[Nek5000-users] Linearised Navier Stokes
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Mon Aug 21 08:11:25 CDT 2017
Hi Adam,
Yes, I had wrongly set it to 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.
However the following line
call gradm1(DTDX,DTDY,DTDZ,T)
which works for the base flow is not working for the perturbation
if I use the below lines:
call gradm1(DTPDX,DTPDY,DTPDZ,TP)
call outpost(DTPDX,DTPDY,DTPDZ,PRP,TP,0,'gdtprt')
Thank you
Swarandeep
On Mon, Aug 21, 2017 at 4:41 PM, <nek5000-users at lists.mcs.anl.gov> wrote:
> 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)
>
> Swarandeep
>
> On Fri, Aug 18, 2017 at 6:14 PM, <nek5000-users at lists.mcs.anl.gov> wrote:
>
>> Strange. Could you send me your log file? (adam at mech.kth.se)
>> Regards
>> Adam
>>
>>
>>
>> On 18/08/17 14:40, 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> 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 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>
>>> 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 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>> 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>:
>>>>>
>>>>> 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>> 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> 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>> 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> 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> 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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