[Nek5000-users] Full restart with a different time step
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Wed Nov 18 15:05:10 CST 2015
Hi Philipp,
That makes sense. Thank you very much!!
Best regards,
Tony
________________________________________
From: nek5000-users-bounces at lists.mcs.anl.gov <nek5000-users-bounces at lists.mcs.anl.gov> on behalf of nek5000-users-request at lists.mcs.anl.gov <nek5000-users-request at lists.mcs.anl.gov>
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2. Re: Full restart with a different time step
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3. Re: Full restart with a different time step
(nek5000-users at lists.mcs.anl.gov)
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Message: 1
Date: Tue, 17 Nov 2015 21:20:58 +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: [Nek5000-users] New Webpage and Documentation
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<mailman.10850.1447795271.24727.nek5000-users at lists.mcs.anl.gov>
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Hi nek5000 users,
As you may have noticed we have a new webpage and a documentation update where we gathered the information on the previous pages. As last week the documentation is accessible in both pdf and browsable form.
Some info may have been missed either by accident or since it seemed redundant. Therefore we welcome your requests and observations in order to improve the current status.
The old page is now hosted statically on the new page but as Aleks pointed out the search button doesn't work anymore. The reason for that is that our systems people couldn't mirror the old page and could barely give us the old page statically.
I realize this may be highly inconvenient to some but the best solution we can see such that we do not short circuit the progress:
1. If there is anything you are looking for and is not available please let us know and we shall update it
2. We try to adapt the search button on the new page to allow users to navigate as they were used to, also the browsable edition of the documentation should be of help
3. The old page source together with the database can be provided to whoever sees any use to it.
Also you may have noticed we link to most of the centers that have a high number of users, and also promote work performed with Nek5000. If you would like to be added either by lining to your homepage or just by citing your work in the Gallery please let us know.
Best,
Oana
------------------------------
Message: 2
Date: Tue, 17 Nov 2015 23:24:07 +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] Full restart with a different time step
Message-ID:
<mailman.10853.1447802672.24727.nek5000-users at lists.mcs.anl.gov>
Content-Type: text/plain; charset="iso-8859-1"
Hi Adam,
Thank you very much for your comments.
I actually thought about loading the 4 restart files in nek and do interpolation between two time steps. But I agree with you that I would introduce some error to the flow fields for restarting. In my case, I want to keep the data of the old simulation and continue from the current checkpoints, so I don't want to ruin the accuracy of the flow fields.
Like you said, changing \dt after restarting from the current flow fields maight be the simplest solution. However, I have one concern about this. When we use 3rd order accuracy in time, the solver would use the history information from the last few time steps and that's why we need to restart the simulation with 4 continuous flow fields. If I change the time step size in the middle of the simulation, how much would it affect the solving process? What do you think?
Best regards,
Tony
________________________________________
From: nek5000-users-bounces at lists.mcs.anl.gov <nek5000-users-bounces at lists.mcs.anl.gov> on behalf of nek5000-users-request at lists.mcs.anl.gov <nek5000-users-request at lists.mcs.anl.gov>
Sent: 17 November 2015 18:00
To: nek5000-users at lists.mcs.anl.gov
Subject: Nek5000-users Digest, Vol 81, Issue 15
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nek5000-users at lists.mcs.anl.gov
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When replying, please edit your Subject line so it is more specific
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Today's Topics:
1. Full restart with a different time step
(nek5000-users at lists.mcs.anl.gov)
2. Re: Full restart with a different time step
(nek5000-users at lists.mcs.anl.gov)
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Message: 1
Date: Mon, 16 Nov 2015 19:19:23 +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: [Nek5000-users] Full restart with a different time step
Message-ID:
<mailman.10777.1447701586.24727.nek5000-users at lists.mcs.anl.gov>
Content-Type: text/plain; charset="iso-8859-1"
Dear Neks,
I use full_restart option for my current simulations. One simulation crashed after restarting for some time with the Courant number going crazy. I suppose I will need to reduce the time step size.
Basically, I want to continue my simulation using full_restart option but with a smaller time step size. Somehow I remember I saw one post saying one shouldn't change the time step size when using the full_restart option. I'm just thinking of a way to work around the problem.
So does anyone have ideas on how I can interpolate the flow fields between two time steps or any other ways to fully restart a simulation with a different time step size?
Thank you very much in advance for any suggestions or comments.
Best regards,
Tony
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Message: 2
Date: Tue, 17 Nov 2015 09:27:47 +0100
From: nek5000-users at lists.mcs.anl.gov
To: nek5000-users at lists.mcs.anl.gov
Subject: Re: [Nek5000-users] Full restart with a different time step
Message-ID:
<mailman.10819.1447748894.24727.nek5000-users at lists.mcs.anl.gov>
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Hi
For full_restart you should have four velocity fields and you could use
nek5000 as a preprocessing tool. You can simply load all 4 fields in
userchk, perform some kind of interpolation in time and finally write
down new restart files. The question is how to deal with pressure. One
solution would be simply interpolate pressure saved in the files. The
other would be to run modified version of pressure solver with uzawa
turned on to get pressure corresponding to interpolated velocity field.
We've played with uzawa for pn-pn-2 and we use our version of
full_restart, but we haven't done this kind of modified restart, so I
don't know what is better. On the other hand you could restart nek with
your current checkpoints and dt corresponding to the old simulation, and
later (after 4th step) gradually decrease time step. I guess this would
be the simplest and probably best solution. If time resolution in old
simulation was insufficient, your restart files do not give correct
evolution of the field and interpolation in time would not remove it.
Anyhow you introduce some initial error to simulation. In this case I
probably would simply play with dt keeping it constant during first 4
steps and gradually decreasing later.
Regards
Adam
On 2015-11-16 20:19, nek5000-users at lists.mcs.anl.gov wrote:
>
> Dear Neks,
>
>
> I use full_restart option for my current simulations. One simulation
> crashed after restarting for some time with the Courant number going
> crazy. I suppose I will need to reduce the time step size.
>
>
> Basically, I want to continue my simulation using full_restart option
> but with a smaller time step size. Somehow I remember I saw one post
> saying one shouldn't change the time step size when using the
> full_restart option. I'm just thinking of a way to work around the
> problem.
>
>
> So does anyone have ideas on how I can interpolate the flow fields
> between two time steps or any other ways to fully restart a simulation
> with a different time step size?
>
>
> Thank you very much in advance for any suggestions or comments.
>
>
> Best regards,
>
> Tony
>
>
>
> _______________________________________________
> Nek5000-users mailing list
> Nek5000-users at lists.mcs.anl.gov
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
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------------------------------
Message: 3
Date: Wed, 18 Nov 2015 00:29:40 +0100
From: nek5000-users at lists.mcs.anl.gov
To: nek5000-users at lists.mcs.anl.gov
Subject: Re: [Nek5000-users] Full restart with a different time step
Message-ID:
<mailman.10854.1447803012.24727.nek5000-users at lists.mcs.anl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed
Hi,
when you change the time step during a simulation, then there is no
problem; the EXT/BDF coefficients are adjusted accordingly, so you will
keep the accuracy/order even with varying time step.
The reason why you cannot do that during restart (i.e. during the first
4 steps) is because the stored fields are at a given time (at which they
were stored, yielding a certain dt), so you cannot assign them a
different time or dt. The solution in memory is then overwritten with
the data loaded from disk, until all lag arrays are correctly filled.
But as soon as the simulation is not reading from the disk any longer,
then you can go ahead and change the time step.
Best,
PHilipp
On 2015-11-18 00:24, nek5000-users at lists.mcs.anl.gov wrote:
> Hi Adam,
>
> Thank you very much for your comments.
>
> I actually thought about loading the 4 restart files in nek and do
> interpolation between two time steps. But I agree with you that I
> would introduce some error to the flow fields for restarting. In my
> case, I want to keep the data of the old simulation and continue from
> the current checkpoints, so I don't want to ruin the accuracy of the
> flow fields.
>
> Like you said, changing \dt after restarting from the current flow
> fields maight be the simplest solution. However, I have one concern
> about this. When we use 3rd order accuracy in time, the solver would
> use the history information from the last few time steps and that's
> why we need to restart the simulation with 4 continuous flow fields.
> If I change the time step size in the middle of the simulation, how
> much would it affect the solving process? What do you think?
>
> Best regards, Tony
>
> ________________________________________ From:
> nek5000-users-bounces at lists.mcs.anl.gov
> <nek5000-users-bounces at lists.mcs.anl.gov> on behalf of
> nek5000-users-request at lists.mcs.anl.gov
> <nek5000-users-request at lists.mcs.anl.gov> Sent: 17 November 2015
> 18:00 To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users
> Digest, Vol 81, Issue 15
>
> Send Nek5000-users mailing list submissions to
> nek5000-users at lists.mcs.anl.gov
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users or, via
> email, send a message with subject or body 'help' to
> nek5000-users-request at lists.mcs.anl.gov
>
> You can reach the person managing the list at
> nek5000-users-owner at lists.mcs.anl.gov
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Nek5000-users digest..."
>
>
> Today's Topics:
>
> 1. Full restart with a different time step
> (nek5000-users at lists.mcs.anl.gov) 2. Re: Full restart with a
> different time step (nek5000-users at lists.mcs.anl.gov)
>
>
> ----------------------------------------------------------------------
>
> Message: 1 Date: Mon, 16 Nov 2015 19:19:23 +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: [Nek5000-users] Full restart with a different time step
> Message-ID:
> <mailman.10777.1447701586.24727.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Neks,
>
>
> I use full_restart option for my current simulations. One simulation
> crashed after restarting for some time with the Courant number going
> crazy. I suppose I will need to reduce the time step size.
>
>
> Basically, I want to continue my simulation using full_restart option
> but with a smaller time step size. Somehow I remember I saw one post
> saying one shouldn't change the time step size when using the
> full_restart option. I'm just thinking of a way to work around the
> problem.
>
>
> So does anyone have ideas on how I can interpolate the flow fields
> between two time steps or any other ways to fully restart a
> simulation with a different time step size?
>
>
> Thank you very much in advance for any suggestions or comments.
>
>
> Best regards,
>
> Tony -------------- next part -------------- An HTML attachment was
> scrubbed... URL:
> <http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20151116/ff31eb4f/attachment-0001.html>
>
> ------------------------------
>
> Message: 2 Date: Tue, 17 Nov 2015 09:27:47 +0100 From:
> nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov
> Subject: Re: [Nek5000-users] Full restart with a different time step
> Message-ID:
> <mailman.10819.1447748894.24727.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
>
> Hi
>
> For full_restart you should have four velocity fields and you could
> use nek5000 as a preprocessing tool. You can simply load all 4 fields
> in userchk, perform some kind of interpolation in time and finally
> write down new restart files. The question is how to deal with
> pressure. One solution would be simply interpolate pressure saved in
> the files. The other would be to run modified version of pressure
> solver with uzawa turned on to get pressure corresponding to
> interpolated velocity field. We've played with uzawa for pn-pn-2 and
> we use our version of full_restart, but we haven't done this kind of
> modified restart, so I don't know what is better. On the other hand
> you could restart nek with your current checkpoints and dt
> corresponding to the old simulation, and later (after 4th step)
> gradually decrease time step. I guess this would be the simplest and
> probably best solution. If time resolution in old simulation was
> insufficient, your restart files do not give correct evolution of the
> field and interpolation in time would not remove it. Anyhow you
> introduce some initial error to simulation. In this case I probably
> would simply play with dt keeping it constant during first 4 steps
> and gradually decreasing later. Regards Adam
>
> On 2015-11-16 20:19, nek5000-users at lists.mcs.anl.gov wrote:
>>
>> Dear Neks,
>>
>>
>> I use full_restart option for my current simulations. One
>> simulation crashed after restarting for some time with the Courant
>> number going crazy. I suppose I will need to reduce the time step
>> size.
>>
>>
>> Basically, I want to continue my simulation using full_restart
>> option but with a smaller time step size. Somehow I remember I saw
>> one post saying one shouldn't change the time step size when using
>> the full_restart option. I'm just thinking of a way to work around
>> the problem.
>>
>>
>> So does anyone have ideas on how I can interpolate the flow fields
>> between two time steps or any other ways to fully restart a
>> simulation with a different time step size?
>>
>>
>> Thank you very much in advance for any suggestions or comments.
>>
>>
>> Best regards,
>>
>> Tony
>>
>>
>>
>> _______________________________________________ Nek5000-users
>> mailing list Nek5000-users at lists.mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>
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