<div dir="ltr">Dear Ketan,<div><br></div><div>Many thanks for your reply. Basically I want to get the averaged velocity, rms velocities and shear stress where I got two questions. </div><div><br></div><div>1. Once the subroutines were writen in usr file, Is calling avg_all still needed? In other words, the post-processing is done after longtime running, and usr file is changed instead of calling avg_all, isn't it?</div><div><br></div><div>2. After trying the subroutines you provided, there isnt no files generated in the directory. Can you give me more infomation about the averaging process.</div><div><br></div><div>Best wishes,</div><div><br></div><div>ZJ</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 30 November 2017 at 18:00, <span dir="ltr"><<a href="mailto:nek5000-users-request@lists.mcs.anl.gov" target="_blank">nek5000-users-request@lists.mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Nek5000-users mailing list submissions to<br>
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1. tools in new version (<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a>)<br>
2. Re: avg_all averaging (<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a>)<br>
3. Re: tools in new version (<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a>)<br>
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Message: 1<br>
Date: Thu, 30 Nov 2017 06:26:10 +0300<br>
From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a><br>
To: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a><br>
Subject: [Nek5000-users] tools in new version<br>
Message-ID:<br>
<<a href="mailto:mailman.3666.1512012374.19102.nek5000-users@lists.mcs.anl.gov">mailman.3666.1512012374.<wbr>19102.nek5000-users@lists.mcs.<wbr>anl.gov</a>><br>
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Hi, Neks!<br>
<br>
I am trying to create a complex geometry and use nektools. I use nekmerge2 script to merge two parts of my mesh, and then I want to use reatore2 and genmap. In previous version the same script worked find, but now (~/Nek5000/bin/) reatore2 gives a note:?<br>
<br>
Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_DENORMAL<br>
<br>
and after that genmap gives a error:<br>
<br>
ABORT: SELF-CHK 1 2 4 0<br>
Try to tighten the mesh tolerance!<br>
<br>
I have tested this script with old tools (on another computer) and it's still works fine. Do you have any ideas why does this problem occur?<br>
<br>
Best regards,<br>
Mark<br>
<br>
<br>
<br>
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Message: 2<br>
Date: Thu, 30 Nov 2017 05:01:23 +0000<br>
From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a><br>
To: "<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a>"<br>
<<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a>><br>
Subject: Re: [Nek5000-users] avg_all averaging<br>
Message-ID:<br>
<<a href="mailto:mailman.3672.1512018086.19102.nek5000-users@lists.mcs.anl.gov">mailman.3672.1512018086.<wbr>19102.nek5000-users@lists.mcs.<wbr>anl.gov</a>><br>
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Hi ZJ,<br>
<br>
A quick search of the archives with keyword ?avg_all? will give you answer to related questions:<br>
<a href="https://lists.mcs.anl.gov/mailman/mmsearch/nek5000-users?config=nek5000-users.htsearch&restrict=&exclude=&method=and&format=short&sort=score&words=avg_all" rel="noreferrer" target="_blank">https://lists.mcs.anl.gov/<wbr>mailman/mmsearch/nek5000-<wbr>users?config=nek5000-users.<wbr>htsearch&restrict=&exclude=&<wbr>method=and&format=short&sort=<wbr>score&words=avg_all</a><br>
<br>
avg_all is a collection of time-averaged information in the avg, rms and rm2 files. The avg files has time-averaged u,v and w; rms has time-averaged u^2, v^2 and w^2; and rm2 has uv, vw, and uw. The avg_all routines is located in navier5.f in case you want to get more information.<br>
<br>
Typically the first step in post processing is to use the routine ?auto_averager? to combine all the files output from avg_all. autoaverager takes as input the name of a file (example: fname1.list) which has a list of all the files that you want to combine (example: the contents of fname1.list will be: avgcasename0.f00001 avgcasename0.f00002 ? Note- there should be only 1 filename per line in the fname1.list file). You can use the auto_averager routine to combine all your avgcasename0.f00* files and output them to a single file or do more post-processing with it. The quantities available in avg, rms and rm2 files are sufficient to get the actual urms, vrms velocities etc? Additionally, once you time-average the data using auto_averager, you can use space averaging routines such as z_avg etc? to average quantities in homogeneous direction of your domain.<br>
<br>
It would also help if you specify what exactly are you trying to get from these avg_all files i.e. are you looking for rms velocities or something else?<br>
<br>
Here is a snippet of my code that I have used in the past to post-process these files:<br>
call auto_averager(fname1)<br>
call copy(uk,vx)<br>
call copy(vk,vy)<br>
call copy(wk,vz)<br>
call col2(uk,uk,lt)<br>
call col2(vk,vk,lt)<br>
call col2(wk,wk,lt)<br>
call auto_averager(fname2)<br>
call sub2(vx,uk,lt)<br>
call sub2(vy,vk,lt)<br>
call sub2(vz,wk,lt)<br>
call z_avg(vxa,vx,gs_avg_hndl,<wbr>nelxy,ifld)<br>
call z_avg(vya,vy,gs_avg_hndl,<wbr>nelxy,ifld)<br>
call z_avg(vza,vz,gs_avg_hndl,<wbr>nelxy,ifld)<br>
call outpost(vxa,vya,vza,vxa,vya,' ')<br>
<br>
Here fname1 has the list of all avgcasename0.f00* files and fname2 has the list of all the rmscasename0.f00* files.<br>
<br>
<br>
Ketan<br>
<br>
<br>
<br>
<br>
<br>
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Message: 3<br>
Date: Thu, 30 Nov 2017 11:11:43 +0100<br>
From: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a><br>
To: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a> <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a>><br>
Subject: Re: [Nek5000-users] tools in new version<br>
Message-ID:<br>
<<a href="mailto:mailman.3678.1512036715.19102.nek5000-users@lists.mcs.anl.gov">mailman.3678.1512036715.<wbr>19102.nek5000-users@lists.mcs.<wbr>anl.gov</a>><br>
Content-Type: text/plain; charset=utf-8<br>
<br>
Can you try again with the latest version on GitHub (just submitted a potential fix).<br>
<br>
-----Original message-----<br>
> <a href="mailto:From%3Anek5000-users@lists.mcs.anl.gov">From:nek5000-users@lists.mcs.<wbr>anl.gov</a> <<a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a>><br>
> Sent: Thursday 30th November 2017 4:27<br>
> To: <a href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.<wbr>gov</a><br>
> Subject: [Nek5000-users] tools in new version<br>
><br>
> Hi, Neks!<br>
><br>
> I am trying to create a complex geometry and use nektools. I use nekmerge2 script to merge two parts of my mesh, and then I want to use reatore2 and genmap. In previous version the same script worked find, but now (~/Nek5000/bin/) reatore2 gives a note:?<br>
><br>
> Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG IEEE_DENORMAL<br>
><br>
> and after that genmap gives a error:<br>
><br>
> ABORT: SELF-CHK 1 2 4 0<br>
> Try to tighten the mesh tolerance!<br>
><br>
> I have tested this script with old tools (on another computer) and it's still works fine. Do you have any ideas why does this problem occur?<br>
><br>
> Best regards,<br>
> Mark<br>
><br>
><br>
><br>
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</blockquote></div><br></div>