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.
Best, Pascal Boulet — Professor in computational chemistry - DEPARTMENT OF CHEMISTRY Director of the Madirel laboratory Aix-Marseille University - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE Tél: +33(0)4 13 55 18 19 - Fax : +33(0)4 13 55 18 50 Email : [email protected] <mailto:[email protected]> > Le 29 janv. 2019 à 03:08, Paolo Costa <[email protected]> a écrit : > > Dear Pascal, > > thanks a lot for your detailed answer. > I have a doubt regarding the occupation. You suggested me to change from > smearing to fixed. Why? > 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. > 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. > Do you have any advise for me on running efficiently such 'heavy' > calculation? the following is the input file I prepared. > > Thanks. > > &CONTROL > calculation = "relax" > prefix ='PdNP85' > forc_conv_thr = 1.0e-04 > max_seconds = 1.0e+14 > nstep = 800 > pseudo_dir = "/home/pcosta/pseudo" > verbosity ='high' > disk_io ='none' > tprnfor = .TRUE. > tstress = .TRUE. > / > > &SYSTEM > a = 3.50000e+01 > degauss = 1.50000e-02 > ecutrho = 1.84000e+02 > ecutwfc = 1.8400e+01 > lda_plus_u = .FALSE. > ibrav = 1 > nat = 85 > nspin = 1 > ntyp = 1 > occupations = "smearing" > smearing = "gaussian" > starting_magnetization(1) = 2.00000e-01 > vdw_corr = 'grimme-d3' > / > > &ELECTRONS > conv_thr = 1.00000e-08 > diagonalization = "david" > diago_david_ndim=2 > mixing_ndim = 4 > electron_maxstep = 800 > startingpot = "atomic" > startingwfc = "atomic+random" > / > > &IONS > ion_dynamics = "bfgs" > trust_radius_min=1e-5 > / > > K_POINTS {gamma} > > ATOMIC_SPECIES > Pd 106.42000 Pd.pbe-n-kjpaw_psl.1.0.0.UPF > > ATOMIC_POSITIONS {angstrom} > Pd 15.776820 15.903080 18.073770 > Pd 13.861740 15.947890 16.372170 > Pd 15.426330 16.891080 14.607090 > Pd 17.339080 16.844820 16.311460 > Pd 18.903660 17.788010 14.546390 > Pd 19.237700 16.790950 18.028860 > Pd 20.816440 17.748340 16.229570 > Pd 17.689590 15.856780 19.778310 > Pd 16.975260 17.828530 12.847760 > Pd 18.570070 18.796940 11.026040 > Pd 20.500000 18.751390 12.742100 > Pd 22.364760 18.706220 14.403920 > Pd 19.600740 15.810070 21.482820 > Pd 21.206620 16.763870 19.717150 > Pd 22.748800 17.737590 17.835530 > Pd 24.322110 18.688150 16.053790 > Pd 11.886050 15.964270 14.712830 > Pd 13.491300 16.916240 12.952550 > Pd 15.004030 17.840610 11.205900 > Pd 16.545790 18.780840 9.431780 > Pd 10.275990 14.989220 16.543560 > Pd 12.269750 14.998870 18.133740 > Pd 14.170130 14.930450 19.899420 > Pd 16.138350 14.920080 21.533320 > Pd 18.056230 14.884320 23.208070 > Pd 14.812290 19.063690 13.385100 > Pd 16.379960 20.041440 11.613080 > Pd 18.303760 20.017670 13.301860 > Pd 16.728710 19.035300 15.082270 > Pd 18.648070 19.012670 16.763720 > Pd 15.156510 18.054700 16.859480 > Pd 17.076040 18.034690 18.532810 > Pd 13.234570 18.083640 15.155940 > Pd 20.227600 19.993890 14.990690 > Pd 22.151300 19.970120 16.679380 > Pd 20.570710 18.988560 18.452590 > Pd 18.987980 18.008990 20.217740 > Pd 11.679690 17.105560 16.939740 > Pd 13.591300 17.086050 18.604820 > Pd 15.497560 17.050130 20.317280 > Pd 17.401810 17.014340 22.027600 > Pd 14.353250 13.784050 17.521250 > Pd 12.421840 13.836590 15.841810 > Pd 13.994670 14.793240 14.062880 > Pd 15.935220 14.740470 15.750230 > Pd 17.500910 15.694120 13.975160 > Pd 17.872280 14.687800 17.434540 > Pd 19.429680 15.639620 15.658700 > Pd 16.284240 13.728290 19.210540 > Pd 15.567540 15.749910 12.283910 > Pd 17.140290 16.706510 10.505080 > Pd 19.073920 16.650450 12.197390 > Pd 20.999510 16.591890 13.891230 > Pd 18.226670 13.682240 20.878200 > Pd 19.776270 14.629820 19.109600 > Pd 21.374640 15.586780 17.349740 > Pd 22.970990 16.542650 15.591720 > Pd 17.813280 14.564160 11.809350 > Pd 16.272540 13.570020 13.595860 > Pd 14.725500 12.579240 15.366950 > Pd 18.215930 13.541560 15.273450 > Pd 16.666980 12.552890 17.036500 > Pd 19.760790 14.538960 13.480320 > Pd 21.688380 14.503850 15.165370 > Pd 20.145540 13.519610 16.919810 > Pd 18.618160 12.524270 18.720940 > Pd 12.824840 19.253220 17.422890 > Pd 14.389300 20.188650 15.625310 > Pd 15.937510 21.120970 13.823770 > Pd 16.330060 20.205960 17.306090 > Pd 17.870000 21.136320 15.503860 > Pd 14.759580 19.267480 19.108760 > Pd 16.705570 19.291080 20.772730 > Pd 18.237800 20.217270 18.977850 > Pd 19.818670 21.153740 17.191370 > Pd 18.518490 12.413770 12.842670 > Pd 16.923030 11.449920 14.609650 > Pd 18.863830 11.377970 16.278280 > Pd 20.420780 12.330080 14.518590 > Pd 15.802800 22.375450 16.028650 > Pd 14.249000 21.410550 17.831820 > Pd 16.203800 21.434420 19.485420 > Pd 17.719490 22.386670 17.690140 > Pd 15.573820 23.543960 18.485200 > Pd 19.033400 10.228370 14.054610 > > > Il giorno lun 28 gen 2019 alle ore 11:31 pboulet <[email protected] > <mailto:[email protected]>> ha scritto: > As a supplement to Giuseppe’s and Lorenzo's comments: > > 1- forc_conv_thr should be smaller: about 1e-4 or 1e-5 (why using 1.94469e-03 > with that many digits?) > 2- add: etot_conv_thr= 1e-7 > 2- I would use ibrav=0 together with CELL-PARAMETERS (see online manual) > 3- occupation=fixed, no smearing, and nbnd=number of occupied states+ a few > virtual ones. It should work as you have a dimer. > 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)… > 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). > 6- &CELL … / section is not necessary as you only optimise atomic positions. > 7- K_POINTS {Gamma} is all right as you have a molecule (k-points are only > meaningful for slabs and bulk structures) > > HTH, > Best > > > Pascal Boulet > — > Professor in computational chemistry - DEPARTMENT OF CHEMISTRY > Director of the Madirel laboratory > Aix-Marseille University - Avenue Escadrille Normandie Niemen - F-13013 > Marseille - FRANCE > Tél: +33(0)4 13 55 18 19 - Fax : +33(0)4 13 55 18 50 > Email : [email protected] <mailto:[email protected]> > > > > >> Le 28 janv. 2019 à 16:44, Paolo Costa <[email protected] >> <mailto:[email protected]>> a écrit : >> >> Dear QE users, >> >> I am trying to optimize (relax) Pd dimer (Pd2) as cluster placed on cubic >> lattice. >> 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). >> Am I doing something wrong? Here below the input file: >> >> &CONTROL >> calculation = "relax" >> prefix ='Pd2' >> forc_conv_thr = 1.94469e-03 >> max_seconds = 1.34369e+14 >> nstep = 800 >> pseudo_dir = "/home/pcosta/pseudo" >> verbosity ='high' >> disk_io ='none' >> tprnfor = .TRUE. >> tstress = .TRUE. >> / >> >> &SYSTEM >> a = 4.50000e+01 >> degauss = 1.00000e-02 >> ecutrho = 1.83747e+01 >> ecutwfc = 1.46997e+00 >> lda_plus_u = .FALSE. >> ibrav = 1 >> nat = 2 >> nspin = 2 >> ntyp = 1 >> occupations = "smearing" >> smearing = "gaussian" >> starting_magnetization(1) = 2.00000e-01 >> assume_isolated = 'makov-payne' >> vdw_corr = 'grimme-d3' >> / >> >> &ELECTRONS >> conv_thr = 1.00000e-08 >> diagonalization = "david" >> electron_maxstep = 800 >> mixing_beta = 4.00000e-01 >> startingpot = "atomic" >> startingwfc = "atomic+random" >> / >> >> &IONS >> ion_dynamics = "bfgs" >> trust_radius_min=1e-5 >> / >> >> &CELL >> cell_dofree = "all" >> cell_dynamics = "bfgs" >> press_conv_thr = 5.00000e-01 >> / >> >> K_POINTS {automatic} >> 3 3 1 0 0 0 >> >> ATOMIC_SPECIES >> Pd 106.42000 Pd.pbe-n-kjpaw_psl.1.0.0.UPF >> >> ATOMIC_POSITIONS {angstrom} >> Pd 16.194860 19.259990 18.659720 >> Pd 18.251640 18.665930 18.594650 >> >> Thanks. >> -- >> Paolo Costa, Ph.D. >> Postdoctoral Researcher >> Department of Chemistry and Biomolecular Sciences >> University of Ottawa >> 10 Marie Curie, Ottawa, ON K1N 6N5, Canada >> Room number: DRO 326 (D'Iorio Hall) >> _______________________________________________ >> users mailing list >> [email protected] <mailto:[email protected]> >> https://lists.quantum-espresso.org/mailman/listinfo/users >> <https://lists.quantum-espresso.org/mailman/listinfo/users> > _______________________________________________ > users mailing list > [email protected] <mailto:[email protected]> > https://lists.quantum-espresso.org/mailman/listinfo/users > <https://lists.quantum-espresso.org/mailman/listinfo/users> > > -- > Paolo Costa, Ph.D. > Postdoctoral Researcher > Department of Chemistry and Biomolecular Sciences > University of Ottawa > 10 Marie Curie, Ottawa, ON K1N 6N5, Canada > Room number: DRO 326 (D'Iorio Hall) > _______________________________________________ > users mailing list > [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users
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