Dear all,
I'm calculating parameters like adsorption energy, geometric parameters, NMR
chemical shifts of adsorbates on a surface. In this specific case I calculated
the adsorption energy of an ethyl anion on an anatase 001 surface of titania. I
got the following energies:
Esurface + adsorbate = -4301.05337244
Esurface = -4258.9387474
Eadsorbate = -42.37757742
So Eads = Esurface + adsorbate - (Esurface + Eadsorbate) = 0.26
Now this seems wrong. If Eads is positive, so adsorption is not favourable,
then the ethyl-anion should migrate away from the surface in the relax
calculation of a001cti. correct? I executed the three calculations with the
exact same parameters as the other ones so I don't see how this is possible. I
attached my input files of the calculations. I hope someone can guide me
through this.
Thanks in advance,
Laurens Siemons
Master student chemistry
University of Antwerp
&control
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'a001cti'
tstress = .false.
tprnfor = .true.
pseudo_dir =
'/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/PSEUDOPOTENTIALS'
outdir = '/data/antwerpen/204/vsc20442'
wf_collect = .true.
verbosity='high'
nstep = 100
/
&SYSTEM
ibrav = 0
A = 7.5703200
nat = 55
ntyp = 4
ecutwfc = 60
ecutrho = 600
spline_ps = .true.
tot_charge = -1
occupations = 'smearing'
smearing ='gaussian'
degauss = 0.01
/
&electrons
electron_maxstep = 800
diagonalization = 'david'
conv_thr = 1.0d-8
diago_thr_init = 1e-4
mixing_mode = 'local-TF'
mixing_beta = 0.10
/
&ions
ion_dynamics = 'bfgs'
ion_positions = 'default'
/
ATOMIC_SPECIES
O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF
Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF
H 1.0079 H.wc-kjpaw_psl.1.0.0.UPF
C 12.0107 C.wc-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
Ti 0.0000000 0.0000000 1.9087670 0 0 0
Ti 3.7851600 3.7851500 1.9087670 0 0 0
Ti 3.7851600 0.0000000 1.9087670 0 0 0
Ti 0.0000000 3.7851500 1.9087670 0 0 0
Ti 1.8987801 1.9072538 6.6653189
Ti 5.6847274 5.6910109 6.6668078
Ti 5.6829787 1.9073371 6.6660252
Ti 1.8988482 5.6908822 6.6673040
Ti 7.5556487 1.8925750 4.2620477
Ti 3.7707991 5.6777250 4.2626203
Ti 3.7706326 1.8925750 4.2612651
Ti 7.5563300 5.6777250 4.2619331
Ti 1.8209799 0.0147848 8.9752324
Ti 5.6042776 3.7983526 8.9766449
Ti 5.6063519 0.0134524 8.9757859
Ti 1.8188148 3.7978378 8.9763395
O 7.5578290 0.0000000 3.8386641
O 3.7728582 3.7851500 3.8379196
O 3.7728658 0.0000000 3.8383777
O 7.5578214 3.7851500 3.8381296
O 2.0533736 1.9066709 8.6237139
O 5.8371104 5.6904280 8.6250500
O 5.8301987 1.9065346 8.6250309
O 2.0455686 5.6908670 8.6248591
O 7.5448913 1.9081774 6.2507347
O 3.7603899 5.6924947 6.2503530
O 3.7599887 1.9082834 6.2488260
O 7.5457165 5.6921388 6.2497422
O 1.8925800 0.0000000 1.5017606 0 0 0
O 5.6777400 3.7851500 1.5017606 0 0 0
O 5.6777400 0.0000000 1.5017606 0 0 0
O 1.8925800 3.7851500 1.5017606 0 0 0
O 1.7713489 0.0137931 7.0572842
O 5.5548131 3.7984964 7.0573797
O 5.5558351 0.0131875 7.0575705
O 1.7694639 3.7983299 7.0573415
O 0.0000000 1.8925750 2.3162697 0 0 0
O 3.7851600 5.6777250 2.3162697 0 0 0
O 3.7851600 1.8925750 2.3162697 0 0 0
O 0.0000000 5.6777250 2.3162697 0 0 0
O 1.8768640 1.8913335 4.6819764
O 5.6628340 5.6747953 4.6816710
O 5.6621754 1.8903645 4.6819191
O 1.8775453 5.6755599 4.6822055
O 0.1607103 0.0185624 9.5272860
O 3.9456886 3.8013277 9.5290611
O 3.9459006 0.0124531 9.5278586
O 0.1607179 3.7978681 9.5300537
C 3.3681670 3.6634367 11.7587988
H 3.9107122 2.8615381 11.2166472
H 3.2707791 3.2800956 12.8197770
H 4.0867365 4.5064364 11.8259000
C 2.1131000 4.0648547 11.0384011
H 1.4171240 3.1988251 11.0020987
H 1.5828076 4.8499215 11.6216489
K_POINTS {automatic}
3 3 1 1 1 0
CELL_PARAMETERS {alat}
1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 2.5213822
&control
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'anatase001-2x2-4'
tstress = .false.
tprnfor = .true.
pseudo_dir =
'/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/PSEUDOPOTENTIALS'
outdir = '/data/antwerpen/204/vsc20442'
wf_collect = .true.
verbosity='high'
nstep = 100
/
&SYSTEM
ibrav = 0
A = 7.5703200
nat = 48
ntyp = 2
ecutwfc = 60
ecutrho = 600
spline_ps = .true.
occupations = 'smearing'
smearing ='gaussian'
degauss = 0.01
/
&electrons
electron_maxstep = 400
diagonalization = 'david'
conv_thr = 1.0d-8
diago_thr_init = 1e-4
mixing_mode = 'local-TF'
mixing_beta = 0.10
/
&ions
ion_dynamics = 'bfgs'
ion_positions = 'default'
/
ATOMIC_SPECIES
O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF
Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF
K_POINTS automatic
3 3 1 1 1 0
ATOMIC_POSITIONS {crystal}
Ti -0.000000000000000 0.000000000000000 0.100000000000000 0 0 0
Ti 0.500000000000000 0.500000000000000 0.100000000000000 0 0 0
Ti 0.500000000000000 0.000000000000000 0.100000000000000 0 0 0
Ti -0.000000000000000 0.500000000000000 0.100000000000000 0 0 0
Ti 0.250000000000000 0.250000000000000 0.350000000000000
Ti 0.750000000000000 0.750000000000000 0.350000000000000
Ti 0.750000000000000 0.250000000000000 0.350000000000000
Ti 0.250000000000000 0.750000000000000 0.350000000000000
Ti -0.000000000000000 0.250000000000000 0.225000000000000
Ti 0.500000000000000 0.750000000000000 0.225000000000000
Ti 0.500000000000000 0.250000000000000 0.225000000000000
Ti -0.000000000000000 0.750000000000000 0.225000000000000
Ti 0.250000000000000 0.000000000000000 0.475011500000000
Ti 0.750000000000000 0.500000000000000 0.475011500000000
Ti 0.750000000000000 0.000000000000000 0.475011500000000
Ti 0.250000000000000 0.500000000000000 0.475011500000000
O -0.000000000000000 0.000000000000000 0.203676500000000
O 0.500000000000000 0.500000000000000 0.203676500000000
O 0.500000000000000 0.000000000000000 0.203676500000000
O -0.000000000000000 0.500000000000000 0.203676500000000
O 0.250000000000000 0.250000000000000 0.453677000000000
O 0.750000000000000 0.750000000000000 0.453677000000000
O 0.750000000000000 0.250000000000000 0.453677000000000
O 0.250000000000000 0.750000000000000 0.453677000000000
O -0.000000000000000 0.250000000000000 0.328677000000000
O 0.500000000000000 0.750000000000000 0.328677000000000
O 0.500000000000000 0.250000000000000 0.328677000000000
O -0.000000000000000 0.750000000000000 0.328677000000000
O 0.250000000000000 -0.000000000000000 0.078677500000000 0 0 0
O 0.750000000000000 0.500000000000000 0.078677500000000 0 0 0
O 0.750000000000000 -0.000000000000000 0.078677500000000 0 0 0
O 0.250000000000000 0.500000000000000 0.078677500000000 0 0 0
O 0.250000000000000 0.000000000000000 0.371349500000000
O 0.750000000000000 0.500000000000000 0.371349500000000
O 0.750000000000000 0.000000000000000 0.371349500000000
O 0.250000000000000 0.500000000000000 0.371349500000000
O -0.000000000000000 0.250000000000000 0.121349000000000 0 0 0
O 0.500000000000000 0.750000000000000 0.121349000000000 0 0 0
O 0.500000000000000 0.250000000000000 0.121349000000000 0 0 0
O 0.000000000000000 0.750000000000000 0.121349000000000 0 0 0
O 0.250000000000000 0.250000000000000 0.246349000000000
O 0.750000000000000 0.750000000000000 0.246349000000000
O 0.750000000000000 0.250000000000000 0.246349000000000
O 0.250000000000000 0.750000000000000 0.246349000000000
O 0.000000000000000 0.000000000000000 0.496349500000000
O 0.510000000000000 0.509000000000000 0.496345000000000
O 0.520000000000000 0.050000000000000 0.496849500000000
O 0.000000000000000 0.500000000000000 0.496349500000000
CELL_PARAMETERS {alat}
1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 2.5213822
&CONTROL
calculation = "relax",
restart_mode = "from_scratch",
prefix = "test",
pseudo_dir =
"/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/PSEUDOPOTENTIALS",
outdir = "/data/antwerpen/204/vsc20442/TMP",
wf_collect = .true.
verbosity='high'
nstep = 100
/
&SYSTEM
ibrav = 0,
nat = 7,
ntyp = 2,
ecutwfc = 60,
ecutrho = 600,
tot_charge = -1
spline_ps = .true.
occupations = 'smearing'
smearing = 'gaussian'
degauss = 0.01
/
&ELECTRONS
electron_maxstep = 750
conv_thr = 1.D-8,
diago_thr_init = 1e-4
mixing_mode = 'local-TF'
mixing_beta = 0.10,
/
&IONS
ion_dynamics = 'bfgs'
ion_positions = 'default'
/
CELL_PARAMETERS {bohr}
20.0 0.0 0.0
0.0 20.0 0.0
0.0 0.0 20.0
ATOMIC_SPECIES
H 1.0079 H.wc-kjpaw_psl.1.0.0.UPF
C 12.0107 C.wc-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
C -0.0213930 -0.0427728 0.0002253
H 0.0313362 0.0553059 1.0639646
H 0.8989264 -0.4468014 -0.3672035
H -0.8267851 -0.6981517 -0.2585316
C -0.2626932 1.3408221 -0.6319211
H 0.1135877 1.5552039 -1.6103653
H -0.8066307 2.0877692 -0.0923832
K_POINTS {Gamma}
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