[QE-users] Unexpected adsorption energy
Mohamed Safy
msafy505 at gmail.com
Wed Dec 5 21:04:54 CET 2018
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
>
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