[Nek5000-users] Linearised Navier Stokes

nek5000-users at lists.mcs.anl.gov nek5000-users at lists.mcs.anl.gov
Mon Aug 21 06:11:29 CDT 2017


Hi,
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?
Regards
Adam


On 18/08/17 15:06, nek5000-users at lists.mcs.anl.gov wrote:
> Hi Adam,
>        I have send the logfile to your email: adam at mech.kth.se 
> <mailto:adam at mech.kth.se>)
>
> Swarandeep
>
> On Fri, Aug 18, 2017 at 6:14 PM, <nek5000-users at lists.mcs.anl.gov 
> <mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
>
>     Strange. Could you send me your log file? (adam at mech.kth.se
>     <mailto:adam at mech.kth.se>)
>     Regards
>     Adam
>
>
>
>     On 18/08/17 14:40, nek5000-users at lists.mcs.anl.gov
>     <mailto:nek5000-users at lists.mcs.anl.gov> wrote:
>>     Hi Adam,
>>
>>           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:
>>
>>     [PROBLEMTYPE]
>>     perturbations = yes
>>     solveBaseflow = no
>>     variableProperties = yes
>>
>>        Can you please let me know where I am am mistaken.
>>
>>     Swarandeep
>>
>>
>>     On Fri, Aug 18, 2017 at 4:52 PM, <nek5000-users at lists.mcs.anl.gov
>>     <mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
>>
>>         Hi,
>>
>>         ###.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.
>>         regards
>>         adam
>>
>>
>>         On 18/08/17 10:49, nek5000-users at lists.mcs.anl.gov
>>         <mailto:nek5000-users at lists.mcs.anl.gov> wrote:
>>>         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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>>
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