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<div class="moz-cite-prefix">Hi,<br>
The first problem I could see is pressure mesh size. From the log
file it seems you are using P_n-P_n instead P_n-P_n-2. Only
P_n-P_n-2 has perturbation mode, so please check you SIZE file and
compare it with the SIZE file in dfh_cav example. You should have
lx2=lx1-2 instead of lx2=lx1. Is it the case?<br>
Regards<br>
Adam<br>
<br>
<br>
On 18/08/17 15:06, <a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> wrote:<br>
</div>
<blockquote type="cite"
cite="mid:mailman.1948.1503061600.6680.nek5000-users@lists.mcs.anl.gov">
<div dir="ltr">Hi Adam,
<div> I have send the logfile to your email: <a
class="gmail-m_-538237651637850933moz-txt-link-abbreviated"
href="mailto:adam@mech.kth.se" target="_blank"
moz-do-not-send="true">adam@mech.kth.se</a>)</div>
<div><br>
</div>
<div>Swarandeep<br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Aug 18, 2017 at 6:14 PM, <span
dir="ltr"><<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank" moz-do-not-send="true">nek5000-users@lists.mcs.anl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<div
class="gmail-m_-538237651637850933moz-cite-prefix">Strange.
Could you send me your log file? (<a
class="gmail-m_-538237651637850933moz-txt-link-abbreviated"
href="mailto:adam@mech.kth.se" target="_blank"
moz-do-not-send="true">adam@mech.kth.se</a>)<br>
Regards<br>
Adam
<div>
<div class="gmail-h5"><br>
<br>
<br>
On 18/08/17 14:40, <a
class="gmail-m_-538237651637850933moz-txt-link-abbreviated"
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank" moz-do-not-send="true">nek5000-users@lists.mcs.anl.<wbr>gov</a>
wrote:<br>
</div>
</div>
</div>
<div>
<div class="gmail-h5">
<blockquote type="cite">
<div dir="ltr">Hi Adam,
<div><br>
<div> Thank you for the continued
support. I managed to get the base flow
and then I used it in a perturbation
calculation following the dfh_cav case.
Peculiarly, I an finding that the basic
state is getting time stepped and the
perturbations are not (in contrast to the
dfh_cav case). I have used the same .par
file from the dfh_cav case and has used
the follwoing settings:</div>
<div><br>
</div>
<div>
<div>[PROBLEMTYPE]</div>
<div>perturbations = yes</div>
<div>solveBaseflow = no</div>
<div>variableProperties = yes</div>
</div>
<div><br>
</div>
<div> Can you please let me know where I
am am mistaken.</div>
<div><br>
</div>
<div>Swarandeep</div>
<div><br>
</div>
<div> </div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Aug 18, 2017
at 4:52 PM, <span dir="ltr"><<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank" moz-do-not-send="true">nek5000-users@lists.mcs.anl.<wbr>gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<div
class="gmail-m_-538237651637850933m_-9042198792866845286moz-cite-prefix">Hi,<br>
<br>
###.ma2 is the binary version of
###.map file and you need only one of
them (it is a new feature). The map
(or ma2) is generated by travis during
testing by running genmap, so we do
not keep it in repository.<br>
regards<br>
adam
<div>
<div
class="gmail-m_-538237651637850933h5"><br>
<br>
On 18/08/17 10:49, <a
class="gmail-m_-538237651637850933m_-9042198792866845286moz-txt-link-abbreviated"
href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a>
wrote:<br>
</div>
</div>
</div>
<div>
<div
class="gmail-m_-538237651637850933h5">
<blockquote type="cite">
<div dir="ltr">Hi
<div> I could no find the
###.ma2 file for the dfh_cav
example. Hence I suppose I
require the ###.box or the
###.map file to proceed for
the base flow. Please correct
me if I have misunderstood.</div>
<div><br>
</div>
<div>Swarandeep</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri,
Aug 18, 2017 at 1:03 AM, <span
dir="ltr"><<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.g<wbr>ov</a>></span>
wrote:<br>
<blockquote
class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">Hi Swarandeep,<br>
<br>
For computing the base flow
you can use the same mesh
and map file. What you need
to change is 1) the boundary
conditions such that they
are valid for the base flow
and 2) the flags that you
run a nonlinear instead of a
linear case.<br>
<br>
As Clio was saying, in that
particular case the base
flow was computed using a
Newton method. For lower
Rayleigh numbers, you should
however be able to just run
(nonlinear) DNS to reach the
steady state.<br>
<br>
Best regards,<br>
Philipp<span><br>
<br>
On 2017-08-17 20:23, <a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a>
wrote:<br>
</span>
<blockquote
class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px
solid
rgb(204,204,204);padding-left:1ex"><span>
Hi Clio and Adam,<br>
<br>
Thanks for the
information.<br>
<br>
I think in order to
compute the base flow I
need the ###.box file as
well as a different
###.usr file as I think
the boundary and initial
conditions for the
###.usr file in the
short_tests/dfh_cav
directory is applicable
for the perturbations
only. Please send me the
###.box and the
corresponding ###.usr
file applicable for the
base flow for dfh_cav
case.<br>
<br>
Swarandeep<br>
<br>
<br>
</span>
<div>
<div
class="gmail-m_-538237651637850933m_-9042198792866845286h5">
On Thu, Aug 17, 2017
at 7:03 PM, <<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.g<wbr>ov</a>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>>
wrote:<br>
<br>
Hi Swarandeep,<br>
<br>
The baseflow has
been computed with a
Newton solver (which
is not<br>
available in the
nek examples). The
additional code had
been<br>
implemented in the
version 1040 of
nek5000, and there is
no .par<br>
file for that.
However, in general,
if your case is
laminar, to<br>
compute a
baseflow, you just
need to evaluate the
steady state of<br>
your nonlinear
case. For that, you
can use the same .par
file, and<br>
just change to the
nonlinear solver
(perturbationmodes =
0,<br>
perturbations =
no, solveBaseflow =
yes).<br>
<br>
The non
dimensionalization is
based on Hellums and
Churchill (1962).<br>
<br>
The equations are:<br>
<br>
Pr (du/dt +
(U*nabla)u +
(u*nabla)U) =
1/sqrt(Ra)laplacian(u)
-grad<br>
p + e_g theta<br>
d theta/dt +
(u*nabla)Theta +
(U*nabla)theta =<br>
1/sqrt(Ra)laplacian(theta)<br>
div(u)=0<br>
<br>
where u, theta are
respectively the
velocity and
temperature of the<br>
perturbation, U,
Theta the velocity and
temperature of the
baseflow.<br>
<br>
You can find more
information in the
paper "Saglietti,
Clio, et al.<br>
"Adjoint
optimization of
natural convection
problems:
differentially<br>
heated cavity."
Theoretical and
Computational Fluid
Dynamics (2016):<br>
1-17." on which
the example is based.<br>
<br>
Regards,<br>
<br>
clio<br>
<br>
<br>
Quoting <a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a><br>
</div>
</div>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>:<span><br>
<br>
Hi Adam,<br>
<br>
Thanks for the
clarification. Can you
please send me a sample<br>
.par file for<br>
the baseflow for
the case of "dfh_cav".
Also is it possible to<br>
get the<br>
equations solved
for this
problem(dfh_cav). I
would like to know<br>
the way<br>
that this has
been made dimensionless.<br>
<br>
For your kind
information I briefly
describe my case which I<br>
have been used<br>
to solve with
the regular non-linear
framework using older<br>
versions (.rea<br>
files). My setup
is as follows:<br>
Geometry is a 3D
cylindrical annullus.<br>
Temperature are
fixed at inner and outer
cylinders.<br>
Gravity is
acting in -z direction<br>
There is a back
ground rotation which is
constant.<br>
<br>
Please let me
know if any other info
is required. Thanks for
the<br>
help.<br>
<br>
Swarandeep<br>
<br>
<br>
<br>
<br>
On Thu, Aug 17,
2017 at 1:48 PM,<br>
<<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.g<wbr>ov</a><br>
</span><span>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>>
wrote:<br>
<br>
Hi
Swarandeep,<br>
<br>
Yes. You
generate ###.rea in the
standard way. In the old<br>
version it
was<br>
txt and
contained both mesh
information and runtime<br>
parameter.
One could<br>
split mesh
information (###.re2,
binary file) and runtime<br>
parameters<br>
(###.rea
with negative number of
elements or currently<br>
###.par)
using<br>
reatore2
tool. The map file is
generated with genmap
(can be<br>
txt or<br>
binary). So
the procedure is more or
less the same. If you<br>
have ###.rea<br>
with mesh
you split it and
generate ###.re2. Next
you<br>
generate
###.map with<br>
genmap and
finally ###.par by hand.
Be careful to use tolls<br>
from the
same<br>
release, as
they've been changed
significantly (e.g.
binary<br>
###.map
file).<br>
Regards<br>
Adam<br>
<br>
<br>
On 16/08/17
18:52, <a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.go<wbr>v</a><br>
</span><span>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>
wrote:<br>
<br>
Hi Adam,<br>
<br>
Thank you very much for
the help.<br>
<br>
Does the ###.map,
###.box file and from
them the<br>
###.rea file<br>
(in the
dfh_cav case: the
###.re2 files) are
created as<br>
done for the<br>
earlier
versions i.e., by using
genbox and genmap.
Please<br>
clarify.<br>
<br>
Swarandeep<br>
<br>
<br>
<br>
On Wed, Aug
16, 2017 at 5:35 PM,<br>
<<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mcs.anl.g<wbr>ov</a><br>
</span><span>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>>
wrote:<br>
<br>
Hi,<br>
<br>
The
simplest way would be to
look into existing
example<br>
under<br>
Nek5000/short_test/dfh_cav/<br>
It is a
differentially heated
cavity case and covers<br>
both
direct and<br>
adjoint
linear solver. It is
compatible with the
current<br>
git
version and<br>
uses
###.par file instead of
###.rea.<br>
Regards<br>
Adam<br>
<br>
<br>
<br>
<br>
<br>
On
11/08/17 11:05, <a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
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</span><span>
<mailto:<a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>
wrote:<br>
<br>
This
information might be
outdated (old version)
but<br>
previously the base<br>
flow
was read in using the
restart option in the
rea<br>
file. The disturbance<br>
you
can read in yourself in
userchk.<br>
<br>
Philipp<br>
<br>
On
2017-08-11 10:49, <a
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"
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</span><span>
<mailto:<a
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target="_blank"
moz-do-not-send="true">nek5000-users@lists.mc<wbr>s.anl.gov</a>>
wrote:<br>
<br>
Hi Philipp,<br>
<br>
That was very
much helpful. I have a<br>
steady base flow and<br>
temperature state.
Please let me know where
to<br>
provide the base flow.<br>
<br>
<br>
Thank you<br>
Swarandeep<br>
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<pre>______________________________<wbr>_________________
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<pre wrap="">_______________________________________________
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