<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">Dear Giuseppe,</span><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">The structure of the clay I have in the input file is a (110) surface of Fe containing clay with 2:1 ration of tetrahedral sheet to octahedral sheet.</div><div style="font-family:arial,sans-serif;font-size:13px">I have *tried* to center the surface at the origin of my simulation supercell. The surface was created in Materials Studio. Xcrysden does not orient the surface to the center of the supercell.</div><div style="font-family:arial,sans-serif;font-size:13px">I have attached a picture of the structure using Discovery Studio.</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">If the attached structure is reasonable (I think it is!), is there any other place in the input file that I should look into to solve this problem?</div><div style="font-family:arial,sans-serif;font-size:13px">Please let me know!</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Thanks again,</div><div style="font-family:arial,sans-serif;font-size:13px">Sai</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">PS: Sorry if this is duplicate, the original message was larger than 200kB. So shortened the size of the figure. </div><div style="font-family:arial,sans-serif;font-size:13px">---</div><div style="font-family:arial,sans-serif;font-size:13px">Sai Ramadugu</div><div style="font-family:arial,sans-serif;font-size:13px">Post-Doctoral Scholar</div><div style="font-family:arial,sans-serif;font-size:13px">University of Iowa</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Dec 2, 2014 at 5:10 PM, Giuseppe Mattioli <span dir="ltr"><<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Sai<br>
I've opened your input file with xcrysden. I do not know the structure<br>
of your clay, but the structure contained in your file is *very*<br>
strange, and I doubt it is what you are tryng to simulate... Check the<br>
atom positions first of all!<br>
HTH<br>
Giuseppe<br>
<br>
Giuseppe Mattioli<br>
ISM-CNR<br>
Italy<br>
<div><div class="h5"><br>
Quoting Sai Kumar Ramadugu <<a href="mailto:sramadugu@gmail.com">sramadugu@gmail.com</a>>:<br>
<br>
> Dear All,<br>
><br>
> I performing a relaxation of a monoclinic surface supercell of clay mineral.<br>
> The system has Fe, Si, O, H atoms and I am using Hubbard U for Fe atom and<br>
> according a previous paper (JPCC 2013, 117, 22800) I am using ferromagnetic<br>
> ordering for Fe. The supercell has 116 atoms. After the first optimization<br>
> cycle, there are NAN for forces and atomic coordinates and the job quits<br>
> with "some of the original symmetry operations not satisfied" message. I<br>
> read some of the previous threads on this but even after using nosym=true,<br>
> I cannot prevent this outcome. I am using QE v. 5.1, USPP.<br>
> Here is my input file:<br>
><br>
> &CONTROL<br>
> pseudo_dir = '/import/u/u1/uaf/uasramadugu1/pseudo',<br>
> calculation = 'relax',<br>
> prefix = 'nga1',<br>
> outdir = './tmp/',<br>
> restart_mode = 'restart',<br>
> /<br>
> &SYSTEM<br>
> ibrav = 0,<br>
> nat = 116,<br>
> ntyp = 4,<br>
> ecutwfc = 40,<br>
> ecutrho = 320,<br>
> occupations = 'smearing',<br>
> smearing = 'mv',<br>
> degauss = 0.02,<br>
> nspin = 2,<br>
> starting_magnetization(4) = 0.5,<br>
> lda_plus_u = .TRUE.<br>
> Hubbard_U(4) = 4.0,<br>
> nosym = .TRUE.<br>
> /<br>
> &ELECTRONS<br>
> conv_thr = 1.D-7,<br>
> mixing_beta = 0.20D0,<br>
> electron_maxstep = 200,<br>
> /<br>
> &IONS<br>
> /<br>
> ATOMIC_SPECIES<br>
> Si 1.00 Si.pbe-n-rrkjus_psl.0.1.UPF<br>
> O 1.00 O.pbe-rrkjus.UPF<br>
> H 1.00 H.pbe-rrkjus_psl.0.1.UPF<br>
> Fe 1.00 Fe.pbe-nd-rrkjus.UPF<br>
> CELL_PARAMETERS {bohr}<br>
> 18.4815288646 0 0<br>
> -3.8055093495 39.4697757527 0<br>
> 0.0 0 81.1208726003<br>
> K_POINTS {automatic}<br>
> 2 1 1 1 1 1<br>
> ATOMIC_POSITIONS {Angstrom}<br>
> Si 3.244236583 -0.172014720 -1.094825338<br>
> Si 2.228369492 2.411697260 3.448017655<br>
> O 2.736303038 5.113595723 -1.094825338<br>
> O 2.736303038 -2.873913184 3.448017655<br>
> O -2.981392825 0.184537563 -0.467912953<br>
> O -3.997259916 2.768249543 4.074930040<br>
> O -2.473459279 -5.101072881 -0.467912953<br>
> Si -3.489326371 -2.517360901 4.074930040<br>
> Si -1.970779189 -5.092209359 -3.448018036<br>
> O -2.981392825 -2.563165356 1.094824954<br>
> O -2.473459279 0.138733107 -3.448018038<br>
> O -3.489326371 2.722445087 1.094824954<br>
> O 3.244236583 5.067791268 -4.074930424<br>
> O 3.244236583 -2.919717639 0.467912569<br>
> Si 3.752170129 -0.217819176 -4.074930424<br>
> Si 2.736303038 2.365892804 0.467912569<br>
> O 1.484554833 -0.225310670 -1.467338541<br>
> O 0.468687742 2.358401311 3.075504451<br>
> O 0.976621287 5.060299774 -1.467338541<br>
> O 0.976621287 -2.927209133 3.075504451<br>
> O -0.205843983 -2.106252953 -4.774528173<br>
> Si -1.221711074 0.477459027 -0.231685180<br>
> Si -2.237578166 3.061171007 4.311157813<br>
> O -0.713777529 3.179357491 -4.774528173<br>
> O -0.713777529 -4.808151417 -0.231685180<br>
> O -1.729644620 -2.224439436 4.311157813<br>
> O -0.205843983 -5.093581387 -3.075504835<br>
> O -1.221711074 -2.509869407 1.467338158<br>
> Si -0.713777529 0.192029056 -3.075504835<br>
> Si -1.729644620 2.775741037 1.467338158<br>
> O 1.484554833 4.774869803 -4.311158196<br>
> O 1.484554833 -3.212639104 0.231684797<br>
> O 0.468687742 -0.628927124 4.774527789<br>
> O 1.992488379 -0.510740641 -4.311158196<br>
> O 0.976621287 2.072971340 0.231684797<br>
> Si -0.039245804 4.656683320 4.774527789<br>
> Si 3.634300016 6.536830035 -4.592814486<br>
> O 3.629046564 -1.396010889 -0.049971498<br>
> O 2.613179472 1.187701091 4.492871495<br>
> O 4.136980109 1.305887574 -4.592814491<br>
> O 3.121113018 3.889599555 -0.049971498<br>
> O 3.121113018 -4.097909353 4.492871495<br>
> Si -2.350335714 -3.922881168 -4.492871878<br>
> Si -3.366202805 -1.339169188 0.049971115<br>
> O -4.382069896 1.244542793 4.592814107<br>
> O -2.858269259 1.362729276 -4.492871878<br>
> O -3.874136351 3.946441256 0.049971115<br>
> O -3.874136351 -4.041067651 4.592814107<br>
> O 4.179848986 3.963518711 -4.919899104<br>
> Si 4.179848986 -4.023990196 -0.377056111<br>
> Si 3.163981894 -1.440278216 4.165786881<br>
> O 4.687782531 -1.322091733 -4.919899104<br>
> O 3.671915440 1.261620248 -0.377056111<br>
> O 2.656048349 3.845332228 4.165786881<br>
> O -2.901138136 -4.985131076 -2.066993745<br>
> O -3.917005227 -2.401419096 2.475849247<br>
> O -3.409071682 0.300479368 -2.066993745<br>
> O -4.424938773 2.884191348 2.475849247<br>
> O -2.901138136 -1.294901861 -4.165787265<br>
> H -3.917005227 1.288810119 0.377055728<br>
> H -4.932872319 3.872522099 4.919898721<br>
> O -2.398458040 -6.525844328 -4.165787266<br>
> O -3.409071682 -3.996800325 0.377055728<br>
> O -4.424938773 -1.413088344 4.919898721<br>
> H 4.179848986 -0.333760981 -2.475849631<br>
> H 3.163981894 2.249950999 2.066993362<br>
> O 3.671915440 4.951849462 -2.475849631<br>
> O 3.671915440 -3.035659445 2.066993362<br>
> O 1.452047081 2.357458364 -2.743877369<br>
> H 0.436179989 4.941170344 1.798965624<br>
> H 1.959980626 -2.928152080 -2.743877369<br>
> O 0.944113535 -0.344440100 1.798965624<br>
> O -1.189203322 2.894870467 -1.798966007<br>
> O -1.189203322 -5.092638441 2.743876985<br>
> H -0.681269776 -2.390739977 -1.798966007<br>
> H -1.697136868 0.192972003 2.743876985<br>
> O -0.665406237 -1.837117046 -0.825551760<br>
> O -1.681273329 0.746594934 3.717291232<br>
> O -1.173339783 3.448493397 -0.825551760<br>
> O -1.173339783 -4.539015510 3.717291232<br>
> O 1.944117087 -3.481775011 -3.717291616<br>
> O 0.928249996 -0.898063030 0.825551377<br>
> O 1.436183541 1.803835433 -3.717291616<br>
> O 0.420316450 4.387547413 0.825551377<br>
> Fe 0.639355425 -3.993359982 -1.512766928<br>
> Fe -0.376511666 -1.409648002 3.030076065<br>
> Fe 0.131421879 1.292250462 -1.512766928<br>
> Fe -0.884445212 3.875962442 3.030076065<br>
> Fe 0.639355425 -1.325532075 -3.030076448<br>
> Fe -0.376511666 1.258179905 1.512766544<br>
> Fe 0.131421879 3.960078369 -3.030076448<br>
> Fe 0.131421879 -4.027430539 1.512766544<br>
> H -0.330486013 -1.370310935 4.983743911<br>
> H -0.380473528 0.085683105 4.755623060<br>
> H -0.658084122 5.576125416 4.713164954<br>
> H -0.652159651 3.742806044 4.628702666<br>
> H -4.427569708 3.782916231 5.904144710<br>
> H -3.602562722 1.472178451 5.349550961<br>
> H -3.633502006 -1.231158556 5.676621530<br>
> H -3.230548684 -3.888975775 5.484308909<br>
> H 2.080475062 3.564355425 5.072355961<br>
> H 1.955333207 0.980964115 5.362698017<br>
> H 2.538530040 -1.610432101 5.066873837<br>
> H 2.397170127 -4.136241468 5.333429287<br>
> H 0.205066887 2.556899870 -4.755254151<br>
> H 0.516960094 -2.927561392 -4.587160198<br>
> H 0.654975044 -1.407396893 -4.826401650<br>
> H -0.023070297 4.048169258 -4.788300904<br>
> H -1.517074941 -3.838757062 -5.221363272<br>
> H -1.486326426 -6.574176125 -4.796485322<br>
> H -2.091934330 1.505338311 -5.283120860<br>
> H -2.257230613 -1.219591574 -5.066793073<br>
> H 3.859525324 -1.289248815 -5.658147957<br>
> H 3.530413611 1.325355867 -5.522221885<br>
> H 3.397463119 4.028877693 -5.704565012<br>
> H 3.132772235 6.610409095 -5.580314384<br>
> -----<br>
><br>
> The crash file writes the following:<br>
><br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> task # 0<br>
> from checkallsym : error # 1<br>
> some of the original symmetry operations not satisfied<br>
><br>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
> Any suggestions could be of great help.<br>
><br>
> Thanks for your time in advance.<br>
><br>
> Regards<br>
> Sai<br>
><br>
> -------------<br>
> Sai Ramadugu<br>
> Post-Doctoral Scholar,<br>
> Department of Chemistry,<br>
> University of Iowa.<br>
<br>
<br>
</div></div>--<br>
********************************************************<br>
- Article premier - Les hommes naissent et demeurent<br>
libres et ègaux en droits. Les distinctions sociales<br>
ne peuvent être fondèes que sur l'utilitè commune<br>
- Article 2 - Le but de toute association politique<br>
est la conservation des droits naturels et<br>
imprescriptibles de l'homme. Ces droits sont la libertè,<br>
la propriètè, la sùretè et la rèsistance à l'oppression.<br>
********************************************************<br>
<br>
Giuseppe Mattioli<br>
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
v. Salaria Km 29,300 - C.P. 10<br>
I 00015 - Monterotondo Stazione (RM)<br>
Tel <a href="tel:%2B%2039%2006%2090672836" value="+390690672836">+ 39 06 90672836</a> - Fax <a href="tel:%2B39%2006%2090672316" value="+390690672316">+39 06 90672316</a><br>
E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><br>
<br>
_______________________________________________<br>
Pw_forum mailing list<br>
<a href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br>
<a href="http://pwscf.org/mailman/listinfo/pw_forum" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a></blockquote></div><br></div>