<div dir="ltr"><div dir="ltr"><div dir="ltr">Dear Pascal,<div><br></div><div>thanks a lot for your detailed answer. </div><div>I have a doubt regarding the occupation. You suggested me to change from smearing to fixed. Why? </div><div>Moreover, the Pd dimer is just a starting point since I have to calculate a larger cluster of Pd (e.g. Pd85). I need to compute adsoprtion energies of organic substrate on Pd85 cluster. </div><div>I read in lit. (J. Phys. Chem. A 2008, 112, 8911–8915) that Pd85 is a diamagnetic cluster, thus I will not run any spin-polarization calculation. </div><div>Do you have any advise for me on running efficiently such 'heavy' calculation? the following is the input file I prepared. </div><div><br></div><div>Thanks.</div><div><br></div><div><div>&CONTROL</div><div> calculation = "relax"</div><div> prefix ='PdNP85'</div><div> forc_conv_thr = 1.0e-04</div><div> max_seconds = 1.0e+14</div><div> nstep = 800</div><div> pseudo_dir = "/home/pcosta/pseudo"</div><div><span style="white-space:pre"> </span>verbosity ='high'</div><div> disk_io ='none'</div><div> tprnfor = .TRUE.</div><div> tstress = .TRUE.</div><div>/</div><div><br></div><div>&SYSTEM</div><div> a = 3.50000e+01</div><div> degauss = 1.50000e-02</div><div> ecutrho = 1.84000e+02</div><div> ecutwfc = 1.8400e+01</div><div> lda_plus_u = .FALSE.</div><div> ibrav = 1</div><div> nat = 85</div><div> nspin = 1</div><div> ntyp = 1</div><div> occupations = "smearing"</div><div> smearing = "gaussian"</div><div> starting_magnetization(1) = 2.00000e-01</div><div> vdw_corr = 'grimme-d3'</div><div>/</div><div><br></div><div>&ELECTRONS</div><div> conv_thr = 1.00000e-08</div><div> diagonalization = "david"</div><div> diago_david_ndim=2</div><div> mixing_ndim = 4</div><div> electron_maxstep = 800</div><div> startingpot = "atomic"</div><div> startingwfc = "atomic+random"</div><div>/</div><div><br></div><div>&IONS</div><div> ion_dynamics = "bfgs"</div><div><span style="white-space:pre"> </span>trust_radius_min=1e-5</div><div>/</div><div><br></div><div>K_POINTS {gamma}</div><div><br></div><div>ATOMIC_SPECIES</div><div>Pd 106.42000 Pd.pbe-n-kjpaw_psl.1.0.0.UPF</div><div><br></div><div>ATOMIC_POSITIONS {angstrom}</div><div>Pd 15.776820 15.903080 18.073770</div><div>Pd 13.861740 15.947890 16.372170</div><div>Pd 15.426330 16.891080 14.607090</div><div>Pd 17.339080 16.844820 16.311460</div><div>Pd 18.903660 17.788010 14.546390</div><div>Pd 19.237700 16.790950 18.028860</div><div>Pd 20.816440 17.748340 16.229570</div><div>Pd 17.689590 15.856780 19.778310</div><div>Pd 16.975260 17.828530 12.847760</div><div>Pd 18.570070 18.796940 11.026040</div><div>Pd 20.500000 18.751390 12.742100</div><div>Pd 22.364760 18.706220 14.403920</div><div>Pd 19.600740 15.810070 21.482820</div><div>Pd 21.206620 16.763870 19.717150</div><div>Pd 22.748800 17.737590 17.835530</div><div>Pd 24.322110 18.688150 16.053790</div><div>Pd 11.886050 15.964270 14.712830</div><div>Pd 13.491300 16.916240 12.952550</div><div>Pd 15.004030 17.840610 11.205900</div><div>Pd 16.545790 18.780840 9.431780</div><div>Pd 10.275990 14.989220 16.543560</div><div>Pd 12.269750 14.998870 18.133740</div><div>Pd 14.170130 14.930450 19.899420</div><div>Pd 16.138350 14.920080 21.533320</div><div>Pd 18.056230 14.884320 23.208070</div><div>Pd 14.812290 19.063690 13.385100</div><div>Pd 16.379960 20.041440 11.613080</div><div>Pd 18.303760 20.017670 13.301860</div><div>Pd 16.728710 19.035300 15.082270</div><div>Pd 18.648070 19.012670 16.763720</div><div>Pd 15.156510 18.054700 16.859480</div><div>Pd 17.076040 18.034690 18.532810</div><div>Pd 13.234570 18.083640 15.155940</div><div>Pd 20.227600 19.993890 14.990690</div><div>Pd 22.151300 19.970120 16.679380</div><div>Pd 20.570710 18.988560 18.452590</div><div>Pd 18.987980 18.008990 20.217740</div><div>Pd 11.679690 17.105560 16.939740</div><div>Pd 13.591300 17.086050 18.604820</div><div>Pd 15.497560 17.050130 20.317280</div><div>Pd 17.401810 17.014340 22.027600</div><div>Pd 14.353250 13.784050 17.521250</div><div>Pd 12.421840 13.836590 15.841810</div><div>Pd 13.994670 14.793240 14.062880</div><div>Pd 15.935220 14.740470 15.750230</div><div>Pd 17.500910 15.694120 13.975160</div><div>Pd 17.872280 14.687800 17.434540</div><div>Pd 19.429680 15.639620 15.658700</div><div>Pd 16.284240 13.728290 19.210540</div><div>Pd 15.567540 15.749910 12.283910</div><div>Pd 17.140290 16.706510 10.505080</div><div>Pd 19.073920 16.650450 12.197390</div><div>Pd 20.999510 16.591890 13.891230</div><div>Pd 18.226670 13.682240 20.878200</div><div>Pd 19.776270 14.629820 19.109600</div><div>Pd 21.374640 15.586780 17.349740</div><div>Pd 22.970990 16.542650 15.591720</div><div>Pd 17.813280 14.564160 11.809350</div><div>Pd 16.272540 13.570020 13.595860</div><div>Pd 14.725500 12.579240 15.366950</div><div>Pd 18.215930 13.541560 15.273450</div><div>Pd 16.666980 12.552890 17.036500</div><div>Pd 19.760790 14.538960 13.480320</div><div>Pd 21.688380 14.503850 15.165370</div><div>Pd 20.145540 13.519610 16.919810</div><div>Pd 18.618160 12.524270 18.720940</div><div>Pd 12.824840 19.253220 17.422890</div><div>Pd 14.389300 20.188650 15.625310</div><div>Pd 15.937510 21.120970 13.823770</div><div>Pd 16.330060 20.205960 17.306090</div><div>Pd 17.870000 21.136320 15.503860</div><div>Pd 14.759580 19.267480 19.108760</div><div>Pd 16.705570 19.291080 20.772730</div><div>Pd 18.237800 20.217270 18.977850</div><div>Pd 19.818670 21.153740 17.191370</div><div>Pd 18.518490 12.413770 12.842670</div><div>Pd 16.923030 11.449920 14.609650</div><div>Pd 18.863830 11.377970 16.278280</div><div>Pd 20.420780 12.330080 14.518590</div><div>Pd 15.802800 22.375450 16.028650</div><div>Pd 14.249000 21.410550 17.831820</div><div>Pd 16.203800 21.434420 19.485420</div><div>Pd 17.719490 22.386670 17.690140</div><div>Pd 15.573820 23.543960 18.485200</div><div>Pd 19.033400 10.228370 14.054610</div></div><div><br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il giorno lun 28 gen 2019 alle ore 11:31 pboulet <<a href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">As a supplement to Giuseppe’s and Lorenzo's comments:<div><br><div>1- forc_conv_thr should be smaller: about 1e-4 or 1e-5 (why using 1.94469e-03 with that many digits?)</div><div>2- add: etot_conv_thr= 1e-7</div><div>2- I would use ibrav=0 together with CELL-PARAMETERS (see online manual)</div><div>3- occupation=fixed, no smearing, and nbnd=number of occupied states+ a few virtual ones. It should work as you have a dimer.</div><div>4- why using vdW corrections? not sure they are significant. Furthermore, as a remember Grimme’s corrections are not that good for metals. I got too large bond distances for gold (but it was for a solid)… </div><div>5- mixing_beta=0.2 should do the job and you eventually avoid oscillations in the SCF convergence if you use a too large value (or even no convergence at all).</div><div>6- &CELL … / section is not necessary as you only optimise atomic positions.</div><div>7- K_POINTS {Gamma} is all right as you have a molecule (k-points are only meaningful for slabs and bulk structures)</div><div><br></div><div>HTH,</div><div>Best</div><div><br></div><div><br><div>
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<div><br><blockquote type="cite"><div>Le 28 janv. 2019 à 16:44, Paolo Costa <<a href="mailto:paolo.costa85@gmail.com" target="_blank">paolo.costa85@gmail.com</a>> a écrit :</div><br class="gmail-m_2195822157104886705Apple-interchange-newline"><div><div dir="ltr"><div dir="ltr">Dear QE users,<div><br></div><div>I am trying to optimize (relax) Pd dimer (Pd2) as cluster placed on cubic lattice.</div><div>However I got a value of Pd-Pd bond length which is far too long (3.36 A) compare to the experimental one (about 2.6 A).</div><div>Am I doing something wrong? Here below the input file:</div><div><div><br></div><div>&CONTROL</div><div> calculation = "relax"</div><div>prefix ='Pd2'</div><div> forc_conv_thr = 1.94469e-03</div><div> max_seconds = 1.34369e+14</div><div> nstep = 800</div><div> pseudo_dir = "/home/pcosta/pseudo"</div><div><span style="white-space:pre-wrap"> </span>verbosity ='high'</div><div>disk_io ='none'</div><div> tprnfor = .TRUE.</div><div> tstress = .TRUE.</div><div>/</div><div><br></div><div>&SYSTEM</div><div> a = 4.50000e+01</div><div> degauss = 1.00000e-02</div><div> ecutrho = 1.83747e+01</div><div> ecutwfc = 1.46997e+00</div><div><span style="white-space:pre-wrap"> </span>lda_plus_u = .FALSE.</div><div> ibrav = 1</div><div> nat = 2</div><div> nspin = 2</div><div> ntyp = 1</div><div> occupations = "smearing"</div><div> smearing = "gaussian"</div><div> starting_magnetization(1) = 2.00000e-01</div><div> assume_isolated = 'makov-payne'</div><div><span style="white-space:pre-wrap"> </span>vdw_corr = 'grimme-d3'</div><div>/</div><div><br></div><div>&ELECTRONS</div><div> conv_thr = 1.00000e-08</div><div> diagonalization = "david"</div><div> electron_maxstep = 800</div><div> mixing_beta = 4.00000e-01</div><div> startingpot = "atomic"</div><div> startingwfc = "atomic+random"</div><div>/</div><div><br></div><div>&IONS</div><div> ion_dynamics = "bfgs"</div><div><span style="white-space:pre-wrap"> </span>trust_radius_min=1e-5</div><div>/</div><div><br></div><div>&CELL</div><div> cell_dofree = "all"</div><div> cell_dynamics = "bfgs"</div><div> press_conv_thr = 5.00000e-01</div><div>/</div><div><br></div><div>K_POINTS {automatic}</div><div> 3 3 1 0 0 0</div><div> </div><div>ATOMIC_SPECIES</div><div>Pd 106.42000 Pd.pbe-n-kjpaw_psl.1.0.0.UPF</div><div><br></div><div>ATOMIC_POSITIONS {angstrom}</div><div>Pd 16.194860 19.259990 18.659720</div><div>Pd 18.251640 18.665930 18.594650</div><div><br></div><div>Thanks.</div>-- <br><div dir="ltr" class="gmail-m_2195822157104886705gmail-m_6880443592494725121gmail_signature"><div dir="ltr">Paolo Costa, Ph.D.<div>Postdoctoral Researcher</div><div>Department of Chemistry and Biomolecular Sciences</div><div>University of Ottawa</div><div>10 Marie Curie, Ottawa, ON K1N 6N5, Canada</div><div>Room number: DRO 326 (D'Iorio Hall)</div></div></div></div></div></div>
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<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr">Paolo Costa, Ph.D.<div>Postdoctoral Researcher</div><div>Department of Chemistry and Biomolecular Sciences</div><div>University of Ottawa</div><div>10 Marie Curie, Ottawa, ON K1N 6N5, Canada</div><div>Room number: DRO 326 (D'Iorio Hall)</div></div></div>