[QE-users] Wrong prediction for Pd-Pd bond length
pboulet
pascal.boulet at univ-amu.fr
Tue Jan 29 10:03:24 CET 2019
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 : pascal.boulet at univ-amu.fr <mailto:pascal.boulet at univ-amu.fr>
> Le 29 janv. 2019 à 03:08, Paolo Costa <paolo.costa85 at gmail.com> 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 <pascal.boulet at univ-amu.fr <mailto:pascal.boulet at univ-amu.fr>> 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 : pascal.boulet at univ-amu.fr <mailto:pascal.boulet at univ-amu.fr>
>
>
>
>
>> Le 28 janv. 2019 à 16:44, Paolo Costa <paolo.costa85 at gmail.com <mailto:paolo.costa85 at gmail.com>> 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)
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>
> --
> 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
> users at lists.quantum-espresso.org
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