[Nek5000-users] Nek5000-users Digest, Vol 103, Issue 9
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Fri Sep 15 02:51:15 CDT 2017
Hi Goran,
First of all thanks for having a look, my box file is as follows:
plume_v2_largeIni.rea
2 spatial dimension
2 number of fields
#
#
#
#========================================================
#
Box_1
-20 -50 nel_1, nel_2
0. 50. 0.8 x0, x1
0. 100. 1.1 y0, y1
W ,E ,W ,W (bc's) velocity (west, east, south, north)
T ,E ,t ,W (bc's) temperature (west, east, south, north)
Box_2
-20 -50 nel_1, nel_2
50. 100. 1.2 x0, x1
0. 100. 1.1 y0, y1
E ,W ,W ,W (bc's) velocity (west, east, south, north)
E ,T ,t ,W (bc's) temperature (west, east, south, north)
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.
Thanks again,
Daniel
________________________________
From: Nek5000-users <nek5000-users-bounces at lists.mcs.anl.gov> on behalf of nek5000-users-request at lists.mcs.anl.gov <nek5000-users-request at lists.mcs.anl.gov>
Sent: 14 September 2017 17:29:13
To: nek5000-users at lists.mcs.anl.gov
Subject: Nek5000-users Digest, Vol 103, Issue 9
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Today's Topics:
1. Problems with post-processing multiple-boxes in MATLAB and
Python (nek5000-users at lists.mcs.anl.gov)
2. Re: Problems with post-processing multiple-boxes in MATLAB
and Python (nek5000-users at lists.mcs.anl.gov)
3. Re: Problems with post-processing multiple-boxes in MATLAB
and Python (nek5000-users at lists.mcs.anl.gov)
4. Re: proj_ortho error in pipe flow
(nek5000-users at lists.mcs.anl.gov)
5. problem with applying boundary conditions
(nek5000-users at lists.mcs.anl.gov)
----------------------------------------------------------------------
Message: 1
Date: Thu, 14 Sep 2017 14:57:27 +0000
From: nek5000-users at lists.mcs.anl.gov
To: "nek5000-users at lists.mcs.anl.gov"
<nek5000-users at lists.mcs.anl.gov>
Subject: [Nek5000-users] Problems with post-processing multiple-boxes
in MATLAB and Python
Message-ID:
<mailman.763.1505402018.10190.nek5000-users at lists.mcs.anl.gov>
Content-Type: text/plain; charset="iso-8859-1"
Hi All,
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.
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.
Best regards,
Daniel Ward
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Message: 2
Date: Thu, 14 Sep 2017 15:20:27 +0000
From: nek5000-users at lists.mcs.anl.gov
To: shivang agarwal <nek5000-users at lists.mcs.anl.gov>
Subject: Re: [Nek5000-users] Problems with post-processing
multiple-boxes in MATLAB and Python
Message-ID:
<mailman.765.1505402478.10190.nek5000-users at lists.mcs.anl.gov>
Content-Type: text/plain; charset="utf-8"
Hi Daniel,
I've had a similar problem before. Can you send your .box file so we can have a look?
Best regards,
Goran
On Sep 14, 2017, at 11:13, "nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>" <nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
Hi All,
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.
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.
Best regards,
Daniel Ward
_______________________________________________
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Message: 3
Date: Thu, 14 Sep 2017 15:33:07 +0000
From: nek5000-users at lists.mcs.anl.gov
To: "nek5000-users at lists.mcs.anl.gov"
<nek5000-users at lists.mcs.anl.gov>
Subject: Re: [Nek5000-users] Problems with post-processing
multiple-boxes in MATLAB and Python
Message-ID:
<mailman.767.1505403191.10190.nek5000-users at lists.mcs.anl.gov>
Content-Type: text/plain; charset="us-ascii"
Hi All,
Genbox generates a tensor-product array of elements with layout:
(ix , iy, iz) (ix fastest moving, iy 2nd fastest, iz 3rd fastest)
If you want to have multiple boxes that continue in this ordering, you could
do the following, say:
box (1)
-5 -5 -5
-1 1 1.0
-1 1 1.0
0 2 1.0
box(2)
-5 -5 -10
-1 1 1
-1 1 1
1.0 9.0
etc
This would stack a 5x5x10 box on top of a 5x5x5 box
and topologically is the same as a 5x5 x (15) box
... i.e., things get concatenated in the z direction.
Also, note that you can use custom distributions in each direction, e.g.,
box
3 3 -5
0 0.1 0.3 10
0 .9 22 33
-5 9 1.5
which would give spacing [ 0 .1 .3 10] in the x direction
[0 .9 22 33] in y
and geometric partition of 5 elements in z on [-5:9]
with size ratio 1.5 between each adjacent z level.
hth
Paul
________________________________
From: Nek5000-users <nek5000-users-bounces at lists.mcs.anl.gov> on behalf of nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
Sent: Thursday, September 14, 2017 10:20:27 AM
To: shivang agarwal
Subject: Re: [Nek5000-users] Problems with post-processing multiple-boxes in MATLAB and Python
Hi Daniel,
I've had a similar problem before. Can you send your .box file so we can have a look?
Best regards,
Goran
On Sep 14, 2017, at 11:13, "nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>" <nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
Hi All,
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.
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.
Best regards,
Daniel Ward
_______________________________________________
Nek5000-users mailing list
Nek5000-users at lists.mcs.anl.gov<mailto:Nek5000-users at lists.mcs.anl.gov>
https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
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Message: 4
Date: Thu, 14 Sep 2017 15:34:39 +0000
From: nek5000-users at lists.mcs.anl.gov
To: "nek5000-users at lists.mcs.anl.gov"
<nek5000-users at lists.mcs.anl.gov>
Subject: Re: [Nek5000-users] proj_ortho error in pipe flow
Message-ID:
<mailman.770.1505403282.10190.nek5000-users at lists.mcs.anl.gov>
Content-Type: text/plain; charset="windows-1252"
Hi Steffen,
Thanks for bringing this to our attention.
Adam and I have been looking into this... (no doubt, it's something
stupid done by me awhile back).
Hope to have it resolved by next week.
Best,
Paul
________________________________
From: Nek5000-users <nek5000-users-bounces at lists.mcs.anl.gov> on behalf of nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
Sent: Thursday, September 14, 2017 8:18:27 AM
To: nek5000-users at lists.mcs.anl.gov
Subject: Re: [Nek5000-users] proj_ortho error in pipe flow
Hi,
I have made some more tests to find the cause of this issue.
Attached is a laminar pipe flow simulation with temperature and one
passive scalar. The original setup is from Paul's "nusselt.tgz", where
he answered another question of mine.
I found that I can reproduce the same error I see in my turbulent
simulations when there is an additional passive scalar with a different
type of boundary condition, i.e. Neumann boundary condition at the pipe
wall for temperature and Dirichlet boundary condition for the passive
scalar.
Can someone please check my setup and tell me why this causes the
projection to fail?
I hope to save some computational resources by using the projection.
However, if it is not possible, I will keep param(94) = 0.
Kind Regards,
Steffen Straub
--
Karlsruhe Institute of Technology (KIT)
Institute of Fluid Mechanics
M.Sc. Steffen Straub
Doctoral Researcher
Kaiserstra?e 10
Building 10.23
76131 Karlsruhe, Germany
Phone: +49 721 608-43027
E-mail: steffen.straub at kit.edu
Web: http://www.istm.kit.edu
KIT ? The Research University in the Helmholtz Association
Since 2010, the KIT has been certified as a family-friendly university.
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Message: 5
Date: Thu, 14 Sep 2017 12:29:10 -0400
From: nek5000-users at lists.mcs.anl.gov
To: nek5000-users at lists.mcs.anl.gov
Subject: [Nek5000-users] problem with applying boundary conditions
Message-ID:
<mailman.778.1505406553.10190.nek5000-users at lists.mcs.anl.gov>
Content-Type: text/plain; charset="utf-8"
Dear Neks,
I am trying to run a simulation, replicating the Nek5000 run from this
youtube video:
https://www.youtube.com/watch?v=RmmN-KFSvAY
The inlet BC is constant velocity (which is set to 1.0), and as can be seen
from the video, the velocity magnitude reasonably away from the inlet is
zero at starting times. However, in all of my simulations, I see the
velocity magnitude as one at all the interior points away from the inlet
from the beginning (the inlet BC ux=1.0 I am applying is somehow propagated
to all interior elements). Am I doing something wrong somewhere, or is this
the expected behavior? Please see my userbc() and useric() from my .usr
file below:
subroutine userbc (ix,iy,iz,iside,eg)
include 'SIZE'
include 'TOTAL'
include 'NEKUSE'
integer ix,iy,iz,eg,e,i,n
CC "My inlet is at x=0"
if (x.le.1e-4) then
ux=1.0
endif
return
end
subroutine useric (ix,iy,iz,eg)
include 'SIZE'
include 'TOTAL'
include 'NEKUSE'
ux=0
uy=0
return
end
I believe userbc() is executed for only 'v' in my case. For the other
constraints on the elements (like 'W', 'O', 'E'), I think userbc() would
not run (please correct me if I am wrong, I am learning here). Since the
above functions wouldn't work as expected, I changed userchk() and removed
the above if statements in userbc(). My userchk() is as follows:
subroutine userchk
include 'SIZE'
include 'TOTAL'
integer i,n
n = nx1*ny1*nz1*nelv
if (istep.eq.0) then
do i=1,n
if (xm1(i,1,1,1).le.1e-4) then
vx(i,1,1,1)=1
endif
enddo
endif
return
end
This didn't work either. Can somebody point me in the right direction?
Thanks,
Ajay
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