[QE-users] Unexpected adsorption energy

Mohamed Safy msafy505 at gmail.com
Sun Dec 9 13:37:28 CET 2018


Dear  Giuseppe
Many thanks for your response.
I will try with your advice and give you the response
Thanks

On Thu, 6 Dec 2018 at 12:24, Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
wrote:

>
> Dear Mohamed
>
> charged ions are tricky in DFT for multiple reasons. The excess and
> well localized charge can suffer a very strong delocalization error
> which may lead to unbound electronic states. Moreover, charged ions
> are generally not stable in gas phase. They often require a polar
> solvent to exist. Finally, in periodic boundary conditions a
> distribution of charge (aka "jellium") is required to compensate the
> positive/negative charge in a supercell, and the reference potential
> is affected by the insertion of such charge, so that for example you
> cannot calculate the ionization energy of a molecule as
> E[q=+1]-E[q=0], as you do when you use GTO codes.
>
> This said, it is not impossible to calculate the adsorption energy of
> charged ions on a given substrate, provided that:
>
> 1) You use a hybrid EXX-GGA functional. This is not mandatory, but it
> is recommended because it generally avoids the accommodation of excess
> electrons in unbound states.
>
> 2) You embed your system in an implicit dielectric medium (maybe
> "water", in your case). In QE this is easily provided by the
> QUANTUM-ENVIRON plug-in.
>
> Then you can calculate the adsorption energy in two ways:
>
> A) you can start from the interacting configuration of your system and
> progressively remove the ion in several snapshots (or a few snapshot,
> depending on the computational resources you can afford). Then you
> build an interaction potential curve and yiu try to estimate its
> asymptotic value. It requires also a large supercell, of course.
>
> B) you can use a little trick (which however requires 1 and 2 above).
> Put a cation in a part of your supercell where the interaction energy
> with you polymer+anion system is negligible. Then calculate the energy
> of your cation+anion system in a neutral supercell where their charge
> is exactly compensated. The energy difference between three neutral
> supercells E[polymer+anion+cation]-E[polymer]-E[cation+anion] should
> be a sensible estimate of the anion adsorption energy
>
> HTH
> Giuseppe
>
> Mohamed Safy <msafy505 at gmail.com> ha scritto:
>
> > Thanks for your valuable information but I have experimental results
> which
> > indicate the presence of adsorption. is this can be considered a
> > conflict?.  I tried to validate the method using a smaller system. I
> > studied the adsorption of H2 on Graphene.
> > The adsorption energy was 17.17 kcal/mol.
> > the systems are below
> > Complex
> > &CONTROL
> >     calculation   = "scf"
> >     forc_conv_thr =  1.00000e-03
> >     max_seconds   =  1.72800e+05
> >     nstep         = 1000
> >     verbosity='high'
> >     restart_mode='from_scratch'
> >     iprint=1
> >     tprnfor=.true.
> >  pseudo_dir = '/lfs01/workdirs/val/Test/pseudo',
> > outdir='/lfs01/workdirs/val/Test/Out/C',
> > /
> >
> > &SYSTEM
> >     a     =  7.40525e+00
> >     c     =  9.99906e+00
> >     ibrav = 4
> >     nat   = 19
> >     ntyp  = 2
> >     ecutwfc = 45.0 ,
> > ecutrho = 450.0 ,
> > input_DFT = 'PBE-D2' ,
> > occupations = 'smearing' ,
> > degauss = 1.0d-4 ,
> > vdw_corr = 'Grimme-D2'
> > assume_isolated = 'mt'
> > smearing = 'marzari-vanderbilt' ,
> > /
> >
> > &ELECTRONS
> > conv_thr = 1.0d-7 ,
> > electron_maxstep = 1000
> > mixing_mode = 'plain' ,
> > mixing_beta = 0.3d0 ,
> > /
> >
> > &IONS
> > ion_dynamics='bfgs'
> > upscale=20.0
> > /
> >
> > &CELL
> > /
> >
> > K_POINTS {automatic}
> >  3  3  3  0 0 0
> >
> > ATOMIC_SPECIES
> > C      12.01070  C.pbe-n-kjpaw_psl.1.0.0.UPF
> > H       1.00794  H.pbe-kjpaw_psl.1.0.0.UPF
> > ATOMIC_POSITIONS {angstrom}
> > C        1.280642168   0.685951341  -0.000431048
> > C       -1.236653977   3.539880413  -0.001566184
> > C       -0.000377617   2.903279130  -0.002911997
> > C       -2.489554615   5.710262290  -0.000852594
> > C       -1.229721248   4.990709007  -0.000338911
> > C        2.449440629   1.438897112   0.002319254
> > C        3.702198081   0.707454065  -0.001265064
> > C        1.236237242   3.539760579   0.000958837
> > C        2.478517989   2.856386275   0.004841971
> > C       -0.000246038   5.700684987  -0.000997560
> > C        1.229347070   4.990770096  -0.000716604
> > C        4.955272233   1.438694069  -0.002138838
> > C        6.124721243   0.686321393   0.000987763
> > C        3.702044434   3.562937903   0.001926384
> > C        4.925831271   2.856536000  -0.001755553
> > C        2.489209922   5.710445901  -0.000342579
> > C        3.702309214   4.976078918  -0.000048704
> > H        3.360489134   2.350036356  -3.014528460
> > H        2.719672863   2.741584163  -3.037540110
> >
> >
> > Graphen
> > &CONTROL
> >     calculation   = "scf"
> >     forc_conv_thr =  1.00000e-03
> >     max_seconds   =  1.72800e+05
> >     nstep         = 1000
> >     verbosity='high'
> >     restart_mode='from_scratch'
> >     iprint=1
> >     tprnfor=.true.
> >  pseudo_dir = '/lfs01/Val/cairo010u1/Test/pseudo',
> > outdir='/lfs01/workdirs/Val/Test/Out/G',
> > /
> >
> > &SYSTEM
> >     a     =  7.40525e+00
> >     c     =  9.99906e+00
> >     ibrav = 4
> >     nat   = 17
> >     ntyp  = 1
> >     ecutwfc = 45.0 ,
> > ecutrho = 450.0 ,
> > input_DFT = 'PBE-D2' ,
> > occupations = 'smearing' ,
> > degauss = 1.0d-4 ,
> > vdw_corr = 'Grimme-D2'
> > assume_isolated = 'mt'
> > smearing = 'marzari-vanderbilt' ,
> > /
> >
> > &ELECTRONS
> > conv_thr = 1.0d-10 ,
> > electron_maxstep = 1000
> > mixing_mode = 'plain' ,
> > mixing_beta = 0.3d0 ,
> > /
> >
> > &IONS
> > ion_dynamics='bfgs'
> > upscale=20.0
> > /
> >
> > &CELL
> > /
> >
> > K_POINTS {automatic}
> >  3  3  3  0 0 0
> >
> > ATOMIC_SPECIES
> > C      12.01070  C.pbe-n-kjpaw_psl.1.0.0.UPF
> >
> > ATOMIC_POSITIONS {angstrom}
> > C        1.280642168   0.685951341  -0.000431048
> > C       -1.236653977   3.539880413  -0.001566184
> > C       -0.000377617   2.903279130  -0.002911997
> > C       -2.489554615   5.710262290  -0.000852594
> > C       -1.229721248   4.990709007  -0.000338911
> > C        2.449440629   1.438897112   0.002319254
> > C        3.702198081   0.707454065  -0.001265064
> > C        1.236237242   3.539760579   0.000958837
> > C        2.478517989   2.856386275   0.004841971
> > C       -0.000246038   5.700684987  -0.000997560
> > C        1.229347070   4.990770096  -0.000716604
> > C        4.955272233   1.438694069  -0.002138838
> > C        6.124721243   0.686321393   0.000987763
> > C        3.702044434   3.562937903   0.001926384
> > C        4.925831271   2.856536000  -0.001755553
> > C        2.489209922   5.710445901  -0.000342579
> > C        3.702309214   4.976078918  -0.000048704
> >
> >
> >
> > Hydrogen
> > &CONTROL
> >     calculation   = "scf"
> >     forc_conv_thr =  1.00000e-03
> >     max_seconds   =  1.72800e+05
> >     nstep         = 1000
> >     verbosity='high'
> >     restart_mode='from_scratch'
> >     iprint=1
> >     tprnfor=.true.
> >  pseudo_dir = '/lfs01/workdirs/Val/Test/pseudo',
> > outdir='/lfs01/workdirs/Val/Test/Out/HY',
> > /
> >
> > &SYSTEM
> >     a     =  7.40525e+00
> >     c     =  9.99906e+00
> >     ibrav = 4
> >     nat   = 2
> >     ntyp  = 1
> >     ecutwfc = 45.0 ,
> > ecutrho = 450.0 ,
> > input_DFT = 'PBE-D2' ,
> > occupations = 'smearing' ,
> > degauss = 1.0d-4 ,
> > vdw_corr = 'Grimme-D2'
> > assume_isolated = 'mt'
> > smearing = 'marzari-vanderbilt' ,
> >
> > /
> >
> > &ELECTRONS
> > conv_thr = 1.0d-7 ,
> > electron_maxstep = 1000
> > mixing_mode = 'plain' ,
> > mixing_beta = 0.3d0 ,
> > /
> >
> > &IONS
> > ion_dynamics='bfgs'
> > upscale=20.0
> > /
> >
> > &CELL
> > /
> >
> > K_POINTS {automatic}
> >  3  3  3  0 0 0
> >
> > ATOMIC_SPECIES
> > H       1.00794  H.pbe-kjpaw_psl.1.0.0.UPF
> > ATOMIC_POSITIONS {angstrom}
> > H        3.360489134   2.350036356  -3.014528460
> > H        2.719672863   2.741584163  -3.037540110
> >
> >
> > On Wed, 5 Dec 2018 at 21:09, Stefano Baroni <baroni at sissa.it> wrote:
> >
> >> I know nothing about your system, but what you report simply seem the
> >> evidence of an endothermal adsorption, stabilized by a  energy barrier.
> >> Have you got strong reasons to believe that this cannot be the case?
> >> Regards, Stefano B
> >>
> >> ___
> >> Stefano Baroni, Trieste -- http://stefano.baroni.me
> >>
> >> > On 5 Dec 2018, at 18:45, Mohamed Safy <msafy505 at gmail.com> wrote:
> >> >
> >> > Dear QE users
> >> > I am trying to study the adsorption of a negatively charged molecule
> on
> >> a core of polymer. The relaxed cell showed the formation of four
> hydrogen
> >> bonds (with O...H distance range between 1.7 and 1.95 angstrom). But,
> when
> >> I calculated the adsorption energy I found it a positive value (44
> >> kcal/mol). any advice or suggestion please.
> >> > Thanks in advance
> >> > _______________________________________________
> >> > users mailing list
> >> > users at lists.quantum-espresso.org
> >> > https://lists.quantum-espresso.org/mailman/listinfo/users
> >>
> >> _______________________________________________
> >> users mailing list
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> >>
>
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
>
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