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<p><span style="font-size:11pt">Hi Paul,</span></p>
<p><br>
</p>
<p><span style="font-size:11pt">Sorry for not replying earlier, I didn't see your reply last week unfortunately. So in my case I'm creating a partition as follows:</span></p>
<p><br>
</p>
<p><font size="2"><span style="font-size:10pt"><span style="font-size:11pt">Box_1</span><br>
<span style="font-size:11pt">-20 -50 nel_1, nel_2</span><br>
<span style="font-size:11pt">0. 50. 0.8 x0, x1</span><br>
<span style="font-size:11pt">0. 100. 1.1 y0, y1</span><br>
<span style="font-size:11pt">W ,E ,W ,W (bc's) velocity (west, east, south, north)</span><br>
<span style="font-size:11pt">T ,E ,t ,W (bc's) temperature (west, east, south, north)</span><br>
<span style="font-size:11pt">Box_2</span><br>
<span style="font-size:11pt">-20 -50 nel_1, nel_2</span><br>
<span style="font-size:11pt">50. 100. 1.2 x0, x1</span><br>
<span style="font-size:11pt">0. 100. 1.1 y0, y1</span><br>
<span style="font-size:11pt">E ,W ,W ,W (bc's) velocity (west, east, south, north)</span><br>
<span style="font-size:11pt">E ,T ,t ,W (bc's) temperature (west, east, south, north)</span></span></font></p>
<p><br>
</p>
<p><span style="font-size:11pt">This makes two boxes, separated in the x-direction. Is what you're saying, then, that my two 20x50 boxes are stacked one on top of the other to, in effect, create one 20x100 box? If that's the case, how do I take my element
map (which is just a list of 2000 numbers mapping local to global elements) and make sure that my two boxes are concatenated in the x-direction, instead of the z?</span></p>
<p><br>
</p>
<p><span style="font-size:11pt">Thanks in advance,</span></p>
<p><br>
</p>
<p><span style="font-size:11pt">Daniel</span><br>
</p>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Nek5000-users <nek5000-users-bounces@lists.mcs.anl.gov> on behalf of nek5000-users-request@lists.mcs.anl.gov <nek5000-users-request@lists.mcs.anl.gov><br>
<b>Sent:</b> 15 September 2017 13:05:25<br>
<b>To:</b> nek5000-users@lists.mcs.anl.gov<br>
<b>Subject:</b> Nek5000-users Digest, Vol 103, Issue 12</font>
<div> </div>
</div>
</div>
<font size="2"><span style="font-size:10pt;">
<div class="PlainText">Send Nek5000-users mailing list submissions to<br>
nek5000-users@lists.mcs.anl.gov<br>
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Today's Topics:<br>
<br>
1. Re: time integration scheme for temperature/scalar equations<br>
(nek5000-users@lists.mcs.anl.gov)<br>
2. Re: Nek5000-users Digest, Vol 103, Issue 9<br>
(nek5000-users@lists.mcs.anl.gov)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 15 Sep 2017 13:02:20 +0200<br>
From: nek5000-users@lists.mcs.anl.gov<br>
To: nek5000-users@lists.mcs.anl.gov<br>
Subject: Re: [Nek5000-users] time integration scheme for<br>
temperature/scalar equations<br>
Message-ID:<br>
<mailman.839.1505473384.10190.nek5000-users@lists.mcs.anl.gov><br>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br>
<br>
Hi,<br>
To be more precise. Routines "makeabq" and "makebdq" are called if you <br>
use hemholtz solver for passive scalars. The other option is cvode, <br>
which uses slightly different scheme. I guess hemholtz is default and to <br>
use cvode you have to add CVODE to preprocessing flag. About the link to <br>
doxygen. This one is outdated so it could be dangerous to use it. There <br>
is doxygen showing current beta2 version under<br>
<a href="https://adampep.github.io/KTH_Framework/files.html">https://adampep.github.io/KTH_Framework/files.html</a><br>
Regards<br>
Adam<br>
<br>
On 15/09/17 12:11, nek5000-users@lists.mcs.anl.gov wrote:<br>
><br>
> Hi Bolun Xu,<br>
><br>
> Yes,<br>
><br>
> you can see that in the conduct.f file( in which convection-diffusion <br>
> equation for temperature is solved): <br>
> <a href="http://www.mcs.anl.gov/research/projects/nek5/docs/html/conduct_8f_source.html">
http://www.mcs.anl.gov/research/projects/nek5/docs/html/conduct_8f_source.html</a><br>
><br>
> In the subroutine "makeabq" the same Adam-Bashforth coefficients AB() <br>
> are called and in the subroutine "makebdq", the BD() coefficients are <br>
> used again.<br>
><br>
> best,<br>
> Pierre-Emmanuel<br>
><br>
><br>
> On 2017-09-15 11:47, nek5000-users@lists.mcs.anl.gov wrote:<br>
>> Hi! All,<br>
>><br>
>> I learned from the subroutines makeabf and makebdf in navier1.f that the<br>
>> time integration scheme for momentum equation is the AB-CN scheme, that<br>
>> explicit schemes for nonlinear and forcing term, and implicit ones for<br>
>> viscous term. The prefactors of those schemes are stored in AB() and BD()<br>
>> arrays. Now my question is, whether the temperature/scalar equations also<br>
>> use the same schemes as momentum ones and also share the same prefactors in<br>
>> AB() / BD() arrays.<br>
>><br>
>> Any help is appreciated.<br>
>><br>
>> Regards.<br>
>><br>
>> ----------------------------------------------------------------<br>
>><br>
>> Bolun Xu<br>
>><br>
>> University of Science and Technology of China<br>
>><br>
>> Department of Modern Mechanics<br>
>><br>
>> Hefei, Anhui, China<br>
>><br>
>> <br>
>><br>
>><br>
>><br>
>><br>
>> _______________________________________________<br>
>> Nek5000-users mailing list<br>
>> Nek5000-users@lists.mcs.anl.gov<br>
>> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
><br>
><br>
><br>
> _______________________________________________<br>
> Nek5000-users mailing list<br>
> Nek5000-users@lists.mcs.anl.gov<br>
> <a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
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Message: 2<br>
Date: Fri, 15 Sep 2017 07:51:15 +0000<br>
From: nek5000-users@lists.mcs.anl.gov<br>
To: "nek5000-users@lists.mcs.anl.gov"<br>
<nek5000-users@lists.mcs.anl.gov><br>
Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 103, Issue 9<br>
Message-ID:<br>
<mailman.845.1505477125.10190.nek5000-users@lists.mcs.anl.gov><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi Goran,<br>
<br>
<br>
First of all thanks for having a look, my box file is as follows:<br>
<br>
<br>
plume_v2_largeIni.rea<br>
2 spatial dimension<br>
2 number of fields<br>
#<br>
#<br>
#<br>
#========================================================<br>
#<br>
Box_1<br>
-20 -50 nel_1, nel_2<br>
0. 50. 0.8 x0, x1<br>
0. 100. 1.1 y0, y1<br>
W ,E ,W ,W (bc's) velocity (west, east, south, north)<br>
T ,E ,t ,W (bc's) temperature (west, east, south, north)<br>
Box_2<br>
-20 -50 nel_1, nel_2<br>
50. 100. 1.2 x0, x1<br>
0. 100. 1.1 y0, y1<br>
E ,W ,W ,W (bc's) velocity (west, east, south, north)<br>
E ,T ,t ,W (bc's) temperature (west, east, south, north)<br>
<br>
I think where I'm struggling is in working out how the output (0.f#####) files are structured, or how their structure relates to the actual solution. I've managed to get the (2000, in this case) element mappings out of the files, I just can't then get this
mapping to actually map the elements correctly.<br>
<br>
Thanks again,<br>
<br>
Daniel<br>
<br>
<br>
________________________________<br>
From: Nek5000-users <nek5000-users-bounces@lists.mcs.anl.gov> on behalf of nek5000-users-request@lists.mcs.anl.gov <nek5000-users-request@lists.mcs.anl.gov><br>
Sent: 14 September 2017 17:29:13<br>
To: nek5000-users@lists.mcs.anl.gov<br>
Subject: Nek5000-users Digest, Vol 103, Issue 9<br>
<br>
Send Nek5000-users mailing list submissions to<br>
nek5000-users@lists.mcs.anl.gov<br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
nek5000-users-request@lists.mcs.anl.gov<br>
<br>
You can reach the person managing the list at<br>
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When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of Nek5000-users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Problems with post-processing multiple-boxes in MATLAB and<br>
Python (nek5000-users@lists.mcs.anl.gov)<br>
2. Re: Problems with post-processing multiple-boxes in MATLAB<br>
and Python (nek5000-users@lists.mcs.anl.gov)<br>
3. Re: Problems with post-processing multiple-boxes in MATLAB<br>
and Python (nek5000-users@lists.mcs.anl.gov)<br>
4. Re: proj_ortho error in pipe flow<br>
(nek5000-users@lists.mcs.anl.gov)<br>
5. problem with applying boundary conditions<br>
(nek5000-users@lists.mcs.anl.gov)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 14 Sep 2017 14:57:27 +0000<br>
From: nek5000-users@lists.mcs.anl.gov<br>
To: "nek5000-users@lists.mcs.anl.gov"<br>
<nek5000-users@lists.mcs.anl.gov><br>
Subject: [Nek5000-users] Problems with post-processing multiple-boxes<br>
in MATLAB and Python<br>
Message-ID:<br>
<mailman.763.1505402018.10190.nek5000-users@lists.mcs.anl.gov><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi All,<br>
<br>
<br>
I am using Nek5000 to simulate a buoyant plume rising from the centre of the floor of a square 2D domain. I am trying to use MATLAB and/or Python to post-process my data. Everything works fine when I post-process a simulation that was initialised with only
one box in my .box file. When, however, I run a simulation with multiple boxes (i.e. to cluster nodes), the local to global mapping of elements appears to go wrong and puts data into the wrong places. When plotting a contour plot of coordinates for example,
where I would expect a constantly changing colour gradient, I instead get back colour gradients in four quarters.<br>
<br>
<br>
I haven't used this list before so if I need to provide examples of images or code I can do. If anybody else has had this problem and has found a way to overcome it by finding the correct mapping some help would be very much appreciated.<br>
<br>
<br>
Best regards,<br>
<br>
<br>
Daniel Ward<br>
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<br>
Message: 2<br>
Date: Thu, 14 Sep 2017 15:20:27 +0000<br>
From: nek5000-users@lists.mcs.anl.gov<br>
To: shivang agarwal <nek5000-users@lists.mcs.anl.gov><br>
Subject: Re: [Nek5000-users] Problems with post-processing<br>
multiple-boxes in MATLAB and Python<br>
Message-ID:<br>
<mailman.765.1505402478.10190.nek5000-users@lists.mcs.anl.gov><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Daniel,<br>
<br>
I've had a similar problem before. Can you send your .box file so we can have a look?<br>
<br>
Best regards,<br>
<br>
Goran<br>
<br>
On Sep 14, 2017, at 11:13, "nek5000-users@lists.mcs.anl.gov<mailto:nek5000-users@lists.mcs.anl.gov>" <nek5000-users@lists.mcs.anl.gov<mailto:nek5000-users@lists.mcs.anl.gov>> wrote:<br>
<br>
<br>
Hi All,<br>
<br>
<br>
I am using Nek5000 to simulate a buoyant plume rising from the centre of the floor of a square 2D domain. I am trying to use MATLAB and/or Python to post-process my data. Everything works fine when I post-process a simulation that was initialised with only
one box in my .box file. When, however, I run a simulation with multiple boxes (i.e. to cluster nodes), the local to global mapping of elements appears to go wrong and puts data into the wrong places. When plotting a contour plot of coordinates for example,
where I would expect a constantly changing colour gradient, I instead get back colour gradients in four quarters.<br>
<br>
<br>
I haven't used this list before so if I need to provide examples of images or code I can do. If anybody else has had this problem and has found a way to overcome it by finding the correct mapping some help would be very much appreciated.<br>
<br>
<br>
Best regards,<br>
<br>
<br>
Daniel Ward<br>
<br>
_______________________________________________<br>
Nek5000-users mailing list<br>
Nek5000-users@lists.mcs.anl.gov<mailto:Nek5000-users@lists.mcs.anl.gov><br>
<a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
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<br>
Message: 3<br>
Date: Thu, 14 Sep 2017 15:33:07 +0000<br>
From: nek5000-users@lists.mcs.anl.gov<br>
To: "nek5000-users@lists.mcs.anl.gov"<br>
<nek5000-users@lists.mcs.anl.gov><br>
Subject: Re: [Nek5000-users] Problems with post-processing<br>
multiple-boxes in MATLAB and Python<br>
Message-ID:<br>
<mailman.767.1505403191.10190.nek5000-users@lists.mcs.anl.gov><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
<br>
Hi All,<br>
<br>
<br>
Genbox generates a tensor-product array of elements with layout:<br>
<br>
<br>
(ix , iy, iz) (ix fastest moving, iy 2nd fastest, iz 3rd fastest)<br>
<br>
<br>
If you want to have multiple boxes that continue in this ordering, you could<br>
<br>
do the following, say:<br>
<br>
<br>
box (1)<br>
<br>
-5 -5 -5<br>
<br>
-1 1 1.0<br>
<br>
-1 1 1.0<br>
<br>
0 2 1.0<br>
<br>
<br>
box(2)<br>
<br>
-5 -5 -10<br>
<br>
-1 1 1<br>
<br>
-1 1 1<br>
<br>
1.0 9.0<br>
<br>
<br>
etc<br>
<br>
<br>
This would stack a 5x5x10 box on top of a 5x5x5 box<br>
<br>
<br>
and topologically is the same as a 5x5 x (15) box<br>
<br>
<br>
... i.e., things get concatenated in the z direction.<br>
<br>
<br>
<br>
Also, note that you can use custom distributions in each direction, e.g.,<br>
<br>
<br>
box<br>
<br>
3 3 -5<br>
<br>
0 0.1 0.3 10<br>
<br>
0 .9 22 33<br>
<br>
-5 9 1.5<br>
<br>
<br>
which would give spacing [ 0 .1 .3 10] in the x direction<br>
<br>
<br>
[0 .9 22 33] in y<br>
<br>
<br>
and geometric partition of 5 elements in z on [-5:9]<br>
<br>
with size ratio 1.5 between each adjacent z level.<br>
<br>
<br>
hth<br>
<br>
<br>
Paul<br>
<br>
<br>
________________________________<br>
From: 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>
Sent: Thursday, September 14, 2017 10:20:27 AM<br>
To: shivang agarwal<br>
Subject: Re: [Nek5000-users] Problems with post-processing multiple-boxes in MATLAB and Python<br>
<br>
Hi Daniel,<br>
<br>
I've had a similar problem before. Can you send your .box file so we can have a look?<br>
<br>
Best regards,<br>
<br>
Goran<br>
<br>
On Sep 14, 2017, at 11:13, "nek5000-users@lists.mcs.anl.gov<mailto:nek5000-users@lists.mcs.anl.gov>" <nek5000-users@lists.mcs.anl.gov<mailto:nek5000-users@lists.mcs.anl.gov>> wrote:<br>
<br>
<br>
Hi All,<br>
<br>
<br>
I am using Nek5000 to simulate a buoyant plume rising from the centre of the floor of a square 2D domain. I am trying to use MATLAB and/or Python to post-process my data. Everything works fine when I post-process a simulation that was initialised with only
one box in my .box file. When, however, I run a simulation with multiple boxes (i.e. to cluster nodes), the local to global mapping of elements appears to go wrong and puts data into the wrong places. When plotting a contour plot of coordinates for example,
where I would expect a constantly changing colour gradient, I instead get back colour gradients in four quarters.<br>
<br>
<br>
I haven't used this list before so if I need to provide examples of images or code I can do. If anybody else has had this problem and has found a way to overcome it by finding the correct mapping some help would be very much appreciated.<br>
<br>
<br>
Best regards,<br>
<br>
<br>
Daniel Ward<br>
<br>
_______________________________________________<br>
Nek5000-users mailing list<br>
Nek5000-users@lists.mcs.anl.gov<mailto:Nek5000-users@lists.mcs.anl.gov><br>
<a href="https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users">https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users</a><br>
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<br>
Message: 4<br>
Date: Thu, 14 Sep 2017 15:34:39 +0000<br>
From: nek5000-users@lists.mcs.anl.gov<br>
To: "nek5000-users@lists.mcs.anl.gov"<br>
<nek5000-users@lists.mcs.anl.gov><br>
Subject: Re: [Nek5000-users] proj_ortho error in pipe flow<br>
Message-ID:<br>
<mailman.770.1505403282.10190.nek5000-users@lists.mcs.anl.gov><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
<br>
Hi Steffen,<br>
<br>
<br>
Thanks for bringing this to our attention.<br>
<br>
<br>
Adam and I have been looking into this... (no doubt, it's something<br>
<br>
stupid done by me awhile back).<br>
<br>
<br>
Hope to have it resolved by next week.<br>
<br>
<br>
Best,<br>
<br>
<br>
Paul<br>
<br>
<br>
________________________________<br>
From: 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>
Sent: Thursday, September 14, 2017 8:18:27 AM<br>
To: nek5000-users@lists.mcs.anl.gov<br>
Subject: Re: [Nek5000-users] proj_ortho error in pipe flow<br>
<br>
Hi,<br>
<br>
I have made some more tests to find the cause of this issue.<br>
Attached is a laminar pipe flow simulation with temperature and one<br>
passive scalar. The original setup is from Paul's "nusselt.tgz", where<br>
he answered another question of mine.<br>
<br>
I found that I can reproduce the same error I see in my turbulent<br>
simulations when there is an additional passive scalar with a different<br>
type of boundary condition, i.e. Neumann boundary condition at the pipe<br>
wall for temperature and Dirichlet boundary condition for the passive<br>
scalar.<br>
<br>
Can someone please check my setup and tell me why this causes the<br>
projection to fail?<br>
<br>
<br>
I hope to save some computational resources by using the projection.<br>
However, if it is not possible, I will keep param(94) = 0.<br>
<br>
Kind Regards,<br>
Steffen Straub<br>
<br>
--<br>
Karlsruhe Institute of Technology (KIT)<br>
Institute of Fluid Mechanics<br>
<br>
M.Sc. Steffen Straub<br>
Doctoral Researcher<br>
<br>
Kaiserstra?e 10<br>
Building 10.23<br>
76131 Karlsruhe, Germany<br>
<br>
Phone: +49 721 608-43027<br>
E-mail: steffen.straub@kit.edu<br>
Web: <a href="http://www.istm.kit.edu">http://www.istm.kit.edu</a><br>
<br>
KIT ? The Research University in the Helmholtz Association<br>
<br>
Since 2010, the KIT has been certified as a family-friendly university.<br>
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Message: 5<br>
Date: Thu, 14 Sep 2017 12:29:10 -0400<br>
From: nek5000-users@lists.mcs.anl.gov<br>
To: nek5000-users@lists.mcs.anl.gov<br>
Subject: [Nek5000-users] problem with applying boundary conditions<br>
Message-ID:<br>
<mailman.778.1505406553.10190.nek5000-users@lists.mcs.anl.gov><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Neks,<br>
<br>
I am trying to run a simulation, replicating the Nek5000 run from this<br>
youtube video:<br>
<a href="https://www.youtube.com/watch?v=RmmN-KFSvAY">https://www.youtube.com/watch?v=RmmN-KFSvAY</a><br>
<br>
The inlet BC is constant velocity (which is set to 1.0), and as can be seen<br>
from the video, the velocity magnitude reasonably away from the inlet is<br>
zero at starting times. However, in all of my simulations, I see the<br>
velocity magnitude as one at all the interior points away from the inlet<br>
from the beginning (the inlet BC ux=1.0 I am applying is somehow propagated<br>
to all interior elements). Am I doing something wrong somewhere, or is this<br>
the expected behavior? Please see my userbc() and useric() from my .usr<br>
file below:<br>
<br>
subroutine userbc (ix,iy,iz,iside,eg)<br>
include 'SIZE'<br>
include 'TOTAL'<br>
include 'NEKUSE'<br>
integer ix,iy,iz,eg,e,i,n<br>
<br>
CC "My inlet is at x=0"<br>
<br>
if (x.le.1e-4) then<br>
ux=1.0<br>
endif<br>
<br>
return<br>
end<br>
<br>
subroutine useric (ix,iy,iz,eg)<br>
include 'SIZE'<br>
include 'TOTAL'<br>
include 'NEKUSE'<br>
<br>
ux=0<br>
uy=0<br>
<br>
return<br>
end<br>
<br>
I believe userbc() is executed for only 'v' in my case. For the other<br>
constraints on the elements (like 'W', 'O', 'E'), I think userbc() would<br>
not run (please correct me if I am wrong, I am learning here). Since the<br>
above functions wouldn't work as expected, I changed userchk() and removed<br>
the above if statements in userbc(). My userchk() is as follows:<br>
<br>
subroutine userchk<br>
include 'SIZE'<br>
include 'TOTAL'<br>
integer i,n<br>
<br>
n = nx1*ny1*nz1*nelv<br>
<br>
if (istep.eq.0) then<br>
do i=1,n<br>
if (xm1(i,1,1,1).le.1e-4) then<br>
vx(i,1,1,1)=1<br>
endif<br>
enddo<br>
endif<br>
<br>
return<br>
end<br>
<br>
This didn't work either. Can somebody point me in the right direction?<br>
<br>
Thanks,<br>
Ajay<br>
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