<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">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">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">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">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">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">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">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">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">nek5000-users@lists.mcs.anl.g<wbr>ov</a>
<mailto:<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">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">nek5000-users@lists.mcs.anl.go<wbr>v</a><br>
</div>
</div>
<mailto:<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">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">nek5000-users@lists.mcs.anl.g<wbr>ov</a><br>
</span><span> <mailto:<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">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">nek5000-users@lists.mcs.anl.go<wbr>v</a><br>
</span><span> <mailto:<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">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">nek5000-users@lists.mcs.anl.g<wbr>ov</a><br>
</span><span> <mailto:<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">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">nek5000-users@lists.mcs.anl.go<wbr>v</a><br>
</span><span> <mailto:<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">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">nek5000-users@lists.mcs.anl.go<wbr>v</a><br>
</span><span>
<mailto:<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">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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