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<p style="margin-top:0;margin-bottom:0">Hi Jon,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">You raise two separate issues --- </p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"> 1. periodic-auto is simply the way that prenek assigns the P-P matching between</p>
<p style="margin-top:0;margin-bottom:0"> a pair of faces. It requires the faces to be parallel, aligned, and with unit normals </p>
<p style="margin-top:0;margin-bottom:0">point in opposite directions. Generally under these circumstances prenek/pretex will </p>
<p style="margin-top:0;margin-bottom:0">find the matched pairs and thus generate the correct .rea file. From there, genmap</p>
<p style="margin-top:0;margin-bottom:0">and Nek5000 will establish the correct connectivity to execute the code (primarily,</p>
<p style="margin-top:0;margin-bottom:0">direct stiffness summation).</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">2. If the faces are not aligned, you need to have a way to assign the P-P association.</p>
<p style="margin-top:0;margin-bottom:0"> Assuming you can do this then <span style="font-size: 12pt;">there are two possible cases:</span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;"><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"> a) The unit normals on P-P face pairs are aligned and in </font>opposite<font size="3"> direction.</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"> This case will go through genmap/Nek5000 without any issue.</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"><br>
</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"> b) The unit normals on P-P faces are not aligned, i.e., you're running the CYCLIC</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"> case (ifcyc=.true.). Here, there's going to be an issues in setting up the .map</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"> file. genmap likely will not work. You can recover this inside nek because</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"> we allow the user to prescribe some connectivity information, but it's clear</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"> that this will have to be done on a case-by-case basis.</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"><br>
</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3">One of things we often do is to have a fake mesh with the same topology but</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3">with a geometry such that the normals are aligned (Case 2.a). Then generate</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3">the .map file and use it with Case 2.b.</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"><br>
</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3">If this isn't possible, I'd suggest you contact me off-list and I can try to give</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3">some guidance.</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"><br>
</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3">In the meantime, for your model problem, I'd suggest proceeding with one of </font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3">the approaches outlined above, just so you can familiarize yourself with the</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3">overall process for the cyclic bcs.</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"><br>
</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3">hth,</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"><br>
</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3">Paul</font></p>
<p style="margin-top:0;margin-bottom:0"><font size="3"><br>
</font></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0"> a) Unit normals are parallel and in </p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Nek5000-users <nek5000-users-bounces@lists.mcs.anl.gov> on behalf of nek5000-users@lists.mcs.anl.gov <nek5000-users@lists.mcs.anl.gov><br>
<b>Sent:</b> Saturday, January 13, 2018 2:34:58 PM<br>
<b>To:</b> nek5000-users@lists.mcs.anl.gov<br>
<b>Subject:</b> Re: [Nek5000-users] Periodicity with curvature</font>
<div> </div>
</div>
<div>
<div dir="ltr">Hi Paul,
<div>In the future, I will need a more complex geometry where cyclic BCs are not in-line. This simple example I presented here is simply a proof of concept for another mesh.</div>
<div>What would be the best method do this, when the geometry isn't simple enough to use auto-periodic?</div>
<div><br>
</div>
<div>Thank you,</div>
<div>Jon</div>
</div>
<div class="x_gmail_extra"><br>
<div class="x_gmail_quote">On Sat, Jan 13, 2018 at 2:28 PM, <span dir="ltr"><<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a>></span> wrote:<br>
<blockquote class="x_gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div id="x_m_-5858926404772448990divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:#000000; font-family:Calibri,Helvetica,sans-serif">
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Hi Jon,</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">It's been awhile since I've run the cyclic BCs that you're trying to use.</p>
<p style="margin-top:0; margin-bottom:0">(Here: cyclic = periodic + turning through an angle.)</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">I can't recall the full workflow at the moment (and am not in a position</p>
<p style="margin-top:0; margin-bottom:0">to check), but I think you'll have better luck if you build a straight mesh,</p>
<p style="margin-top:0; margin-bottom:0">run genmap, and then morph the geometry into the desired curved</p>
<p style="margin-top:0; margin-bottom:0">shape in usrdat2().</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">The reason for doing so is that you'll then be guaranteed to have</p>
<p style="margin-top:0; margin-bottom:0">the correct mesh connectivity.</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">hth,</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Paul</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
</div>
<hr style="display:inline-block; width:98%">
<div id="x_m_-5858926404772448990divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Nek5000-users <<a href="mailto:nek5000-users-bounces@lists.mcs.anl.gov" target="_blank">nek5000-users-bounces@lists.<wbr>mcs.anl.gov</a>>
on behalf of <a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.<wbr>gov</a> <<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.<wbr>gov</a>><br>
<b>Sent:</b> Saturday, January 13, 2018 1:00:48 PM<br>
<b>To:</b> <a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.<wbr>gov</a><br>
<b>Subject:</b> Re: [Nek5000-users] Periodicity with curvature</font>
<div> </div>
</div>
<div>
<div class="x_h5">
<div>
<div dir="ltr">My apologies, can you clarify what you mean?
<div>I made global refinements one more time, and re-assigned the periodic BCs within prex. For this 2D case (attached), I have linked the 8 element sides with the right 8 sides. All other sides are walls.</div>
<div><br>
</div>
<div>Thank you,<br>
Jon</div>
</div>
<div class="x_m_-5858926404772448990x_gmail_extra"><br>
<div class="x_m_-5858926404772448990x_gmail_quote">On Sat, Jan 13, 2018 at 12:49 PM,
<span dir="ltr"><<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.<wbr>gov</a>></span> wrote:<br>
<blockquote class="x_m_-5858926404772448990x_gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="auto">
<div></div>
<div>can you try again with at least 3 elements in other direction.</div>
<div>
<div class="x_m_-5858926404772448990x_h5">
<div><br>
On 13 Jan 2018, at 19:42, "<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.g<wbr>ov</a>" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.g<wbr>ov</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<div dir="ltr">Thanks for the quick response. I made some global refinements but it seems I'm still getting the same error with genmap.
<div><br>
</div>
<div>Attached is the new .rea file with 4 elements in the periodic direction.</div>
<div><br>
</div>
</div>
<div class="x_m_-5858926404772448990x_gmail_extra"><br>
<div class="x_m_-5858926404772448990x_gmail_quote">On Sat, Jan 13, 2018 at 12:32 PM,
<span dir="ltr"><<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.g<wbr>ov</a>></span> wrote:<br>
<blockquote class="x_m_-5858926404772448990x_gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="auto">
<div></div>
<div>You need to have at least three elements in the periodic direction. </div>
<div>
<div class="x_m_-5858926404772448990x_m_2972450520427343467h5">
<div><br>
On 13 Jan 2018, at 19:19, "<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.g<wbr>ov</a>" <<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.g<wbr>ov</a>> wrote:<br>
<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div dir="ltr">
<div>
<div class="x_m_-5858926404772448990x_m_2972450520427343467h5">Dear Nek Users,
<div><br>
</div>
<div>I am trying to get periodicity to work in the lastest version of Nek. I've made an extremely simple mesh within prenek (prex) in polar coordinates and cannot seem to run this case. When I run genmap, I get the error below. Did I do something wrong in setting
up this mesh?</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>>> genmap</div>
<div>
<div> reading a.rea</div>
<div>Input mesh tolerance (default 0.2):</div>
<div>NOTE: smaller is better, but generous is more forgiving for bad meshes.</div>
<div>0.01</div>
<div> reading mesh data ...</div>
<div> start locglob_lexico: 4 2 8 1.0000000000000000E-002</div>
<div> locglob: 1 1 8</div>
<div> locglob: 2 5 8</div>
<div> locglob: 1 6 8</div>
<div> locglob: 2 6 8</div>
<div> done locglob_lexico: 6 6 8 2</div>
<div> start periodic vtx: 2 6</div>
<div> 1 4 4 Matrix: x0</div>
<div> 1 x0 1.0000E+00 1.0000E+00 5.4347-323 4.9407-324</div>
<div> 2 x0 -3.5355E-01 3.5355E-01 6.9423-310 6.9423-310</div>
<div> 3 x0 3.5355E-01 -3.5355E-01 6.9529-310 6.9529-310</div>
<div> 4 x0 6.9423-310 6.9529-310 2.3477-313 3.1632-317</div>
<div> 2 4 4 Matrix: x1</div>
<div> 1 x1 1.0000E+00 1.0000E+00 6.3240-322 0.0000E+00</div>
<div> 2 x1 -3.5355E-01 3.5355E-01 0.0000E+00 6.9423-310</div>
<div> 3 x1 -3.5355E-01 3.5355E-01 6.9423-310 6.9529-310</div>
<div> 4 x1 6.9423-310 6.9423-310 6.9423-310 6.9529-310</div>
<div> 1 4 4 Matrix: z0</div>
<div> 1 z0 1.0000E+00 1.0000E+00 5.4347-323 4.9407-324</div>
<div> 2 z0 -2.1213E+00 -1.4142E+00 6.9423-310 6.9423-310</div>
<div> 3 z0 2.1213E+00 1.4142E+00 6.9529-310 6.9529-310</div>
<div> 4 z0 6.9423-310 6.9529-310 2.3477-313 3.1632-317</div>
<div> 2 4 4 Matrix: z1</div>
<div> 1 z1 1.0000E+00 1.0000E+00 6.3240-322 0.0000E+00</div>
<div> 2 z1 1.4142E+00 2.1213E+00 0.0000E+00 6.9423-310</div>
<div> 3 z1 1.4142E+00 2.1213E+00 6.9423-310 6.9529-310</div>
<div> 4 z1 6.9423-310 6.9423-310 6.9423-310 6.9529-310</div>
<div> 1 3 0 1.00000000E-03 2.12132000E+00 abort: FACE MATCH FAIL</div>
<div> 2 4 3 2.12132000E-03 1.00000031E+00 abort: FACE MATCH FAIL</div>
<div><br>
</div>
<div> 0 quit</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>The mesh within my .rea file is as follows:</div>
<div>
<div> 20.0000 20.0000 -8.00000 -4.00000 XFAC,YFAC,XZERO,YZERO</div>
<div> **MESH DATA** 1st line is X of corner 1,2,3,4. 2nd line is Y.</div>
<div> 2 2 2 NEL,NDIM,NELV</div>
<div> ELEMENT 1 [ 1A] GROUP 0</div>
<div> -2.121320 -1.414213 -0.8742276E-07 -0.1311341E-06</div>
<div> 2.121320 1.414213 2.000000 3.000000</div>
<div> ELEMENT 2 [ 1B] GROUP 0</div>
<div> -0.1311341E-06 -0.8742276E-07 1.414213 2.121320</div>
<div> 3.000000 2.000000 1.414213 2.121320</div>
<div> ***** CURVED SIDE DATA *****</div>
<div> 4 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE</div>
<div> 2 1 -2.00000 0.00000 0.00000 0.00000 0.00000 C</div>
<div> 4 1 3.00000 0.00000 0.00000 0.00000 0.00000 C</div>
<div> 2 2 -2.00000 0.00000 0.00000 0.00000 0.00000 C</div>
<div> 4 2 3.00000 0.00000 0.00000 0.00000 0.00000 C</div>
<div> ***** BOUNDARY CONDITIONS *****</div>
<div> ***** FLUID BOUNDARY CONDITIONS *****</div>
<div> P 1 1 2.00000 3.00000 0.00000 0.00000 0.00000</div>
<div> W 1 2 0.00000 0.00000 0.00000 0.00000 0.00000</div>
<div> E 1 3 2.00000 1.00000 0.00000 0.00000 0.00000</div>
<div> W 1 4 0.00000 0.00000 0.00000 0.00000 0.00000</div>
<div> E 2 1 1.00000 3.00000 0.00000 0.00000 0.00000</div>
<div> W 2 2 0.00000 0.00000 0.00000 0.00000 0.00000</div>
<div> P 2 3 1.00000 1.00000 0.00000 0.00000 0.00000</div>
<div> W 2 4 0.00000 0.00000 0.00000 0.00000 0.00000</div>
<div> ***** NO THERMAL BOUNDARY CONDITIONS *****</div>
</div>
<div><br>
</div>
</div>
</div>
<div><mime-attachment.png><br>
</div>
</div>
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