[Nek5000-users] Linearised Navier Stokes

nek5000-users at lists.mcs.anl.gov nek5000-users at lists.mcs.anl.gov
Fri Aug 18 10:33:00 CDT 2017


Hi,
I guess we can continue the discussion directly using email. Adam has 
your logfile, so he will probably get back to you early next week.

Best,
Philipp

On 2017-08-18 17:26, nek5000-users at lists.mcs.anl.gov wrote:
> Hi clio,
> 
>       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. I have used the same .par file from 
> the dfh_cav case and has used the follwoing settings:
> 
> [PROBLEMTYPE]
> perturbations = yes
> solveBaseflow = no
> variableProperties = yes
> 
>     Can you please let me know where I may be mistaken.
> 
> Swarandeep
> 
> On Fri, Aug 18, 2017 at 3:32 PM, <nek5000-users at lists.mcs.anl.gov 
> <mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
> 
>     Hi Swarandeep,
> 
>     The binary mesh is saved in the re2 file, you can use that file to
>     generate a map file with genmap.
> 
>     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.
> 
>     Regards,
> 
>     clio
> 
> 
>     Quoting nek5000-users at lists.mcs.anl.gov
>     <mailto:nek5000-users at lists.mcs.anl.gov>:
> 
>         Hi
>              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.
> 
>         Swarandeep
> 
>         On Fri, Aug 18, 2017 at 1:03 AM,
>         <nek5000-users at lists.mcs.anl.gov
>         <mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
> 
>             Hi Swarandeep,
> 
>             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.
> 
>             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.
> 
>             Best regards,
>             Philipp
> 
>             On 2017-08-17 20:23, nek5000-users at lists.mcs.anl.gov
>             <mailto:nek5000-users at lists.mcs.anl.gov> wrote:
> 
>                 Hi Clio and Adam,
> 
>                          Thanks for the information.
> 
>                    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.
> 
>                 Swarandeep
> 
> 
>                 On Thu, Aug 17, 2017 at 7:03 PM,
>                 <nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>
>                 <mailto:nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>>> wrote:
> 
>                      Hi Swarandeep,
> 
>                      The baseflow has been computed with a Newton solver
>                 (which is not
>                      available in the nek examples). The additional code
>                 had been
>                      implemented in the version 1040 of nek5000, and
>                 there is no .par
>                      file for that. However, in general, if your case is
>                 laminar, to
>                      compute a baseflow, you just need to evaluate the
>                 steady state of
>                      your nonlinear case. For that, you can use the same
>                 .par file, and
>                      just change to the nonlinear solver
>                 (perturbationmodes = 0,
>                      perturbations = no, solveBaseflow = yes).
> 
>                      The non dimensionalization is based on Hellums and
>                 Churchill (1962).
> 
>                      The equations are:
> 
>                      Pr (du/dt + (U*nabla)u + (u*nabla)U) =
>                 1/sqrt(Ra)laplacian(u) -grad
>                      p + e_g theta
>                      d theta/dt + (u*nabla)Theta + (U*nabla)theta =
>                      1/sqrt(Ra)laplacian(theta)
>                      div(u)=0
> 
>                      where u, theta are respectively the velocity and
>                 temperature of the
>                      perturbation, U, Theta the velocity and temperature
>                 of the baseflow.
> 
>                      You can find more information in the paper
>                 "Saglietti, Clio, et al.
>                      "Adjoint optimization of natural convection
>                 problems: differentially
>                      heated cavity." Theoretical and Computational Fluid
>                 Dynamics (2016):
>                      1-17." on which the example is based.
> 
>                      Regards,
> 
>                      clio
> 
> 
>                      Quoting nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>
>                      <mailto:nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>>:
> 
>                          Hi Adam,
> 
>                          Thanks for the clarification. Can you please
>                 send me a sample
>                          .par file for
>                          the baseflow for the case of "dfh_cav". Also is
>                 it possible to
>                          get the
>                          equations solved for this problem(dfh_cav). I
>                 would like to know
>                          the way
>                          that this has been made dimensionless.
> 
>                          For your kind information I briefly describe my
>                 case which I
>                          have been used
>                          to solve with the regular non-linear framework
>                 using older
>                          versions (.rea
>                          files). My setup is as follows:
>                          Geometry is a 3D cylindrical annullus.
>                          Temperature are fixed at inner and outer cylinders.
>                          Gravity is acting in -z direction
>                          There is a back ground rotation which is constant.
> 
>                          Please let me know if any other info is
>                 required. Thanks for the
>                          help.
> 
>                          Swarandeep
> 
> 
> 
> 
>                          On Thu, Aug 17, 2017 at 1:48 PM,
>                          <nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>
>                          <mailto:nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>>> wrote:
> 
>                              Hi Swarandeep,
> 
>                              Yes. You generate ###.rea in the standard
>                 way. In the old
>                              version it was
>                              txt and contained both mesh information and
>                 runtime
>                              parameter. One could
>                              split mesh information (###.re2, binary
>                 file) and runtime
>                              parameters
>                              (###.rea with negative number of elements
>                 or currently
>                              ###.par) using
>                              reatore2 tool. The map file is generated
>                 with genmap (can be
>                              txt or
>                              binary). So the procedure is more or less
>                 the same. If you
>                              have ###.rea
>                              with mesh you split it and generate
>                 ###.re2. Next you
>                              generate ###.map with
>                              genmap and finally ###.par by hand. Be
>                 careful to use tolls
>                              from the same
>                              release, as they've been changed
>                 significantly (e.g. binary
>                              ###.map file).
>                              Regards
>                              Adam
> 
> 
>                              On 16/08/17 18:52,
>                 nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>
>                              <mailto:nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
> 
>                              Hi Adam,
> 
>                                        Thank you very much for the help.
> 
>                                        Does the ###.map, ###.box file 
>                 and from them the
>                              ###.rea file
>                              (in the dfh_cav case: the ###.re2 files) 
>                 are created as
>                              done for the
>                              earlier versions i.e., by using genbox and
>                 genmap. Please
>                              clarify.
> 
>                              Swarandeep
> 
> 
> 
>                              On Wed, Aug 16, 2017 at 5:35 PM,
>                              <nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>
>                              <mailto:nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>>> wrote:
> 
>                                  Hi,
> 
>                                  The simplest way would be to look into
>                 existing example
>                                  under
>                                  Nek5000/short_test/dfh_cav/
>                                  It is a differentially heated cavity
>                 case and covers
>                                  both direct and
>                                  adjoint linear solver. It is compatible
>                 with the current
>                                  git version and
>                                  uses ###.par file instead of ###.rea.
>                                  Regards
>                                  Adam
> 
> 
> 
> 
> 
>                                  On 11/08/17 11:05,
>                 nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>
>                                  <mailto:nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
> 
>                                      This information might be outdated
>                 (old version) but
>                                      previously the base
>                                      flow was read in using the restart
>                 option in the rea
>                                      file. The disturbance
>                                      you can read in yourself in userchk.
> 
>                                      Philipp
> 
>                                      On 2017-08-11 10:49,
>                 nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>
>                                     
>                 <mailto:nek5000-users at lists.mcs.anl.gov
>                 <mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
> 
>                                          Hi Philipp,
> 
>                                                 That was very much
>                 helpful. I have a
>                                          steady base flow and
>                                          temperature state. Please let
>                 me know where to
>                                          provide the base flow.
> 
> 
>                                          Thank you
>                                          Swarandeep
>                                         
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