[QE-users] Adsorption of molecules on the slab
khouini_f at znu.ac.ir
khouini_f at znu.ac.ir
Sat Oct 8 10:58:20 CEST 2022
Thank you dear Hervé Bulou
What do you mean by larger side mesh size?
Any answer from you is valuable for me.
On Sat, Oct 8, 2022 at 12:37 AM, bulou wrote: Have you tried with a larger side mesh size?
I may be wrong but it seems to me that the size you used is too small to prevent the molecule to interact with itself, which could induce undesirable effects especially if the starting configuration is too far from the most stable configuration.
Hervé
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Hervé Bulou
IPCMS-DSI
23 rue du Loess
BP43
F-67034 Strasbourg Cedex 2 (FRANCE)
tel +33 (0)3 88 10 70 95
herve.bulou at ipcms.unistra.fr (mailto:herve.bulou at ipcms.unistra.fr)
http://www.ipcms.unistra.fr/?page_id=9707&lang=en (http://www.ipcms.unistra.fr/?page_id=9707&lang=en) (http://www.ipcms.unistra.fr/?page_id=9707&lang=en)
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On 07/10/2022 21:26, kh_f_69 via users wrote:
Hi I am investigating the adsorption configuration of an organic molecule on platinum metal. When relaxing the molecule on the surface, after several steps, unfortunately, the structure of my molecule changes and actually breaks its bonds and the molecule loses its original structure. I have no idea how to solve this problem so that the structure of the molecule is fixed and only the configuration is optimized on the surface, any help would be great. My input file is below Thank you in advance
&CONTROL
calculation = "relax"
restart_mode='from_scratch',
prefix='.',
pseudo_dir = '.',
outdir='.',
verbosity = 'high' ,
tstress = .true. ,
tprnfor = .true. ,
forc_conv_thr = 1.94469e-03
nstep=200
/
&SYSTEM
ibrav = 0
nat = 75
nspin = 2
ntyp = 4
occupations= "smearing",
smearing= 'methfessel-paxton',
degauss=0.02,
assume_isolated='2D',
ecutwfc=30,
ecutrho=240,
starting_magnetization = 0.2
nosym=.true.
/
&ELECTRONS
conv_thr = 1.00000e-07
electron_maxstep = 300
mixing_beta = 3.00000e-01
mixing_mode = "local-TF"
/
&IONS
ion_dynamics = "bfgs"
/
K_POINTS {automatic}
3 3 1 0 0 0
CELL_PARAMETERS {angstrom}
10.922466325 -0.000000001 0.000000000
-5.461233163 9.459132775 0.000000000
0.000000000 0.000000000 18.000000000
ATOMIC_SPECIES
Pt 195.07800 pt_pbe_v1.4.uspp.F.UPF
H 1.00784 H.pbe-rrkjus_psl.1.0.0.UPF
O 15.999 O.pbe-n-kjpaw_psl.0.1.UPF
C 12.0107 C.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
Pt 0.0000077644 1.5765353552 16.3472430825
Pt 1.3653138403 0.7882699234 13.9807271384
Pt 0.0000000000 0.0000000000 11.6344210000 0 0 0
Pt -0.0000000001 1.5765263758 9.3594310000 0 0 0
Pt -1.3652992973 3.9413174027 16.3472432565
Pt 0.0000056911 3.1530542088 13.9807237385
Pt -1.3653117209 2.3647890738 11.6344210000 0 0 0
Pt -1.3653117210 3.9413154497 9.3594310000 0 0 0
Pt -2.7306069919 6.3060985669 16.3472454145
Pt -1.3653034692 5.5178371573 13.9807247039
Pt -2.7306234418 4.7295791277 11.6344210000 0 0 0
Pt -2.7306234419 6.3061045235 9.3594310000 0 0 0
Pt -4.0959140592 8.6708836324 16.3472472241
Pt -2.7306117082 7.8826191304 13.9807317397
Pt -4.0959361427 7.0943682015 11.6344210000 0 0 0
Pt -4.0959361428 8.6708945773 9.3594310000 0 0 0
Pt 2.7306236460 1.5765362703 16.3472408801
Pt 4.0959318247 0.7882691829 13.9807260288
Pt 2.7306234415 -0.0000000002 11.6344210000 0 0 0
Pt 2.7306234414 1.5765263756 9.3594310000 0 0 0
Pt 1.3653164814 3.9413181222 16.3472414781
Pt 2.7306235902 3.1530536188 13.9807225982
Pt 1.3653117206 2.3647890736 11.6344210000 0 0 0
Pt 1.3653117205 3.9413154495 9.3594310000 0 0 0
Pt 0.0000090139 6.3060992417 16.3472433990
Pt 1.3653145269 5.5178365556 13.9807237339
Pt -0.0000000003 4.7295791275 11.6344210000 0 0 0
Pt -0.0000000004 6.3061045233 9.3594310000 0 0 0
Pt -1.3652981764 8.6708842497 16.3472450356
Pt 0.0000064858 7.8826185842 13.9807309194
Pt -1.3653117212 7.0943682013 11.6344210000 0 0 0
Pt -1.3653117213 8.6708945771 9.3594310000 0 0 0
Pt 5.4612372260 1.5765360174 16.3472433993
Pt 6.8265475346 0.7882704581 13.9807287820
Pt 5.4612478630 -0.0000000004 11.6344210000 0 0 0
Pt 5.4612478629 1.5765263755 9.3594310000 0 0 0
Pt 4.0959301298 3.9413179086 16.3472437141
Pt 5.4612392613 3.1530548263 13.9807252600
Pt 4.0959361421 2.3647890735 11.6344210000 0 0 0
Pt 4.0959361420 3.9413154493 9.3594310000 0 0 0
Pt 2.7306226904 6.3060990582 16.3472459231
Pt 4.0959300283 5.5178377680 13.9807261407
Pt 2.7306234412 4.7295791273 11.6344210000 0 0 0
Pt 2.7306234411 6.3061045231 9.3594310000 0 0 0
Pt 1.3653155429 8.6708839957 16.3472473898
Pt 2.7306221715 7.8826197992 13.9807332565
Pt 1.3653117203 7.0943682011 11.6344210000 0 0 0
Pt 1.3653117202 8.6708945770 9.3594310000 0 0 0
Pt 8.1918529878 1.5765365561 16.3472470691
Pt 9.5571618390 0.7882735064 13.9807363341
Pt 8.1918713045 -0.0000000006 11.6344210000 0 0 0
Pt 8.1918713044 1.5765263753 9.3594310000 0 0 0
Pt 6.8265457985 3.9413184184 16.3472476089
Pt 8.1918536386 3.1530577791 13.9807330558
Pt 6.8265595836 2.3647890733 11.6344210000 0 0 0
Pt 6.8265595835 3.9413154491 9.3594310000 0 0 0
Pt 5.4612382544 6.3060995578 16.3472497009
Pt 6.8265444294 5.5178407507 13.9807341494
Pt 5.4612478627 4.7295791271 11.6344210000 0 0 0
Pt 5.4612478626 6.3061045229 9.3594310000 0 0 0
Pt 4.0959311982 8.6708847198 16.3472515327
Pt 5.4612362969 7.8826227379 13.9807416081
Pt 4.0959361418 7.0943682009 11.6344210000 0 0 0
Pt 4.0959361417 8.6708945768 9.3594310000 0 0 0
C 3.95619779 5.17747681 18.32291712
C 2.95442915 6.17887277 18.34491198
C 1.74931835 5.51976820 18.42013420
O 1.93930433 4.17782698 18.45089274
H 5.03101126 5.30666171 18.24637459
H 3.09401738 7.25466563 18.30950534
H 0.71613894 5.85334029 18.44987249
C 3.75049106 2.58712572 18.41614957
H 2.92137736 1.83776279 18.44425772
O 4.92983530 2.23931121 18.40363741
C 3.28030354 4.06768486 18.39728890
-- khouini fahime,PH.D student
physical chemistry, university of zanjan
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