[Nek5000-users] Contents of Nek5000-users digest Corner elements giving large values
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Mon Jun 5 12:26:01 CDT 2017
Swarandeep,
Another issue that can arise in RBC simulations is poor numerical
conditioning due to the non-dimensionalization. The non-dimensional form
of the equations used in the Nek5000 examples is based off the conduction
scales which result in a very small time-step and large velocities at
larger Ra. I don't think you're case is high enough for it to be a
problem, but you might try using the "freefall" scales if you aren't
already.
I suggest consulting the Scheel, Emran and Schumacher paper for some
details on running an RBC simulation with Nek5000.
Scheel, Janet D., Mohammad S. Emran, and Jörg Schumacher. "Resolving the
fine-scale structure in turbulent Rayleigh–Bénard convection." *New Journal
of Physics* 15.11 (2013): 113063.
Kind Regards,
Phil S.
On Mon, Jun 5, 2017 at 10:00 AM, <nek5000-users-request at lists.mcs.anl.gov>
wrote:
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> 1. Re: Corner elements giving large values
> (nek5000-users at lists.mcs.anl.gov)
> 2. Re: Corner elements giving large values
> (nek5000-users at lists.mcs.anl.gov)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 5 Jun 2017 01:12:39 +0530
> From: nek5000-users at lists.mcs.anl.gov
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Corner elements giving large values
> Message-ID:
> <mailman.7988.1496605362.2967.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Nek Forum, Paul
>
> Thanks for the suggestions. I implemented them. Waiting for the
> simulation to be over.
>
> Another issue I have is that the BC for T at the inner cylinder wall
> does not stay at 0 as I have given in userbc. It becomes 0.2 over some
> time.
>
> Thank you
> Swarandeep
>
>
>
>
>
> On Fri, Jun 2, 2017 at 10:28 PM, <nek5000-users at lists.mcs.anl.gov> wrote:
> >
> > Hi Swarandeep,
> >
> > Set p26 in the .rea file to be 0.1 and make certain IFCHAR is F (a few
> lines below);
> >
> > Make certain your dt is positive (param 12)
> >
> > Paul
> >
> > ________________________________________
> > From: nek5000-users-bounces at lists.mcs.anl.gov [
> nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> > Sent: Friday, June 02, 2017 10:31 AM
> > To: nek5000-users at lists.mcs.anl.gov
> > Subject: Re: [Nek5000-users] Corner elements giving large values
> >
> > Dear Nek Forum, Paul
> >
> > Yes, I have user defined grid such that the locations of the
> > elements are distributed to lie on the chebyshev grid at the top and
> > bottom and near the side walls.
> > Also please tell which param sets the CFL.
> >
> > Thank you
> > Swarandeep
> >
> >
> > On Fri, Jun 2, 2017 at 8:00 PM, <nek5000-users at lists.mcs.anl.gov>
> wrote:
> >>
> >> Dear Swarandeep,
> >>
> >> Did you refine your element size at the top and bottom and near the
> side walls?
> >>
> >> Please set your CFL to 0.05 in order to get the flow started.
> >>
> >> Best,
> >>
> >>
> >> Paul
> >>
> >> ________________________________________
> >> From: nek5000-users-bounces at lists.mcs.anl.gov [
> nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> >> Sent: Friday, June 02, 2017 1:04 AM
> >> To: nek5000-users at lists.mcs.anl.gov
> >> Subject: Re: [Nek5000-users] Corner elements giving large values
> >>
> >> Hi Nek Forum, Paul
> >>
> >> The top and bottom BC are zero heat flux. Please let me n=know
> >> how to control the CFL. It is 0.5 in the logfile. I am having no
> >> particular difficulty except these corner elements at the junction of
> >> inner cylinder and the top/bottom planes. Is there a better way to
> >> treat edge boundary elements. Also is it possible to have different
> >> order of elements at different locations.
> >>
> >> Thank you
> >> Swarandeep
> >>
> >> On Fri, Jun 2, 2017 at 12:50 AM, <nek5000-users at lists.mcs.anl.gov>
> wrote:
> >>>
> >>> Hi Swarandeep,
> >>>
> >>> Sorry - I misunderstood. I guess my question was more about the
> >>> temperature bcs at the bottom and top of the domain?
> >>>
> >>> In general, however, there should be no difficulty. What happens
> >>> when you reduce your dt ?
> >>>
> >>> You need to keep the CFL < ~0.5 in general. CFL is printed in the
> logfile,
> >>>
> >>> grep tep logfile
> >>>
> >>> and you'll see it "C= ....."
> >>>
> >>> Paul
> >>>
> >>>
> >>>
> >>>
> >>> ________________________________________
> >>> From: nek5000-users-bounces at lists.mcs.anl.gov [
> nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> >>> Sent: Thursday, June 01, 2017 1:57 PM
> >>> To: nek5000-users at lists.mcs.anl.gov
> >>> Subject: Re: [Nek5000-users] Corner elements giving large values
> >>>
> >>> Hi NekForum, Paul
> >>>
> >>> I intent to have isothermal conditions at the inner and outer
> >>> cylinders. The differential heating is achieved by imposing a
> >>> temperature difference across the two cylinders. I have used T = 1 and
> >>> 0 values for non-dimensional temperature. I think it should be fine.
> >>> Do you see any problem here.
> >>>
> >>> Thank you
> >>> Swarandeep
> >>>
> >>> On Thu, Jun 1, 2017 at 11:28 PM, <nek5000-users at lists.mcs.anl.gov>
> wrote:
> >>>>
> >>>> Hi Swarandeep,
> >>>>
> >>>> Is 0/1 a realistic BC for T ?
> >>>>
> >>>> Best,
> >>>>
> >>>> Paul
> >>>>
> >>>> ________________________________________
> >>>> From: nek5000-users-bounces at lists.mcs.anl.gov [
> nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> >>>> Sent: Thursday, June 01, 2017 12:53 PM
> >>>> To: nek5000-users at lists.mcs.anl.gov
> >>>> Subject: Re: [Nek5000-users] Corner elements giving large values
> >>>>
> >>>> Hi Nek Forum, Paul
> >>>>
> >>>> I am having temp = 1 and temp = 0 at the inner and outer
> >>>> boundaries. Gravity is pointing in the -ve z-direction along the axis
> >>>> of the
> >>>> annulus. The top and bottom planes have zero heat flux
> conditions.
> >>>> I have Coriolis force added as a body force.
> >>>> The Rayleigh number is around 10000. The resolution is 8, 25,
> >>>> 24 elements in the r, phi and z directions respectively with order 9.
> >>>> My initial condition is very low arbitrary velocity
> >>>> perturbation (~10^(-8)). The time resolution is set to 10^(-5) for
> >>>> param12. The CFL is
> >>>> set to 0.5. Please indicate how to control it.
> >>>>
> >>>> As you have rightly mentioned, I start the simulation with a
> >>>> very low value of the Rayleigh number and gradually increase it. Yet,
> >>>> the corner values only get large. Other regions of the domain are
> >>>> fine.
> >>>>
> >>>> Thank you
> >>>> Swarandeep
> >>>>
> >>>> On Thu, Jun 1, 2017 at 7:38 PM, <nek5000-users at lists.mcs.anl.gov>
> wrote:
> >>>>>
> >>>>> Hi Swarandeep,
> >>>>>
> >>>>> How large is your Rayleigh number and what is your resolution?
> >>>>> What are your thermal bcs? What are your ICs?
> >>>>>
> >>>>> There should be no particular issue with your configuration - but
> you do need to
> >>>>> control spatial and temporal resolution.
> >>>>>
> >>>>>
> >>>>> For RB, you often have to start at low Ra and/or small dt because
> the nonlinear
> >>>>> response can often drive the velocities to be quite high very
> rapidly before the
> >>>>> CFL constraint kicks in. RB flows are one of the rare instances
> where I use
> >>>>> variable time step size (param 12 > 0), but even then you have to
> keep the target
> >>>>> CFL quite small until the flow is established.
> >>>>>
> >>>>> hth,
> >>>>>
> >>>>> Paul
> >>>>>
> >>>>> ________________________________________
> >>>>> From: nek5000-users-bounces at lists.mcs.anl.gov [
> nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> >>>>> Sent: Thursday, June 01, 2017 7:27 AM
> >>>>> To: nek5000-users at lists.mcs.anl.gov
> >>>>> Subject: [Nek5000-users] Corner elements giving large values
> >>>>>
> >>>>> Dear Nek forum,
> >>>>>
> >>>>> I am simulating Rayleigh Benard flow in a 3D finite
> cylindrical annulus.
> >>>>> I am getting spurious large values of velocity at the corner
> regions
> >>>>> of the annulus i.e. the edges where the inner cylinder joins
> the
> >>>>> top and bottom
> >>>>> planes. The boundary condition is no-slip and no penetration
> for velocity
> >>>>> at these edges. Can someone point out a plausible reason.
> >>>>>
> >>>>> Thank you
> >>>>> Swarandeep
> >>>>> _______________________________________________
> >>>>> Nek5000-users mailing list
> >>>>> Nek5000-users at lists.mcs.anl.gov
> >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >>>>> _______________________________________________
> >>>>> Nek5000-users mailing list
> >>>>> Nek5000-users at lists.mcs.anl.gov
> >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >>>> _______________________________________________
> >>>> Nek5000-users mailing list
> >>>> Nek5000-users at lists.mcs.anl.gov
> >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >>>> _______________________________________________
> >>>> Nek5000-users mailing list
> >>>> Nek5000-users at lists.mcs.anl.gov
> >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >>> _______________________________________________
> >>> Nek5000-users mailing list
> >>> Nek5000-users at lists.mcs.anl.gov
> >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >>> _______________________________________________
> >>> Nek5000-users mailing list
> >>> Nek5000-users at lists.mcs.anl.gov
> >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >> _______________________________________________
> >> Nek5000-users mailing list
> >> Nek5000-users at lists.mcs.anl.gov
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >> _______________________________________________
> >> Nek5000-users mailing list
> >> Nek5000-users at lists.mcs.anl.gov
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> > _______________________________________________
> > Nek5000-users mailing list
> > Nek5000-users at lists.mcs.anl.gov
> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> > _______________________________________________
> > Nek5000-users mailing list
> > Nek5000-users at lists.mcs.anl.gov
> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 5 Jun 2017 01:20:04 +0000
> From: nek5000-users at lists.mcs.anl.gov
> To: "nek5000-users at lists.mcs.anl.gov"
> <nek5000-users at lists.mcs.anl.gov>
> Subject: Re: [Nek5000-users] Corner elements giving large values
> Message-ID:
> <mailman.7989.1496625605.2967.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Swarandeep,
>
> if you send me your .rea/.usr/SIZE file off-list, I'll take a look.
>
> Paul
> ________________________________________
> From: nek5000-users-bounces at lists.mcs.anl.gov [
> nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> Sent: Sunday, June 04, 2017 2:42 PM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Corner elements giving large values
>
> Hi Nek Forum, Paul
>
> Thanks for the suggestions. I implemented them. Waiting for the
> simulation to be over.
>
> Another issue I have is that the BC for T at the inner cylinder wall
> does not stay at 0 as I have given in userbc. It becomes 0.2 over some
> time.
>
> Thank you
> Swarandeep
>
>
>
>
>
> On Fri, Jun 2, 2017 at 10:28 PM, <nek5000-users at lists.mcs.anl.gov> wrote:
> >
> > Hi Swarandeep,
> >
> > Set p26 in the .rea file to be 0.1 and make certain IFCHAR is F (a few
> lines below);
> >
> > Make certain your dt is positive (param 12)
> >
> > Paul
> >
> > ________________________________________
> > From: nek5000-users-bounces at lists.mcs.anl.gov [
> nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> > Sent: Friday, June 02, 2017 10:31 AM
> > To: nek5000-users at lists.mcs.anl.gov
> > Subject: Re: [Nek5000-users] Corner elements giving large values
> >
> > Dear Nek Forum, Paul
> >
> > Yes, I have user defined grid such that the locations of the
> > elements are distributed to lie on the chebyshev grid at the top and
> > bottom and near the side walls.
> > Also please tell which param sets the CFL.
> >
> > Thank you
> > Swarandeep
> >
> >
> > On Fri, Jun 2, 2017 at 8:00 PM, <nek5000-users at lists.mcs.anl.gov>
> wrote:
> >>
> >> Dear Swarandeep,
> >>
> >> Did you refine your element size at the top and bottom and near the
> side walls?
> >>
> >> Please set your CFL to 0.05 in order to get the flow started.
> >>
> >> Best,
> >>
> >>
> >> Paul
> >>
> >> ________________________________________
> >> From: nek5000-users-bounces at lists.mcs.anl.gov [
> nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> >> Sent: Friday, June 02, 2017 1:04 AM
> >> To: nek5000-users at lists.mcs.anl.gov
> >> Subject: Re: [Nek5000-users] Corner elements giving large values
> >>
> >> Hi Nek Forum, Paul
> >>
> >> The top and bottom BC are zero heat flux. Please let me n=know
> >> how to control the CFL. It is 0.5 in the logfile. I am having no
> >> particular difficulty except these corner elements at the junction of
> >> inner cylinder and the top/bottom planes. Is there a better way to
> >> treat edge boundary elements. Also is it possible to have different
> >> order of elements at different locations.
> >>
> >> Thank you
> >> Swarandeep
> >>
> >> On Fri, Jun 2, 2017 at 12:50 AM, <nek5000-users at lists.mcs.anl.gov>
> wrote:
> >>>
> >>> Hi Swarandeep,
> >>>
> >>> Sorry - I misunderstood. I guess my question was more about the
> >>> temperature bcs at the bottom and top of the domain?
> >>>
> >>> In general, however, there should be no difficulty. What happens
> >>> when you reduce your dt ?
> >>>
> >>> You need to keep the CFL < ~0.5 in general. CFL is printed in the
> logfile,
> >>>
> >>> grep tep logfile
> >>>
> >>> and you'll see it "C= ....."
> >>>
> >>> Paul
> >>>
> >>>
> >>>
> >>>
> >>> ________________________________________
> >>> From: nek5000-users-bounces at lists.mcs.anl.gov [
> nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> >>> Sent: Thursday, June 01, 2017 1:57 PM
> >>> To: nek5000-users at lists.mcs.anl.gov
> >>> Subject: Re: [Nek5000-users] Corner elements giving large values
> >>>
> >>> Hi NekForum, Paul
> >>>
> >>> I intent to have isothermal conditions at the inner and outer
> >>> cylinders. The differential heating is achieved by imposing a
> >>> temperature difference across the two cylinders. I have used T = 1 and
> >>> 0 values for non-dimensional temperature. I think it should be fine.
> >>> Do you see any problem here.
> >>>
> >>> Thank you
> >>> Swarandeep
> >>>
> >>> On Thu, Jun 1, 2017 at 11:28 PM, <nek5000-users at lists.mcs.anl.gov>
> wrote:
> >>>>
> >>>> Hi Swarandeep,
> >>>>
> >>>> Is 0/1 a realistic BC for T ?
> >>>>
> >>>> Best,
> >>>>
> >>>> Paul
> >>>>
> >>>> ________________________________________
> >>>> From: nek5000-users-bounces at lists.mcs.anl.gov [
> nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> >>>> Sent: Thursday, June 01, 2017 12:53 PM
> >>>> To: nek5000-users at lists.mcs.anl.gov
> >>>> Subject: Re: [Nek5000-users] Corner elements giving large values
> >>>>
> >>>> Hi Nek Forum, Paul
> >>>>
> >>>> I am having temp = 1 and temp = 0 at the inner and outer
> >>>> boundaries. Gravity is pointing in the -ve z-direction along the axis
> >>>> of the
> >>>> annulus. The top and bottom planes have zero heat flux
> conditions.
> >>>> I have Coriolis force added as a body force.
> >>>> The Rayleigh number is around 10000. The resolution is 8, 25,
> >>>> 24 elements in the r, phi and z directions respectively with order 9.
> >>>> My initial condition is very low arbitrary velocity
> >>>> perturbation (~10^(-8)). The time resolution is set to 10^(-5) for
> >>>> param12. The CFL is
> >>>> set to 0.5. Please indicate how to control it.
> >>>>
> >>>> As you have rightly mentioned, I start the simulation with a
> >>>> very low value of the Rayleigh number and gradually increase it. Yet,
> >>>> the corner values only get large. Other regions of the domain are
> >>>> fine.
> >>>>
> >>>> Thank you
> >>>> Swarandeep
> >>>>
> >>>> On Thu, Jun 1, 2017 at 7:38 PM, <nek5000-users at lists.mcs.anl.gov>
> wrote:
> >>>>>
> >>>>> Hi Swarandeep,
> >>>>>
> >>>>> How large is your Rayleigh number and what is your resolution?
> >>>>> What are your thermal bcs? What are your ICs?
> >>>>>
> >>>>> There should be no particular issue with your configuration - but
> you do need to
> >>>>> control spatial and temporal resolution.
> >>>>>
> >>>>>
> >>>>> For RB, you often have to start at low Ra and/or small dt because
> the nonlinear
> >>>>> response can often drive the velocities to be quite high very
> rapidly before the
> >>>>> CFL constraint kicks in. RB flows are one of the rare instances
> where I use
> >>>>> variable time step size (param 12 > 0), but even then you have to
> keep the target
> >>>>> CFL quite small until the flow is established.
> >>>>>
> >>>>> hth,
> >>>>>
> >>>>> Paul
> >>>>>
> >>>>> ________________________________________
> >>>>> From: nek5000-users-bounces at lists.mcs.anl.gov [
> nek5000-users-bounces at lists.mcs.anl.gov] on behalf of
> nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov]
> >>>>> Sent: Thursday, June 01, 2017 7:27 AM
> >>>>> To: nek5000-users at lists.mcs.anl.gov
> >>>>> Subject: [Nek5000-users] Corner elements giving large values
> >>>>>
> >>>>> Dear Nek forum,
> >>>>>
> >>>>> I am simulating Rayleigh Benard flow in a 3D finite
> cylindrical annulus.
> >>>>> I am getting spurious large values of velocity at the corner
> regions
> >>>>> of the annulus i.e. the edges where the inner cylinder joins
> the
> >>>>> top and bottom
> >>>>> planes. The boundary condition is no-slip and no penetration
> for velocity
> >>>>> at these edges. Can someone point out a plausible reason.
> >>>>>
> >>>>> Thank you
> >>>>> Swarandeep
> >>>>> _______________________________________________
> >>>>> Nek5000-users mailing list
> >>>>> Nek5000-users at lists.mcs.anl.gov
> >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >>>>> _______________________________________________
> >>>>> Nek5000-users mailing list
> >>>>> Nek5000-users at lists.mcs.anl.gov
> >>>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >>>> _______________________________________________
> >>>> Nek5000-users mailing list
> >>>> Nek5000-users at lists.mcs.anl.gov
> >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >>>> _______________________________________________
> >>>> Nek5000-users mailing list
> >>>> Nek5000-users at lists.mcs.anl.gov
> >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >>> _______________________________________________
> >>> Nek5000-users mailing list
> >>> Nek5000-users at lists.mcs.anl.gov
> >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >>> _______________________________________________
> >>> Nek5000-users mailing list
> >>> Nek5000-users at lists.mcs.anl.gov
> >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >> _______________________________________________
> >> Nek5000-users mailing list
> >> Nek5000-users at lists.mcs.anl.gov
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> >> _______________________________________________
> >> Nek5000-users mailing list
> >> Nek5000-users at lists.mcs.anl.gov
> >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> > _______________________________________________
> > Nek5000-users mailing list
> > Nek5000-users at lists.mcs.anl.gov
> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> > _______________________________________________
> > Nek5000-users mailing list
> > Nek5000-users at lists.mcs.anl.gov
> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>
>
> ------------------------------
>
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>
>
> End of Nek5000-users Digest, Vol 100, Issue 4
> *********************************************
>
--
Phil Sakievich
Post Doctoral Research Associate - Mechanical and Aerospace Engineering
Arizona State University - Ira A. Fulton School for Engineering of Matter
Transport and Energy
Tempe, Arizona
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