Thank you for your reply!<div>I need to compare adsorption energy for organic molecules on different surfaces (Na, Au, Si, and C). I successfully used diagonalization for Na and Au as they are metals. However, I am not sure if I use OT for Si and C, it would be accurate to compare Eads with those of Na and Au. What do you think?</div><div>Do you have any suggestion how to expand Si surface to allow reconstructing?</div><div>Do you think fo graphite I also cannot use unitary cell?</div><div><br></div><div>Regards,</div><div>Dmitrii</div><div><br></div><div> <br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">On Monday, November 30, 2020 at 2:21:43 PM UTC+11 Lucas Lodeiro 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">Hi DMITRII,<div><br></div><div>I am not an expert on silicon systems, but I read plenty times that (001) silicon surfaces presents reconstruction when the surface is expanded (the reconstruction is not possible for the unitary surface cell), as your case. This could explain why do you have this problem with silicon and not with Au and Na. The first time that I read about this was "density functional theory: a practical introduction" of Janice Steckel and David Scholl, and in some papers, like this: <a href="https://www.researchgate.net/figure/Pictorial-view-of-the-100-surface-of-silicon-a-unrelaxed-surface-b-relaxed_fig5_282648906" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://www.researchgate.net/figure/Pictorial-view-of-the-100-surface-of-silicon-a-unrelaxed-surface-b-relaxed_fig5_282648906&source=gmail&ust=1606794473681000&usg=AFQjCNGXSBjTsOQgEYqAibjy62p-74pk1A">https://www.researchgate.net/figure/Pictorial-view-of-the-100-surface-of-silicon-a-unrelaxed-surface-b-relaxed_fig5_282648906</a></div><div><br></div><div>Another thing is, Why do you use diagonalization instead of OT method? I expect that silicon system (even surface systems) were not metals... then the OT method will be faster.</div><div><br></div><div>Regards </div><div>Lucas Lodeiro</div></div><br><div class="gmail_quote"></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El dom, 29 nov 2020 a las 22:24, DMITRII Drugov (<<a href data-email-masked rel="nofollow">dre...@gmail.com</a>>) escribió:<br></div></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Good day dear CP2K users, could you please have a look at my .in file to see did I specify ABC cell parameters and ALPHA_BETA_GAMMA for Si(100) with 16.29210*16.29210*5.76 A^3. I am using TZVP-MOLOPT-GTH and I allowed two top layer to relax while other bulk part is frozen. In total it only 42 atoms our of 85 is under relaxation. My system didn't reach any convergence yet, despite I run it for 30 hour on supercomputer with 120 GB memory and 36 CPU. However, I used same .in file for gold and Na slabs and with around 70-60 atoms with DZVP, and it converged within 1-2 hours. Do you think it's normal for TZVP, should I wait longer? Or smth wrong with my .in setting?<div><br></div><div>Regards,</div><div>Dmitrii<br><div><div><br></div><div><div> -------- Informations at step = 3 ------------</div><div> Optimization Method = LBFGS</div><div> Total Energy = 2.<a href="tel:(903)%20833-5460" value="+19038335460" target="_blank" rel="nofollow">9038335460</a></div><div> Real energy change = -14.0555995686</div><div> Decrease in energy = YES</div><div> Used time = 15200.012</div><div><br></div><div> Convergence check :</div><div> Max. step size = 0.3482436711</div><div> Conv. limit for step size = 0.0030000000</div><div> Convergence in step size = NO</div><div> RMS step size = 0.0816981844</div><div> Conv. limit for RMS step = 0.0015000000</div><div> Convergence in RMS step = NO</div><div> Max. gradient = <a href="tel:(681)%20309-1629" value="+16813091629" target="_blank" rel="nofollow">1.6813091629</a></div><div> Conv. limit for gradients = 0.0004500000</div><div> Conv. for gradients = NO</div><div> RMS gradient = 0.4396446909</div><div> Conv. limit for RMS grad. = 0.0003000000</div><div> Conv. for gradients = NO</div></div></div><div><br></div><div>my setting are:</div><div><div>&GLOBAL</div><div> PROJECT Si100_optimisation </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 20</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-wrap"> </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-wrap"> </span>&PBE</div><div><span style="white-space:pre-wrap"> </span>&END PBE</div><div> &END XC_FUNCTIONAL</div><div> &vdW_POTENTIAL</div><div> <span style="white-space:pre-wrap"> </span>DISPERSION_FUNCTIONAL PAIR_POTENTIAL</div><div> <span style="white-space:pre-wrap"> </span> &PAIR_POTENTIAL</div><div> <span style="white-space:pre-wrap"> </span> PARAMETER_FILE_NAME dftd3.dat</div><div> <span style="white-space:pre-wrap"> </span>TYPE DFTD3</div><div> <span style="white-space:pre-wrap"> </span>REFERENCE_FUNCTIONAL PBE</div><div> <span style="white-space:pre-wrap"> </span>R_CUTOFF 15.0</div><div> <span style="white-space:pre-wrap"> </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 16.404 16.404 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> Si 17.64977 -17.64977 -4.07302</div><div> Si 17.64977 -12.21907 -4.07302</div><div> Si 17.64977 -6.78837 -4.07302</div><div> Si 17.64977 -1.35767 -4.07302</div><div> Si 12.21907 -17.64977 -4.07302</div><div> Si 16.29210 -16.29210 -5.43070</div><div> Si 13.57675 -13.57675 -5.43070</div><div> Si 14.93442 -14.93442 -4.07302</div><div> Si 12.21907 -12.21907 -4.07302</div><div> Si 16.29210 -10.86140 -5.43070</div><div> Si 13.57675 -8.14605 -5.43070</div><div> Si 14.93442 -9.50372 -4.07302</div><div> Si 12.21907 -6.78837 -4.07302</div><div> Si 16.29210 -5.43070 -5.43070</div><div> Si 13.57675 -2.71535 -5.43070</div><div> Si 14.93442 -4.07302 -4.07302</div><div> Si 12.21907 -1.35767 -4.07302</div><div> Si 6.78837 -17.64977 -4.07302</div><div> Si 10.86140 -16.29210 -5.43070</div><div> Si 8.14605 -13.57675 -5.43070</div><div> Si 9.50372 -14.93442 -4.07302</div><div> Si 6.78837 -12.21907 -4.07302</div><div> Si 10.86140 -10.86140 -5.43070</div><div> Si 8.14605 -8.14605 -5.43070</div><div> Si 9.50372 -9.50372 -4.07302</div><div> Si 6.78837 -6.78837 -4.07302</div><div> Si 10.86140 -5.43070 -5.43070</div><div> Si 8.14605 -2.71535 -5.43070</div><div> Si 9.50372 -4.07302 -4.07302</div><div> Si 6.78837 -1.35767 -4.07302</div><div> Si 1.35767 -17.64977 -4.07302</div><div> Si 5.43070 -16.29210 -5.43070</div><div> Si 2.71535 -13.57675 -5.43070</div><div> Si 4.07302 -14.93442 -4.07302</div><div> Si 1.35767 -12.21907 -4.07302</div><div> Si 5.43070 -10.86140 -5.43070</div><div> Si 2.71535 -8.14605 -5.43070</div><div> Si 4.07302 -9.50372 -4.07302</div><div> Si 1.35767 -6.78837 -4.07302</div><div> Si 5.43070 -5.43070 -5.43070</div><div> Si 2.71535 -2.71535 -5.43070</div><div> Si 4.07302 -4.07302 -4.07302</div><div> Si 1.35767 -1.35767 -4.07302</div><div> Si 17.64977 -14.93442 -1.35767</div><div> Si 17.64977 -9.50372 -1.35767</div><div> Si 17.64977 -4.07302 -1.35767</div><div> Si 14.93442 -17.64977 -1.35767</div><div> Si 13.57675 -16.29210 -2.71535</div><div> Si 16.29210 -13.57675 -2.71535</div><div> Si 14.93442 -12.21907 -1.35767</div><div> Si 12.21907 -14.93442 -1.35767</div><div> Si 13.57675 -10.86140 -2.71535</div><div> Si 16.29210 -8.14605 -2.71535</div><div> Si 14.93442 -6.78837 -1.35767</div><div> Si 12.21907 -9.50372 -1.35767</div><div> Si 13.57675 -5.43070 -2.71535</div><div> Si 16.29210 -2.71535 -2.71535</div><div> Si 14.93442 -1.35767 -1.35767</div><div> Si 12.21907 -4.07302 -1.35767</div><div> Si 9.50372 -17.64977 -1.35767</div><div> Si 8.14605 -16.29210 -2.71535</div><div> Si 10.86140 -13.57675 -2.71535</div><div> Si 9.50372 -12.21907 -1.35767</div><div> Si 6.78837 -14.93442 -1.35767</div><div> Si 8.14605 -10.86140 -2.71535</div><div> Si 10.86140 -8.14605 -2.71535</div><div> Si 9.50372 -6.78837 -1.35767</div><div> Si 6.78837 -9.50372 -1.35767</div><div> Si 8.14605 -5.43070 -2.71535</div><div> Si 10.86140 -2.71535 -2.71535</div><div> Si 9.50372 -1.35767 -1.35767</div><div> Si 6.78837 -4.07302 -1.35767</div><div> Si 4.07302 -17.64977 -1.35767</div><div> Si 2.71535 -16.29210 -2.71535</div><div> Si 5.43070 -13.57675 -2.71535</div><div> Si 4.07302 -12.21907 -1.35767</div><div> Si 1.35767 -14.93442 -1.35767</div><div> Si 2.71535 -10.86140 -2.71535</div><div> Si 5.43070 -8.14605 -2.71535</div><div> Si 4.07302 -6.78837 -1.35767</div><div> Si 1.35767 -9.50372 -1.35767</div><div> Si 2.71535 -5.43070 -2.71535</div><div> Si 5.43070 -2.71535 -2.71535</div><div> Si 4.07302 -1.35767 -1.35767</div><div> Si 1.35767 -4.07302 -1.35767</div><div> &END COORD</div><div> &KIND Au</div><div> BASIS_SET DZVP-MOLOPT-SR-GTH </div><div> POTENTIAL GTH-PBE-q11</div><div> &END KIND</div><div> &KIND F</div><div> BASIS_SET TZVP-MOLOPT-GTH </div><div> POTENTIAL GTH-PBE-q7</div><div> &END KIND</div><div> &KIND O</div><div> BASIS_SET TZVP-MOLOPT-GTH</div><div> POTENTIAL GTH-PBE-q6</div><div> &END KIND</div><div> &KIND C</div><div> BASIS_SET TZVP-MOLOPT-GTH</div><div> POTENTIAL GTH-PBE-q4</div><div> &END KIND</div><div> &KIND Si</div><div> BASIS_SET TZVP-MOLOPT-GTH</div><div> POTENTIAL GTH-PBE-q4</div><div> &END KIND</div><div> &KIND S</div><div> BASIS_SET TZVP-MOLOPT-GTH</div><div> POTENTIAL GTH-PBE-q6</div><div> &END KIND</div><div> &KIND N</div><div> BASIS_SET TZVP-MOLOPT-GTH</div><div> POTENTIAL GTH-PBE-q5</div><div> &END KIND</div><div> &KIND Na</div><div> BASIS_SET DZVP-MOLOPT-SR-GTH</div><div> POTENTIAL GTH-PBE-q9</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..43 </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><div><img alt="Screen Shot 2020-11-30 at 12.12.28 pm.png" width="534px" height="399px" src="https://groups.google.com/group/cp2k/attach/81f6ba637acc1/Screen%20Shot%202020-11-30%20at%2012.12.28%20pm.png?part=0.1&view=1"><br></div></div>
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