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<p class="MsoNormal"><span lang="EN-US">Dear QE users,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I recently learned that you have to apply a dipole correction when adsorbing molecules onto a surface when working under PBC. I know you can do this manually via the dipfield option, but the assume_isolated=”2D” option
should have the same effect with the added benefit of truncating the Coulomb interaction in the z-direction. I have tried to re-do one of my calculations with this option enabled but I get the following error:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">2D CODE WILL NOT WORK, 2D MATERIAL NOT IN X-Y PLANE!!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> Error in routine vloc_of_g (1):<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"> 2D cutoff is smaller than pseudo cutoff radius: increase interlayer distance (or see Modules/read_pseudo.f90)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Can somebody tell me how I can get this to work in my system? I don’t see how my material is not in the X-Y plane when looking at my structure. Could it be a problem because my cell is not orthogonal?</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I don’t know if attachments work, so I’ll add my input description here (I only added the assume_isolated=”2D” flag compared to the original calculation):</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">&CONTROL</p>
<p class="MsoNormal"> calculation = 'relax'</p>
<p class="MsoNormal"> restart_mode = 'from_scratch'</p>
<p class="MsoNormal"> prefix = 'a101-3mppa-md1-2d'</p>
<p class="MsoNormal"> pseudo_dir = '/data/antwerpen/206/vsc20615/temp/quantumespresso/PSEUDOPOTENTIALS'</p>
<p class="MsoNormal"> outdir = '/scratch/antwerpen/206/vsc20615/quantumespresso/a101-3mppa-md1-2d'
</p>
<p class="MsoNormal"> nstep = 200</p>
<p class="MsoNormal"> verbosity = 'high'</p>
<p class="MsoNormal">/</p>
<p class="MsoNormal">&SYSTEM</p>
<p class="MsoNormal"> ibrav = 0</p>
<p class="MsoNormal"> A = 3.77449</p>
<p class="MsoNormal"> nat = 125</p>
<p class="MsoNormal"> ntyp = 6</p>
<p class="MsoNormal"> ecutwfc = 60</p>
<p class="MsoNormal"> ecutrho = 600</p>
<p class="MsoNormal"> spline_ps = .true.</p>
<p class="MsoNormal"> vdw_corr = "grimme-d2"</p>
<p class="MsoNormal"> assume_isolated = "2D"</p>
<p class="MsoNormal">! nr1 = 180</p>
<p class="MsoNormal">! nr2 = 160</p>
<p class="MsoNormal">! nr3 = 480</p>
<p class="MsoNormal">/</p>
<p class="MsoNormal">&ELECTRONS</p>
<p class="MsoNormal"> electron_maxstep = 500</p>
<p class="MsoNormal"> diagonalization = 'david'</p>
<p class="MsoNormal"> conv_thr = 1.0d-10</p>
<p class="MsoNormal"> mixing_beta = 0.70</p>
<p class="MsoNormal">/</p>
<p class="MsoNormal">&IONS</p>
<p class="MsoNormal"> ion_dynamics = 'bfgs'</p>
<p class="MsoNormal">/</p>
<p class="MsoNormal">ATOMIC_SPECIES</p>
<p class="MsoNormal"> C 12.0107 C.wc-n-kjpaw_psl.1.0.0.UPF</p>
<p class="MsoNormal"> H 1.0079 H.wc-kjpaw_psl.1.0.0.UPF</p>
<p class="MsoNormal"> O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF</p>
<p class="MsoNormal"> P 30.973761 P.wc-n-kjpaw_psl.1.0.0.UPF</p>
<p class="MsoNormal"> S 32.0600 S.wc-n-kjpaw_psl.1.0.0.UPF</p>
<p class="MsoNormal"> Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF</p>
<p class="MsoNormal">ATOMIC_POSITIONS {crystal}</p>
<p class="MsoNormal">Ti 0.000000000 0.000000000 0.026316000 0 0 0</p>
<p class="MsoNormal">Ti 0.666667000 0.000000000 0.026316000 0 0 0</p>
<p class="MsoNormal">Ti 0.333333000 0.000000000 0.026316000 0 0 0</p>
<p class="MsoNormal">Ti 0.166667000 0.500000000 0.026316000 0 0 0</p>
<p class="MsoNormal">Ti 0.500000000 0.500000000 0.026316000 0 0 0</p>
<p class="MsoNormal">Ti 0.833333000 0.500000000 0.026316000 0 0 0</p>
<p class="MsoNormal">Ti 0.000824658 0.992331197 0.264938249</p>
<p class="MsoNormal">Ti 0.334135046 0.995049704 0.264624893</p>
<p class="MsoNormal">Ti 0.667613401 0.992398327 0.264893895</p>
<p class="MsoNormal">Ti 0.168926625 0.489197175 0.261993802</p>
<p class="MsoNormal">Ti 0.499777376 0.489341171 0.261832125</p>
<p class="MsoNormal">Ti 0.834286595 0.493562288 0.264858957</p>
<p class="MsoNormal">Ti 0.000057357 0.987892876 0.144759568</p>
<p class="MsoNormal">Ti 0.333795375 0.994450512 0.144007883</p>
<p class="MsoNormal">Ti 0.667723487 0.987841633 0.144749798</p>
<p class="MsoNormal">Ti 0.167624322 0.486336635 0.144288179</p>
<p class="MsoNormal">Ti 0.833927173 0.487390518 0.144773288</p>
<p class="MsoNormal">Ti 0.500148725 0.486358394 0.144260258</p>
<p class="MsoNormal">Ti 0.000460100 0.237804472 0.170484800</p>
<p class="MsoNormal">Ti 0.667233312 0.237885209 0.170448961</p>
<p class="MsoNormal">Ti 0.333852171 0.235526018 0.175041344</p>
<p class="MsoNormal">Ti 0.168398115 0.741530329 0.169439965</p>
<p class="MsoNormal">Ti 0.499182489 0.741792231 0.169370400</p>
<p class="MsoNormal">Ti 0.833844439 0.738095532 0.170226827</p>
<p class="MsoNormal">Ti 0.000000000 0.250000000 0.055556000 0 0 0</p>
<p class="MsoNormal">Ti 0.333333000 0.250000000 0.055556000 0 0 0</p>
<p class="MsoNormal">Ti 0.666667000 0.250000000 0.055556000 0 0 0</p>
<p class="MsoNormal">Ti 0.166667000 0.750000000 0.055556000 0 0 0</p>
<p class="MsoNormal">Ti 0.833333000 0.750000000 0.055556000 0 0 0</p>
<p class="MsoNormal">Ti 0.500000000 0.750000000 0.055556000 0 0 0</p>
<p class="MsoNormal">Ti -0.000849135 0.241620902 0.283991654</p>
<p class="MsoNormal">Ti 0.334211578 0.229486912 0.294789499</p>
<p class="MsoNormal">Ti 0.669259871 0.241661770 0.283943878</p>
<p class="MsoNormal">Ti 0.167941078 0.743027462 0.282833203</p>
<p class="MsoNormal">Ti 0.500298838 0.743518834 0.282674577</p>
<p class="MsoNormal">Ti 0.834126861 0.742296000 0.283914549</p>
<p class="MsoNormal">O 0.000000000 0.792604000 0.050573000 0 0 0</p>
<p class="MsoNormal">O 0.666667000 0.792604000 0.050573000 0 0 0</p>
<p class="MsoNormal">O 0.333333000 0.792604000 0.050573000 0 0 0</p>
<p class="MsoNormal">O 0.166667000 0.292603000 0.050573000 0 0 0</p>
<p class="MsoNormal">O 0.500000000 0.292603000 0.050573000 0 0 0</p>
<p class="MsoNormal">O 0.833333000 0.292603000 0.050573000 0 0 0</p>
<p class="MsoNormal">O 0.000999902 0.783997574 0.290644302</p>
<p class="MsoNormal">O 0.334194354 0.782131036 0.289864123</p>
<p class="MsoNormal">O 0.667315797 0.784210346 0.290600729</p>
<p class="MsoNormal">O 0.165022435 0.285293931 0.288688459</p>
<p class="MsoNormal">O 0.503402803 0.285414366 0.288633679</p>
<p class="MsoNormal">O 0.834202275 0.284726475 0.291829067</p>
<p class="MsoNormal">O 0.000328547 0.782573684 0.166458648</p>
<p class="MsoNormal">O 0.333763074 0.782094072 0.166486451</p>
<p class="MsoNormal">O 0.667375878 0.782525490 0.166428258</p>
<p class="MsoNormal">O 0.167196314 0.280774534 0.168158388</p>
<p class="MsoNormal">O 0.833857737 0.281487490 0.166486492</p>
<p class="MsoNormal">O 0.500533758 0.280806577 0.168126558</p>
<p class="MsoNormal">O 0.000646472 0.446942502 0.148138954</p>
<p class="MsoNormal">O 0.667028635 0.447056244 0.148130898</p>
<p class="MsoNormal">O 0.333832262 0.446912009 0.149006038</p>
<p class="MsoNormal">O 0.167435932 0.948443020 0.148023522</p>
<p class="MsoNormal">O 0.500160423 0.948420706 0.147970167</p>
<p class="MsoNormal">O 0.833815451 0.948371263 0.148089448</p>
<p class="MsoNormal">O 0.000000000 0.457396000 0.031299000 0 0 0</p>
<p class="MsoNormal">O 0.333333000 0.457396000 0.031299000 0 0 0</p>
<p class="MsoNormal">O 0.666667000 0.457396000 0.031299000 0 0 0</p>
<p class="MsoNormal">O 0.166667000 0.957398000 0.031298000 0 0 0</p>
<p class="MsoNormal">O 0.833333000 0.957398000 0.031298000 0 0 0</p>
<p class="MsoNormal">O 0.500000000 0.957398000 0.031298000 0 0 0</p>
<p class="MsoNormal">O 0.000182502 0.455103259 0.265406655</p>
<p class="MsoNormal">O 0.334217463 0.454182236 0.265386721</p>
<p class="MsoNormal">O 0.668275913 0.455113562 0.265283540</p>
<p class="MsoNormal">O 0.167329550 0.952869715 0.266041159</p>
<p class="MsoNormal">O 0.500976826 0.953007465 0.266063759</p>
<p class="MsoNormal">O 0.834173758 0.954309912 0.266193670</p>
<p class="MsoNormal">O 0.167225159 0.528205014 0.079851481</p>
<p class="MsoNormal">O 0.833501149 0.528933548 0.079684771</p>
<p class="MsoNormal">O 0.499798809 0.528195196 0.079854300</p>
<p class="MsoNormal">O 0.000112744 0.028909917 0.079703966</p>
<p class="MsoNormal">O 0.333513512 0.029310025 0.079609205</p>
<p class="MsoNormal">O 0.666824884 0.028885840 0.079701780</p>
<p class="MsoNormal">O 0.168927393 0.552195069 0.311862455</p>
<p class="MsoNormal">O 0.500571116 0.552647575 0.311599738</p>
<p class="MsoNormal">O 0.834128121 0.554244676 0.312443095</p>
<p class="MsoNormal">O 0.001667002 0.053292910 0.312465752</p>
<p class="MsoNormal">O 0.334125750 0.041489697 0.314643237</p>
<p class="MsoNormal">O 0.666824841 0.053356919 0.312418201</p>
<p class="MsoNormal">O 0.167074901 0.534322574 0.197303614</p>
<p class="MsoNormal">O 0.500957026 0.534453287 0.197252476</p>
<p class="MsoNormal">O 0.834095888 0.534153834 0.197415660</p>
<p class="MsoNormal">O 0.000656870 0.033252329 0.197686285</p>
<p class="MsoNormal">O 0.667173613 0.033248085 0.197668359</p>
<p class="MsoNormal">O 0.334064313 0.032371261 0.198159864</p>
<p class="MsoNormal">O 0.001261584 0.194859151 0.119262607</p>
<p class="MsoNormal">O 0.666176302 0.194863415 0.119249014</p>
<p class="MsoNormal">O 0.333617170 0.195806181 0.120022086</p>
<p class="MsoNormal">O 0.166511195 0.693813129 0.119146228</p>
<p class="MsoNormal">O 0.833748973 0.694242339 0.119183090</p>
<p class="MsoNormal">O 0.500653091 0.693865672 0.119119289</p>
<p class="MsoNormal">O 0.000000000 0.207396000 0.002059000 0 0 0</p>
<p class="MsoNormal">O 0.333333000 0.207396000 0.002059000 0 0 0</p>
<p class="MsoNormal">O 0.666667000 0.207396000 0.002059000 0 0 0</p>
<p class="MsoNormal">O 0.166667000 0.707397000 0.002059000 0 0 0</p>
<p class="MsoNormal">O 0.500000000 0.707397000 0.002059000 0 0 0</p>
<p class="MsoNormal">O 0.833333000 0.707397000 0.002059000 0 0 0</p>
<p class="MsoNormal">O -0.002833921 0.208797549 0.233695444</p>
<p class="MsoNormal">O 0.334081147 0.205057932 0.237064131</p>
<p class="MsoNormal">O 0.671094794 0.208883738 0.233641915</p>
<p class="MsoNormal">O 0.165998811 0.710283185 0.232877352</p>
<p class="MsoNormal">O 0.501855504 0.710591340 0.232747947</p>
<p class="MsoNormal">O 0.834046683 0.710385014 0.233486355</p>
<p class="MsoNormal">P 0.337744915 0.299655874 0.389987571</p>
<p class="MsoNormal">O 0.334392761 0.232493133 0.354696138</p>
<p class="MsoNormal">O 0.454064087 0.383366154 0.386837757</p>
<p class="MsoNormal">H 0.475874889 0.456048986 0.354982614</p>
<p class="MsoNormal">O 0.224881710 0.388759446 0.387378347</p>
<p class="MsoNormal">H 0.199773273 0.457858542 0.355474070</p>
<p class="MsoNormal">C 0.338658788 0.171092313 0.445085474</p>
<p class="MsoNormal">H 0.258917787 0.106622145 0.448843615</p>
<p class="MsoNormal">H 0.415955064 0.103932102 0.447364310</p>
<p class="MsoNormal">C 0.343855835 0.236865735 0.480533751</p>
<p class="MsoNormal">H 0.421119565 0.306204721 0.474551370</p>
<p class="MsoNormal">H 0.264862358 0.301600934 0.478018945</p>
<p class="MsoNormal">C 0.351618891 0.124349150 0.526761244</p>
<p class="MsoNormal">H 0.432463886 0.062465297 0.529674497</p>
<p class="MsoNormal">H 0.274773960 0.054552295 0.532970920</p>
<p class="MsoNormal">S 0.354786587 0.207513983 0.567892849</p>
<p class="MsoNormal">H 0.359959849 0.088820581 0.604398345</p>
<p class="MsoNormal">CELL_PARAMETERS {alat}</p>
<p class="MsoNormal"> 0.000000000000000 3.000000000000000 0.000000000000000 </p>
<p class="MsoNormal"> 1.000000000000000 -0.000000000000000 -2.539341738883929 </p>
<p class="MsoNormal"> 8.550000000000001 0.000000000000000 0.000000000000000 </p>
<p class="MsoNormal">K_POINTS {automatic}</p>
<p class="MsoNormal">2 2 1 1 1 0</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks in advance and kind regards,</p>
<p class="MsoNormal">Léon Luntadila Lufungula</p>
<p class="MsoNormal">PhD student</p>
<p class="MsoNormal">University of Antwerp</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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