<div dir="ltr">Hi Adam,<div><br></div><div>        Yes, I had wrongly  set it to <span style="font-size:12.8px"> </span><span style="font-size:12.8px">lx2=lx1. I corrected it and now the running is correct. The base flow is held in place and the perturbations are time stepped.  Thank you very much for this.</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">         However the following line </span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">   call gradm1(DTDX,DTDY,DTDZ,T)</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">         which works for the base flow is not working for the perturbation if I use the below lines:</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">         call gradm1(DTPDX,DTPDY,DTPDZ,TP)</span></div><div><span style="font-size:12.8px">       call outpost(DTPDX,DTPDY,DTPDZ,PRP,TP,0,'gdtprt') </span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Thank you</span></div><div><span style="font-size:12.8px">Swarandeep</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Aug 21, 2017 at 4:41 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">
  
    
  
  <div text="#000000" bgcolor="#FFFFFF">
    <div class="m_-2614846919753584310moz-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<div><div class="h5"><br>
      <br>
      <br>
      On 18/08/17 15:06, <a class="m_-2614846919753584310moz-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="h5">
    <blockquote type="cite">
      <div dir="ltr">Hi Adam,
        <div>       I have send the logfile to your email: <a class="m_-2614846919753584310gmail-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.<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="m_-2614846919753584310gmail-m_-538237651637850933moz-cite-prefix">Strange.
                    Could you send me your log file? (<a class="m_-2614846919753584310gmail-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="m_-2614846919753584310gmail-h5"><br>
                        <br>
                        <br>
                        On 18/08/17 14:40, <a class="m_-2614846919753584310gmail-m_-538237651637850933moz-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="m_-2614846919753584310gmail-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.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">
                              <div bgcolor="#FFFFFF">
                                <div class="m_-2614846919753584310gmail-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="m_-2614846919753584310gmail-m_-538237651637850933h5"><br>
                                      <br>
                                      On 18/08/17 10:49, <a class="m_-2614846919753584310gmail-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="m_-2614846919753584310gmail-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="m_-2614846919753584310gmail-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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                                      <br>
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</pre>
                                    </blockquote>
                                    <p><br>
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                        <br>
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</pre>
                      </blockquote>
                      <p><br>
                      </p>
                    </div>
                  </div>
                </div>
                <br>
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          </div>
        </div>
      </div>
      <br>
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      <br>
      <pre>______________________________<wbr>_________________
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</pre>
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    <p><br>
    </p>
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