Hi guys, could you suggest the right cell setting for graphite simulation. Should I use extra space in xy dimension to get right optimised geometry? I build slab from Avogadro with 384 atoms and xyz 17.04000000 14.75707288 13.20000000 A. I froze two bottom layer and allowed remaining top two layer to equilibrate. <div><br><div>I am using following parameters:</div><div><div>&GLOBAL</div><div> PROJECT Graphite_geometry_optimization_moreMOs </div><div> RUN_TYPE GEO_OPT</div><div> PRINT_LEVEL MEDIUM</div><div>&END GLOBAL</div><div>&FORCE_EVAL</div><div> METHOD QS</div><div> &DFT</div><div> BASIS_SET_FILE_NAME BASIS_MOLOPT</div><div> POTENTIAL_FILE_NAME GTH_POTENTIALS</div><div> CHARGE 0</div><div> MULTIPLICITY 1</div><div> &MGRID</div><div> CUTOFF 800</div><div> NGRIDS 5</div><div> REL_CUTOFF 70</div><div> &END MGRID</div><div> &QS</div><div> EPS_DEFAULT 1.0E-12</div><div> WF_INTERPOLATION ASPC</div><div> &END QS</div><div> &SCF</div><div> SCF_GUESS ATOMIC</div><div> EPS_SCF 1.0E-7</div><div> MAX_SCF 1000</div><div> CHOLESKY INVERSE</div><div> ADDED_MOS 100</div><div> &SMEAR ON</div><div> METHOD FERMI_DIRAC</div><div> ELECTRONIC_TEMPERATURE [K] 300</div><div> &END SMEAR</div><div> &DIAGONALIZATION</div><div> ALGORITHM STANDARD</div><div> &END DIAGONALIZATION</div><div> &MIXING</div><div> METHOD BROYDEN_MIXING</div><div> ALPHA 0.4<span style="white-space:pre"> </span> </div><div> NBROYDEN 8</div><div> &END MIXING</div><div> &END SCF</div><div> &XC</div><div> &XC_FUNCTIONAL</div><div><span style="white-space:pre"> </span>&PBE</div><div><span style="white-space:pre"> </span>&END PBE</div><div> &END XC_FUNCTIONAL</div><div> &vdW_POTENTIAL</div><div> <span style="white-space:pre"> </span>DISPERSION_FUNCTIONAL PAIR_POTENTIAL</div><div> <span style="white-space:pre"> </span> &PAIR_POTENTIAL</div><div> <span style="white-space:pre"> </span> PARAMETER_FILE_NAME dftd3.dat</div><div> <span style="white-space:pre"> </span>TYPE DFTD3</div><div> <span style="white-space:pre"> </span>REFERENCE_FUNCTIONAL PBE</div><div> <span style="white-space:pre"> </span>R_CUTOFF 15.0</div><div> <span style="white-space:pre"> </span>&END PAIR_POTENTIAL</div><div> &END vdW_POTENTIAL</div><div> &END XC</div><div> &POISSON</div><div> PERIODIC xy</div><div> POISSON_SOLVER ANALYTIC</div><div> &END POISSON</div><div> &END DFT</div><div> &SUBSYS</div><div> &CELL</div><div> ABC 18.46 13.53 50.0</div><div> ALPHA_BETA_GAMMA 90.0 90.0 120.0</div><div> PERIODIC xy</div><div> &END CELL</div><div> &COORD</div><div> C 0.00000000 0.00000000 0.00000000</div><div> ...</div><div> C 17.75000000 13.52731681 9.90000000<br></div><div> &END COORD</div><div> &KIND C</div><div> BASIS_SET DZVP-MOLOPT-GTH</div><div> POTENTIAL GTH-PBE-q4</div><div> &END KIND</div><div> &END SUBSYS</div><div>&END FORCE_EVAL</div><div>&MOTION</div><div> &CONSTRAINT</div><div> &FIXED_ATOMS</div><div> COMPONENTS_TO_FIX XYZ</div><div> LIST 1..194</div><div> &END FIXED_ATOMS</div><div> &END CONSTRAINT</div><div> &GEO_OPT</div><div> OPTIMIZER LBFGS</div><div> MAX_ITER 300</div><div> &END GEO_OPT</div><div> &END MOTION</div><div><br></div><div>I spend 34 hours with 36 CPU and 120 GB of memory and still didn't optimised it yet. It seems that energy does not decrease much. </div><div><div> 384</div><div> i = 1, E = -2025.9045014398</div></div><div><div> 384</div><div> i = 6, E = -2075.1262328870</div></div><div> If I change cell parameters to </div><div><div> &SUBSYS</div><div> &CELL</div><div> ABC 18.46 13.53 50.0</div><div> PERIODIC xy</div><div> SYMMETRY ORTHORHOMBIC</div><div> &END CELL</div><div><div> 384</div><div> i = 1, E = -2132.8940479508</div></div><div><div> 384</div><div> i = 11, E = -2146.1458464543</div></div><div><br></div><div>It does not help much.</div><div><br></div><div>Regards,</div><div>Dmitrii</div><br></div></div></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Friday, December 4, 2020 at 2:52:34 PM UTC+11 DMITRII Drugov wrote:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Thank you for your reply! I am still running optimisation, I will share update once its done.<div><br></div><div>Regards,</div><div>Dmitrii</div><div><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, December 3, 2020 at 1:10:48 PM UTC+11 Travis wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi,<div><br></div><div>Graphite unit cell is hexagonal (<a href="https://materialsproject.org/materials/mp-48/" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://materialsproject.org/materials/mp-48/&source=gmail&ust=1607232141380000&usg=AFQjCNH63dnB7vPb6pqRwhcZtq_PwCYvDQ">https://materialsproject.org/materials/mp-48/</a>). You can orthogonalize any cell though. Do it by hand or use a program like atomsk (<a href="https://atomsk.univ-lille.fr/" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://atomsk.univ-lille.fr/&source=gmail&ust=1607232141380000&usg=AFQjCNHbblnv2_D1mmMr2FTUCpEjUTMRKQ">https://atomsk.univ-lille.fr/</a>),</div><div><br></div><div>atomsk foo.cif -orthogonal-cell bar.cif</div><div><br></div><div>-T<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Wednesday, December 2, 2020 at 6:38:50 PM UTC-5 <a rel="nofollow">dre...@gmail.com</a> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Good day dear CP2K users, do you think its right to use 90 90 90 orthorhombic symmetry for Graphite cell?<div>Should it be hexagonal 90 90 120 alpha betta gamma?</div><div><br></div><div>Regrads,</div><div>Dmitrii <br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Thursday, May 29, 2014 at 8:01:13 PM UTC+10 <a rel="nofollow">mic...@gmail.com</a> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div>Thanks for the clarification, Matthias. <br></div><br> I must admit that as someone who started off with PWs it is quite surprising to see that changing basis set within the same "class of complexity" can mess up things to the point of not being able to converge the SCF. In the future I'll pay more attention to testing the basis set when using CP2K, and take due note that there is much more than the number of polarization functions to define the quality of the basis!<br>
<br></div>Best wishes,<br>Michele<br><br><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, May 29, 2014 at 9:17 AM, Matthias Krack <span dir="ltr"><<a rel="nofollow">mat...@psi.ch</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear Michele,<br><br>I would not consider graphite as a specifically nasty system. As Matt already wrote, the basis sets in GTH_BASIS_SETS resulted from atomic calculations using the actual GTH pseudopotential. Such an atomic basis set optimisation gives in the case of carbon only a set of exponents and contraction coefficients for a 2s and 2p function. The SZV (single-valence) basis sets in GTH_BASIS_SETS are the results of such optimisations. You may try the C SZV basis set and you will see that is behaves at least reasonably for your system (you may also add a prmitive d polarisation function -> SZVP) However, experience has shown that such a minimal basis set is by far not accurate enough in most cases as it does not provide sufficient flexibility. Thus it is not suited for production runs. The double-zeta (DZV) GTH basis sets are derived from the corresponding SZV basis sets just by using the smallest exponent as a primitive function for the second valence function. This exponent is often rather small which results in a quite diffuse valence function without any nodal structure. These DZV basis sets were tested in molecular calculations in which they worked. You see, however, that the procedure is not based on any strict optimisation method. This deficiency may become apparent for condensed phase systems like your system. For such systems I would always recommend the use of the MOLOPT SR basis sets as already suggested which provide results closer to PW calculations. The generation procedure of the MOLOPT basis sets performs an optimisation of the contraction coefficients of all included valence functions. In this respect the MOLOPT SR basis sets can be considered as a kind of "second generation" CP2K basis sets.<br>
Nevertheless, I would like to note that there are many cases in which the GTH_BASIS_SETS work fine and their use may become beneficial as they are computionally less demanding. I know that these basis set issues are quite annoying, especially for people coming from the PW community.<br>
<br>Best regards,<br><br>Matthias<div><br><br>On Wednesday, May 28, 2014 9:57:05 PM UTC+2, Michele Ceriotti wrote:</div><blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><p dir="ltr">Dear Matt (and Marcella who basically replied the same in private),</p>
<p dir="ltr"> Thanks a million, using the molopt basis set does fix things. I had tried both the dzvp from basis_sets and gth_basis_set, and I was getting similar nonsense.</p>
<p dir="ltr">I am a bit scared seeing how much difference it makes changing the basis set. Any idea why graphite should be such a nasty beast? I had experimented with different basis sets for water and never saw such a dramatic effect.</p>
<p dir="ltr">All the best,<br>
Michele</p>
</div><div><div><div class="gmail_quote">On 28 May 2014 19:23, "Matt W" <<a rel="nofollow">Mat...@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Michele,<div><br></div><div>please try using the MOLOPT basis sets provided with CP2K ($CP2K_root/tests/QS/BASIS_<u></u>MOLOPT) that prehaps give a more suitable starting point for describing a "molecular" system like graphite than atomic optimization based ones.</div>
<div><br></div><div>Using a DZVP-MOLOPT-SR-GTH basis - I get SCF convergence in ~10 cycles and geometry converges in ~10 steps (with BFGS).</div><div><br></div><div>Matt<br><br>On Wednesday, May 28, 2014 5:19:30 PM UTC+1, Michele Ceriotti wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">
<p dir="ltr">Hi Matthias, <br>
Thanks for the quick answer. I have already played with the obvious parameters, point is it is impossible to converge the scf properly. <br>
Everything looks like what you get when the geometry is crazy, and indeed my student tried to enlarge the cell (by almost 10%!) and got converged scf and more reasonable forces. <br>
However this is inconsistent with the literature and the results from siesta.<br>
We have been trying to fiddle with the scf parameters for days, but get consistently 100au forces on a geometry that should be very close to optimum.<br>
Do you see something wrong with how we define the cell or the positions?<br>
Best<br>
Michele</p>
<div class="gmail_quote">On 28 May 2014 17:47, "Matthias Krack" <<a rel="nofollow">mat...@psi.ch</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Michele,<br><br>I would suggest to set EPS_DEFAULT in @QS section at least to 1.0E-12 or lower and for the ALPHA in &MIXING I would also use a smaller value like 0.2. Maybe this will help to converge your system properly.<br>
<br>Matthias<br><br>On Wednesday, May 28, 2014 4:20:44 PM UTC+2, Michele Ceriotti wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Dear CP2K community, <br>
<br> I have been trying for a few days to set up calculations of graphite as an exercise for a student but I am getting the weirdest results. I am sure in the it will end up being a silly mistake in the input, but I can't get to see it so perhaps someone can help. <br>
<br>Despite using a fairly large FD smearing, the SCF cycle has a hard time converging, and when the maximum number of steps is reached <br><br> 50 Broy./Diag. 0.50E+00 1.2 0.00014351 -819.2909959720 -2.28E-09<br>
*** SCF run NOT converged ***<br><br>and the calculation carries on with what it has got, diagnostics are really strange. <br><br>For a start, eigenvalues show two weird very low-energy states<br> MO EIGENVALUES AND MO OCCUPATION NUMBERS<br>
# MO index MO eigenvalue [a.u.] MO occupation<br> 1 -21.523076 2.000000<br> 2 -21.517160 2.000000<br> 3 -1.383548 2.000000<br>
4 -0.510418 2.000000<br><br>forces on the atoms are insane<br> ATOMIC FORCES in [a.u.]<br> # Atom Kind Element X Y Z<br> 1 1 C 4.68736611 4.63921800 -222.86999309<br>
2 1 C -1.57720920 -4.48651652 124.33822840<br> 3 1 C -5.01734639 3.10518104 176.16292919<br><br>and so is the stress tensor<br> STRESS TENSOR [GPa]<br> X Y Z<br>
X -8233.84728056 8.05482610 0.90481573<br> Y 8.05482610 -9552.76932222 -0.49445437<br> Z 0.90481573 -0.49445437 -2526.59040628<br><br>I was thinking of an error in the structure or the cell parameters, but I checked it many times and everything seems in order. The same structure, with same functional and similar parameters in SIESTA converges like a stone, and gives no problem whatsoever. <br>
<br>Can you spot something obvious that I am missing? I'd really like to use CP2K for this exercise, but I can't seem to figure out what is going wrong. <br><br>Many thanks,<br>Michele<br><br></div></blockquote>
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