[Nek5000-users] Linearised Navier Stokes
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Tue Aug 22 03:21:32 CDT 2017
Hi,
Nek uses static memory allocation so you have the max memory amount you
can use. In this case the max number of elements depends on the size of
given element (lx1) and can be pretty high for 2D runs but for 3D is
bounded. There are possible compiler options to increase memory limit
(e.g. -mcmodel for gfortran), but we usually do not bother bother about
it as nek is well parallelised and one can easily increase amount of
global memory by adding more nodes. That is the proper way to go.
Otherwise you would wait for result forever.
regards
Adam
On 22/08/17 10:11, nek5000-users at lists.mcs.anl.gov wrote:
> 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
> <mailto: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
> <mailto: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
> <mailto: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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