[QE-users] Wrong prediction for Pd-Pd bond length
BARRETEAU Cyrille
cyrille.barreteau at cea.fr
Tue Jan 29 10:37:38 CET 2019
Just a small comment on Palladium which is an element very close to magnetism.
GGA functional slightly overestimates the lattice parameter and incorrectly predict a magnetic ground state...
Therefore if you turn-on magnetism you will probably find a magnetic Pd cluster.
LDA gives the right non-magnetic ground state.
best
Cyrille
========================
Cyrille Barreteau
CEA Saclay, IRAMIS, SPEC Bat. 771
91191 Gif sur Yvette Cedex, FRANCE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+33 1 69 08 38 56 /+33 6 47 53 66 52 (mobile)
email: cyrille.barreteau at cea.fr
Web: http://iramis.cea.fr/Pisp/cyrille.barreteau/
========================
________________________________
De : users [users-bounces at lists.quantum-espresso.org] de la part de pboulet [pascal.boulet at univ-amu.fr]
Envoyé : mardi 29 janvier 2019 10:03
À : Quantum Espresso users Forum
Objet : Re: [QE-users] Wrong prediction for Pd-Pd bond length
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<mailto: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)
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