[QE-users] Unexpected adsorption energy
Mohamed Safy
msafy505 at gmail.com
Wed Dec 19 08:12:59 CET 2018
Dear Giuseppe
I took your advice but the E[cation+anion] system was very difficult to be
converged.
I tried to reduce the mixing_beta and conv_thr with no results.
Thanks
On Sun, 9 Dec 2018 at 14:37, Mohamed Safy <msafy505 at gmail.com> wrote:
> 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
>> >> users at lists.quantum-espresso.org
>> >> https://lists.quantum-espresso.org/mailman/listinfo/users
>> >>
>>
>>
>>
>> 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>
>>
>> _______________________________________________
>> users mailing list
>> users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20181219/f7a6d731/attachment.html>
More information about the users
mailing list