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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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
> [email protected]
> https://lists.quantum-espresso.org/mailman/listinfo/users
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GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
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