[Nek5000-users] Linearised Navier Stokes
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Tue Aug 22 03:11:27 CDT 2017
Hi Adam,
For running a 3D case , I am setting: parameter (lelg=500). This
gives some compilations errors as follows:
obj/bdry.o: In function `faceiv_..0':
/home/Nek5000/core/bdry.f:(.text+0x8b8c): relocation truncated to fit:
R_X86_64_32S against symbol `screv_' defined in COMMON section in
obj/postpro.o
This does not occur if lelg<300. Please let me know a higher lelg can be
used.
Thank you
Swarandeep
On Mon, Aug 21, 2017 at 6:41 PM, <nek5000-users at lists.mcs.anl.gov> wrote:
> 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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