I just built a flow chart based on case expansion. I hope it useful for all beginner later.<br><br>Zhenyu<br><blockquote name="replyContent" style="padding-left:5px;margin-left:5px;border-left:#b6b6b6 2px solid;margin-right:0">-----原始邮件-----<br>
<b>发件人:</b> nek5000-users@lists.mcs.anl.gov<br>
<b>发送时间:</b> 2014-04-14 08:30:27 (星期一)<br>
<b>收件人:</b> nek5000-users@lists.mcs.anl.gov<br>
<b>抄送:</b> <br>
<b>主题:</b> Re: [Nek5000-users] usr file - Vol 62, Issue 9<br><br><p>Dear Murph,</p><p>I carried on along your suggested way and at least got some expected results</p><p>for case expanson.</p><p>Thank you very much for your guidance. </p><p>Yours,</p><p>Zhenyu</p><p><br><br><br></p><blockquote style="padding-left: 5px; margin-right: 0px; margin-left: 5px; border-left-color: rgb(182, 182, 182); border-left-width: 2px; border-left-style: solid;" name="replyContent">-----原始邮件-----<br>
<b>发件人:</b> <a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a><br>
<b>发送时间:</b> 2014-04-13 23:47:28 (星期日)<br>
<b>收件人:</b> <a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a><br>
<b>抄送:</b> <br>
<b>主题:</b> Re: [Nek5000-users] usr file - Vol 62, Issue 9<br><br>
Zhenyu,<br>
<br>
Hi... In general, you do the following:<br>
<br>
Use an existing run files as templates to start with. You need the
.rea, SIZE, .box, and .usr files. Rename the rea,box, and usr files
to a unique name for your run, like your_run.rea, your_run.box,
your_run.usr.<br>
<ul>
<li>Edit the .box file to define your grid, geometry, and BCs.<br>
</li>
<li>Edit the .rea file with all the basic run parameters. If you
have an .rea template that is ascii (without the .re2 option)
and it has geometry information at the end, ignore this
information as it will be regenerated.</li>
<li>Edit the SIZE file to set your array sizes and GLL DOF (this
must also be set correctly in .rea).</li>
<li>Edit the .usr file per instructions, including the information
for boundary conditions if applicable.</li>
</ul>
<p>Then, you generate a new .rea file with the grid geometry by
running genbox: "genbox ./your_run.box". This will create the
files box.rea and box.tmp. You rename box.rea to your_run.rea.
This will overwrite the one you edited with a new one with all
your changes in the settings sections intact, and new geometry
information at the end. Delete box.tmp.<br>
</p>
<p>Next, you run genmap to create a new map file: "genmap
./your_run". This will create the new map file.<br>
</p>
<p>Next, compile the code with: "./makenek ./your_run". If
successful, you will get a new binary copy of nek5000.<br>
</p>
<p>Then you run with one of the scripts like: "./nekbmpi ./your_run
24"<br>
</p>
<p>You will probably get a lot of errors initially based on improper
makenek setting for your compiler and target platform, geometry
issues, etc... Read all the documentation and look at the
examples to figure this stuff out for your application...<br>
</p>
<p>See Ya,<br>
</p>
<p>Murph<br>
<a class="moz-txt-link-abbreviated" href="mailto:mlodea@oakland.edu" target="_blank">mlodea@oakland.edu</a><br>
</p>
<blockquote cite="mid:mailman.78.1397149209.8253.nek5000-users@lists.mcs.anl.gov" type="cite"><br>
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<div class="headerdisplayname" style="display: inline;">Subject:
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[Nek5000-users] How to create .usr file</td>
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<td>
<div class="headerdisplayname" style="display: inline;">From:
</div>
<a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a></td>
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<div class="headerdisplayname" style="display: inline;">Date:
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4/10/2014 10:49 AM</td>
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<div class="headerdisplayname" style="display: inline;">To:
</div>
<a class="moz-txt-link-abbreviated" href="mailto:Nek5000-users@lists.mcs.anl.gov" target="_blank">Nek5000-users@lists.mcs.anl.gov</a></td>
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<br>
<div class="moz-text-html">Dear All,<br>
<br>
I am trying nek5000 under ubuntu.<br>
<br>
As a beginner, I just wonder which is the best way to create
the .usr file, should I copy one from the examples and change it
for my case or use a tool just like genbox, genmap, etc. to
generate it? I have the same question for creation of SIZE<br>
<br>
By the way, I can only find the usage of prenek and
demonstrative cases from the old manual of nekton, what is the
current way of generating meshes for public uses?<br>
<br>
Thank you very much in advance.<br>
<br>
Zhenyu<br>
</div>
<br>
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<div class="headerdisplayname" style="display: inline;">Subject:
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Re: [Nek5000-users] How to create .usr file</td>
</tr>
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<td>
<div class="headerdisplayname" style="display: inline;">From:
</div>
<a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a></td>
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<div class="headerdisplayname" style="display: inline;">Date:
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4/9/2014 11:17 AM</td>
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<div class="headerdisplayname" style="display: inline;">To:
</div>
<a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a></td>
</tr>
</tbody>
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<br>
<div class="moz-text-html" lang="x-western">
Hi Zhenyu,<br>
<br>
The *.usr is to be copied from the examples and change it
according to your needs like Boundary condition and Initial
condition. <br>
<br>
The SIZE file too should be copied (change the number of element
per processor according to yours) . <br>
<br>
See the example 'Expansion ' --> mkmesh file, which will give
you an insight about how to write a script to create a mesh
using prenek. <br>
<br>
Best Regards,<br>
Kamal.<br>
<br>
<br>
<div class="moz-cite-prefix">On 10/04/2014 16:49, <a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank" moz-do-not-send="true">nek5000-users@lists.mcs.anl.gov</a>
wrote:<br>
</div>
<blockquote cite="mid:mailman.4966.1397142449.3880.nek5000-users@lists.mcs.anl.gov" type="cite">Dear All,<br>
<br>
I am trying nek5000 under ubuntu.<br>
<br>
As a beginner, I just wonder which is the best way to create
the .usr file, should I copy one from the examples and change
it for my case or use a tool just like genbox, genmap, etc. to
generate it? I have the same question for creation of SIZE<br>
<br>
By the way, I can only find the usage of prenek and
demonstrative cases from the old manual of nekton, what is the
current way of generating meshes for public uses?<br>
<br>
Thank you very much in advance.<br>
<br>
Zhenyu<br>
<br>
<br>
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