<!DOCTYPE html><html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /></head><body><div data-crea="font-wrapper" style="font-family: Tahoma; font-size: 16px; direction: ltr"><div style="font-family: Tahoma; font-size: 16px"></div><div><span class="VIiyi" jsaction="mouseup:BR6jm" jsname="jqKxS" lang="en"><span jsaction="agoMJf:PFBcW;jhKsnd:P7O7bd;uFUCPb:pvnm0e,pfE8Hb,PFBcW;f56efd:dJXsye;zimBkd:iXtTIf;oFN6Ye:hij5Wb;bmeZHc:iURhpf;Oxj3Xe:qAKMYb,yaf12d" jsname="txFAF" class="JLqJ4b ChMk0b" jscontroller="Zl5N8"><span class="Q4iAWc" jsaction="click:E6Tfl,GFf3ac,tMZCfe; contextmenu:Nqw7Te,QP7LD; mouseout:Nqw7Te; mouseover:E6Tfl,c2aHje" jsname="W297wb">Thank you dear Hervé Bulou</span></span><span jsaction="agoMJf:PFBcW;jhKsnd:P7O7bd;uFUCPb:pvnm0e,pfE8Hb,PFBcW;f56efd:dJXsye;zimBkd:iXtTIf;oFN6Ye:hij5Wb;bmeZHc:iURhpf;Oxj3Xe:qAKMYb,yaf12d" jsname="txFAF" class="JLqJ4b" jscontroller="Zl5N8"><span class="Q4iAWc" jsaction="click:E6Tfl,GFf3ac,tMZCfe; contextmenu:Nqw7Te,QP7LD; mouseout:Nqw7Te; mouseover:E6Tfl,c2aHje" jsname="W297wb"><br></span></span></span></div><div><span class="VIiyi" jsaction="mouseup:BR6jm" jsname="jqKxS" lang="en"><span jsaction="agoMJf:PFBcW;jhKsnd:P7O7bd;uFUCPb:pvnm0e,pfE8Hb,PFBcW;f56efd:dJXsye;zimBkd:iXtTIf;oFN6Ye:hij5Wb;bmeZHc:iURhpf;Oxj3Xe:qAKMYb,yaf12d" jsname="txFAF" class="JLqJ4b ChMk0b" jscontroller="Zl5N8"><span class="Q4iAWc" jsaction="click:E6Tfl,GFf3ac,tMZCfe; contextmenu:Nqw7Te,QP7LD; mouseout:Nqw7Te; mouseover:E6Tfl,c2aHje" jsname="W297wb">What do you mean by larger side mesh size?</span></span><span jsaction="agoMJf:PFBcW;jhKsnd:P7O7bd;uFUCPb:pvnm0e,pfE8Hb,PFBcW;f56efd:dJXsye;zimBkd:iXtTIf;oFN6Ye:hij5Wb;bmeZHc:iURhpf;Oxj3Xe:qAKMYb,yaf12d" jsname="txFAF" class="JLqJ4b" jscontroller="Zl5N8"><span class="Q4iAWc" jsaction="click:E6Tfl,GFf3ac,tMZCfe; contextmenu:Nqw7Te,QP7LD; mouseout:Nqw7Te; mouseover:E6Tfl,c2aHje" jsname="W297wb">
</span></span><span jsaction="agoMJf:PFBcW;jhKsnd:P7O7bd;uFUCPb:pvnm0e,pfE8Hb,PFBcW;f56efd:dJXsye;zimBkd:iXtTIf;oFN6Ye:hij5Wb;bmeZHc:iURhpf;Oxj3Xe:qAKMYb,yaf12d" jsname="txFAF" class="JLqJ4b ChMk0b" jscontroller="Zl5N8"><span class="Q4iAWc" jsaction="click:E6Tfl,GFf3ac,tMZCfe; contextmenu:Nqw7Te,QP7LD; mouseout:Nqw7Te; mouseover:E6Tfl,c2aHje" jsname="W297wb"><br></span></span></span></div><div><span class="VIiyi" jsaction="mouseup:BR6jm" jsname="jqKxS" lang="en"><span jsaction="agoMJf:PFBcW;jhKsnd:P7O7bd;uFUCPb:pvnm0e,pfE8Hb,PFBcW;f56efd:dJXsye;zimBkd:iXtTIf;oFN6Ye:hij5Wb;bmeZHc:iURhpf;Oxj3Xe:qAKMYb,yaf12d" jsname="txFAF" class="JLqJ4b ChMk0b" jscontroller="Zl5N8"><span class="Q4iAWc" jsaction="click:E6Tfl,GFf3ac,tMZCfe; contextmenu:Nqw7Te,QP7LD; mouseout:Nqw7Te; mouseover:E6Tfl,c2aHje" jsname="W297wb">Any answer from you is valuable for me.</span></span></span></div><br><div></div><br><br><div data-anchor="reply-title">On Sat, Oct 8, 2022 at 12:37 AM, bulou <herve.bulou@ipcms.unistra.fr> wrote:</div><blockquote><div><div>
Have you tried with a larger side mesh size? <br><br>
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.<br>
Hervé<br>
**********************************************************
<br>
Hervé Bulou
<br>
IPCMS-DSI
<br>
23 rue du Loess
<br>
BP43
<br>
F-67034 Strasbourg Cedex 2 (FRANCE)
<br>
tel +33 (0)3 88 10 70 95
<br><a href="mailto:herve.bulou@ipcms.unistra.fr" target="_blank" tabindex="-1" rel="external">herve.bulou@ipcms.unistra.fr</a>
<br><a href="http://www.ipcms.unistra.fr/?page_id=9707&lang=en" target="_blank" tabindex="-1" rel="external">http://www.ipcms.unistra.fr/?page_id=9707&lang=en</a>
<a href="http://www.ipcms.unistra.fr/?page_id=9707&lang=en" target="_blank" tabindex="-1" rel="external"><http://www.ipcms.unistra.fr/?page_id=9707&lang=en></a>
<br>
**********************************************************
<br><div>On 07/10/2022 21:26, kh_f_69 via users
wrote:<br></div>
<blockquote type="cite" cite="mid:3dc777a9ca5417ad27d7bbc4c310845c@mail.znu.ac.ir">
<div data-crea="font-wrapper" style="font-family: Tahoma;font-size: 16px;direction: ltr">
<div dir="ltr" data-setdir="false" style='font-family: "Helvetica Neue", Helvetica, Arial, sans-serif'>
<div dir="ltr" data-setdir="false">Hi</div>
<div dir="ltr" data-setdir="false">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.</div>
<div dir="ltr" data-setdir="false">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.</div>
<div dir="ltr" data-setdir="false">My input file is below</div>
<div dir="ltr" data-setdir="false">Thank you in advance</div>
</div>
<div><br></div>
<div>&CONTROL</div>
<div> calculation = "relax"</div>
<div> restart_mode='from_scratch',</div>
<div> prefix='.',</div>
<div> pseudo_dir = '.',</div>
<div> outdir='.',</div>
<div> verbosity = 'high' ,</div>
<div> tstress = .true. ,</div>
<div> tprnfor = .true. , </div>
<div> forc_conv_thr = 1.94469e-03</div>
<div> nstep=200</div>
<div>/</div>
<div><br></div>
<div>&SYSTEM</div>
<div> </div>
<div> ibrav = 0</div>
<div> nat = 75</div>
<div> nspin = 2</div>
<div> ntyp = 4</div>
<div> occupations= "smearing",</div>
<div> smearing= 'methfessel-paxton',</div>
<div> degauss=0.02,</div>
<div> assume_isolated='2D',</div>
<div> ecutwfc=30,</div>
<div> ecutrho=240,</div>
<div> starting_magnetization = 0.2</div>
<div> nosym=.true.</div>
<div>/</div>
<div><br></div>
<div>&ELECTRONS</div>
<div> conv_thr = 1.00000e-07</div>
<div> electron_maxstep = 300</div>
<div> mixing_beta = 3.00000e-01</div>
<div> mixing_mode = "local-TF"</div>
<div> </div>
<div>/</div>
<div><br></div>
<div>&IONS</div>
<div> ion_dynamics = "bfgs"</div>
<div><br></div>
<div>/</div>
<div><br></div>
<div>K_POINTS {automatic}</div>
<div> 3 3 1 0 0 0</div>
<div><br></div>
<div>CELL_PARAMETERS {angstrom}</div>
<div> 10.922466325 -0.000000001 0.000000000</div>
<div> -5.461233163 9.459132775 0.000000000</div>
<div> 0.000000000 0.000000000 18.000000000</div>
<div> </div>
<div>ATOMIC_SPECIES</div>
<div>Pt 195.07800 pt_pbe_v1.4.uspp.F.UPF</div>
<div> H 1.00784 H.pbe-rrkjus_psl.1.0.0.UPF</div>
<div> O 15.999 O.pbe-n-kjpaw_psl.0.1.UPF</div>
<div> C 12.0107 C.pbe-n-kjpaw_psl.1.0.0.UPF</div>
<div>ATOMIC_POSITIONS {angstrom}</div>
<div><br></div>
<div>Pt 0.0000077644 1.5765353552
16.3472430825</div>
<div>Pt 1.3653138403 0.7882699234
13.9807271384</div>
<div>Pt 0.0000000000 0.0000000000
11.6344210000 0 0 0</div>
<div>Pt -0.0000000001 1.5765263758
9.3594310000 0 0 0</div>
<div>Pt -1.3652992973 3.9413174027
16.3472432565</div>
<div>Pt 0.0000056911 3.1530542088
13.9807237385</div>
<div>Pt -1.3653117209 2.3647890738
11.6344210000 0 0 0</div>
<div>Pt -1.3653117210 3.9413154497
9.3594310000 0 0 0</div>
<div>Pt -2.7306069919 6.3060985669
16.3472454145</div>
<div>Pt -1.3653034692 5.5178371573
13.9807247039</div>
<div>Pt -2.7306234418 4.7295791277
11.6344210000 0 0 0</div>
<div>Pt -2.7306234419 6.3061045235
9.3594310000 0 0 0</div>
<div>Pt -4.0959140592 8.6708836324
16.3472472241</div>
<div>Pt -2.7306117082 7.8826191304
13.9807317397</div>
<div>Pt -4.0959361427 7.0943682015
11.6344210000 0 0 0</div>
<div>Pt -4.0959361428 8.6708945773
9.3594310000 0 0 0</div>
<div>Pt 2.7306236460 1.5765362703
16.3472408801</div>
<div>Pt 4.0959318247 0.7882691829
13.9807260288</div>
<div>Pt 2.7306234415 -0.0000000002
11.6344210000 0 0 0</div>
<div>Pt 2.7306234414 1.5765263756
9.3594310000 0 0 0</div>
<div>Pt 1.3653164814 3.9413181222
16.3472414781</div>
<div>Pt 2.7306235902 3.1530536188
13.9807225982</div>
<div>Pt 1.3653117206 2.3647890736
11.6344210000 0 0 0</div>
<div>Pt 1.3653117205 3.9413154495
9.3594310000 0 0 0</div>
<div>Pt 0.0000090139 6.3060992417
16.3472433990</div>
<div>Pt 1.3653145269 5.5178365556
13.9807237339</div>
<div>Pt -0.0000000003 4.7295791275
11.6344210000 0 0 0</div>
<div>Pt -0.0000000004 6.3061045233
9.3594310000 0 0 0</div>
<div>Pt -1.3652981764 8.6708842497
16.3472450356</div>
<div>Pt 0.0000064858 7.8826185842
13.9807309194</div>
<div>Pt -1.3653117212 7.0943682013
11.6344210000 0 0 0</div>
<div>Pt -1.3653117213 8.6708945771
9.3594310000 0 0 0</div>
<div>Pt 5.4612372260 1.5765360174
16.3472433993</div>
<div>Pt 6.8265475346 0.7882704581
13.9807287820</div>
<div>Pt 5.4612478630 -0.0000000004
11.6344210000 0 0 0</div>
<div>Pt 5.4612478629 1.5765263755
9.3594310000 0 0 0</div>
<div>Pt 4.0959301298 3.9413179086
16.3472437141</div>
<div>Pt 5.4612392613 3.1530548263
13.9807252600</div>
<div>Pt 4.0959361421 2.3647890735
11.6344210000 0 0 0</div>
<div>Pt 4.0959361420 3.9413154493
9.3594310000 0 0 0</div>
<div>Pt 2.7306226904 6.3060990582
16.3472459231</div>
<div>Pt 4.0959300283 5.5178377680
13.9807261407</div>
<div>Pt 2.7306234412 4.7295791273
11.6344210000 0 0 0</div>
<div>Pt 2.7306234411 6.3061045231
9.3594310000 0 0 0</div>
<div>Pt 1.3653155429 8.6708839957
16.3472473898</div>
<div>Pt 2.7306221715 7.8826197992
13.9807332565</div>
<div>Pt 1.3653117203 7.0943682011
11.6344210000 0 0 0</div>
<div>Pt 1.3653117202 8.6708945770
9.3594310000 0 0 0</div>
<div>Pt 8.1918529878 1.5765365561
16.3472470691</div>
<div>Pt 9.5571618390 0.7882735064
13.9807363341</div>
<div>Pt 8.1918713045 -0.0000000006
11.6344210000 0 0 0</div>
<div>Pt 8.1918713044 1.5765263753
9.3594310000 0 0 0</div>
<div>Pt 6.8265457985 3.9413184184
16.3472476089</div>
<div>Pt 8.1918536386 3.1530577791
13.9807330558</div>
<div>Pt 6.8265595836 2.3647890733
11.6344210000 0 0 0</div>
<div>Pt 6.8265595835 3.9413154491
9.3594310000 0 0 0</div>
<div>Pt 5.4612382544 6.3060995578
16.3472497009</div>
<div>Pt 6.8265444294 5.5178407507
13.9807341494</div>
<div>Pt 5.4612478627 4.7295791271
11.6344210000 0 0 0</div>
<div>Pt 5.4612478626 6.3061045229
9.3594310000 0 0 0</div>
<div>Pt 4.0959311982 8.6708847198
16.3472515327</div>
<div>Pt 5.4612362969 7.8826227379
13.9807416081</div>
<div>Pt 4.0959361418 7.0943682009
11.6344210000 0 0 0</div>
<div>Pt 4.0959361417 8.6708945768
9.3594310000 0 0 0</div>
<div> C 3.95619779 5.17747681 18.32291712</div>
<div> C 2.95442915 6.17887277 18.34491198</div>
<div> C 1.74931835 5.51976820 18.42013420</div>
<div> O 1.93930433 4.17782698 18.45089274</div>
<div> H 5.03101126 5.30666171 18.24637459</div>
<div> H 3.09401738 7.25466563 18.30950534</div>
<div> H 0.71613894 5.85334029 18.44987249</div>
<div> C 3.75049106 2.58712572 18.41614957</div>
<div> H 2.92137736 1.83776279 18.44425772</div>
<div> O 4.92983530 2.23931121 18.40363741</div>
<div> C 3.28030354 4.06768486 18.39728890</div>
<div><br></div>
<div data-anchor="reply-title"><br><div data-crea="font-wrapper" style="font-family: Tahoma;direction: ltr">--</div>
<div data-crea="font-wrapper" style="font-family: Tahoma;direction: ltr">khouini fahime,PH.D student<br>
physical chemistry, university of zanjan</div>
</div>
<br><div><br></div>
</div>
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