<div dir="ltr">Hi clio,<div><br></div><div>     Thank you for the suggestion. I have got the base flow now. But when I tried to run the perturbation using the sample .par file for the dfh_cav case for a different problem, the base flow is getting tmestepped instead of perturbation. <span style="color:rgb(80,0,80);font-size:12.8px">I have used the same .par file from the dfh_cav case and has used the follwoing settings:</span></div><div style="color:rgb(80,0,80);font-size:12.8px"><br></div><div style="color:rgb(80,0,80);font-size:12.8px"><div>[PROBLEMTYPE]</div><div>perturbations = yes</div><div>solveBaseflow = no</div><div>variableProperties = yes</div></div><div style="color:rgb(80,0,80);font-size:12.8px"><br></div><div style="color:rgb(80,0,80);font-size:12.8px">   Can you please let me know where I may be mistaken.</div><div style="color:rgb(80,0,80);font-size:12.8px"><br></div><div style="color:rgb(80,0,80);font-size:12.8px">Swarandeep</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Aug 18, 2017 at 3:32 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Swarandeep,<br>
<br>
The binary mesh is saved in the re2 file, you can use that file to generate a map file with genmap.<br>
<br>
You don't need to start from the box file, because for this specific case the type of the boundary conditions is the same for the linear and nonlinear simulations.<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>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Hi<br>
    I could no find the ###.ma2 file for the dfh_cav example. Hence I<br>
suppose I require the ###.box or the ###.map file to proceed for the base<br>
flow. Please correct me if I have misunderstood.<br>
<br>
Swarandeep<br>
<br>
On Fri, Aug 18, 2017 at 1:03 AM, <<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.g<wbr>ov</a>> wrote:<br>
<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Hi Swarandeep,<br>
<br>
For computing the base flow you can use the same mesh and map file. What<br>
you need to change is 1) the boundary conditions such that they are valid<br>
for the base flow and 2) the flags that you run a nonlinear instead of a<br>
linear case.<br>
<br>
As Clio was saying, in that particular case the base flow was computed<br>
using a Newton method. For lower Rayleigh numbers, you should however be<br>
able to just run (nonlinear) DNS to reach the steady state.<br>
<br>
Best regards,<br>
Philipp<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>
<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
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<br>
well as a different ###.usr file as I think the boundary and initial<br>
conditions for the ###.usr file in the short_tests/dfh_cav directory is<br>
applicable for the perturbations only. Please send me the ###.box and the<br>
corresponding ###.usr file applicable for the base flow for dfh_cav case.<br>
<br>
Swarandeep<br>
<br>
<br>
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><br>
<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>
    <mailto:<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mc<wbr>s.anl.gov</a>>:<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>
        <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>
            <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>
            <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>
                <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>
                    <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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