.0 >> > 0 6 0 0.0 >> > 0 0 1 0.0 >> > %endblock kgrid_Monkhorst_Pack >> > >> > which still includes the high-symmetry point K, but has a much less >> dense >> > grid. Do it still with MD.VariableCell .true., and look at the >> > structural parameters. Use a 800 Ry cutoff in all of them, since this >> will >> > help avoid the infamous egg-box effect. Please tell me if you see any >> > difference in the structural parameters from each of the calculations. >> You >> > can use, if you wish, an automatically generated DZP basis set with an >> > EnergyShift 0.2 eV. An anticipation on the results: if there is no >> > difference between these results, there is something wrong :) >> > >> > The fact that you use Stephan Roche's results as a benchmark is good - >> his >> > calculations are very reliable. Nevertheless, I would say that you are >> > somehow inadvertently forcing symmetry in your system, which is the >> cause >> > of >> > the - much likely fortuitous - agreement of whatever result you are >> > obtaining in your calculations, with those of S. Roche. >> > >> > Some years ago, there were several posts on graphene on the list, with >> > some >> > very enlightening paricipations by Stephanie Reich. Search the list >> > archives >> > for these posts - you will learn a lot from them. I did, when I was >> still >> > working with graphene. >> > >> > Later on we can deal with different beasts like GNRs. >> > >> > Cheers, >> > >> > Marcos >> > >> > On Thu, Apr 22, 2010 at 11:32 PM, Artem Baskin <[email protected]> >> wrote: >> > >> >> Dear Marcos, >> >> Thanks for your help, but the situation looks really WEIRD or I don't >> >> understand anything at all (that may be also true). >> >> When I was calculating the BS for graphene and zigzag NR I did not >> use >> >> any >> >> specific supercell (I did not use the supercell block, the naive >> >> supercell >> >> factors were 6*6*1 for graphene (initially my elementary unit cell >> >> consisted of 2 atoms) and 6*1*1 for Zigzag NR (with 22 atoms - 5 >> rings >> >> width)). Of course, the SCF procedure converged in these two cases. >> >> As to criterion to determine whether my calculations are good or not, >> I >> >> used the comparison both with tight-bonding method results and the >> DFT >> >> calculations that were already done (using Siesta) by Pr. Stephan >> Roche >> >> and co-workers. My results tallied with the those ones perfectly. >> >> >> >> As to convergence in case with the zigzag NR (with k-point grid), >> double >> >> unit cell of armchair NR and its flakes, the procedure did not >> >> converged, >> >> and I don't know how to have it converged. Moreover, form one step >> of >> >> the >> >> iteration to another one the charges on the edge H-atoms are >> fluctuating >> >> getting more and more asymmetrical. This is another manifestation of >> the >> >> non-zero dipole moment. >> >> >> >> Best, >> >> Artem Baskin, >> >> PhD student, >> >> University of Illinois at Chicago >> >> >> >> >> >> On Thu, April 22, 2010 1:16 pm, Marcos Veríssimo Alves wrote: >> >> > Artem, >> >> > >> >> > Good results for graphene without any k-point sampling (only Gamma >> >> point)? >> >> > And also for a zigzag NR? Now THAT's weird... unless you are using >> a >> >> huge >> >> > supercell for each of them. What is your criterion for saying that >> >> your >> >> > calculation is good? For a zigzag NR you might get away with a >> smaller >> >> > supercell, if it's a semiconductor (I guess it is, I don't remember >> it >> >> > right >> >> > now). >> >> > >> >> > What is your procedure for calculating the band structure? Are you >> >> making >> >> > sure you re-use the converged DM file? >> >> > >> >> > Marcos >> >> > >> >> > >> >> > On Thu, Apr 22, 2010 at 8:06 PM, Artem Baskin <[email protected]> >> wrote: >> >> > >> >> >> Dear all users, >> >> >> I am involved in band structure calculations for armchair and >> zigzag >> >> >> nanoribbons and I have problems with the appropriate k-point >> >> sampling. >> >> >> My >> >> >> problem is like this: >> >> >> Initially, I calculated the band structure for graphene and zigzag >> NR >> >> >> without specifying any k-points. The results (with Meshcutoff >> level >> >> 800 >> >> >> Ry >> >> >> and 400 Ry respectively) were quite good. But when I tried to >> >> calculate >> >> >> the band structure for armchair (5 rings width) NR I got >> absolutely >> >> >> wrong >> >> >> results, moreover, in spite of symmetrical configuration I >> obtained >> >> the >> >> >> non-zero significant dipole moment perpendicular to the ribbon >> (even >> >> >> with 400 Ry MCutoff). >> >> >> Then I generated a k-point grid using >> >> >> %block kgrid_Monkhorst_Pack >> >> >> 45 0 0 0.5 >> >> >> 0 1 0 0.5 >> >> >> 0 0 1 0.5 >> >> >> %endblock kgrid_Monkhorst_Pack >> >> >> and I got correct results (no dipole moment and reasonable FE and >> >> band >> >> >> structure). >> >> >> >> >> >> FIRST problem that I encountered was that when I tried to >> recalculate >> >> BS >> >> >> for zigzag NR with the SAME k-point grid I got an enormous dipole >> >> moment >> >> >> (perpendicular to the ribbon) and wrong BS and FE level. Why is it >> >> so? >> >> >> >> >> >> SECOND problem is that when I doubled the elementary cell for >> 5-rings >> >> >> width armchair ribbon (using the SAME k-point grid and 400 Ry >> MCoff >> >> >> level) >> >> >> just to make sure that I will get the same good results I got >> again >> >> an >> >> >> enormous Dip moment and incorrect Band Structure. >> >> >> >> >> >> And THIRD (mysterious) problem is that when I tried to calculate >> Band >> >> >> Structure for an isolated flake of armchair NR (3*5 rings size) I >> got >> >> >> non >> >> >> zero Dip moment (in this case for x- and y- directions) that is >> >> >> nonsense. >> >> >> >> >> >> I guess, the problem is how to define correctly k-grid in these >> three >> >> >> cases, but I don't know how. I performed the convergence test >> >> increasing >> >> >> the number of k-points but neither dipole moment nor FE level >> >> >> demonstrate >> >> >> the monotonic behaviour, so I could not reach the correct results. >> >> >> >> >> >> Any help will be appreciated. >> >> >> >> >> >> Artem Baskin, >> >> >> PhD student, >> >> >> University of Illinois at Chicago >> >> >> >> >> >> >> >> >> >> >> >> >> >> > >> >> > >> >> >> >> >> >> >> > >> >> >> >
