<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yui_3_16_0_1_1447699371956_48501">Pascal:</div><div id="yui_3_16_0_1_1447699371956_48567">Do not you think z-vector will shrink till it reaches the optimal length?</div><div id="yui_3_16_0_1_1447699371956_48502"> </div><div id="yui_3_16_0_1_1447699371956_48146"><span></span></div> <br><div class="qtdSeparateBR"><br><br></div><div style="display: block;" class="yahoo_quoted"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"> <font face="Arial" size="2"> On Tuesday, November 17, 2015 12:35 AM, Pascal Boulet <pascal.boulet@univ-amu.fr> wrote:<br> </font> </div> <br><br> <div class="y_msg_container"><div id="yiv4889452832"><div>So, I think in this case you should also relax the z-axis: The system tends to fill the vacuum by moving atoms since it cannot adapt the cell parameter.<div><br clear="none"><div>Pascal</div><div><br clear="none"><div class="yiv4889452832yqt8008647212" id="yiv4889452832yqt02663"><div><div>Le 16 nov. 2015 à 21:49, Jaret Qi <<a rel="nofollow" shape="rect" ymailto="mailto:jaretqi@yahoo.com" target="_blank" href="mailto:jaretqi@yahoo.com">jaretqi@yahoo.com</a>> a écrit :</div><br class="yiv4889452832Apple-interchange-newline" clear="none"><blockquote type="cite"><div style="background-color:rgb(255, 255, 255);font-family:HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif;font-size:16px;"><div id="yiv4889452832yui_3_16_0_1_1447699371956_11156">To make it clear, I am not adding vacuum to isolate my system like in graphene where we make the z-axis large enough to make it graphene not graphite. My system is a (001) interface between semi-metallic and semiconductor, so i am trying to minimize the interaction along the interface which is along the z-axis and study some properties and match it with experimental results. I need a reasonable vacuum so I began with 4A.</div><div id="yiv4889452832yui_3_16_0_1_1447699371956_11157"><br clear="none"></div><div id="yiv4889452832yui_3_16_0_1_1447699371956_11158"> <br clear="none"></div><br clear="none"><div class="yiv4889452832qtdSeparateBR"><br clear="none"><br clear="none"></div><div class="yiv4889452832yahoo_quoted" style="display:block;"> <div style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"> <div style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"> <div dir="ltr"> <font face="Arial" size="2"> On Monday, November 16, 2015 1:31 PM, Nicola Marzari <<a rel="nofollow" shape="rect" ymailto="mailto:nicola.marzari@epfl.ch" target="_blank" href="mailto:nicola.marzari@epfl.ch">nicola.marzari@epfl.ch</a>> wrote:<br clear="none"> </font> </div> <br clear="none"><br clear="none"> <div class="yiv4889452832y_msg_container">On 16/11/2015 21:17, Jaret Qi wrote:<br clear="none">> but that will cost time!<br clear="none"><br clear="none">you are right! just keep the 4 angstroms, no one will notice.<br clear="none"><br clear="none">(actually, skip the calculations altogether, and make up some<br clear="none">plausible numbers in your paper - that will be even faster).<br clear="none"><br clear="none"> nicola<br clear="none"><br clear="none">><br clear="none">><br clear="none">><br clear="none">> On Monday, November 16, 2015 9:26 AM, Pascal Boulet<br clear="none">> <<a rel="nofollow" shape="rect" ymailto="mailto:pascal.boulet@univ-amu.fr" target="_blank" href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a>> wrote:<br clear="none">><br clear="none">><br clear="none">> Hello,<br clear="none">><br clear="none">> 4 angstroms wide seems to be very small for the vacuum. As a rule of<br clear="none">> thumb you should use at least 2.5 times the thickness of your slab. This<br clear="none">> is what we observed in the calculations of semiconductor slabs. This has<br clear="none">> to be tested.<br clear="none">><br clear="none">> Pascal<br clear="none">><br clear="none">> Le 16 nov. 2015 à 16:40, Jaret Qi <<a rel="nofollow" shape="rect" ymailto="mailto:jaretqi@yahoo.com" target="_blank" href="mailto:jaretqi@yahoo.com">jaretqi@yahoo.com</a><br clear="none">> <mailto:<a rel="nofollow" shape="rect" ymailto="mailto:jaretqi@yahoo.com" target="_blank" href="mailto:jaretqi@yahoo.com">jaretqi@yahoo.com</a>>> a écrit :<br clear="none">><br clear="none">>> Hello all,<br clear="none">>> I am trying to minimize the interaction between my system and its<br clear="none">>> periodic images. To do so, I introduced a layer of vacuum along the<br clear="none">>> z-axis by increasing the lattice vector along the z-axis by 4A. At the<br clear="none">>> same time, I fixed it by using this parameter: cell_dofree='2Dxy',<br clear="none">>> But I have noticed atoms that are close to the vacuum move along the<br clear="none">>> z-axis and vacuum is decreasing, is this wrong or I should use<br clear="none">>> different cell_dofree?<br clear="none">>> note:relaxation still ongoing, not relaxed yet.<br clear="none">>><br clear="none">>><br clear="none">>> JARET,<br clear="none">>> ASU<br clear="none">>> _______________________________________________<br clear="none">>> Pw_forum mailing list<br clear="none">>> <a rel="nofollow" shape="rect" ymailto="mailto:Pw_forum@pwscf.org" target="_blank" href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a> <mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Pw_forum@pwscf.org" target="_blank" href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a>><br clear="none">>> <a rel="nofollow" shape="rect" target="_blank" href="http://pwscf.org/mailman/listinfo/pw_forum">http://pwscf.org/mailman/listinfo/pw_forum</a><br clear="none">><br clear="none">> --<br clear="none">> Pascal Boulet /- MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE/<br clear="none">> Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie<br clear="none">> Niemen - 13013 Marseille<br clear="none">> Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50<br clear="none">> Site : <a rel="nofollow" shape="rect" target="_blank" href="http://allos.up.univ-mrs.fr/pascal">http://allos.up.univ-mrs.fr/pascal </a>- Email :<br clear="none">> <a rel="nofollow" shape="rect" ymailto="mailto:pascal.boulet@univ-amu.fr" target="_blank" href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a> <mailto:<a rel="nofollow" shape="rect" ymailto="mailto:pascal.boulet@univ-amu.fr" target="_blank" href="mailto:pascal.boulet@univ-amu.fr">pascal.boulet@univ-amu.fr</a>><br clear="none">> /Afin de respecter l'environnement, merci de n'imprimer cet email que si<br clear="none">> nécessaire./<div class="yiv4889452832yqt2621883996" id="yiv4889452832yqtfd08559"><br clear="none">><br clear="none">><br clear="none">><br clear="none">><br clear="none">><br clear="none">> _______________________________________________<br clear="none">> Pw_forum mailing list<br clear="none">> <a rel="nofollow" shape="rect" ymailto="mailto:Pw_forum@pwscf.org" target="_blank" href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a><br clear="none">> <a rel="nofollow" shape="rect" target="_blank" href="http://pwscf.org/mailman/listinfo/pw_forum">http://pwscf.org/mailman/listinfo/pw_forum</a></div><br clear="none">><br clear="none"><br clear="none">-- <br clear="none">----------------------------------------------------------------------<br clear="none">Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL<br clear="none">Director, National Centre for Competence in Research NCCR MARVEL, EPFL<br clear="none"><a rel="nofollow" shape="rect" target="_blank" href="http://theossrv1.epfl.ch/Main/Contact">http://theossrv1.epfl.ch/Main/Contact </a><a rel="nofollow" shape="rect" target="_blank" href="http://nccr-marvel.ch/en/project">http://nccr-marvel.ch/en/project</a><div class="yiv4889452832yqt2621883996" id="yiv4889452832yqtfd09972"><br clear="none"></div><br clear="none"><br clear="none"></div> </div> </div> </div></div></blockquote></div></div><br clear="none"><div>
--<br clear="none"><div style="color:rgb(0, 0, 0);font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-family:Tahoma, Verdana, Arial, Helvetica, sans-serif;font-size:15px;line-height:22px;"><span style="color:rgb(34, 187, 234);font-size:14px;font-family:verdana;font-weight:700;">Pascal Boulet</span> <span style="color:rgb(34, 187, 234);font-size:11px;font-family:verdana;"><em>- MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE</em></span></div><div style="color:rgb(0, 0, 0);font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-family:Tahoma, Verdana, Arial, Helvetica, sans-serif;font-size:15px;line-height:22px;"><span style="font-size:11px;font-family:verdana;">Aix-Marseille Université - </span><span style="font-size:11px;font-family:verdana;">ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille</span></div><div style="color:rgb(0, 0, 0);font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-family:Tahoma, Verdana, Arial, Helvetica, sans-serif;font-size:15px;line-height:22px;"><span style="font-size:11px;font-family:verdana;">Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50</span></div><div style="color:rgb(0, 0, 0);font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-family:Tahoma, Verdana, Arial, Helvetica, sans-serif;font-size:15px;line-height:22px;"><span style="font-size:12px;font-family:verdana;">Site : <a rel="nofollow" shape="rect" target="_blank" href="http://allos.up.univ-mrs.fr/pascal" title="http://allos.up.univ-mrs.fr/pascal" style="line-height:20px;color:rgb(34, 187, 234);text-decoration:none;">http://allos.up.univ-mrs.fr/pascal</a> - Email : <a rel="nofollow" shape="rect" ymailto="mailto:pascal.boulet@univ-amu.fr" target="_blank" href="mailto:pascal.boulet@univ-amu.fr" style="line-height:20px;color:rgb(34, 187, 234);text-decoration:none;">pascal.boulet@univ-amu.fr</a></span></div><div style="color:rgb(0, 0, 0);font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-family:Tahoma, Verdana, Arial, Helvetica, sans-serif;font-size:15px;line-height:22px;"><span style="line-height:25px;color:rgb(0, 113, 185);font-size:11px;font-family:verdana;"><em>Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire.</em></span></div>
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