<div dir="ltr">Dear Gan <div>That helps a lot. Thank you!</div><div>Best</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Linfeng Gan <<a href="mailto:linfe...@gmail.com">linfe...@gmail.com</a>> 于2020年5月15日周五 上午8:29写道：<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>
<p class="MsoNormal"><span lang="EN-US">Hi, Sun</span></p>
<p class="MsoNormal"><span lang="EN-US">I would like to share some of my experience
with you.</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">(1) CUTOFF</span></p>
<p class="MsoNormal"><span lang="EN-US">As you can see from the cutoff test, you must
increase cutoff at least up to 1000 Ry. I had test cutoff ranged from 600 to 2500,
the highest the best. At 1200 Ry, the cell optimization result is very close
to the experimental data. <br></span></p><p class="MsoNormal"><span lang="EN-US"><br></span></p>
<p class="MsoNormal"><span lang="EN-US"># Grid cutoff vs total energy</span></p>
<p class="MsoNormal"><span lang="EN-US"># Date: Tue Apr<span> </span>7 10:28:38 2020</span></p><p class="MsoNormal"><span lang="EN-US"># rel_cutoff = 60 </span></p>
<p class="MsoNormal"><span lang="EN-US"># Cutoff (Ry) | Total Energy (Ha) | Energy
per Atom (eV) | NG on grid 1 | NG on grid 2 | NG on grid 3 | NG on grid 4 | NG
on grid 5 </span></p>
<p class="MsoNormal"><span lang="EN-US">50<span> </span>-511.8311527382<span> </span>-145.0795204885<span> </span>1191545<span> </span>55218<span> </span>480<span> </span>0<span> </span>0</span></p>
<p class="MsoNormal"><span lang="EN-US">100<span> </span>-498.0188507854<span> </span>-141.1643970471<span> </span>1191545<span> </span>55218<span> </span>480<span> </span>0<span> </span>0</span></p>
<p class="MsoNormal"><span lang="EN-US">150<span> </span>-498.1333770910<span> </span>-141.1968597477<span> </span>1084277<span> </span>152208<span> </span>10758<span> </span>0<span> </span>0</span></p>
<p class="MsoNormal"><span lang="EN-US">200<span>
</span><span> </span>-498.0596390179<span> </span>-141.1759585497<span> </span>1011045<span> </span>180500<span> </span>55218<span> </span>480<span> </span>0</span></p>
<p class="MsoNormal"><span lang="EN-US">250<span> </span>-498.0576533189<span> </span>-141.1753956995<span> </span>894935<span> </span>264998<span> </span>86030<span> </span>1280<span> </span>0</span></p>
<p class="MsoNormal"><span lang="EN-US">300<span> </span>-498.0561376050<span> </span>-141.1749660675<span> </span>839389<span> </span>277782<span> </span>127992<span> </span>2080<span> </span>0</span></p>
<p class="MsoNormal"><span lang="EN-US">350<span> </span>-498.0556031621<span> </span>-141.1748145786<span> </span>784888<span> </span>299389<span> </span>152208<span> </span>10758<span> </span>0</span></p>
<p class="MsoNormal"><span lang="EN-US">400<span> </span>-498.0546430297<span> </span>-141.1745424273<span> </span>743542<span> </span>307599<span> </span>172215<span> </span>23887<span> </span>0</span></p>
<p class="MsoNormal"><span lang="EN-US">450<span> </span>-498.0543833523<span> </span>-141.1744688212<span> </span>715246<span> </span>305115<span> </span>187987<span> </span>38415<span> </span>480</span></p>
<p class="MsoNormal"><span lang="EN-US">500<span> </span>-498.0547962093 <span> </span>-141.1745858463<span> </span>664938<span> </span>346107<span> </span>180500<span> </span>55218<span> </span>480</span></p>
<p class="MsoNormal"><span lang="EN-US">550<span> </span>-498.0548813984<span> </span>-141.1746099933<span> </span>648732<span> </span>310339<span> </span>223070<span> </span>63822<span> </span>1280</span></p>
<p class="MsoNormal"><span lang="EN-US">600<span> </span>-498.0548597218<span> </span>-141.1746038491<span> </span>597516<span> </span>325211<span> </span>250210<span> </span>73026<span>
</span>1280</span></p>
<p class="MsoNormal"><span lang="EN-US">650<span> </span>-498.0549993006<span> </span>-141.1746434129<span> </span>558534<span> </span>336401<span> </span>264998<span> </span>86030<span> </span>1280</span></p>
<p class="MsoNormal"><span lang="EN-US">700<span> </span>-498.0548179649<span> </span>-141.1745920130<span> </span>513592<span> </span>356057<span> </span>290284<span> </span>85230<span> </span>2080</span></p>
<p class="MsoNormal"><span lang="EN-US">750<span> </span>-498.0547555671<span> </span>-141.1745743262<span> </span>499950<span> </span>340239<span> </span>294170<span> </span>110804<span> </span>2080</span></p>
<p class="MsoNormal"><span lang="EN-US">800<span> </span>-498.0547613057<span> </span>-141.1745759528<span> </span><span> </span>452398<span> </span>386991<span> </span>277782<span> </span>127992<span> </span>2080</span></p>
<p class="MsoNormal"><span lang="EN-US">850<span> </span>-498.0547622822<span> </span>-141.1745762296<span> </span>415918<span> </span>410299<span> </span>267688<span> </span>147908<span> </span>5430</span></p>
<p class="MsoNormal"><span lang="EN-US">900<span> </span>-498.0547014016<span> </span>-141.1745589729<span> </span>403034<span> </span>388334<span> </span>292909<span> </span>157536<span> </span>5430</span></p>
<p class="MsoNormal"><span lang="EN-US">950<span> </span>-498.0547014005<span> </span>-141.1745589726<span> </span>390150<span> </span>394738<span> </span>299389<span> </span>152208<span> </span>10758</span></p>
<p class="MsoNormal"><span lang="EN-US">1000<span> </span>-498.0546629837<span> </span>-141.1745480833<span> </span>374096<span> </span><span> </span>381572<span> </span>318409<span> </span>162408<span> </span>10758</span></p>
<p class="MsoNormal"><span lang="EN-US">1050<span> </span>-498.0546627095<span> </span>-141.1745480056<span> </span>372626<span> </span>379024<span> </span>308511<span> </span>172231<span> </span>14851</span></p>
<p class="MsoNormal"><span lang="EN-US">1100<span> </span>-498.0546627489<span> </span>-141.1745480167<span> </span>333972<span> </span>409570<span> </span>307599<span> </span>172215<span> </span>23887</span></p>
<p class="MsoNormal"><span lang="EN-US">1150<span> </span>-498.0546599853<span> </span>-141.1745472334<span> </span>291540<span> </span>452002<span> </span>287140<span> </span>192674<span> </span>23887</span></p>
<p class="MsoNormal"><span lang="EN-US">1200<span> </span>-498.0546599398<span> </span>-141.1745472205<span> </span>283078<span> </span>459664<span> </span><span> </span>282659<span>
</span>188911<span> </span>32931</span></p>
<p class="MsoNormal"><span lang="EN-US">1250<span> </span>-498.0546664857<span> </span>-141.1745490759<span> </span>265352<span> </span>449894<span> </span>305115<span> </span>187987<span> </span>38895</span></p>
<p class="MsoNormal"><span lang="EN-US">1300<span> </span>-498.0546695315<span> </span>-141.1745499393<span> </span>257340<span> </span>430648<span> </span>331573<span> </span>180200<span> </span>47482</span></p>
<p class="MsoNormal"><span lang="EN-US">1350<span> </span>-498.0546694852<span> </span>-141.1745499261<span> </span>249304<span> </span>433344<span> </span>336433<span> </span>172464<span> </span>55698</span></p>
<p class="MsoNormal"><span lang="EN-US">1400<span> </span>-498.0546619268<span> </span>-141.1745477837<span> </span>249304<span> </span>415634<span> </span>346107<span>
</span><span> </span>180500<span> </span>55698</span></p>
<p class="MsoNormal"><span lang="EN-US">1450<span> </span>-498.0546657092<span> </span>-141.1745488558<span> </span>237064<span> </span>427874<span> </span>330835<span> </span>195772<span> </span>55698</span></p>
<p class="MsoNormal"><span lang="EN-US">1500<span> </span>-498.0546657265<span> </span>-141.1745488607<span> </span>237064<span> </span>419238<span> </span>322207<span> </span>203632<span> </span>65102</span></p>
<p class="MsoNormal"><span lang="EN-US">1550<span> </span>-498.0546649445<span> </span>-141.1745486391<span> </span>232240<span> </span>416492<span> </span>310339<span> </span>223070<span> </span>65102</span></p>
<p class="MsoNormal"><span lang="EN-US">1600<span> </span>-498.0546621702<span> </span>-141.1745478527<span> </span>232240<span> </span>400820<span> </span>312383<span> </span>236698<span> </span><span> </span>65102</span></p>
<p class="MsoNormal"><span lang="EN-US">1650<span> </span>-498.0546580786<span> </span>-141.1745466929<span> </span>224234<span> </span>392132<span> </span>329077<span> </span>228294<span> </span>73506</span></p>
<p class="MsoNormal"><span lang="EN-US">1700<span> </span>-498.0546579920<span> </span>-141.1745466684<span> </span>224234<span> </span>373282<span> </span>325211<span> </span>250210<span> </span>74306</span></p>
<p class="MsoNormal"><span lang="EN-US">1750<span> </span>-498.0546626389<span> </span>-141.1745479855<span> </span>224234<span> </span>368338<span> </span>318615<span> </span>255886<span> </span>80170</span></p>
<p class="MsoNormal"><span lang="EN-US">1800<span> </span>-498.0546626425<span> </span>-141.1745479866<span> </span>216222<span> </span>347172<span> </span>339757<span> </span>263922<span> </span>80170</span></p>
<p class="MsoNormal"><span lang="EN-US">1850 <span> </span>-498.0546624400<span> </span>-141.1745479292<span> </span>216222<span> </span>342312<span> </span>336401<span> </span>264998<span> </span>87310</span></p>
<p class="MsoNormal"><span lang="EN-US">1900<span> </span>-498.0546624669<span> </span>-141.1745479368<span> </span>196998<span> </span>345386<span> </span>332173<span> </span>285376<span> </span>87310</span></p>
<p class="MsoNormal"><span lang="EN-US">1950<span>
</span><span> </span>-498.0546619107<span> </span>-141.1745477791<span> </span>153670<span> </span>372770<span> </span>343209<span> </span>290284<span> </span>87310</span></p>
<p class="MsoNormal"><span lang="EN-US">2000<span> </span>-498.0546645404<span> </span>-141.1745485245<span> </span>127866<span> </span>385726<span> </span>356057<span> </span>290284<span> </span>87310</span></p>
<p class="MsoNormal"><span lang="EN-US">2050<span> </span>-498.0546619783<span> </span>-141.1745477983<span> </span>107134<span> </span>406458<span> </span>356057<span> </span>285100<span> </span>92494</span></p>
<p class="MsoNormal"><span lang="EN-US">2100<span> </span>-498.0546619823<span> </span>-141.1745477994<span> </span>82148<span> </span>431444<span> </span>339841<span> </span>296252<span> </span>97558</span></p>
<p class="MsoNormal"><span lang="EN-US">2150<span> </span>-498.0546619947<span> </span>-141.1745478029<span> </span>77348<span> </span>422602<span> </span>340239<span> </span>294170<span> </span>112884</span></p>
<p class="MsoNormal"><span lang="EN-US">2200<span> </span>-498.0546617280<span> </span>-141.1745477273<span> </span>69312<span> </span>400926<span> </span>369951<span> </span>294170<span> </span>112884</span></p>
<p class="MsoNormal"><span lang="EN-US">2250<span> </span>-498.0546617309<span> </span><span> </span>-141.1745477282<span> </span>64488<span> </span>392818<span> </span>382883<span> </span>285546<span> </span>121508</span></p>
<p class="MsoNormal"><span lang="EN-US">2300<span> </span>-498.0546623124<span> </span>-141.1745478930<span> </span>64488<span> </span>387910<span> </span>386991<span> </span>277782<span> </span>130072</span></p>
<p class="MsoNormal"><span lang="EN-US">2350<span> </span>-498.0546623561<span> </span>-141.1745479054<span> </span>53548<span> </span>378466<span> </span>399339<span> </span>285818<span> </span>130072</span></p>
<p class="MsoNormal"><span lang="EN-US">2400<span> </span>-498.0546621789<span> </span>-141.1745478552<span> </span>53548<span> </span>370382<span> </span>407423<span> </span>270648<span> </span>145242</span></p>
<p class="MsoNormal"><span lang="EN-US">2450<span> </span>-498.0546621769<span> </span>-141.1745478546<span> </span>43948<span> </span>371970<span> </span>410299<span> </span>267688<span> </span>153338</span></p>
<p class="MsoNormal"><span lang="EN-US">2500<span> </span>-498.0546611280<span> </span>-141.1745475573<span> </span>35936<span> </span>379982<span> </span>402203<span> </span>274984<span> </span>154138</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">(2) CELL_REF</span></p>
<p class="MsoNormal"><span lang="EN-US">I had tested the CELL_REF vectors A, B, and
C from 1 to 3 times of origin CELL corresponding vectors with 0.2 interval. I think
1.2 time of the CELL vectors ABC is enough which has a good balancing the computational
time and accuracy.</span></p>
</div><div><br></div><div><br></div>On Thursday, May 14, 2020 at 6:54:53 PM UTC+8, shixun sun wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi, Gan<div>I had the same problem with you now, and could you tell me how much you increase your cutoff. and did you change your c axis, like you want 6, so you increase it to 10 in your input</div><div>Millions of thanks for your help</div><div>best</div></div><br><div class="gmail_quote"><div dir="ltr">Linfeng Gan <<a rel="nofollow">li...@gmail.com</a>> 于2020年5月14日周四 下午6:48写道：<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">
<p class="MsoNormal"><span lang="EN-US">I had carefully tested the CUTOFF and the CELL_REF.
The test results showed that increased the CUTOFF had most helpful.</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<div><span style="font-size:10.5pt;font-family:等线" lang="EN-US">So, the problem solved</span></div><div><span style="font-size:10.5pt;font-family:等线" lang="EN-US"><br></span></div>On Tuesday, April 7, 2020 at 4:11:46 PM UTC+8, Linfeng Gan wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Thanks Juerg. I will try as you suggest and update a few days later.</div><div><br></div><br>On Monday, April 6, 2020 at 3:32:56 PM UTC+8, jgh wrote:<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi
<br>
<br>I assume your system is weakly bound in z-direction. Small force
<br>changes in that direction can cause large changes.
<br>The only obvious problem I could spot is the definition of the
<br>reference cell. In order to minimize the effect of a change in
<br>volume, the reference cell should be larger than the initial
<br>and final cell. I would set c=10 or 12 and I would also increase
<br>the cutoff.
<br>You could test this by just scan the energy as function of c and
<br>correctly adapt the geometry of course.
<br>
<br>regards
<br>
<br>Juerg Hutter
<br>--------------------------------------------------------------
<br>Juerg Hutter Phone : ++41 44 635 4491
<br>Institut für Chemie C FAX : ++41 44 635 6838
<br>Universität Zürich E-mail: <a rel="nofollow">h...@chem.uzh.ch</a>
<br>Winterthurerstrasse 190
<br>CH-8057 Zürich, Switzerland
<br>---------------------------------------------------------------
<br>
<br>-----<a rel="nofollow">c...@googlegroups.com</a> wrote: -----
<br>To: "cp2k" <<a rel="nofollow">c...@googlegroups.com</a>>
<br>From: "Linfeng Gan"
<br>Sent by: <a rel="nofollow">c...@googlegroups.com</a>
<br>Date: 04/05/2020 04:27AM
<br>Subject: [CP2K:13056] COF cell optimize exploded
<br>
<br>
<br> Hello all,
<br> I need some help about the covalent-organic frameworks (COF) 2D sheet cell optimize. After I optimized the COF with a 2X2X2 supercell, the cell size was totally exploded. I had kept the cell vectors and symmetry constant, changed different basis sets and different XC functions but the cell exploded anyway.
<br> I had tried basis sets DZVP-MOLOPT-GTH and DZVP-MOLOPT-SR-GTH with PADE, PBE and BLYP. And the DFTD3 correction was also add to each calculation. The GAPW method I also had tried, but none of them worked.
<br>
<br> Any suggestion is welcome, thanks!
<br> Linfeng
<br>
<br> The COF-5-2X2X2 supercell vectors should be:
<br> CELL_TOP| Volume [angstrom^3]: 21253.270
<br> CELL_TOP| Vector a [angstrom 60.040 0.000 0.000 |a| = 60.040
<br> CELL_TOP| Vector b [angstrom -30.020 51.996 0.000 |b| = 60.040
<br> CELL_TOP| Vector c [angstrom 0.000 0.000 6.808 |c| = 6.808
<br> CELL_TOP| Angle (b,c), alpha [degree]: 90.000
<br> CELL_TOP| Angle (a,c), beta [degree]: 90.000
<br> CELL_TOP| Angle (a,b), gamma [degree]: 120.000
<br>
<br> But after cell optimized calculation the output cell vectors are:
<br> *******************************************************************************
<br> *** GEOMETRY OPTIMIZATION COMPLETED ***
<br> *******************************************************************************
<br>
<br> Reevaluating energy at the minimum
<br>
<br> CELL| Volume [angstrom^3]: 25653.623
<br> CELL| Vector a [angstrom]: 60.345 0.000 0.000 |a| = 60.345
<br> CELL| Vector b [angstrom]: -30.173 52.260 0.000 |b| = 60.345
<br> CELL| Vector c [angstrom]: 0.000 -0.000 8.135 |c| = 8.135
<br> CELL| Angle (b,c), alpha [degree]: 90.000
<br> CELL| Angle (a,c), beta [degree]: 90.000
<br> CELL| Angle (a,b), gamma [degree]: 120.000
<br>
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<br>[attachment "COF-5-2X2X2.xyz" removed by Jürg Hutter/at/UZH]
<br>[attachment "opt_cell.inp" removed by Jürg Hutter/at/UZH]
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