[Nek5000-users] Courant for passive scalar
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Tue Jun 20 04:04:17 CDT 2017
Hi Paul and Stephan
how does the blow up manifests itself : I didnt dig a lot into the blow up. the flow converges nicely, and once its at steady state I inject the scalar at the inlet through the boundary condition (localized source). it develops a nice turbulent plume, that keeps going for a long time and then suddenly it produces lots of NaN.
this picture is consistent with the idea that sometimes passive scalars develop fronts, where abrupt changes occur across a small scale (bachelor scale; for me ~ kolmogorov scale cause diffusivity = viscosity). the classic Courant condition for advection will miss the presence of fronts, cause these are completely uncorrelated to the velocity field. (see eg PRL 84:2385, 2000).
i am thinking of including a further check to account for the presence of fronts. but i am sure others have faced similar problems, and so i wanted to check whether someone has already implemented something.
in the meantime, i’m using courant 0.25 and see if this is enough, although its clearly suboptimal.
cheers
Agnese
ps. Paul : filtering was already on.
>
> Have you tried reducing dt by, say, 2x ?
>
> That should be enough...
>
> Also, you can try filtering by setting p103=0.05
> in the .rea file.
>
> The velocity and passive scalars have the same CFL restriction, but velocity is regularized by pressure so it tends to be more stable than high Peclet passive scalar simulations.
>
> hth,
>
> Paul
>
> From: nek5000-users-bounces at lists.mcs.anl.gov <mailto:nek5000-users-bounces at lists.mcs.anl.gov> <nek5000-users-bounces at lists.mcs.anl.gov <mailto:nek5000-users-bounces at lists.mcs.anl.gov>> on behalf of nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov> <nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>>
> Sent: Thursday, June 15, 2017 3:38:03 AM
> To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>
> Subject: Re: [Nek5000-users] Courant number for passive scalar
>
> How does the blow-up manifest itself?
>
> Try to run it with 2nd order in time and keep the CFL<0.5. This should be stable assuming there is no source term introducing an additional time step constraint.
>
> Does your mesh resolve these steep gradients?
>
> Cheers,
> Stefan
>
> -----Original message-----
> > From:nek5000-users at lists.mcs.anl.gov <mailto:users at lists.mcs.anl.gov> <nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>>
> > Sent: Thursday 15th June 2017 9:29
> > To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>
> > Subject: Re: [Nek5000-users] Courant number for passive scalar
> >
> > I havent seen the equivalent of a Courant criterion for passive scalars.
> > what I meant is the scalar is intermittent, so one should have a way to detect the regions where gradients are extremely large (fronts) and make sure to decrease the timestep there.
> > <br class="" />fronts do not correspond to regions where velocities are especially large, so the classic courant criterion will miss them.
> > <br class="" />does this make sense ?
> > any suggestions ?
> > <br class="" />agnese
> > <br class="" /><br class="" /><br class="" />On Jun 14, 2017, at 2:39 PM, nek5000-users-request at lists.mcs.anl.gov <mailto:nek5000-users-request at lists.mcs.anl.gov> <mailto:nek5000-users-request at lists.mcs.anl.gov <mailto:nek5000-users-request at lists.mcs.anl.gov>> wrote:
> > <br class="Apple-interchange-newline" />Send Nek5000-users mailing list submissions to<br class="" /> 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>><br class="" /><br class="" />To subscribe or unsubscribe via the World Wide Web, visit<br class="" /> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users<br <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users%3Cbr> class="" />or, via email, send a message with subject or body 'help' to<br class="" /> nek5000-users-request at lists.mcs.anl.gov <mailto:nek5000-users-request at lists.mcs.anl.gov><br class="" /><br class="" />You can reach the person managing the list at<br class="" /> nek5000-users-owner at lists.mcs.anl.gov <mailto:nek5000-users-owner at lists.mcs.anl.gov><br class="" /><br class="" />When replying, please edit your Subject line so it is more specific<br class="" />than "Re: Contents of Nek5000-users digest..."<br class="" />Today's Topics:<br class="" /><br class="" /> 1. Re: Courant for passive scalar ? (nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>)<br class="" /> 2. Re: Courant for passiv
> e scalar
> ? (nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>)<br class="" /><br class="" />From: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />Subject: Re: [Nek5000-users] Courant for passive scalar ?<br class="" />Date: June 14, 2017 at 10:44:13 AM GMT+2<br class="" />To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />Reply-To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" /><br class="" /><br class="" />Thanks Jan !
> > <br class="" />so it is confirmed that the tilmestep is based exclusively on the velocity field ?
> > how do people make sure that the passive scalars do not blow up ?
> > anybody ?
> > <br class="" />any help is greatly appreciated !!
> > agnese
> > <br class="" /><br class="" />Agnese Seminara
> > --------------------------------
> > CNRS
> > Institut de Physique de Nice
> > Parc Valrose
> > avenue J Vallot
> > 06108 Nice, France
> > +33 (0) 492 076 775
> > http://sites.unice.fr/site/aseminara/ <http://sites.unice.fr/site/aseminara/> <http://sites.unice.fr/site/aseminara/ <http://sites.unice.fr/site/aseminara/>><br class="" />On Jun 13, 2017, at 7:00 PM, nek5000-users-request at lists.mcs.anl.gov <mailto:nek5000-users-request at lists.mcs.anl.gov> <mailto:nek5000-users-request at lists.mcs.anl.gov <mailto:nek5000-users-request at lists.mcs.anl.gov>> wrote:
> > <br class="Apple-interchange-newline" />Send Nek5000-users mailing list submissions to<br class="" /> 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>><br class="" /><br class="" />To subscribe or unsubscribe via the World Wide Web, visit<br class="" /> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users<br <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users%3Cbr> class="" />or, via email, send a message with subject or body 'help' to<br class="" /> nek5000-users-request at lists.mcs.anl.gov <mailto:nek5000-users-request at lists.mcs.anl.gov><br class="" /><br class="" />You can reach the person managing the list at<br class="" /> nek5000-users-owner at lists.mcs.anl.gov <mailto:nek5000-users-owner at lists.mcs.anl.gov><br class="" /><br class="" />When replying, please edit your Subject line so it is more specific<br class="" />than "Re: Contents of Nek5000-users digest..."<br class="" />Today's Topics:<br class="" /><br class="" /> 1. Re: Courant for passive scalar ? (nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>)<br class="" /> 2. prenek (nek5000-users@
> lists.mc
> s.anl.gov <http://s.anl.gov/>)<br class="" /><br class="" />From: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />Subject: Re: [Nek5000-users] Courant for passive scalar ?<br class="" />Date: June 12, 2017 at 8:00:26 PM GMT+2<br class="" />To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />Reply-To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" /><br class="" /><br class="" />Hi,
> > I haven' t tried this myself, but I guess you could write a subroutine that calculates the maximum timestep from the scalar field and sets dt accordingly. Then simple call the routine from userchk.
> > <br class="" />Best,
> > Jan
> > <br class="" />Am 12.06.2017 um 18:15 schrieb 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>>:<br class="" /><br class="" />Dear Neks
> > <br class="" />I am running a simulation of a channel, with a passive scalar. Using diffusivity=viscosity, the velocity field converges nicely, whereas the passive scalar blows up at some random point down the simulation. Reynolds number is 10 000 so its in the turbulent regime.
> > <br class="" />I suspect this is due to the fact that the passive scalar is intermittent, so sometimes large fluctuations will occur, totally uncorrelated to velocity fluctuations. to avoid the code to blow up, one would need to setup the timestep based on a courant criterion for the scalar, and not for the velocity.
> > <br class="" />has this already been implemented ?
> > or how do people avoid this ?
> > <br class="" />any suggestion is more than welcome.
> > thanks
> > Agnese
> > <br class="" /><br class="" /><br class="" />Agnese Seminara
> > --------------------------------
> > CNRS
> > Institut de Physique de Nice
> > Parc Valrose
> > avenue J Vallot
> > 06108 Nice, France
> > +33 (0) 492 076 775
> > http://sites.unice.fr/site/aseminara/ <http://sites.unice.fr/site/aseminara/> <http://sites.unice.fr/site/aseminara/ <http://sites.unice.fr/site/aseminara/>><br class="" />_______________________________________________<br class="" />Nek5000-users mailing list<br class="" />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>><br class="" />https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>><br class="" /><br class="" /><br class="" /><br class="" />From: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />Subject: [Nek5000-users] prenek<br class="" />Date: June 13, 2017 at 12:12:49 PM GMT+2<br class="" />To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />Reply-To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" /><br class="" /><br class="" />Hi nek,
> > <br class="" />I have a 2D mesh. When I used global refine function, the errors occurred. do you know why?
> > <br class="" /> OCT/Multi-SPLIT
> > quad or multi-split? (q/m)
> > Number of elements after OctSplit operation: 7680
> > Are you sure you want to split (y/n)?
> > inside gencen 7680 F 4
> > done gencen 7680
> > start locglob_lexico: 4 7680 30720 2.00000009E-03
> > locglob: 1 1 30720
> > locglob: 2 3664 30720
> > locglob: 1 7761 30720
> > locglob: 2 7761 30720
> > Performing unique_vertex2 self_chk 30720
> > done locglob_lexico: 7761 7761 30720 4
> > Performing makecell self_chk 30720
> > <br class="" /> RMIN: 0.153545E-03
> > EPS,RMIN: 0.500000E-01 0.153545E-03
> > I/O Error: No String Terminator sent to PRS
> > zeroing y: 1 82 -0.75715434E-10
> > I/O Error: No String Terminator sent to PRS
> > zeroing y: 4 82 -0.14778734E-11
> > I/O Error: No String Terminator sent to PRS
> > zeroing y: 4 83 0.72759583E-10
> > I/O Error: No String Terminator sent to PRS
> > zeroing y: 4 123 0.15279482E-09
> > ......
> > <br class="" />Does it mean my mesh is still not right?
> > <br class="" /><br class="" />_______________________________________________<br class="" />Nek5000-users mailing list<br class="" />Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov><br class="" />https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users><br class="" /><br class="" /><br class="" /><br class="" /><br class="" />From: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />Subject: Re: [Nek5000-users] Courant for passive scalar ?<br class="" />Date: June 14, 2017 at 2:37:35 PM GMT+2<br class="" />To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov> <nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>><br class="" />Reply-To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" /><br class="" /><br class="" />How do you define a courant number for a scalar?<br class="" /><br class="" />-----Original message-----<br class="" />From:nek5000-users at lists.mcs.anl.gov <mailto:users at lists.mcs.anl.gov> <nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>><br class="" />Sent: Wednesday 14th June 2017 10:43<br class="" />To: nek5000-users at lists.mcs <mailto:nek5000-users at lists.mcs>
> .anl.gov <http://anl.gov/>
> <br class="" />Subject: Re: [Nek5000-users] Courant for passive scalar ?<br class="" /><br class="" />Thanks Jan !<br class="" /><br class="" />so it is confirmed that the tilmestep is based exclusively on the velocity field ?<br class="" />how do people make sure that the passive scalars do not blow up ? <br class="" />anybody ?<br class="" /><br class="" />any help is greatly appreciated !!<br class="" />agnese<br class="" /><br class="" /><br class="" />Agnese Seminara<br class="" />--------------------------------<br class="" />CNRS<br class="" />Institut de Physique de Nice<br class="" />Parc Valrose <br class="" />avenue J Vallot<br class="" />06108 Nice, France<br class="" />+33 (0) 492 076 775<br class="" />http://sites.unice.fr/site/aseminara/ <http://sites.unice.fr/site/aseminara/><http://sites.unice.fr/site/aseminara/ <http://sites.unice.fr/site/aseminara/>><br class="" />On Jun 13, 2017, at 7:00 PM, nek5000-users-request at lists.mcs.anl.gov <mailto:nek5000-users-request at lists.mcs.anl.gov> < <applewebdata://6F31B652-02FC-43B9-8559-2E0A96DF5A74>mailto:nek5000-users-request at lists.mcs.a <mailto:nek5000-users-request at lists.mcs.a>
> nl.gov <http://nl.gov/>>
> wrote:<br class="" /><br class="Apple-interchange-newline" />Send Nek5000-users mailing list submissions to<br class="" /> 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>><br class="" /><br class="" />To subscribe or unsubscribe via the World Wide Web, visit<br class="" /> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users<br <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users%3Cbr> class="" />or, via email, send a message with subject or body 'help' to<br class="" /> nek5000-users-request at lists.mcs.anl.gov <mailto:nek5000-users-request at lists.mcs.anl.gov><br class="" /><br class="" />You can reach the person managing the list at<br class="" /> nek5000-users-owner at lists.mcs.anl.gov <mailto:nek5000-users-owner at lists.mcs.anl.gov><br class="" /><br class="" />When replying, please edit your Subject line so it is more specific<br class="" />than "Re: Contents of Nek5000-users digest..."<br class="" />Today's Topics:<br class="" /><br class="" /> 1. Re: Courant for passive scalar ? (nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov>)<br class="" /> 2.
> prenek (
> nek5000-users@<br class="" /> lists.mc<br class="" /> s.anl.gov <http://s.anl.gov/>)<br class="" /><br class="" />From: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />Subject: Re: [Nek5000-users] Courant for passive scalar ?<br class="" />Date: June 12, 2017 at 8:00:26 PM GMT+2<br class="" />To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />Reply-To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" /><br class="" /><br class="" />Hi,<br class="" />I haven' t tried this myself, but I guess you could write a subroutine that calculates the maximum timestep from the scalar field and sets dt accordingly. Then simple call the routine from userchk.<br class="" /><br class="" />Best,<br class="" />Jan<br class="" /><br class="" />Am 12.06.2017 um 18:15 schrieb 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>>:<br class="" /><br class="" />Dear Neks<br class="" /><br class="" />I am running a simulation of a channel, with a passive scalar. Usi
> ng diffu
> sivity=viscosity, the velocity field converges nicely, whereas the passive scalar blows up at some random point down the simulation. Reynolds number is 10 000 so its in the turbulent regime.<br class="" /><br class="" />I suspect this is due to the fact that the passive scalar is intermittent, so sometimes large fluctuations will occur, totally uncorrelated to velocity fluctuations. to avoid the code to blow up, one would need to setup the timestep based on a courant criterion for the scalar, and not for the velocity. <br class="" /><br class="" />has this already been implemented ?<br class="" />or how do people avoid this ?<br class="" /><br class="" />any suggestion is more than welcome.<br class="" />thanks<br class="" />Agnese<br class="" /><br class="" /><br class="" /><br class="" />Agnese Seminara<br class="" />--------------------------------<br class="" />CNRS<br class="" />Institut de Physique de Nice<br class="" />Parc
> Valrose
> <br class="" />avenue J Vallot<br class="" />06108 Nice, France<br class="" />+33 (0) 492 076 775<br class="" />http://sites.unice.fr/site/aseminara/ <http://sites.unice.fr/site/aseminara/> <http://sites.unice.fr/site/aseminara/ <http://sites.unice.fr/site/aseminara/>><br class="" />_______________________________________________<br class="" />Nek5000-users mailing list<br class="" />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>><br class="" />https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users> <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users>><br class="" /><br class="" /><br class="" /><br class="" />From: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />Subject: [Nek5000-users] prenek<br class="" />Date: June 13, 2017 at 12:12:49 PM GMT+2<br class="" />To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" />Reply-To: nek5000-users at lists.mcs.anl.gov <mailto:nek5000-users at lists.mcs.anl.gov><br class="" /><br class="" /><br class="" />Hi nek,<br class="" /><br class="" />I have a 2D mesh. When I used global refine fu
> nction,
> the errors occurred. do you know why?<br class="" /><br class="" /> OCT/Multi-SPLIT<br class="" />quad or multi-split? (q/m)<br class="" />Number of elements after OctSplit operation: 7680<br class="" />Are you sure you want to split (y/n)?<br class="" /> inside gencen 7680 F 4<br class="" /> done gencen 7680<br class="" /> start locglob_lexico: 4 7680 30720 2.00000009E-03<br class="" /> locglob: 1 1 30720<br class="" /> locglob: 2 3664 30720<br class="" /> locglob: 1 7761 � A0 30720
> <br class="" /> locglob: 2 7761 30720<br class="" /> Performing unique_vertex2 self_chk 30720<br class="" /> done locglob_lexico: 7761 7761 30720 4<br class="" /> Performing makecell self_chk 30720<br class="" /><br class="" /> RMIN: 0.153545E-03<br class="" /> EPS,RMIN: 0.500000E-01 0.153545E-03<br class="" /> I/O Error: No String Terminator sent to PRS<br class="" /> zeroing y: 1 82 -0.75715434E-10<br class="" /> I/O Error: No String Terminator sent to PRS<br class="" /> zeroing y: 4 82 -0.14778734E-11<br class="" /> I/O Error: No String Terminator sent to PRS<br class="" /> zeroing y: 4 83 0.72759583E-10<br class=""
> />�=
> 0I/O Error: No String Terminator sent to PRS<br class="" /> zeroing y: 4 123 0.15279482E-09<br class="" />......<br class="" /><br class="" />Does it mean my mesh is still not right?<br class="" /><br class="" /><br class="" />_______________________________________________<br class="" />Nek5000-users mailing list<br class="" />Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov><br class="" />https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users><br class="" /><br class="" />_______________________________________________<br class="" />Nek5000-users mailing list<br class="" />Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov><br class="" />https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users><br class="" /><br class="" /><br class="" /><br class="" />_______________________________________________<br class="" />Nek5000-users mailing list<br class="" />Nek5000-users at lists.mcs.anl.gov <mailto:Nek5000-users at lists.mcs.anl.gov><br class="" />https://lists.mcs.anl.gov/mailman/listinfo <https://lists.mcs.anl.gov/mailman/listinfo>
> /nek5000
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