Dear Marcos, I am not sure if I understood you correctly, but I checked my calculation with graphene (with options that you indicated) and I did not get any changes. The convergence is still reached very fast and the final Pressure is 0.4 GPa. Just to be on save side, I would like you to glance at my input file that I used, perhaps, there is something wrong with that how I handled with these options. But anyway, granting that you are correct (and I missed again something important), what does all this prove? The fact that I have to include relaxation as conditio sine qua non? And without relaxation all previous results are not reliable? But I am quite surprised why this relaxation is so important if I started from (more or less) the equilibrium geometry (I know about it beforehand). Moreover, my questions about the role of k-point sampling in case of GNribbons are still open. Here is my input file:
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 MD.VariableCell .true. MD.TypeOfRun CG MD.NumCGsteps 50 MD.TargetStressTol 0.01 GPa MD.TargetPressure 0.01 GPa Yours respectfully, Artem Baskin PhD student, University of Illinois at Chicago On Thu, April 29, 2010 6:05 pm, Marcos Veríssimo Alves wrote: > Artem, > > For a moment I thought I was completely hallucinating about my previous > experience with graphene :) but then I remembered that if you don't set a > variable explicitly in the input, the default values are used. I have just > run a variable-cell calculation for graphene using your input and, indeed, > if you don't set the target pressure, Siesta's default - 1 GPa, which is > huge!!! - is too high, since the final pressure is 0.4 GPa, which is still > too high. I set MD.TargetPressure and MD.TargetStressTol to 0.01 GPa and > the > lattice parameter comes out extremely bad - check it out. Actually, what I > see is that, at some point, the c-axis length starts to diminish > enormously > (surely a spurious effect) and I didn't even bother letting the > calculation > finish. I think now this should prove my points. > > Marcos > > On Thu, Apr 29, 2010 at 11:49 PM, Artem Baskin <[email protected]> wrote: > >> 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 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > >> >> >> > >> >> >> >> >> >> >> >> >> >> >> > >> >> >> >> >> >> >> > >> >> >> >
