<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">It looks ok for a cluster of this size, but I am not an expert in nanoparticles, except for spin polarization: if Pd85 is diamagnetic I would expect neither spin nor starting_magnetization keywords. You will have to run tests to check convergence with ecutrho and ecutwfc. Nobody can help you with this.<div class=""><br class=""><div class=""><br class=""></div><div class="">Best, <div class=""><br class=""><div class="">
<div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div dir="auto" style="text-align: start; text-indent: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;"><span class="" style="font-size: 16pt; font-family: Mistral;">Pascal Boulet</span></div><div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;"><font face="Lucida Handwriting" class=""><span class="" style="font-size: 21px;">—</span></font></div><div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;"><em class="" style="color: rgb(34, 187, 234); font-family: verdana; font-size: 11px; line-height: 22px;">Professor in computational chemistry - DEPARTMENT OF CHEMISTRY</em></div><div class=""><div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px; font-family: Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 15px; line-height: 22px;"><span class="" style="font-size: 11px; font-family: verdana;">Director of the Madirel laboratory</span></div><div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px; font-family: Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 15px; line-height: 22px;"><span class="" style="font-size: 11px; font-family: verdana;">Aix-Marseille University </span><span class="" style="font-size: 11px; font-family: verdana;">- Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE</span></div><div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px; font-family: Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 15px; line-height: 22px;"><span class="" style="font-size: 11px; font-family: verdana;">Tél: +33(0)4 13 55 18 19 - Fax : +33(0)4 13 55 18 50</span></div><div class="" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; -webkit-text-stroke-width: 0px;"><font face="verdana" class=""><span class="" style="font-size: 12px; line-height: 22px;">Email : </span></font><font color="#22bbea" face="verdana" class=""><span style="font-size: 12px; line-height: 20px;" class=""><a href="mailto:pascal.boulet@univ-amu.fr" class="">pascal.boulet@univ-amu.fr</a></span></font></div><div class="" style="font-size: 14px;"><br class=""></div></div></div></div></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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<div><br class=""><blockquote type="cite" class=""><div class="">Le 29 janv. 2019 à 03:08, Paolo Costa <<a href="mailto:paolo.costa85@gmail.com" class="">paolo.costa85@gmail.com</a>> a écrit :</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class="">Dear Pascal,<div class=""><br class=""></div><div class="">thanks a lot for your detailed answer. </div><div class="">I have a doubt regarding the occupation. You suggested me to change from smearing to fixed. Why? </div><div class="">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 class="">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 class="">Do you have any advise for me on running efficiently such 'heavy' calculation? the following is the input file I prepared. </div><div class=""><br class=""></div><div class="">Thanks.</div><div class=""><br class=""></div><div class=""><div class="">&CONTROL</div><div class=""> calculation = "relax"</div><div class=""> prefix ='PdNP85'</div><div class=""> forc_conv_thr = 1.0e-04</div><div class=""> max_seconds = 1.0e+14</div><div class=""> nstep = 800</div><div class=""> pseudo_dir = "/home/pcosta/pseudo"</div><div class=""><span style="white-space:pre" class=""> </span>verbosity ='high'</div><div class=""> disk_io ='none'</div><div class=""> tprnfor = .TRUE.</div><div class=""> tstress = .TRUE.</div><div class="">/</div><div class=""><br class=""></div><div class="">&SYSTEM</div><div class=""> a = 3.50000e+01</div><div class=""> degauss = 1.50000e-02</div><div class=""> ecutrho = 1.84000e+02</div><div class=""> ecutwfc = 1.8400e+01</div><div class=""> lda_plus_u = .FALSE.</div><div class=""> ibrav = 1</div><div class=""> nat = 85</div><div class=""> nspin = 1</div><div class=""> ntyp = 1</div><div class=""> occupations = "smearing"</div><div class=""> smearing = "gaussian"</div><div class=""> starting_magnetization(1) = 2.00000e-01</div><div class=""> vdw_corr = 'grimme-d3'</div><div class="">/</div><div class=""><br class=""></div><div class="">&ELECTRONS</div><div class=""> conv_thr = 1.00000e-08</div><div class=""> diagonalization = "david"</div><div class=""> diago_david_ndim=2</div><div class=""> mixing_ndim = 4</div><div class=""> electron_maxstep = 800</div><div class=""> startingpot = "atomic"</div><div class=""> startingwfc = "atomic+random"</div><div class="">/</div><div class=""><br class=""></div><div class="">&IONS</div><div class=""> ion_dynamics = "bfgs"</div><div class=""><span style="white-space:pre" class=""> </span>trust_radius_min=1e-5</div><div class="">/</div><div class=""><br class=""></div><div class="">K_POINTS {gamma}</div><div class=""><br class=""></div><div class="">ATOMIC_SPECIES</div><div class="">Pd 106.42000 Pd.pbe-n-kjpaw_psl.1.0.0.UPF</div><div class=""><br class=""></div><div class="">ATOMIC_POSITIONS {angstrom}</div><div class="">Pd 15.776820 15.903080 18.073770</div><div class="">Pd 13.861740 15.947890 16.372170</div><div class="">Pd 15.426330 16.891080 14.607090</div><div class="">Pd 17.339080 16.844820 16.311460</div><div class="">Pd 18.903660 17.788010 14.546390</div><div class="">Pd 19.237700 16.790950 18.028860</div><div class="">Pd 20.816440 17.748340 16.229570</div><div class="">Pd 17.689590 15.856780 19.778310</div><div class="">Pd 16.975260 17.828530 12.847760</div><div class="">Pd 18.570070 18.796940 11.026040</div><div class="">Pd 20.500000 18.751390 12.742100</div><div class="">Pd 22.364760 18.706220 14.403920</div><div class="">Pd 19.600740 15.810070 21.482820</div><div class="">Pd 21.206620 16.763870 19.717150</div><div class="">Pd 22.748800 17.737590 17.835530</div><div class="">Pd 24.322110 18.688150 16.053790</div><div class="">Pd 11.886050 15.964270 14.712830</div><div class="">Pd 13.491300 16.916240 12.952550</div><div class="">Pd 15.004030 17.840610 11.205900</div><div class="">Pd 16.545790 18.780840 9.431780</div><div class="">Pd 10.275990 14.989220 16.543560</div><div class="">Pd 12.269750 14.998870 18.133740</div><div class="">Pd 14.170130 14.930450 19.899420</div><div class="">Pd 16.138350 14.920080 21.533320</div><div class="">Pd 18.056230 14.884320 23.208070</div><div class="">Pd 14.812290 19.063690 13.385100</div><div class="">Pd 16.379960 20.041440 11.613080</div><div class="">Pd 18.303760 20.017670 13.301860</div><div class="">Pd 16.728710 19.035300 15.082270</div><div class="">Pd 18.648070 19.012670 16.763720</div><div class="">Pd 15.156510 18.054700 16.859480</div><div class="">Pd 17.076040 18.034690 18.532810</div><div class="">Pd 13.234570 18.083640 15.155940</div><div class="">Pd 20.227600 19.993890 14.990690</div><div class="">Pd 22.151300 19.970120 16.679380</div><div class="">Pd 20.570710 18.988560 18.452590</div><div class="">Pd 18.987980 18.008990 20.217740</div><div class="">Pd 11.679690 17.105560 16.939740</div><div class="">Pd 13.591300 17.086050 18.604820</div><div class="">Pd 15.497560 17.050130 20.317280</div><div class="">Pd 17.401810 17.014340 22.027600</div><div class="">Pd 14.353250 13.784050 17.521250</div><div class="">Pd 12.421840 13.836590 15.841810</div><div class="">Pd 13.994670 14.793240 14.062880</div><div class="">Pd 15.935220 14.740470 15.750230</div><div class="">Pd 17.500910 15.694120 13.975160</div><div class="">Pd 17.872280 14.687800 17.434540</div><div class="">Pd 19.429680 15.639620 15.658700</div><div class="">Pd 16.284240 13.728290 19.210540</div><div class="">Pd 15.567540 15.749910 12.283910</div><div class="">Pd 17.140290 16.706510 10.505080</div><div class="">Pd 19.073920 16.650450 12.197390</div><div class="">Pd 20.999510 16.591890 13.891230</div><div class="">Pd 18.226670 13.682240 20.878200</div><div class="">Pd 19.776270 14.629820 19.109600</div><div class="">Pd 21.374640 15.586780 17.349740</div><div class="">Pd 22.970990 16.542650 15.591720</div><div class="">Pd 17.813280 14.564160 11.809350</div><div class="">Pd 16.272540 13.570020 13.595860</div><div class="">Pd 14.725500 12.579240 15.366950</div><div class="">Pd 18.215930 13.541560 15.273450</div><div class="">Pd 16.666980 12.552890 17.036500</div><div class="">Pd 19.760790 14.538960 13.480320</div><div class="">Pd 21.688380 14.503850 15.165370</div><div class="">Pd 20.145540 13.519610 16.919810</div><div class="">Pd 18.618160 12.524270 18.720940</div><div class="">Pd 12.824840 19.253220 17.422890</div><div class="">Pd 14.389300 20.188650 15.625310</div><div class="">Pd 15.937510 21.120970 13.823770</div><div class="">Pd 16.330060 20.205960 17.306090</div><div class="">Pd 17.870000 21.136320 15.503860</div><div class="">Pd 14.759580 19.267480 19.108760</div><div class="">Pd 16.705570 19.291080 20.772730</div><div class="">Pd 18.237800 20.217270 18.977850</div><div class="">Pd 19.818670 21.153740 17.191370</div><div class="">Pd 18.518490 12.413770 12.842670</div><div class="">Pd 16.923030 11.449920 14.609650</div><div class="">Pd 18.863830 11.377970 16.278280</div><div class="">Pd 20.420780 12.330080 14.518590</div><div class="">Pd 15.802800 22.375450 16.028650</div><div class="">Pd 14.249000 21.410550 17.831820</div><div class="">Pd 16.203800 21.434420 19.485420</div><div class="">Pd 17.719490 22.386670 17.690140</div><div class="">Pd 15.573820 23.543960 18.485200</div><div class="">Pd 19.033400 10.228370 14.054610</div></div><div class=""><br class=""></div></div></div></div><br class=""><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" class="">pascal.boulet@univ-amu.fr</a>> ha scritto:<br class=""></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;" class="">As a supplement to Giuseppe’s and Lorenzo's comments:<div class=""><br class=""><div class="">1- forc_conv_thr should be smaller: about 1e-4 or 1e-5 (why using 1.94469e-03 with that many digits?)</div><div class="">2- add: etot_conv_thr= 1e-7</div><div class="">2- I would use ibrav=0 together with CELL-PARAMETERS (see online manual)</div><div class="">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 class="">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 class="">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 class="">6- &CELL … / section is not necessary as you only optimise atomic positions.</div><div class="">7- K_POINTS {Gamma} is all right as you have a molecule (k-points are only meaningful for slabs and bulk structures)</div><div class=""><br class=""></div><div class="">HTH,</div><div class="">Best</div><div class=""><br class=""></div><div class=""><br class=""><div class="">
<div dir="auto" style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;" class=""><div dir="auto" style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;" class=""><div dir="auto" style="text-align:start;text-indent:0px" class=""><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;" class=""><span style="font-size:16pt;font-family:Mistral" class="">Pascal Boulet</span></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;" class=""><font face="Lucida Handwriting" class=""><span style="font-size:21px" class="">—</span></font></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;" class=""><em style="color:rgb(34,187,234);font-family:verdana;font-size:11px;line-height:22px" class="">Professor in computational chemistry - DEPARTMENT OF CHEMISTRY</em></div><div class=""><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 15px; line-height: 22px;" class=""><span style="font-size:11px;font-family:verdana" class="">Director of the Madirel laboratory</span></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 15px; line-height: 22px;" class=""><span style="font-size:11px;font-family:verdana" class="">Aix-Marseille University </span><span style="font-size:11px;font-family:verdana" class="">- Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE</span></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none; font-family: Tahoma, Verdana, Arial, Helvetica, sans-serif; font-size: 15px; line-height: 22px;" class=""><span style="font-size:11px;font-family:verdana" class="">Tél: +33(0)4 13 55 18 19 - Fax : +33(0)4 13 55 18 50</span></div><div style="letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; text-decoration: none;" class=""><font face="verdana" class=""><span style="font-size:12px;line-height:22px" class="">Email : </span></font><font color="#22bbea" face="verdana" class=""><span style="font-size:12px;line-height:20px" class=""><a href="mailto:pascal.boulet@univ-amu.fr" target="_blank" class="">pascal.boulet@univ-amu.fr</a></span></font></div><div style="font-size:14px" class=""><br class=""></div></div></div></div></div><br class="gmail-m_2195822157104886705Apple-interchange-newline"><br class="gmail-m_2195822157104886705Apple-interchange-newline">
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<div class=""><br class=""><blockquote type="cite" class=""><div class="">Le 28 janv. 2019 à 16:44, Paolo Costa <<a href="mailto:paolo.costa85@gmail.com" target="_blank" class="">paolo.costa85@gmail.com</a>> a écrit :</div><br class="gmail-m_2195822157104886705Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div dir="ltr" class="">Dear QE users,<div class=""><br class=""></div><div class="">I am trying to optimize (relax) Pd dimer (Pd2) as cluster placed on cubic lattice.</div><div class="">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 class="">Am I doing something wrong? Here below the input file:</div><div class=""><div class=""><br class=""></div><div class="">&CONTROL</div><div class=""> calculation = "relax"</div><div class="">prefix ='Pd2'</div><div class=""> forc_conv_thr = 1.94469e-03</div><div class=""> max_seconds = 1.34369e+14</div><div class=""> nstep = 800</div><div class=""> pseudo_dir = "/home/pcosta/pseudo"</div><div class=""><span style="white-space:pre-wrap" class=""> </span>verbosity ='high'</div><div class="">disk_io ='none'</div><div class=""> tprnfor = .TRUE.</div><div class=""> tstress = .TRUE.</div><div class="">/</div><div class=""><br class=""></div><div class="">&SYSTEM</div><div class=""> a = 4.50000e+01</div><div class=""> degauss = 1.00000e-02</div><div class=""> ecutrho = 1.83747e+01</div><div class=""> ecutwfc = 1.46997e+00</div><div class=""><span style="white-space:pre-wrap" class=""> </span>lda_plus_u = .FALSE.</div><div class=""> ibrav = 1</div><div class=""> nat = 2</div><div class=""> nspin = 2</div><div class=""> ntyp = 1</div><div class=""> occupations = "smearing"</div><div class=""> smearing = "gaussian"</div><div class=""> starting_magnetization(1) = 2.00000e-01</div><div class=""> assume_isolated = 'makov-payne'</div><div class=""><span style="white-space:pre-wrap" class=""> </span>vdw_corr = 'grimme-d3'</div><div class="">/</div><div class=""><br class=""></div><div class="">&ELECTRONS</div><div class=""> conv_thr = 1.00000e-08</div><div class=""> diagonalization = "david"</div><div class=""> electron_maxstep = 800</div><div class=""> mixing_beta = 4.00000e-01</div><div class=""> startingpot = "atomic"</div><div class=""> startingwfc = "atomic+random"</div><div class="">/</div><div class=""><br class=""></div><div class="">&IONS</div><div class=""> ion_dynamics = "bfgs"</div><div class=""><span style="white-space:pre-wrap" class=""> </span>trust_radius_min=1e-5</div><div class="">/</div><div class=""><br class=""></div><div class="">&CELL</div><div class=""> cell_dofree = "all"</div><div class=""> cell_dynamics = "bfgs"</div><div class=""> press_conv_thr = 5.00000e-01</div><div class="">/</div><div class=""><br class=""></div><div class="">K_POINTS {automatic}</div><div class=""> 3 3 1 0 0 0</div><div class=""> </div><div class="">ATOMIC_SPECIES</div><div class="">Pd 106.42000 Pd.pbe-n-kjpaw_psl.1.0.0.UPF</div><div class=""><br class=""></div><div class="">ATOMIC_POSITIONS {angstrom}</div><div class="">Pd 16.194860 19.259990 18.659720</div><div class="">Pd 18.251640 18.665930 18.594650</div><div class=""><br class=""></div><div class="">Thanks.</div>-- <br class=""><div dir="ltr" class="gmail-m_2195822157104886705gmail-m_6880443592494725121gmail_signature"><div dir="ltr" class="">Paolo Costa, Ph.D.<div class="">Postdoctoral Researcher</div><div class="">Department of Chemistry and Biomolecular Sciences</div><div class="">University of Ottawa</div><div class="">10 Marie Curie, Ottawa, ON K1N 6N5, Canada</div><div class="">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" class="">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div dir="ltr" class="gmail_signature"><div dir="ltr" class="">Paolo Costa, Ph.D.<div class="">Postdoctoral Researcher</div><div class="">Department of Chemistry and Biomolecular Sciences</div><div class="">University of Ottawa</div><div class="">10 Marie Curie, Ottawa, ON K1N 6N5, Canada</div><div class="">Room number: DRO 326 (D'Iorio Hall)</div></div></div>
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