[QE-users] Unexpected adsorption energy

Giuseppe Mattioli giuseppe.mattioli at ism.cnr.it
Wed Dec 19 12:18:20 CET 2018


Dear Mohamed
I'm afraid that I cannot help you more than this without seeing your  
input files. If you want, you can send them in private.
HTH
Giuseppe

Mohamed Safy <msafy505 at gmail.com> ha scritto:

> 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
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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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