From nek5000-users at lists.mcs.anl.gov Tue Oct 3 12:12:59 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 3 Oct 2017 19:12:59 +0200 Subject: [Nek5000-users] Strong divergence and Laplacian operator Message-ID: Hi all, I need to compute some operators in the strong form directly for a project, i.e. without the mass matrix included in the operator. For the convection and gradient operators, I am using the functions convop and gradm1 respectively. However, I would also need to compute strong divergence and Laplacian and I did not find the corresponding functions (opdiv and axhelm are computing the weak form if I understand correctly). Do such functions exist? Or what modifications should I bring to the existing routines to change them to strong form? Best regards, Nicolas -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 3 16:25:49 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 3 Oct 2017 21:25:49 +0000 Subject: [Nek5000-users] Strong divergence and Laplacian operator In-Reply-To: References: Message-ID: Hi Nicolas, You can use gradm1 to get your strong divergence. Laplacian is a bit trickier since the 2nd derivative really is well-defined. Some people compute the gradient and then apply dsavg() to each component prior to taking the divergence of that field. Right now there are no tools to do exactly the thing you want, so using gradm1() is as good as any option. Note that gradm1() is as efficient (or more so) than some of the other tools to compute gradient in Nek. In order to get (say) du/dx, you have to compute du/dr , du/ds , du/dt, and then get du/dx from the chain rule. du/dy, du/dz also come from the chain rule, almost for free, even though you don't need them. So you can simplify everything just through repeated use of gradm1. Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 3, 2017 12:12:59 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Strong divergence and Laplacian operator Hi all, I need to compute some operators in the strong form directly for a project, i.e. without the mass matrix included in the operator. For the convection and gradient operators, I am using the functions convop and gradm1 respectively. However, I would also need to compute strong divergence and Laplacian and I did not find the corresponding functions (opdiv and axhelm are computing the weak form if I understand correctly). Do such functions exist? Or what modifications should I bring to the existing routines to change them to strong form? Best regards, Nicolas -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 4 02:19:58 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Oct 2017 09:19:58 +0200 Subject: [Nek5000-users] Strong divergence and Laplacian operator In-Reply-To: References: Message-ID: Dear Paul, Thank you for the answer. I will use gradm1 then. Best, Nicolas On Tue, Oct 3, 2017 at 11:25 PM, wrote: > > Hi Nicolas, > > > You can use gradm1 to get your strong divergence. > > > Laplacian is a bit trickier since the 2nd derivative really is > well-defined. > > Some people compute the gradient and then apply dsavg() to each component > > prior to taking the divergence of that field. > > > Right now there are no tools to do exactly the thing you want, so using > gradm1() > > is as good as any option. > > > Note that gradm1() is as efficient (or more so) than some of the other > tools > > to compute gradient in Nek. In order to get (say) du/dx, you have to > compute > > du/dr , du/ds , du/dt, and then get du/dx from the chain rule. du/dy, > du/dz > > also come from the chain rule, almost for free, even though you don't need > them. > > So you can simplify everything just through repeated use of gradm1. > > > Best, Paul > > > ------------------------------ > *From:* Nek5000-users on behalf > of nek5000-users at lists.mcs.anl.gov > *Sent:* Tuesday, October 3, 2017 12:12:59 PM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* [Nek5000-users] Strong divergence and Laplacian operator > > Hi all, > > I need to compute some operators in the strong form directly for a > project, i.e. without the mass matrix included in the operator. > > For the convection and gradient operators, I am using the functions convop > and gradm1 respectively. However, I would also need to compute strong > divergence and Laplacian and I did not find the corresponding functions > (opdiv and axhelm are computing the weak form if I understand correctly). > Do such functions exist? Or what modifications should I bring to the > existing routines to change them to strong form? > > Best regards, > Nicolas > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 4 04:42:43 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Oct 2017 09:42:43 +0000 Subject: [Nek5000-users] Output file temperature looks corrupted Message-ID: Hi all, after using visnek to create a .nek5000 file and viewing the data in ParaView I found that the temperature data for the bottom half of my domain looks corrupted. As you can see in the image the top half of the domain is correct. This corrupted data only effects the temperature, the velocity and pressure are ok for the whole domain. I only started seeing this issue after switching from 7th order to 11th order. Thanks for any help. Andrew -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: nek_temperature.PNG Type: image/png Size: 59578 bytes Desc: nek_temperature.PNG URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 4 04:46:00 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Oct 2017 11:46:00 +0200 Subject: [Nek5000-users] Output file temperature looks corrupted In-Reply-To: References: Message-ID: What version of Nek5000 are you using? Do you use .fXXXXX field files? Single or double precision? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 4th October 2017 11:43 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Output file temperature looks corrupted > > Hi all, after using visnek to create a .nek5000 file and viewing the data in ParaView I found that the temperature data for the bottom half of my domain looks corrupted. As you can see in the image the top half of the domain is correct. > This corrupted data only effects the temperature, the velocity and pressure are ok for the whole domain. I only started seeing this issue after switching from 7th order to 11th order. > Thanks for any help. > Andrew > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed Oct 4 05:03:10 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Oct 2017 10:03:10 +0000 Subject: [Nek5000-users] Output file temperature looks corrupted In-Reply-To: References: Message-ID: The release file gives Release 17.?.? I am using .fXXXXX files. Parameter 63 is set to zero, which I think should be giving single precision? Thank you -----Original Message----- From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov Sent: 04 October 2017 10:46 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Output file temperature looks corrupted What version of Nek5000 are you using? Do you use .fXXXXX field files? Single or double precision? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 4th October 2017 11:43 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Output file temperature looks corrupted > > Hi all, after using visnek to create a .nek5000 file and viewing the data in ParaView I found that the temperature data for the bottom half of my domain looks corrupted. As you can see in the image the top half of the domain is correct. > This corrupted data only effects the temperature, the velocity and pressure are ok for the whole domain. I only started seeing this issue after switching from 7th order to 11th order. > Thanks for any help. > Andrew > _______________________________________________ > 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: RELEASE.md Type: application/octet-stream Size: 1909 bytes Desc: RELEASE.md URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 4 05:08:30 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Oct 2017 12:08:30 +0200 Subject: [Nek5000-users] Output file temperature looks corrupted In-Reply-To: References: Message-ID: Please provide a download link to your field file. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 4th October 2017 12:05 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Output file temperature looks corrupted > > The release file gives Release 17.?.? > > I am using .fXXXXX files. Parameter 63 is set to zero, which I think should be giving single precision? > > Thank you > > -----Original Message----- > From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov > Sent: 04 October 2017 10:46 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Output file temperature looks corrupted > > What version of Nek5000 are you using? > Do you use .fXXXXX field files? Single or double precision? > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Wednesday 4th October 2017 11:43 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] Output file temperature looks corrupted > > > > Hi all, after using visnek to create a .nek5000 file and viewing the data in ParaView I found that the temperature data for the bottom half of my domain looks corrupted. As you can see in the image the top half of the domain is correct. > > This corrupted data only effects the temperature, the velocity and pressure are ok for the whole domain. I only started seeing this issue after switching from 7th order to 11th order. > > Thanks for any help. > > Andrew > > _______________________________________________ > > 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 > From nek5000-users at lists.mcs.anl.gov Wed Oct 4 05:14:56 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Oct 2017 12:14:56 +0200 Subject: [Nek5000-users] Output file temperature looks corrupted In-Reply-To: References: Message-ID: Is it really temperature or your own scalar? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 4th October 2017 12:05 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Output file temperature looks corrupted > > The release file gives Release 17.?.? > > I am using .fXXXXX files. Parameter 63 is set to zero, which I think should be giving single precision? > > Thank you > > -----Original Message----- > From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov > Sent: 04 October 2017 10:46 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Output file temperature looks corrupted > > What version of Nek5000 are you using? > Do you use .fXXXXX field files? Single or double precision? > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Wednesday 4th October 2017 11:43 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] Output file temperature looks corrupted > > > > Hi all, after using visnek to create a .nek5000 file and viewing the data in ParaView I found that the temperature data for the bottom half of my domain looks corrupted. As you can see in the image the top half of the domain is correct. > > This corrupted data only effects the temperature, the velocity and pressure are ok for the whole domain. I only started seeing this issue after switching from 7th order to 11th order. > > Thanks for any help. > > Andrew > > _______________________________________________ > > 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 > From nek5000-users at lists.mcs.anl.gov Wed Oct 4 05:33:00 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Oct 2017 10:33:00 +0000 Subject: [Nek5000-users] Output file temperature looks corrupted In-Reply-To: References: Message-ID: I have not implemented my own scalar. What email should I use for the file transfer? I'm not sure the list address will work with my university file transfer service. -----Original Message----- From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov Sent: 04 October 2017 11:15 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Output file temperature looks corrupted Is it really temperature or your own scalar? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 4th October 2017 12:05 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Output file temperature looks corrupted > > The release file gives Release 17.?.? > > I am using .fXXXXX files. Parameter 63 is set to zero, which I think should be giving single precision? > > Thank you > > -----Original Message----- > From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov > Sent: 04 October 2017 10:46 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Output file temperature looks corrupted > > What version of Nek5000 are you using? > Do you use .fXXXXX field files? Single or double precision? > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Wednesday 4th October 2017 11:43 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] Output file temperature looks corrupted > > > > Hi all, after using visnek to create a .nek5000 file and viewing the data in ParaView I found that the temperature data for the bottom half of my domain looks corrupted. As you can see in the image the top half of the domain is correct. > > This corrupted data only effects the temperature, the velocity and pressure are ok for the whole domain. I only started seeing this issue after switching from 7th order to 11th order. > > Thanks for any help. > > Andrew > > _______________________________________________ > > 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 From nek5000-users at lists.mcs.anl.gov Wed Oct 4 07:49:25 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 4 Oct 2017 12:49:25 +0000 Subject: [Nek5000-users] Output file temperature looks corrupted In-Reply-To: References: Message-ID: Hopefully this link should work. https://oxfile.ox.ac.uk/oxfile/work/extBox?id=497313071C5665635F -----Original Message----- From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov Sent: 04 October 2017 11:09 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Output file temperature looks corrupted Please provide a download link to your field file. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 4th October 2017 12:05 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Output file temperature looks corrupted > > The release file gives Release 17.?.? > > I am using .fXXXXX files. Parameter 63 is set to zero, which I think should be giving single precision? > > Thank you > > -----Original Message----- > From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov > Sent: 04 October 2017 10:46 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Output file temperature looks corrupted > > What version of Nek5000 are you using? > Do you use .fXXXXX field files? Single or double precision? > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Wednesday 4th October 2017 11:43 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] Output file temperature looks corrupted > > > > Hi all, after using visnek to create a .nek5000 file and viewing the data in ParaView I found that the temperature data for the bottom half of my domain looks corrupted. As you can see in the image the top half of the domain is correct. > > This corrupted data only effects the temperature, the velocity and pressure are ok for the whole domain. I only started seeing this issue after switching from 7th order to 11th order. > > Thanks for any help. > > Andrew > > _______________________________________________ > > 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 From nek5000-users at lists.mcs.anl.gov Wed Oct 4 08:39:41 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 04 Oct 2017 15:39:41 +0200 Subject: [Nek5000-users] Nek5000 Documentation : Low Mach equations In-Reply-To: References: Message-ID: Dear Nek experts, I was going through the documentation in order to better understand the Low Mach Model. I'm wondering : why in eq(1.12) p.8 cp doesn't appear why we have a minus une energy equation contrarily to the eq (1.6) Thank you in advance for your answer, Sam From nek5000-users at lists.mcs.anl.gov Tue Oct 3 07:44:01 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 3 Oct 2017 12:44:01 +0000 Subject: [Nek5000-users] Simulation hanging at 'mapping elements to processors' In-Reply-To: References: Message-ID: As a follow-up, I set up the same problem but generated a map file using a previous version of Nek5000. It run fine. I attached the log file. Marco -------------- next part -------------- A non-text attachment was scrubbed... Name: Actesys.1.0000 Type: application/octet-stream Size: 224757 bytes Desc: Actesys.1.0000 URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ATT00001.txt URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 5 04:22:31 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 05 Oct 2017 12:22:31 +0300 Subject: [Nek5000-users] =?utf-8?q?Full_restart_problem?= Message-ID: Hi, Neks! I am using a my_full_restart subroutine as in cyl_restart example. In logfile it seems that it works well, because Nek reads first 3 steps from previous calculation, but I also write to the file the meaning value of friction velocity (u_tau) and it differs. During first 10-20 dimensionless time there is a huge peak in the instant profile of u_tau. Then it begins to oscyllate near an exact meaning, but such behaviour looks strange in case of full_restart using. Do you have any ideas why is it so? Best regards,? Vladislav -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 5 07:13:49 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Oct 2017 09:13:49 -0300 Subject: [Nek5000-users] Postprocessing *.rm2 files with paraview Message-ID: Hello everyone, am having some troubles postprocessing the rm2 files using paraview, this file should have the , , and also i add the turbulent heat flux , , but when i upload this files to paraview it renames this fields with: pressure temperature x-velocity y-velocity z-velocity velocity-mag velocity so i'm unable to recognize which of this "fields" are which one. how can i postprocessing this rm2 files with paraview? best regards Nicolas Thiers From nek5000-users at lists.mcs.anl.gov Thu Oct 5 08:32:55 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Oct 2017 13:32:55 +0000 Subject: [Nek5000-users] Postprocessing *.rm2 files with paraview In-Reply-To: References: Message-ID: Dear Nicolas, rm2 would typically contain and you would need to post-process in conduction with the avg file that contains to get etc. (I normally do this in userchk, in a separate post-processing run of nek in order to generate the fields. See "auto_averager" in core/navier5.f for an example. You can then call outpost() to write out your post-processed fields.) I don't use paraview, but I do use VisIt, and it indeed names things u,v,w, etc. That's ok --- we've not bothered to make up new names for all the different fields. We simply think of (u,v,w) as three components of a given vector. hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, October 5, 2017 7:13 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Postprocessing *.rm2 files with paraview Hello everyone, am having some troubles postprocessing the rm2 files using paraview, this file should have the , , and also i add the turbulent heat flux , , but when i upload this files to paraview it renames this fields with: pressure temperature x-velocity y-velocity z-velocity velocity-mag velocity so i'm unable to recognize which of this "fields" are which one. how can i postprocessing this rm2 files with paraview? best regards Nicolas Thiers _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 5 10:27:29 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 05 Oct 2017 17:27:29 +0200 Subject: [Nek5000-users] Short test : dfh_cav In-Reply-To: <4e202a7441d884c36b7506a9574b57b8@vki.ac.be> References: <4e202a7441d884c36b7506a9574b57b8@vki.ac.be> Message-ID: Dear Neks, I would like to run the case dfh_cav. The thing is that the .rea file is missing. How can I do ? Best regards, Samuel From nek5000-users at lists.mcs.anl.gov Thu Oct 5 20:35:42 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 6 Oct 2017 09:35:42 +0800 Subject: [Nek5000-users] Short test : dfh_cav Message-ID: Hi, Samuel, The case parameters are specified in .par file and the mesh information is contained in .re2 file, so there is no need to use .rea file any more. You can compile the dfh_cav case with above two files as well as .usr/SIZE files immediately I think. Regards, Bolun Xu University of Science and Technology of China Department of Modern Mechanics Hefei, Anhui, China -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 6 02:02:00 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 6 Oct 2017 09:02:00 +0200 Subject: [Nek5000-users] Short test : dfh_cav In-Reply-To: References: <4e202a7441d884c36b7506a9574b57b8@vki.ac.be> Message-ID: Hi, There are ###.par (runtime parameters) and ###.re2 (mesh) files, so everything necessary to run is there. Regards Adam On 05/10/17 17:27, nek5000-users at lists.mcs.anl.gov wrote: > Dear Neks, > > I would like to run the case dfh_cav. The thing is that the .rea file > is missing. > How can I do ? > > Best regards, > Samuel > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Mon Oct 9 04:48:00 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 09 Oct 2017 11:48:00 +0200 Subject: [Nek5000-users] Short test : dfh_cav Message-ID: Hi, Thank you for your quick answer guys. Best regards, Samuel From nek5000-users at lists.mcs.anl.gov Mon Oct 9 14:37:57 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Oct 2017 19:37:57 +0000 Subject: [Nek5000-users] Issues running on Mira Message-ID: I'm currently attempting to run Nek5000 on the Argonne supercomputer (Mira) using 512 nodes, but if using all available cores (16 per node) the code seems to hang after some point. All attempts have been made with a run time of 1 hour. When running on 512 nodes with a single core on each node, the code runs fine. Is it possible that start-up for ~8000 cores takes more than an hour or is there something else that could be causing this issue? Note that we definitely have a sufficient number of elements to run on ~8000 nodes. Thanks, Jefferson Davis -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Oct 9 21:09:43 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Oct 2017 02:09:43 +0000 Subject: [Nek5000-users] Issues running on Mira In-Reply-To: References: Message-ID: Hi Jefferson, What are lx1 and left set to in your SIZE file? It's possible that you're running out of memory. If you have, say, 16000 elements total, then you would only need lelt=2 to run on 8192 MPI ranks. Note that we generally run with -c32 mode, 2 ranks per core, as this typically makes better use of the same number of node hours. Please let me know if this helps. Thanks, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 9, 2017 2:37:57 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Issues running on Mira I'm currently attempting to run Nek5000 on the Argonne supercomputer (Mira) using 512 nodes, but if using all available cores (16 per node) the code seems to hang after some point. All attempts have been made with a run time of 1 hour. When running on 512 nodes with a single core on each node, the code runs fine. Is it possible that start-up for ~8000 cores takes more than an hour or is there something else that could be causing this issue? Note that we definitely have a sufficient number of elements to run on ~8000 nodes. Thanks, Jefferson Davis -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 10 02:51:42 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Oct 2017 09:51:42 +0200 Subject: [Nek5000-users] Issues running on Mira In-Reply-To: References: Message-ID: Can you please post your logile. On 9 Oct 2017, at 22:26, "nek5000-users at lists.mcs.anl.gov " > wrote: I'm currently attempting to run Nek5000 on the Argonne supercomputer (Mira) using 512 nodes, but if using all available cores (16 per node) the code seems to hang after some point. All attempts have been made with a run time of 1 hour. When running on 512 nodes with a single core on each node, the code runs fine. Is it possible that start-up for ~8000 cores takes more than an hour or is there something else that could be causing this issue? Note that we definitely have a sufficient number of elements to run on ~8000 nodes. Thanks, Jefferson Davis _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 10 04:52:06 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Oct 2017 11:52:06 +0200 Subject: [Nek5000-users] proj_ortho error in pipe flow In-Reply-To: References: Message-ID: Hi Neks, I saw that there was a new commit on Github "import Paul's projection fix"? on October, 4th so I tried the newest Nek5000 version with my setup. Projection seems to be running fine if only temperature is solved additionally to pressure and velocity. However, when I want to solve for an additional passive scalar the projection fails (for both unperturbed initial conditions as well as chaotic fields). I tried to restrict the projection only for velocity and temperature in hsolve subroutine by adding the following code snippet: ... if (ifstdh) then ??? call hmholtz(name,u,r,h1,h2,vmk,vml,imsh,tol,maxit,isd) ! My restriction for using projection only on ifield 1 and 2 but not on 3 (first passive scalar) elseif (ifield.gt.2) then ??? call hmholtz(name,u,r,h1,h2,vmk,vml,imsh,tol,maxit,isd) else ... If I restrict the projection in such a way, I do not get errors for the projection of the temperature field but on the other hand no projection for passive scalar(s) is done either. I have tested this in a simple test case which is uploaded here: https://bwsyncandshare.kit.edu/dl/fiVn2UB9QqWZN7awPsJHJSVF I believe there is a problem when more than one temperature field is present and one activates projection (p94 != 0). Unfortunately, my knowledge of the code is not sufficient enough to really dig deeper and solve this problem. The adjustments from my previous message (to extend approxt and napproxt) only postponed the projection errors to later timesteps. Maybe you can point me in the right direction? Best Regards, Steffen Straub On 09/28/2017 07:00 PM, nek5000-users-request at lists.mcs.anl.gov wrote: > Message: 1 > Date: Thu, 28 Sep 2017 14:40:27 +0200 > From:nek5000-users at lists.mcs.anl.gov > To: > Subject: Re: [Nek5000-users] proj_ortho error in pipe flow > Message-ID: > > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Hi Neks, > > I might have fixed my proj_ortho error issue. At least it is running now > without errors on a small test case on my local machine. However, I am > very much unsure if what I was changing is correct. > Can you please confirm that my adjustments are reasonable? > > In conduct.f when hsolve is called, I have adjusted the argument list > like this: > > -????? napproxt(1) = laxtt? ! Fix this... pff 10/10/15 > +????? napproxt(1,ifield-1) = laxtt? ! Fix this... pff 10/10/15 > > ??????????? call hsolve? (name4t,TA,TB,H1,H2 > ????? $?????????????????? ,tmask(1,1,1,1,ifield-1) > ????? $?????????????????? ,tmult(1,1,1,1,ifield-1) > ????? $?????????????????? ,imesh,tolht(ifield),nmxh,1 > -???? $?????????????????? ,approxt,napproxt,bintm1) > +???? $ ,approxt(1,1,ifield-1),napproxt(1,ifield-1) > +???? $?????????????????? ,bintm1) > > such that approxt and napproxt refers to each ifield, ie. temperature, > passive scalar 1, passive scalar 2, ... similar to velx, vely, velz. > > > Accordingly, I have adjusted ORTHOT: > > -????? integer???????? napproxt(2) > + > +C Add another dimension to (n)approxt for each passive scalar and temp. > +????? integer???????? napproxt(2,ldimt) > ?????? common/trthoi/ napproxt > > -????? real??????????? approxt(ktott,0:laxtt) > +????? real??????????? approxt(ktott,0:laxtt,ldimt) > > and induct.f > > -????? napproxt(1) = laxtt > +????? napproxt(1,ifield-1) = laxtt > > > > > > Message: 2 > Date: Thu, 28 Sep 2017 14:04:58 +0000 > From:nek5000-users at lists.mcs.anl.gov > To:"nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] proj_ortho error in pipe flow > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > > Dear Steffen, > > > I believe this issue may have been resolved in an update to the git repo > > last week. > > > Best, > > > Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 10 08:08:08 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Oct 2017 15:08:08 +0200 Subject: [Nek5000-users] Short test : dfh_cav In-Reply-To: <07ad834f9ad729e75643157066e63c9e@vki.ac.be> References: <07ad834f9ad729e75643157066e63c9e@vki.ac.be> Message-ID: Hi again, As I'm trying to visualize the case using postx, I get the error "can't open the file lin_dfh_cav_dir.rea". It seems normal because this file doesn't exist. I tried to use re2torea to create the file but it is not working. Does anyone has any suggestion ? Thanks, Samuel Le 2017-10-09 11:48, Samuel a ?crit?: > Hi, > > Thank you for your quick answer guys. > > Best regards, > Samuel From nek5000-users at lists.mcs.anl.gov Tue Oct 10 08:13:25 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Oct 2017 13:13:25 +0000 Subject: [Nek5000-users] Short test : dfh_cav In-Reply-To: References: <07ad834f9ad729e75643157066e63c9e@vki.ac.be> Message-ID: Could you post the error messages you are seeing when you are running re2torea script? I believe this script is not working properly. How did you generate your re2 file? > On Oct 10, 2017, at 9:08 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi again, > > As I'm trying to visualize the case using postx, I get the error "can't open the file lin_dfh_cav_dir.rea". It seems normal because this file doesn't exist. > I tried to use re2torea to create the file but it is not working. > Does anyone has any suggestion ? > > Thanks, > Samuel > > Le 2017-10-09 11:48, Samuel a ?crit : >> Hi, >> Thank you for your quick answer guys. >> Best regards, >> Samuel > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue Oct 10 08:20:30 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Oct 2017 13:20:30 +0000 Subject: [Nek5000-users] Short test : dfh_cav In-Reply-To: References: <07ad834f9ad729e75643157066e63c9e@vki.ac.be>, Message-ID: Hi Samuel, try calling gen_rea(0) from your usrdat2() and modify the ASCII mesh & BC file newrea.out for the .rea's header and bottom part taken from, e.g., svn's examples/vortex/r1854a.rea but make sure that your first field file has coordinates. Also note that the .rea's p66 for postx has to be 4 for .fld and 6 for .f field files. Aleks ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 10, 2017 8:08:08 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Short test : dfh_cav Hi again, As I'm trying to visualize the case using postx, I get the error "can't open the file lin_dfh_cav_dir.rea". It seems normal because this file doesn't exist. I tried to use re2torea to create the file but it is not working. Does anyone has any suggestion ? Thanks, Samuel Le 2017-10-09 11:48, Samuel a ?crit : > Hi, > > Thank you for your quick answer guys. > > Best regards, > Samuel _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 10 08:39:23 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Oct 2017 15:39:23 +0200 Subject: [Nek5000-users] Short test : dfh_cav In-Reply-To: References: <07ad834f9ad729e75643157066e63c9e@vki.ac.be> Message-ID: Just call gen_rea_full(0) and you're all set. btw: re2torea works as well but you have to provide (in addition to .re2) a rea template! Cheers, Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Tuesday 10th October 2017 15:21 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Short test : dfh_cav > > Hi Samuel, > > try calling gen_rea(0) from your usrdat2() and modify the ASCII mesh & BC file newrea.out for the .rea's header and bottom part taken from, e.g., svn's examples/vortex/r1854a.rea but make sure that your first field file has coordinates. ? > > Also note that the .rea's p66 for postx has to be 4 for .fld and 6 for .f field files. > > Aleks > ----------- > From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Tuesday, October 10, 2017 8:08:08 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Short test : dfh_cav > Hi again, > > As I'm trying to visualize the case using postx, I get the error "can't > open the file lin_dfh_cav_dir.rea". It seems normal because this file > doesn't exist. > I tried to use re2torea to create the file but it is not working. > Does anyone has any suggestion ? > > Thanks, > Samuel > > Le 2017-10-09 11:48, Samuel a ?crit?: > > Hi, > > > > Thank you for your quick answer guys. > > > > Best regards, > > Samuel > _______________________________________________ > 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 From nek5000-users at lists.mcs.anl.gov Tue Oct 10 08:52:50 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Oct 2017 15:52:50 +0200 Subject: [Nek5000-users] nek and visit vy trouble In-Reply-To: References: <07ad834f9ad729e75643157066e63c9e@vki.ac.be> Message-ID: I'm trying to make some volume integrals of the vorticity in the flow domain. I'm considering a two-dimensional plunging flat plate, in the body frame. Is it possible that variables accessed in nek, such as vy, are different from the one displayed in visit? I mean, in the fld file, and in the usr, vy has a sign, while in visit has the opposite sign. Furthemore, exporting the field files in tecplot format and performing integrations in tecplot, computation goes well. What's happening? Thank you Mario -- Mario Ostieri Ph.D. Student University of Naples Federico II Department of Industrial Engineering Piazzale V. Tecchio 80 80125 Napoli, Italy tel. +390817682184 email: mario.ostieri at unina.it From nek5000-users at lists.mcs.anl.gov Tue Oct 10 08:57:19 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 10 Oct 2017 13:57:19 +0000 Subject: [Nek5000-users] nek and visit vy trouble In-Reply-To: References: <07ad834f9ad729e75643157066e63c9e@vki.ac.be> , Message-ID: Yes, Mario, as far I know, VisIt uses linear interpolation and finite difference derivatives so when I look at the vorticity I either use postnek or compute them in usrchk() with, say, comp_vort3() and dump as a separate field sequence with outpost() and then view them in VisIt Aleks ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 10, 2017 8:52:50 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] nek and visit vy trouble I'm trying to make some volume integrals of the vorticity in the flow domain. I'm considering a two-dimensional plunging flat plate, in the body frame. Is it possible that variables accessed in nek, such as vy, are different from the one displayed in visit? I mean, in the fld file, and in the usr, vy has a sign, while in visit has the opposite sign. Furthemore, exporting the field files in tecplot format and performing integrations in tecplot, computation goes well. What's happening? Thank you Mario -- Mario Ostieri Ph.D. Student University of Naples Federico II Department of Industrial Engineering Piazzale V. Tecchio 80 80125 Napoli, Italy tel. +390817682184 email: mario.ostieri at unina.it _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 11 02:06:22 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Oct 2017 09:06:22 +0200 Subject: [Nek5000-users] Short test : dfh_cav Message-ID: Hi, Thank you very much Stefan and Aleks for your wise advices. Samuel ---------------------------------------------------------------------- Message: 1 Date: Tue, 10 Oct 2017 15:39:23 +0200 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Short test : dfh_cav Message-ID: Content-Type: text/plain; charset=utf-8 Just call gen_rea_full(0) and you're all set. btw: re2torea works as well but you have to provide (in addition to .re2) a rea template! Cheers, Stefan -----Original message----- From:nek5000-users at lists.mcs.anl.gov Sent: Tuesday 10th October 2017 15:21 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Short test : dfh_cav Hi Samuel, try calling gen_rea(0) from your usrdat2() and modify the ASCII mesh & BC file newrea.out for the .rea's header and bottom part taken from, e.g., svn's examples/vortex/r1854a.rea but make sure that your first field file has coordinates. ? Also note that the .rea's p66 for postx has to be 4 for .fld and 6 for .f field files. Aleks ----------- From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 10, 2017 8:08:08 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Short test : dfh_cav Hi again, As I'm trying to visualize the case using postx, I get the error "can't open the file lin_dfh_cav_dir.rea". It seems normal because this file doesn't exist. I tried to use re2torea to create the file but it is not working. Does anyone has any suggestion ? Thanks, Samuel Le 2017-10-09 11:48, Samuel a ?crit?: Hi, Thank you for your quick answer guys. Best regards, Samuel _______________________________________________ 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 From nek5000-users at lists.mcs.anl.gov Wed Oct 11 03:56:52 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Oct 2017 08:56:52 +0000 Subject: [Nek5000-users] Case Setup Tutorial Message-ID: Hi neks, I'm just started with Nek5000 and I was searching for some tutorials (best practices) including the whole method to setup and run cases. Can somebody help me? Thank you very much for your support! Kevin -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 11 11:55:49 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Oct 2017 18:55:49 +0200 Subject: [Nek5000-users] nek and visit vy trouble In-Reply-To: References: <07ad834f9ad729e75643157066e63c9e@vki.ac.be> , Message-ID: Hi Aleks, thanks for your answer. I understand that Visit interpolates. I computed vorticity with comp_vort3, I replaced the temperature with the computed vorticity and I viewed it in VisIt. What I don't understand it's the fact that the y component of the velocity changes sign, but the magnitude is the same. In this way, volume integrations during nek simulations are wrong, while integrations on tecplot with the output field files are correct. How can it be possible? Mario Quoting nek5000-users at lists.mcs.anl.gov: > Yes, Mario, as far I know, VisIt uses linear interpolation and > finite difference derivatives so when I look at the vorticity I > either use postnek or compute them in usrchk() with, say, > comp_vort3() and dump as a separate field sequence with outpost() > and then view them in VisIt > > > Aleks > > ________________________________ > From: Nek5000-users on > behalf of nek5000-users at lists.mcs.anl.gov > > Sent: Tuesday, October 10, 2017 8:52:50 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] nek and visit vy trouble > > I'm trying to make some volume integrals of the vorticity in the flow > domain. I'm considering a two-dimensional plunging flat plate, in the > body frame. > Is it possible that variables accessed in nek, such as vy, are different > from the one displayed in visit? > I mean, in the fld file, and in the usr, vy has a sign, while in visit > has the opposite sign. > Furthemore, exporting the field files in tecplot format and performing > integrations in tecplot, computation goes well. > > What's happening? > > Thank you > > Mario > > -- > Mario Ostieri > > Ph.D. Student > University of Naples Federico II > Department of Industrial Engineering > Piazzale V. Tecchio 80 > 80125 Napoli, Italy > tel. +390817682184 > email: mario.ostieri at unina.it > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > Mario Ostieri Ph.D. Student University of Naples Federico II Department of Industrial Engineering Piazzale V. Tecchio 80 80125 Napoli, Italy tel. +390817682184 email: mario.ostieri at unina.it From nek5000-users at lists.mcs.anl.gov Wed Oct 11 12:26:16 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Oct 2017 14:26:16 -0300 Subject: [Nek5000-users] Interpolation in uservp In-Reply-To: References: Message-ID: Hi, I need run a simulation with a variable param(2) in time. I'd like to have several probing or history points in the temperature field, and every time step calculate the average value in time of each of those points. When these values are stable I increase param(2) in uservp, and repeat the procedure. So my question is, how can I obtain the temperature value at a certain (x,y,z) point every time step so I can store it and calculate the average so far at that time? Thank you, Juan Pablo. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 11 12:30:25 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 11 Oct 2017 19:30:25 +0200 Subject: [Nek5000-users] Interpolation in uservp In-Reply-To: References: Message-ID: Hello Juan, take a look at the hemi example and its use of the interp_v subroutine for the velocity. I assume this also works for the temperature field. Jan > Am 11.10.2017 um 19:26 schrieb nek5000-users at lists.mcs.anl.gov: > > Hi, > > I need run a simulation with a variable param(2) in time. I'd like to have several probing or history points in the temperature field, and every time step calculate the average value in time of each of those points. When these values are stable I increase param(2) in uservp, and repeat the procedure. > > So my question is, how can I obtain the temperature value at a certain (x,y,z) point every time step so I can store it and calculate the average so far at that time? > > Thank you, > > Juan Pablo. > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu Oct 12 16:12:00 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Oct 2017 18:12:00 -0300 Subject: [Nek5000-users] Interpolation in uservp Message-ID: Hi, thank you Jan for the answer. It looks like the recent updates of Nek doesn't include the subroutines "intpts_setup" and "intpts" in postpro.f, which are the subroutines used inside "interp_v(uvw,xyz,n)". Should I add them myself? Or maybe there's a most updated way to do the same? Thank you. JP. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 13 06:49:23 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 13 Oct 2017 11:49:23 +0000 Subject: [Nek5000-users] Interpolation in uservp In-Reply-To: References: Message-ID: Dear JP, Have you updated your Nekexamples and Nek5000 repos? There were changes to some of the interpolation routines that impacted the particle tracking implementation. I believe that both are in sync now so that you can use the current hemi example as a guide to off-grid interpolation. hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, October 12, 2017 4:12:00 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Interpolation in uservp Hi, thank you Jan for the answer. It looks like the recent updates of Nek doesn't include the subroutines "intpts_setup" and "intpts" in postpro.f, which are the subroutines used inside "interp_v(uvw,xyz,n)". Should I add them myself? Or maybe there's a most updated way to do the same? Thank you. JP. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Oct 14 10:40:09 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 14 Oct 2017 15:40:09 +0000 Subject: [Nek5000-users] Nek5000 Hackathon, November 12-14, 2017 Message-ID: Dear Nek Developers and Users, We are excited to announce the first-ever Nek5000 Hackathon. When: Nov. 12 (1 PM, Sunday) -- Nov. 14 (5pm, Tuesday), 2017 Where: NCSA Building, University of Illinois, Urbana-Champaign (UIUC), IL, USA Hackathon Goal: The event will bring together users and developers with the intent to help new and current users bring their applications into production mode. It will also give users a chance to provide the development team with feedback on what features or enhancements they would like to see in future releases. Format: We are asking each of the participants (or as a team) to develop a small example demonstrating the phenomena of interest that could be shared with the rest of the user community through the NekExamples Suite. There will not be a formal presentation agenda. We anticipate, however, several rounds of short presentations describing the problems of interest, the features that make the problem interesting and challenging, and the anticipated ways in which the Nek team can help. Please bring your laptops and come prepared to access your usual work sites remotely, from UIUC. Cost: There is no formal registration fee. Lunches will be covered. We may collect a nominal fee for group dinners on Sunday and Monday. Registration: In order to anticipate the number of attendees, we will post a registration site in the coming week. Please stay tuned for details. Hotels: There are several hotels in the area that are a short walk from the workshop site (Siebel Center, Day 1; NCSA Days 2 & 3). Hampton Inn on University ~ 5 minute walk. Illini Union ~ 10 minute walk. Towne Place Suites by Marriott, Champaign 15 minutes I Hotel - 2 miles Sylvia's Irish Inn B&B 10 minutes We look forward to seeing you next month! Sincerely, The Nek Development Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Oct 16 04:04:02 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 16 Oct 2017 09:04:02 +0000 Subject: [Nek5000-users] Calling subroutine "hpts" for several files Message-ID: Dear Neks, I am post processing my data using the subroutine "hpts" to extract field values at specific points. I want to loop over many files and extract the field values for each file. Therefore I want to rename the file "hpts.out" that is created everytime I call hpts. This code snippet is in userchk, and is looks like this: do i=1,100 write(fname,'(I0.5)') i fname='cav0.f'//trim(fname) call load_fld(fname) call hpts call nekgsync if(nid==0)then call rename('hpts.out',trim(fname)//'_hpts') endif call nekgsync enddo My basename is "cav", so fname is "cav0.f00XXX" for XXX = 1, ..., 100. The code is intended to rename hpts.out for a file "cav0.f00XXX" into "cav0.f00XXX_hpts". However, this does not work. I get only one file; "cav0.f00001_hpts". When I open this file it contains the data from "cav0.f000100 - the last file that was opened in the loop! This makes me wonder if hpts.out is properly closed after beeing written to? And also, how can I change my code to make it work as I indended? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Oct 16 05:22:19 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 16 Oct 2017 10:22:19 +0000 Subject: [Nek5000-users] Output file temperature looks corrupted In-Reply-To: References: Message-ID: Does anyone understand what is causing this problem? -----Original Message----- From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov Sent: 04 October 2017 13:49 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Output file temperature looks corrupted Hopefully this link should work. https://oxfile.ox.ac.uk/oxfile/work/extBox?id=497313071C5665635F -----Original Message----- From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov Sent: 04 October 2017 11:09 To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Output file temperature looks corrupted Please provide a download link to your field file. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Wednesday 4th October 2017 12:05 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Output file temperature looks corrupted > > The release file gives Release 17.?.? > > I am using .fXXXXX files. Parameter 63 is set to zero, which I think should be giving single precision? > > Thank you > > -----Original Message----- > From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov > Sent: 04 October 2017 10:46 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Output file temperature looks corrupted > > What version of Nek5000 are you using? > Do you use .fXXXXX field files? Single or double precision? > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Wednesday 4th October 2017 11:43 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] Output file temperature looks corrupted > > > > Hi all, after using visnek to create a .nek5000 file and viewing the data in ParaView I found that the temperature data for the bottom half of my domain looks corrupted. As you can see in the image the top half of the domain is correct. > > This corrupted data only effects the temperature, the velocity and pressure are ok for the whole domain. I only started seeing this issue after switching from 7th order to 11th order. > > Thanks for any help. > > Andrew > > _______________________________________________ > > 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 From nek5000-users at lists.mcs.anl.gov Mon Oct 16 07:26:20 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 16 Oct 2017 12:26:20 +0000 Subject: [Nek5000-users] Calling subroutine "hpts" for several files In-Reply-To: References: Message-ID: Dear Johan, I would look at the hemi example. There it shows how to interpolate a list of values (interp_v is a routine inside hemi.usr). Once you have a list, you can write it out yourself (again, as shown in hemi.usr). Make certain that your interrogation list is _not_ repeated on every processor. (Otherwise you end up doing P times more work.) hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 16, 2017 4:04:02 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Calling subroutine "hpts" for several files Dear Neks, I am post processing my data using the subroutine "hpts" to extract field values at specific points. I want to loop over many files and extract the field values for each file. Therefore I want to rename the file "hpts.out" that is created everytime I call hpts. This code snippet is in userchk, and is looks like this: do i=1,100 write(fname,'(I0.5)') i fname='cav0.f'//trim(fname) call load_fld(fname) call hpts call nekgsync if(nid==0)then call rename('hpts.out',trim(fname)//'_hpts') endif call nekgsync enddo My basename is "cav", so fname is "cav0.f00XXX" for XXX = 1, ..., 100. The code is intended to rename hpts.out for a file "cav0.f00XXX" into "cav0.f00XXX_hpts". However, this does not work. I get only one file; "cav0.f00001_hpts". When I open this file it contains the data from "cav0.f000100 - the last file that was opened in the loop! This makes me wonder if hpts.out is properly closed after beeing written to? And also, how can I change my code to make it work as I indended? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 17 03:35:58 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Oct 2017 08:35:58 +0000 Subject: [Nek5000-users] Calling subroutine "hpts" for several files In-Reply-To: References: , Message-ID: Thanks. After running the hemi example and looking into hemi.usr, I have some questions about how the interpolation works in parallell. It seems as the interpolation is done by a call to the subroutine "intpts" in from the subroutine "interp_v": "call intpts(wrk,3,pts,n,uvw,.true.,.true.,ihandle)" This call interpolates velocities in wrk to positions in pts and outputs in uvw. The positions "pts" are positions of Lagranian particles. Each process has a local array "pts" and a sees a local piece of the velocity field, "wrk". Is it important that each point of "pts" is within the local piece of "wrk" for a processor? * If this is important; how can I see that this is considered within the code? * If it is not important; Could "intpts" be called only from one process (say nid == 0) in order to simplify the code? Also: Have I understood the hemi example correctly? Best, Johan ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 16, 2017 2:26:20 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Dear Johan, I would look at the hemi example. There it shows how to interpolate a list of values (interp_v is a routine inside hemi.usr). Once you have a list, you can write it out yourself (again, as shown in hemi.usr). Make certain that your interrogation list is _not_ repeated on every processor. (Otherwise you end up doing P times more work.) hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 16, 2017 4:04:02 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Calling subroutine "hpts" for several files Dear Neks, I am post processing my data using the subroutine "hpts" to extract field values at specific points. I want to loop over many files and extract the field values for each file. Therefore I want to rename the file "hpts.out" that is created everytime I call hpts. This code snippet is in userchk, and is looks like this: do i=1,100 write(fname,'(I0.5)') i fname='cav0.f'//trim(fname) call load_fld(fname) call hpts call nekgsync if(nid==0)then call rename('hpts.out',trim(fname)//'_hpts') endif call nekgsync enddo My basename is "cav", so fname is "cav0.f00XXX" for XXX = 1, ..., 100. The code is intended to rename hpts.out for a file "cav0.f00XXX" into "cav0.f00XXX_hpts". However, this does not work. I get only one file; "cav0.f00001_hpts". When I open this file it contains the data from "cav0.f000100 - the last file that was opened in the loop! This makes me wonder if hpts.out is properly closed after beeing written to? And also, how can I change my code to make it work as I indended? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 17 05:11:39 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Oct 2017 12:11:39 +0200 Subject: [Nek5000-users] Calling subroutine "hpts" for several files Message-ID: > Is it important that each point of "pts" is within the local piece of "wrk" for a processor? NO > * If it is not important; Could "intpts" be called only from one process (say nid == 0) in order to simplify the code? All ranks have to call intpts() but you can pass an arbitrary list of points (including no points). > Also: Have I understood the hemi example correctly? You have to ask yourself ;) Cheers, Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Tuesday 17th October 2017 10:36 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files > > Thanks. After running the hemi example and looking into hemi.usr, I have some questions about how the interpolation works in parallell. > It seems as the interpolation is done by a call to the subroutine "intpts" in from the subroutine "interp_v": > > "call intpts(wrk,3,pts,n,uvw,.true.,.true.,ihandle)" > > This call interpolates velocities in wrk to positions in pts and outputs in uvw. > The positions "pts" are positions of Lagranian particles. > > Each process has a local array "pts" and a sees a local piece of the velocity field, "wrk". > Is it important that each point of "pts" is within the local piece of "wrk" for a processor? > > * If this is important; how can I see that this is considered within the code? > > * If it is not important; Could "intpts" be called only from one process (say nid == 0) in order to simplify the code? > > Also: Have I understood the hemi example correctly? > > Best, > > Johan > ----------- > From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Monday, October 16, 2017 2:26:20 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files > Dear Johan, > > I would look at the hemi example. > > There it shows how to interpolate a list of values > (interp_v is a routine inside hemi.usr). > > Once you have a list, you can write it out yourself > (again, as shown in hemi.usr). > > Make certain that your interrogation list is _not_ repeated > on every processor. (Otherwise you end up doing P times > more work.) > > hth, > Paul > > ----------- > From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Monday, October 16, 2017 4:04:02 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Calling subroutine "hpts" for several files > Dear Neks, > > I am post processing my data using the subroutine "hpts" to extract field values at specific points. > I want to loop over many files and extract the field values for each file. > Therefore I want to rename the file "hpts.out" that is created everytime I call hpts. > This code snippet is in userchk, and is looks like this: > ????? > ????? do i=1,100 > > ??????? write(fname,'(I0.5)') i > ??????? fname='cav0.f'//trim(fname) > > ??????? call load_fld(fname) > > ??????? call hpts > > ??????? call nekgsync > ??????? if(nid==0)then > ????????? call rename('hpts.out',trim(fname)//'_hpts') > ??????? endif > ??????? call nekgsync > > ????? enddo > > My basename is "cav", so fname is "cav0.f00XXX" for XXX = 1, ..., 100. > The code is intended to rename hpts.out for a file "cav0.f00XXX" into "cav0.f00XXX_hpts". > > However, this does not work. > I get only one file; "cav0.f00001_hpts". > When I open this file it contains the data from "cav0.f000100 - the last file that was opened in the loop! > > This makes me wonder if hpts.out is properly closed after beeing written to? > And also, how can I change my code to make it work as I indended? > > Best, > > Johan > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue Oct 17 05:27:47 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Oct 2017 10:27:47 +0000 Subject: [Nek5000-users] Calling subroutine "hpts" for several files In-Reply-To: References: , , Message-ID: Hi Johan, Yes -- you can have just one list on node 0 if you wish. Make certain that the list length n=0 on on all other nodes (e.g., if (nid.gt.0) n=0 call the routine (..... , n) The only reason to distribute the list is if it large and you don't want to store it all on node 0. The interpolation routine handles all data movement, as it should. Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 17, 2017 3:35:58 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Thanks. After running the hemi example and looking into hemi.usr, I have some questions about how the interpolation works in parallell. It seems as the interpolation is done by a call to the subroutine "intpts" in from the subroutine "interp_v": "call intpts(wrk,3,pts,n,uvw,.true.,.true.,ihandle)" This call interpolates velocities in wrk to positions in pts and outputs in uvw. The positions "pts" are positions of Lagranian particles. Each process has a local array "pts" and a sees a local piece of the velocity field, "wrk". Is it important that each point of "pts" is within the local piece of "wrk" for a processor? * If this is important; how can I see that this is considered within the code? * If it is not important; Could "intpts" be called only from one process (say nid == 0) in order to simplify the code? Also: Have I understood the hemi example correctly? Best, Johan ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 16, 2017 2:26:20 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Dear Johan, I would look at the hemi example. There it shows how to interpolate a list of values (interp_v is a routine inside hemi.usr). Once you have a list, you can write it out yourself (again, as shown in hemi.usr). Make certain that your interrogation list is _not_ repeated on every processor. (Otherwise you end up doing P times more work.) hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 16, 2017 4:04:02 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Calling subroutine "hpts" for several files Dear Neks, I am post processing my data using the subroutine "hpts" to extract field values at specific points. I want to loop over many files and extract the field values for each file. Therefore I want to rename the file "hpts.out" that is created everytime I call hpts. This code snippet is in userchk, and is looks like this: do i=1,100 write(fname,'(I0.5)') i fname='cav0.f'//trim(fname) call load_fld(fname) call hpts call nekgsync if(nid==0)then call rename('hpts.out',trim(fname)//'_hpts') endif call nekgsync enddo My basename is "cav", so fname is "cav0.f00XXX" for XXX = 1, ..., 100. The code is intended to rename hpts.out for a file "cav0.f00XXX" into "cav0.f00XXX_hpts". However, this does not work. I get only one file; "cav0.f00001_hpts". When I open this file it contains the data from "cav0.f000100 - the last file that was opened in the loop! This makes me wonder if hpts.out is properly closed after beeing written to? And also, how can I change my code to make it work as I indended? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 17 07:22:51 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Oct 2017 12:22:51 +0000 Subject: [Nek5000-users] Calling subroutine "hpts" for several files In-Reply-To: References: , , , Message-ID: Thanks! /Johan ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 17, 2017 12:27:47 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Hi Johan, Yes -- you can have just one list on node 0 if you wish. Make certain that the list length n=0 on on all other nodes (e.g., if (nid.gt.0) n=0 call the routine (..... , n) The only reason to distribute the list is if it large and you don't want to store it all on node 0. The interpolation routine handles all data movement, as it should. Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 17, 2017 3:35:58 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Thanks. After running the hemi example and looking into hemi.usr, I have some questions about how the interpolation works in parallell. It seems as the interpolation is done by a call to the subroutine "intpts" in from the subroutine "interp_v": "call intpts(wrk,3,pts,n,uvw,.true.,.true.,ihandle)" This call interpolates velocities in wrk to positions in pts and outputs in uvw. The positions "pts" are positions of Lagranian particles. Each process has a local array "pts" and a sees a local piece of the velocity field, "wrk". Is it important that each point of "pts" is within the local piece of "wrk" for a processor? * If this is important; how can I see that this is considered within the code? * If it is not important; Could "intpts" be called only from one process (say nid == 0) in order to simplify the code? Also: Have I understood the hemi example correctly? Best, Johan ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 16, 2017 2:26:20 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Dear Johan, I would look at the hemi example. There it shows how to interpolate a list of values (interp_v is a routine inside hemi.usr). Once you have a list, you can write it out yourself (again, as shown in hemi.usr). Make certain that your interrogation list is _not_ repeated on every processor. (Otherwise you end up doing P times more work.) hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 16, 2017 4:04:02 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Calling subroutine "hpts" for several files Dear Neks, I am post processing my data using the subroutine "hpts" to extract field values at specific points. I want to loop over many files and extract the field values for each file. Therefore I want to rename the file "hpts.out" that is created everytime I call hpts. This code snippet is in userchk, and is looks like this: do i=1,100 write(fname,'(I0.5)') i fname='cav0.f'//trim(fname) call load_fld(fname) call hpts call nekgsync if(nid==0)then call rename('hpts.out',trim(fname)//'_hpts') endif call nekgsync enddo My basename is "cav", so fname is "cav0.f00XXX" for XXX = 1, ..., 100. The code is intended to rename hpts.out for a file "cav0.f00XXX" into "cav0.f00XXX_hpts". However, this does not work. I get only one file; "cav0.f00001_hpts". When I open this file it contains the data from "cav0.f000100 - the last file that was opened in the loop! This makes me wonder if hpts.out is properly closed after beeing written to? And also, how can I change my code to make it work as I indended? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 17 08:10:29 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Oct 2017 13:10:29 +0000 Subject: [Nek5000-users] Calling subroutine "hpts" for several files In-Reply-To: References: , , , Message-ID: And if I just want to interpolate one field, can I then pass this field directly into intpts? Or does intpts change the content of the input array? For instance, the i:th passive scalar, like this: call intpts(t(:,:,:,:,i+1),1,pts,n,out,.true.,.true.,ihandle) ? ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 17, 2017 12:27:47 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Hi Johan, Yes -- you can have just one list on node 0 if you wish. Make certain that the list length n=0 on on all other nodes (e.g., if (nid.gt.0) n=0 call the routine (..... , n) The only reason to distribute the list is if it large and you don't want to store it all on node 0. The interpolation routine handles all data movement, as it should. Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 17, 2017 3:35:58 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Thanks. After running the hemi example and looking into hemi.usr, I have some questions about how the interpolation works in parallell. It seems as the interpolation is done by a call to the subroutine "intpts" in from the subroutine "interp_v": "call intpts(wrk,3,pts,n,uvw,.true.,.true.,ihandle)" This call interpolates velocities in wrk to positions in pts and outputs in uvw. The positions "pts" are positions of Lagranian particles. Each process has a local array "pts" and a sees a local piece of the velocity field, "wrk". Is it important that each point of "pts" is within the local piece of "wrk" for a processor? * If this is important; how can I see that this is considered within the code? * If it is not important; Could "intpts" be called only from one process (say nid == 0) in order to simplify the code? Also: Have I understood the hemi example correctly? Best, Johan ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 16, 2017 2:26:20 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Dear Johan, I would look at the hemi example. There it shows how to interpolate a list of values (interp_v is a routine inside hemi.usr). Once you have a list, you can write it out yourself (again, as shown in hemi.usr). Make certain that your interrogation list is _not_ repeated on every processor. (Otherwise you end up doing P times more work.) hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 16, 2017 4:04:02 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Calling subroutine "hpts" for several files Dear Neks, I am post processing my data using the subroutine "hpts" to extract field values at specific points. I want to loop over many files and extract the field values for each file. Therefore I want to rename the file "hpts.out" that is created everytime I call hpts. This code snippet is in userchk, and is looks like this: do i=1,100 write(fname,'(I0.5)') i fname='cav0.f'//trim(fname) call load_fld(fname) call hpts call nekgsync if(nid==0)then call rename('hpts.out',trim(fname)//'_hpts') endif call nekgsync enddo My basename is "cav", so fname is "cav0.f00XXX" for XXX = 1, ..., 100. The code is intended to rename hpts.out for a file "cav0.f00XXX" into "cav0.f00XXX_hpts". However, this does not work. I get only one file; "cav0.f00001_hpts". When I open this file it contains the data from "cav0.f000100 - the last file that was opened in the loop! This makes me wonder if hpts.out is properly closed after beeing written to? And also, how can I change my code to make it work as I indended? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 17 09:18:20 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 17 Oct 2017 14:18:20 +0000 Subject: [Nek5000-users] Calling subroutine "hpts" for several files In-Reply-To: References: , , , , Message-ID: If I were doing it, I'd follow the example in hemi No, it doesn't change the input field. Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 17, 2017 8:10:29 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files And if I just want to interpolate one field, can I then pass this field directly into intpts? Or does intpts change the content of the input array? For instance, the i:th passive scalar, like this: call intpts(t(:,:,:,:,i+1),1,pts,n,out,.true.,.true.,ihandle) ? ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 17, 2017 12:27:47 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Hi Johan, Yes -- you can have just one list on node 0 if you wish. Make certain that the list length n=0 on on all other nodes (e.g., if (nid.gt.0) n=0 call the routine (..... , n) The only reason to distribute the list is if it large and you don't want to store it all on node 0. The interpolation routine handles all data movement, as it should. Best, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 17, 2017 3:35:58 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Thanks. After running the hemi example and looking into hemi.usr, I have some questions about how the interpolation works in parallell. It seems as the interpolation is done by a call to the subroutine "intpts" in from the subroutine "interp_v": "call intpts(wrk,3,pts,n,uvw,.true.,.true.,ihandle)" This call interpolates velocities in wrk to positions in pts and outputs in uvw. The positions "pts" are positions of Lagranian particles. Each process has a local array "pts" and a sees a local piece of the velocity field, "wrk". Is it important that each point of "pts" is within the local piece of "wrk" for a processor? * If this is important; how can I see that this is considered within the code? * If it is not important; Could "intpts" be called only from one process (say nid == 0) in order to simplify the code? Also: Have I understood the hemi example correctly? Best, Johan ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 16, 2017 2:26:20 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Calling subroutine "hpts" for several files Dear Johan, I would look at the hemi example. There it shows how to interpolate a list of values (interp_v is a routine inside hemi.usr). Once you have a list, you can write it out yourself (again, as shown in hemi.usr). Make certain that your interrogation list is _not_ repeated on every processor. (Otherwise you end up doing P times more work.) hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 16, 2017 4:04:02 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Calling subroutine "hpts" for several files Dear Neks, I am post processing my data using the subroutine "hpts" to extract field values at specific points. I want to loop over many files and extract the field values for each file. Therefore I want to rename the file "hpts.out" that is created everytime I call hpts. This code snippet is in userchk, and is looks like this: do i=1,100 write(fname,'(I0.5)') i fname='cav0.f'//trim(fname) call load_fld(fname) call hpts call nekgsync if(nid==0)then call rename('hpts.out',trim(fname)//'_hpts') endif call nekgsync enddo My basename is "cav", so fname is "cav0.f00XXX" for XXX = 1, ..., 100. The code is intended to rename hpts.out for a file "cav0.f00XXX" into "cav0.f00XXX_hpts". However, this does not work. I get only one file; "cav0.f00001_hpts". When I open this file it contains the data from "cav0.f000100 - the last file that was opened in the loop! This makes me wonder if hpts.out is properly closed after beeing written to? And also, how can I change my code to make it work as I indended? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 18 04:48:38 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Oct 2017 10:48:38 +0100 Subject: [Nek5000-users] pipe prenek Message-ID: Hi Nek, Is there anyone knows how to calculate the curvature in .rea file. Recently, I want to generate a pipe mesh but it doesn't seem like a pipe in which I guess there is something wrong in curvature part in .rea file. I have attached the mesh part below. **MESH DATA** 1st line is X of corner 1,2,3,4. 2nd line is Y. 12 2 12 NEL,NDIM,NELV ELEMENT 1 [ 1A] GROUP 0 0.000000 0.350000 0.250000 0.000000 0.000000 0.000000 0.250000 0.350000 ELEMENT 2 [ 1B] GROUP 0 0.500000 0.353554 0.250000 0.350000 0.000000 0.353554 0.250000 0.000000 ELEMENT 3 [ 1C] GROUP 0 0.000000 0.000000 0.250000 0.353554 0.500000 0.350000 0.250000 0.353554 ELEMENT 4 [ 1A] GROUP 0 0.000000 0.000000 0.250000 0.350000 0.000000 -0.350000 -0.250000 0.000000 ELEMENT 5 [ 1B] GROUP 0 0.000000 0.353554 0.250000 0.000000 -0.500000 -0.353554 -0.250000 -0.350000 ELEMENT 6 [ 1C] GROUP 0 0.500000 0.350000 0.250000 0.353554 0.000000 0.000000 -0.250000 -0.353554 ELEMENT 7 [ 1A] GROUP 0 0.000000 -0.350000 -0.250000 0.000000 0.000000 0.000000 -0.250000 -0.350000 ELEMENT 8 [ 1B] GROUP 0 -0.500000 -0.353554 -0.250000 -0.350000 0.000000 -0.353554 -0.250000 0.000000 ELEMENT 9 [ 1C] GROUP 0 0.000000 0.000000 -0.250000 -0.353554 -0.500000 -0.350000 -0.250000 -0.353554 ELEMENT 10 [ 1A] GROUP 0 0.000000 0.000000 -0.250000 -0.350000 0.000000 0.350000 0.250000 0.000000 ELEMENT 11 [ 1B] GROUP 0 0.000000 -0.353554 -0.250000 0.000000 0.500000 0.353554 0.250000 0.350000 ELEMENT 12 [ 1C] GROUP 0 -0.500000 -0.350000 -0.250000 -0.353554 0.000000 0.000000 0.250000 0.353554 ***** CURVED SIDE DATA ***** 8 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE 1 2 0.50000 0.00000 0.00000 0.00000 0.00000 C 4 3 0.50000 0.00000 0.00000 0.00000 0.00000 C 1 5 0.50000 0.00000 0.00000 0.00000 0.00000 C 4 6 0.50000 0.00000 0.00000 0.00000 0.00000 C 1 8 0.50000 0.00000 0.00000 0.00000 0.00000 C 4 9 0.50000 0.00000 0.00000 0.00000 0.00000 C 1 11 0.50000 0.00000 0.00000 0.00000 0.00000 C 4 12 0.50000 0.00000 0.00000 0.00000 0.00000 C Kind regards, ZJ -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 18 07:18:45 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Oct 2017 12:18:45 +0000 Subject: [Nek5000-users] pipe prenek In-Reply-To: References: Message-ID: Dear ZJ, In order to parse the characters in the line, nek uses formatted reads for curve sides and for BC info. The format changes as the number of elements increases in order to accommodate the larger integers (i.e., the element number) in the same line, so you have to check either the reader source or prenek source or a valid .rea file to see what that formatting looks like. I've fixed your pipe mesh here. Note that there is a 2D pipe mesh (but with a different base template) in NekExamples/pipe/w2dcyl020a.rea Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, October 18, 2017 4:48:38 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] pipe prenek Hi Nek, Is there anyone knows how to calculate the curvature in .rea file. Recently, I want to generate a pipe mesh but it doesn't seem like a pipe in which I guess there is something wrong in curvature part in .rea file. I have attached the mesh part below. **MESH DATA** 1st line is X of corner 1,2,3,4. 2nd line is Y. 12 2 12 NEL,NDIM,NELV ELEMENT 1 [ 1A] GROUP 0 0.000000 0.350000 0.250000 0.000000 0.000000 0.000000 0.250000 0.350000 ELEMENT 2 [ 1B] GROUP 0 0.500000 0.353554 0.250000 0.350000 0.000000 0.353554 0.250000 0.000000 ELEMENT 3 [ 1C] GROUP 0 0.000000 0.000000 0.250000 0.353554 0.500000 0.350000 0.250000 0.353554 ELEMENT 4 [ 1A] GROUP 0 0.000000 0.000000 0.250000 0.350000 0.000000 -0.350000 -0.250000 0.000000 ELEMENT 5 [ 1B] GROUP 0 0.000000 0.353554 0.250000 0.000000 -0.500000 -0.353554 -0.250000 -0.350000 ELEMENT 6 [ 1C] GROUP 0 0.500000 0.350000 0.250000 0.353554 0.000000 0.000000 -0.250000 -0.353554 ELEMENT 7 [ 1A] GROUP 0 0.000000 -0.350000 -0.250000 0.000000 0.000000 0.000000 -0.250000 -0.350000 ELEMENT 8 [ 1B] GROUP 0 -0.500000 -0.353554 -0.250000 -0.350000 0.000000 -0.353554 -0.250000 0.000000 ELEMENT 9 [ 1C] GROUP 0 0.000000 0.000000 -0.250000 -0.353554 -0.500000 -0.350000 -0.250000 -0.353554 ELEMENT 10 [ 1A] GROUP 0 0.000000 0.000000 -0.250000 -0.350000 0.000000 0.350000 0.250000 0.000000 ELEMENT 11 [ 1B] GROUP 0 0.000000 -0.353554 -0.250000 0.000000 0.500000 0.353554 0.250000 0.350000 ELEMENT 12 [ 1C] GROUP 0 -0.500000 -0.350000 -0.250000 -0.353554 0.000000 0.000000 0.250000 0.353554 ***** CURVED SIDE DATA ***** 8 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE 1 2 0.50000 0.00000 0.00000 0.00000 0.00000 C 4 3 0.50000 0.00000 0.00000 0.00000 0.00000 C 1 5 0.50000 0.00000 0.00000 0.00000 0.00000 C 4 6 0.50000 0.00000 0.00000 0.00000 0.00000 C 1 8 0.50000 0.00000 0.00000 0.00000 0.00000 C 4 9 0.50000 0.00000 0.00000 0.00000 0.00000 C 1 11 0.50000 0.00000 0.00000 0.00000 0.00000 C 4 12 0.50000 0.00000 0.00000 0.00000 0.00000 C Kind regards, ZJ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: b.rea.gz Type: application/x-gzip Size: 2667 bytes Desc: b.rea.gz URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 18 07:42:25 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Oct 2017 13:42:25 +0100 Subject: [Nek5000-users] Element mesh mismatch in pipe Message-ID: Hi Nek, Do you know what can I do for the pipe running. It was good before, but I dont know why it doesn't work now it shows the error below when using nekmpi. I re-genmap even re-generated the rea file which didn't work. I,J,K,IE: 8 7 8 172686 Near Y = 0.44264699E-01 -0.45639873 9.3750000 , d: 0.0000000 -0.45384730E-01 2.0779221 WARNING2 Element mesh mismatch at: I,J,K,IE: 1 8 8 172687 Near Y = 0.46328000E-01 -0.47523300 9.3750000 , d: 0.55511151E-16 -0.70769971 2.0187379 WARNING2 Element mesh mismatch at: I,J,K,IE: 2 8 8 172687 Near Y = 0.49283703E-01 -0.47473225 9.3750000 , d: 0.0000000 -0.77340445 2.0187379 WARNING2 Element mesh mismatch at: I,J,K,IE: 8 8 8 172688 Near Y = 0.46328000E-01 -0.47523300 9.3750000 , d: 0.0000000 -0.70769971 2.0000000 Mesh consistency check failed. EXITING in VRDSMSH. call exitt: dying ... backtrace(): obtained 8 stack frames. ./nek5000() [0x6af030] ./nek5000() [0x877fa2] ./nek5000() [0x461c91] ./nek5000() [0x4082b1] ./nek5000() [0x406df9] ./nek5000() [0x4034be] /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f23bb3adc05] ./nek5000() [0x4033c9] Kind regards, ZJ -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 18 08:57:48 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Oct 2017 15:57:48 +0200 Subject: [Nek5000-users] pipe prenek (nek5000-users@lists.mcs.anl.gov) In-Reply-To: References: Message-ID: Hi ZJ, I have written a python script to generate a mesh for pipe flow which should follow the nek format of the rea files. Feel free to use it if you want to. You can use "git clone https://git.scc.kit.edu/nek5000_scripts/preprocessing" to clone my repository. Then go into the folder "GenPipeMesh" and follow the instructions in the README.md. As I have just made it public, you might run into trouble when cloning the repo. Moreover, consider the code as a work in progress. So there might be some mesh settings that do not work correctly. If you have problems cloning the repo or generating the mesh, just let me know and I will see what I can do (steffen.straub at kit.edu). HTH, Steffen On 10/18/2017 02:42 PM, nek5000-users-request at lists.mcs.anl.gov wrote: > Message: 2 > Date: Wed, 18 Oct 2017 12:18:45 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] pipe prenek > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > > Dear ZJ, > > > In order to parse the characters in the line, nek uses formatted reads for > > curve sides and for BC info. > > > The format changes as the number of elements increases in order to accommodate the larger integers (i.e., the element number) in the same line, > > so you have to check either the reader source or prenek source or a valid > > .rea file to see what that formatting looks like. > > > I've fixed your pipe mesh here. Note that there is a 2D pipe mesh (but with a different base template) in NekExamples/pipe/w2dcyl020a.rea > > > Paul > > > ________________________________ > From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Wednesday, October 18, 2017 4:48:38 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] pipe prenek > > Hi Nek, > > Is there anyone knows how to calculate the curvature in .rea file. Recently, I want to generate a pipe mesh but it doesn't seem like a pipe in which I guess there is something wrong in curvature part in .rea file. I have attached the mesh part below. > > **MESH DATA** 1st line is X of corner 1,2,3,4. 2nd line is Y. > 12 2 12 NEL,NDIM,NELV > ELEMENT 1 [ 1A] GROUP 0 > 0.000000 0.350000 0.250000 0.000000 > 0.000000 0.000000 0.250000 0.350000 > ELEMENT 2 [ 1B] GROUP 0 > 0.500000 0.353554 0.250000 0.350000 > 0.000000 0.353554 0.250000 0.000000 > ELEMENT 3 [ 1C] GROUP 0 > 0.000000 0.000000 0.250000 0.353554 > 0.500000 0.350000 0.250000 0.353554 > ELEMENT 4 [ 1A] GROUP 0 > 0.000000 0.000000 0.250000 0.350000 > 0.000000 -0.350000 -0.250000 0.000000 > ELEMENT 5 [ 1B] GROUP 0 > 0.000000 0.353554 0.250000 0.000000 > -0.500000 -0.353554 -0.250000 -0.350000 > ELEMENT 6 [ 1C] GROUP 0 > 0.500000 0.350000 0.250000 0.353554 > 0.000000 0.000000 -0.250000 -0.353554 > ELEMENT 7 [ 1A] GROUP 0 > 0.000000 -0.350000 -0.250000 0.000000 > 0.000000 0.000000 -0.250000 -0.350000 > ELEMENT 8 [ 1B] GROUP 0 > -0.500000 -0.353554 -0.250000 -0.350000 > 0.000000 -0.353554 -0.250000 0.000000 > ELEMENT 9 [ 1C] GROUP 0 > 0.000000 0.000000 -0.250000 -0.353554 > -0.500000 -0.350000 -0.250000 -0.353554 > ELEMENT 10 [ 1A] GROUP 0 > 0.000000 0.000000 -0.250000 -0.350000 > 0.000000 0.350000 0.250000 0.000000 > ELEMENT 11 [ 1B] GROUP 0 > 0.000000 -0.353554 -0.250000 0.000000 > 0.500000 0.353554 0.250000 0.350000 > ELEMENT 12 [ 1C] GROUP 0 > -0.500000 -0.350000 -0.250000 -0.353554 > 0.000000 0.000000 0.250000 0.353554 > ***** CURVED SIDE DATA ***** > 8 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE > 1 2 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 3 0.50000 0.00000 0.00000 0.00000 0.00000 C > 1 5 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 6 0.50000 0.00000 0.00000 0.00000 0.00000 C > 1 8 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 9 0.50000 0.00000 0.00000 0.00000 0.00000 C > 1 11 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 12 0.50000 0.00000 0.00000 0.00000 0.00000 C > > > Kind regards, > > ZJ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: b.rea.gz > Type: application/x-gzip > Size: 2667 bytes > Desc: b.rea.gz > URL: > > ------------------------------ From nek5000-users at lists.mcs.anl.gov Wed Oct 18 09:44:46 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Oct 2017 15:44:46 +0100 Subject: [Nek5000-users] Nek5000-users Digest, Vol 104, Issue 15 In-Reply-To: References: Message-ID: Hi Paul, Even I used the 2d mesh in example directory with quad multi-split and n2to3, there still some errors showing element mesh mismatch. I do think things gonna changed since using genmap where there is always one or some errors showing some elements were with shift. How can I do that? ...... ...... ...... WARNING2 Element mesh mismatch at: I,J,K,IE: 8 7 8 175498 Near Y = 0.42311775 0.79128327 18.648600 , d: 0.48220174E-01 0.0000000 1.2026574 WARNING2 Element mesh mismatch at: I,J,K,IE: 1 8 8 175499 Near Y = 0.40657800 0.75559000 18.648600 , d: 0.75191377 0.0000000 1.3234691 WARNING2 Element mesh mismatch at: I,J,K,IE: 2 8 8 175499 Near Y = 0.41137682 0.75312483 18.648600 , d: 1.0321964 0.0000000 1.3234691 WARNING2 Element mesh mismatch at: I,J,K,IE: 8 8 8 175500 Near Y = 0.40657800 0.75559000 18.648600 , d: 0.75191377 -0.33306691E-15 1.2647709 Mesh consistency check failed. EXITING in VRDSMSH. call exitt: dying ... backtrace(): obtained 8 stack frames. ./nek5000() [0x6aee70] ./nek5000() [0x877e12] ./nek5000() [0x461c1a] ./nek5000() [0x4082d1] ./nek5000() [0x406e19] ./nek5000() [0x4034be] /lib64/libc.so.6(__libc_start_main+0xf5) [0x7fe817d58c05] ./nek5000() [0x4033c9] Regards, ZJ On 18 October 2017 at 13:42, wrote: > 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. pipe prenek (nek5000-users at lists.mcs.anl.gov) > 2. Re: pipe prenek (nek5000-users at lists.mcs.anl.gov) > 3. Element mesh mismatch in pipe (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 18 Oct 2017 10:48:38 +0100 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] pipe prenek > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Nek, > > Is there anyone knows how to calculate the curvature in .rea file. > Recently, I want to generate a pipe mesh but it doesn't seem like a pipe in > which I guess there is something wrong in curvature part in .rea file. I > have attached the mesh part below. > > **MESH DATA** 1st line is X of corner 1,2,3,4. 2nd line is Y. > 12 2 12 NEL,NDIM,NELV > ELEMENT 1 [ 1A] GROUP 0 > 0.000000 0.350000 0.250000 0.000000 > 0.000000 0.000000 0.250000 0.350000 > ELEMENT 2 [ 1B] GROUP 0 > 0.500000 0.353554 0.250000 0.350000 > 0.000000 0.353554 0.250000 0.000000 > ELEMENT 3 [ 1C] GROUP 0 > 0.000000 0.000000 0.250000 0.353554 > 0.500000 0.350000 0.250000 0.353554 > ELEMENT 4 [ 1A] GROUP 0 > 0.000000 0.000000 0.250000 0.350000 > 0.000000 -0.350000 -0.250000 0.000000 > ELEMENT 5 [ 1B] GROUP 0 > 0.000000 0.353554 0.250000 0.000000 > -0.500000 -0.353554 -0.250000 -0.350000 > ELEMENT 6 [ 1C] GROUP 0 > 0.500000 0.350000 0.250000 0.353554 > 0.000000 0.000000 -0.250000 -0.353554 > ELEMENT 7 [ 1A] GROUP 0 > 0.000000 -0.350000 -0.250000 0.000000 > 0.000000 0.000000 -0.250000 -0.350000 > ELEMENT 8 [ 1B] GROUP 0 > -0.500000 -0.353554 -0.250000 -0.350000 > 0.000000 -0.353554 -0.250000 0.000000 > ELEMENT 9 [ 1C] GROUP 0 > 0.000000 0.000000 -0.250000 -0.353554 > -0.500000 -0.350000 -0.250000 -0.353554 > ELEMENT 10 [ 1A] GROUP 0 > 0.000000 0.000000 -0.250000 -0.350000 > 0.000000 0.350000 0.250000 0.000000 > ELEMENT 11 [ 1B] GROUP 0 > 0.000000 -0.353554 -0.250000 0.000000 > 0.500000 0.353554 0.250000 0.350000 > ELEMENT 12 [ 1C] GROUP 0 > -0.500000 -0.350000 -0.250000 -0.353554 > 0.000000 0.000000 0.250000 0.353554 > ***** CURVED SIDE DATA ***** > 8 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE > 1 2 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 3 0.50000 0.00000 0.00000 0.00000 0.00000 C > 1 5 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 6 0.50000 0.00000 0.00000 0.00000 0.00000 C > 1 8 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 9 0.50000 0.00000 0.00000 0.00000 0.00000 C > 1 11 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 12 0.50000 0.00000 0.00000 0.00000 0.00000 C > > > Kind regards, > > ZJ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20171018/f347a7fa/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Wed, 18 Oct 2017 12:18:45 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] pipe prenek > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > > Dear ZJ, > > > In order to parse the characters in the line, nek uses formatted reads for > > curve sides and for BC info. > > > The format changes as the number of elements increases in order to > accommodate the larger integers (i.e., the element number) in the same line, > > so you have to check either the reader source or prenek source or a valid > > .rea file to see what that formatting looks like. > > > I've fixed your pipe mesh here. Note that there is a 2D pipe mesh (but > with a different base template) in NekExamples/pipe/w2dcyl020a.rea > > > Paul > > > ________________________________ > From: Nek5000-users on behalf > of nek5000-users at lists.mcs.anl.gov > Sent: Wednesday, October 18, 2017 4:48:38 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] pipe prenek > > Hi Nek, > > Is there anyone knows how to calculate the curvature in .rea file. > Recently, I want to generate a pipe mesh but it doesn't seem like a pipe in > which I guess there is something wrong in curvature part in .rea file. I > have attached the mesh part below. > > **MESH DATA** 1st line is X of corner 1,2,3,4. 2nd line is Y. > 12 2 12 NEL,NDIM,NELV > ELEMENT 1 [ 1A] GROUP 0 > 0.000000 0.350000 0.250000 0.000000 > 0.000000 0.000000 0.250000 0.350000 > ELEMENT 2 [ 1B] GROUP 0 > 0.500000 0.353554 0.250000 0.350000 > 0.000000 0.353554 0.250000 0.000000 > ELEMENT 3 [ 1C] GROUP 0 > 0.000000 0.000000 0.250000 0.353554 > 0.500000 0.350000 0.250000 0.353554 > ELEMENT 4 [ 1A] GROUP 0 > 0.000000 0.000000 0.250000 0.350000 > 0.000000 -0.350000 -0.250000 0.000000 > ELEMENT 5 [ 1B] GROUP 0 > 0.000000 0.353554 0.250000 0.000000 > -0.500000 -0.353554 -0.250000 -0.350000 > ELEMENT 6 [ 1C] GROUP 0 > 0.500000 0.350000 0.250000 0.353554 > 0.000000 0.000000 -0.250000 -0.353554 > ELEMENT 7 [ 1A] GROUP 0 > 0.000000 -0.350000 -0.250000 0.000000 > 0.000000 0.000000 -0.250000 -0.350000 > ELEMENT 8 [ 1B] GROUP 0 > -0.500000 -0.353554 -0.250000 -0.350000 > 0.000000 -0.353554 -0.250000 0.000000 > ELEMENT 9 [ 1C] GROUP 0 > 0.000000 0.000000 -0.250000 -0.353554 > -0.500000 -0.350000 -0.250000 -0.353554 > ELEMENT 10 [ 1A] GROUP 0 > 0.000000 0.000000 -0.250000 -0.350000 > 0.000000 0.350000 0.250000 0.000000 > ELEMENT 11 [ 1B] GROUP 0 > 0.000000 -0.353554 -0.250000 0.000000 > 0.500000 0.353554 0.250000 0.350000 > ELEMENT 12 [ 1C] GROUP 0 > -0.500000 -0.350000 -0.250000 -0.353554 > 0.000000 0.000000 0.250000 0.353554 > ***** CURVED SIDE DATA ***** > 8 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE > 1 2 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 3 0.50000 0.00000 0.00000 0.00000 0.00000 C > 1 5 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 6 0.50000 0.00000 0.00000 0.00000 0.00000 C > 1 8 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 9 0.50000 0.00000 0.00000 0.00000 0.00000 C > 1 11 0.50000 0.00000 0.00000 0.00000 0.00000 C > 4 12 0.50000 0.00000 0.00000 0.00000 0.00000 C > > > Kind regards, > > ZJ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20171018/fbc775d5/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: b.rea.gz > Type: application/x-gzip > Size: 2667 bytes > Desc: b.rea.gz > URL: attachments/20171018/fbc775d5/attachment-0001.gz> > > ------------------------------ > > Message: 3 > Date: Wed, 18 Oct 2017 13:42:25 +0100 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Element mesh mismatch in pipe > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Nek, > > Do you know what can I do for the pipe running. It was good before, but I > dont know why it doesn't work now it shows the error below when using > nekmpi. I re-genmap even re-generated the rea file which didn't work. > > I,J,K,IE: 8 7 8 172686 > Near Y = 0.44264699E-01 -0.45639873 9.3750000 , d: 0.0000000 > -0.45384730E-01 2.0779221 > WARNING2 Element mesh mismatch at: > I,J,K,IE: 1 8 8 172687 > Near Y = 0.46328000E-01 -0.47523300 9.3750000 , d: > 0.55511151E-16 -0.70769971 2.0187379 > WARNING2 Element mesh mismatch at: > I,J,K,IE: 2 8 8 172687 > Near Y = 0.49283703E-01 -0.47473225 9.3750000 , d: 0.0000000 > -0.77340445 2.0187379 > WARNING2 Element mesh mismatch at: > I,J,K,IE: 8 8 8 172688 > Near Y = 0.46328000E-01 -0.47523300 9.3750000 , d: 0.0000000 > -0.70769971 2.0000000 > Mesh consistency check failed. EXITING in VRDSMSH. > > call exitt: dying ... > > backtrace(): obtained 8 stack frames. > ./nek5000() [0x6af030] > ./nek5000() [0x877fa2] > ./nek5000() [0x461c91] > ./nek5000() [0x4082b1] > ./nek5000() [0x406df9] > ./nek5000() [0x4034be] > /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f23bb3adc05] > ./nek5000() [0x4033c9] > > > Kind regards, > > ZJ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: attachments/20171018/c2eea72e/attachment.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > 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 104, Issue 15 > ********************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 19 03:50:23 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 19 Oct 2017 10:50:23 +0200 Subject: [Nek5000-users] fix projection for multiple passive scalars Message-ID: Hi Neks, in order to use projection (p94!=0) for one temperature field and at least one additional passive scalar, I believe that the variables napproxt and approxt need to be extended by the size of ldimt. See the attached git-diff.txt for my changes to the code. When I adjust the code like that, projection for veloctity, temperature and all passive scalars works, otherwise it fails with: ... 22? Error Hmholtz TEMP???? 100????????? NaN????????? NaN 1.0000E-08 22proj_ortho:??? 1?? 2 TEMP?? Detect rank deficiency: NaN???????? NaN 22? Project PS 1????????????????? NaN????????? NaN????????? NaN 1?? 0 22? Error Hmholtz PS 1???? 100????????? NaN????????? NaN 1.0000E-08 22proj_ortho:??? 1?? 2 PS 1?? Detect rank deficiency: NaN???????? NaN 22? Project PS 2????????????????? NaN????????? NaN????????? NaN 1?? 0 22? Error Hmholtz PS 2???? 100????????? NaN????????? NaN 1.0000E-08 22proj_ortho:??? 1?? 2 PS 2?? Detect rank deficiency: NaN???????? NaN ... Can one of the developers please confirm and if confirmed include it in the master branch? Best, Steffen Straub -- Karlsruhe Institute of Technology (KIT) Institute of Fluid Mechanics M.Sc. Steffen Straub Doctoral Researcher Kaiserstra?e 10 Building 10.23 76131 Karlsruhe, Germany Phone: +49 721 608-43027 E-mail: steffen.straub at kit.edu Web: http://www.istm.kit.edu Registered office: Kaiserstra?e 12, 76131 Karlsruhe, Germany KIT ? The Research University in the Helmholtz Association -------------- next part -------------- diff --git a/core/ORTHOT b/core/ORTHOT index dfd3efd..5a87743 100644 --- a/core/ORTHOT +++ b/core/ORTHOT @@ -5,10 +5,13 @@ c c parameter (ktott = 1) c parameter (laxtt = 1) c - integer napproxt(2) +C Each approximation space for passive scalars should have +C its own approximation space. +C Hence, extend napproxt and approxt by ldimt. + integer napproxt(2,ldimt) common /trthoi/ napproxt - real approxt(ktott,0:laxtt) + real approxt(ktott,0:laxtt,ldimt) common /trthov/ approxt character*4 name4t diff --git a/core/conduct.f b/core/conduct.f index 301dc3b..d0f7bd9 100644 --- a/core/conduct.f +++ b/core/conduct.f @@ -27,7 +27,11 @@ C endif - napproxt(1) = laxtt ! Fix this... pff 10/10/15 +c napproxt(1) = laxtt ! Fix this... pff 10/10/15 +C napproxt has been extended to account for each passive scalar +C individually + napproxt(1,ifield-1) = laxtt ! for each ifield + nel = nelfld(ifield) n = nx1*ny1*nz1*nel @@ -82,12 +86,17 @@ c $ ,tmult(1,1,1,1,ifield-1) c $ ,imesh,tolht(ifield),nmxh,isd) if(iftmsh(ifield)) then +C When calling hsolve, we need to pass the correct approxt and napproxt +C depending on which ifield (passive scalar) we are working on. call hsolve (name4t,TA,TB,H1,H2 $ ,tmask(1,1,1,1,ifield-1) $ ,tmult(1,1,1,1,ifield-1) $ ,imesh,tolht(ifield),nmxh,1 - $ ,approxt,napproxt,bintm1) + $ ,approxt(1,1,ifield-1),napproxt(1,ifield-1) + & ,bintm1) else +C For Cases where iftmsh(ifield)=False, I do not know whether something +C needs to be adjusted too. call hsolve (name4t,TA,TB,H1,H2 $ ,tmask(1,1,1,1,ifield-1) $ ,tmult(1,1,1,1,ifield-1) diff --git a/core/perturb.f b/core/perturb.f index 59c16ea..359b326 100644 --- a/core/perturb.f +++ b/core/perturb.f @@ -599,7 +599,8 @@ C $ ,H2(LX1,LY1,LZ1,LELT) c include 'ORTHOT' - napproxt(1) = laxtt +C napproxt(1) = laxtt + napproxt(1,ifield-1) = laxtt C IF (IGEOM.EQ.1) THEN C From nek5000-users at lists.mcs.anl.gov Thu Oct 19 07:38:12 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 19 Oct 2017 14:38:12 +0200 Subject: [Nek5000-users] fix projection for multiple passive scalars In-Reply-To: References: Message-ID: If you think this is a bug, please report it on GitHub. On 19 Oct 2017, at 10:52, "nek5000-users at lists.mcs.anl.gov " > wrote: Hi Neks, in order to use projection (p94!=0) for one temperature field and at least one additional passive scalar, I believe that the variables napproxt and approxt need to be extended by the size of ldimt. See the attached git-diff.txt for my changes to the code. When I adjust the code like that, projection for veloctity, temperature and all passive scalars works, otherwise it fails with: ... 22? Error Hmholtz TEMP???? 100????????? NaN????????? NaN 1.0000E-08 22proj_ortho:??? 1?? 2 TEMP?? Detect rank deficiency: NaN???????? NaN 22? Project PS 1????????????????? NaN????????? NaN????????? NaN 1?? 0 22? Error Hmholtz PS 1???? 100????????? NaN????????? NaN 1.0000E-08 22proj_ortho:??? 1?? 2 PS 1?? Detect rank deficiency: NaN???????? NaN 22? Project PS 2????????????????? NaN????????? NaN????????? NaN 1?? 0 22? Error Hmholtz PS 2???? 100????????? NaN????????? NaN 1.0000E-08 22proj_ortho:??? 1?? 2 PS 2?? Detect rank deficiency: NaN???????? NaN ... Can one of the developers please confirm and if confirmed include it in the master branch? Best, Steffen Straub -- Karlsruhe Institute of Technology (KIT) Institute of Fluid Mechanics M.Sc. Steffen Straub Doctoral Researcher Kaiserstra?e 10 Building 10.23 76131 Karlsruhe, Germany Phone: +49 721 608-43027 E-mail: steffen.straub at kit.edu Web: http://www.istm.kit.edu Registered office: Kaiserstra?e 12, 76131 Karlsruhe, Germany KIT ? The Research University in the Helmholtz Association _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 19 07:51:59 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 19 Oct 2017 12:51:59 +0000 Subject: [Nek5000-users] par file and moving mesh Message-ID: Hi all, I am trying to switch from a rea file to a par file and I am having difficulties with the moving mesh capabilities. When visualizing the numerical solution, the mesh is not moving, whereas it was moving with a previous version of Nek5000. I copied the par file from the my_cyl examples as a start point. The main different between my session and the mv_cyl session is the way the mesh motion is handled. I believe the mesh velocity is provided by the user through a function, whereas in my session the mesh velocity is solved for. Below is the par file I am currently using: # # nek parameter file # [GENERAL] #startFrom = restart.fld stopAt = numSteps endTime = 0 numSteps = 1000 dt = 1e-03 timeStepper = bdf #bdf #char #steady tOrder = 3 variableDt = no maxCFL = 2.0 writeControl = timeStep #runTime writeInterval = 50 dealiasing = yes userParam01 = 1.16 userParam02 = 1.8550800E-05 [PROBLEMTYPE] lowMachNumber = no variableProperties = yes dp0dt = no [MESH] motion = yes meshVelocity = no [PRESSURE] residualTol = 1e-10 residualProj = no #preconditioner = amg [VELOCITY] residualTol = 1e-12 residualProj = no Any help will be appreciated. Thanks, Marco From nek5000-users at lists.mcs.anl.gov Thu Oct 19 06:17:36 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 19 Oct 2017 11:17:36 +0000 Subject: [Nek5000-users] Using mshconvert With Curves Message-ID: Hey Neks, I want to convert a 3D pipe mesh (.msh) with periodic BC at inlet and outlet with mshconvert.py. Geometry and Mesh information: D=0.1 L=0.3 (0 "Zone Sections") 9 fluid PART() 11 wall PER2)()) 12 wall PER1)()) 13 wall WALL)()) --> convert('pipe_4.msh',bcs={9:'E',13:'W'},periodic_dx={(12,11):[0.0,0.0,0.3]},curves={????}) Can somebody tell me, what I have to write as input for curve? G Kevin -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 19 09:13:13 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 19 Oct 2017 14:13:13 +0000 Subject: [Nek5000-users] fix projection for multiple passive scalars In-Reply-To: References: Message-ID: Yes, this is a bug. Sorry - Because of another issue (now resolved), I hadn't been attending to this part of projection yet (since it was essentially broken before). I'll try to get this fixed asap. Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, October 19, 2017 3:50:23 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] fix projection for multiple passive scalars Hi Neks, in order to use projection (p94!=0) for one temperature field and at least one additional passive scalar, I believe that the variables napproxt and approxt need to be extended by the size of ldimt. See the attached git-diff.txt for my changes to the code. When I adjust the code like that, projection for veloctity, temperature and all passive scalars works, otherwise it fails with: ... 22 Error Hmholtz TEMP 100 NaN NaN 1.0000E-08 22proj_ortho: 1 2 TEMP Detect rank deficiency: NaN NaN 22 Project PS 1 NaN NaN NaN 1 0 22 Error Hmholtz PS 1 100 NaN NaN 1.0000E-08 22proj_ortho: 1 2 PS 1 Detect rank deficiency: NaN NaN 22 Project PS 2 NaN NaN NaN 1 0 22 Error Hmholtz PS 2 100 NaN NaN 1.0000E-08 22proj_ortho: 1 2 PS 2 Detect rank deficiency: NaN NaN ... Can one of the developers please confirm and if confirmed include it in the master branch? Best, Steffen Straub -- Karlsruhe Institute of Technology (KIT) Institute of Fluid Mechanics M.Sc. Steffen Straub Doctoral Researcher Kaiserstra?e 10 Building 10.23 76131 Karlsruhe, Germany Phone: +49 721 608-43027 E-mail: steffen.straub at kit.edu Web: http://www.istm.kit.edu Registered office: Kaiserstra?e 12, 76131 Karlsruhe, Germany KIT ? The Research University in the Helmholtz Association -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 20 03:03:38 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Oct 2017 15:03:38 +0700 Subject: [Nek5000-users] g2gi in new version Message-ID: Hello I try to interpolate my solution from coarse to fine mesh with g2gi function, but compilation of my problem crashed: per.f:(.text+0x3bfd): undefined reference to `g2gi_'. I use the example from manual, but It seems like there is no g2gi function in new version of the nek (I look in "core" folder and especially in postpro.f file, like in older version). May be this function has been renamed. Regards, Vatslav -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 20 03:06:58 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Oct 2017 10:06:58 +0200 Subject: [Nek5000-users] g2gi in new version In-Reply-To: References: Message-ID: Please read the Release Notes. This function was replaced by gflr. On 20 Oct 2017, at 10:04, "nek5000-users at lists.mcs.anl.gov " > wrote: Hello I try to interpolate my solution from coarse to fine mesh with g2gi function, but compilation of my problem crashed: per.f:(.text+0x3bfd): undefined reference to `g2gi_'. I use the example from manual, but It seems like there is no g2gi function in new version of the nek (I look in "core" folder and especially in postpro.f file, like in older version). May be this function has been renamed. Regards, Vatslav _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 20 09:06:29 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Oct 2017 14:06:29 +0000 Subject: [Nek5000-users] Error when loading file Message-ID: Hi, I load a file in userchk for postprocessing like this: subroutine userchk include 'SIZE' include 'TOTAL' character(64)::filen filen="cha0.f00027" call load_fld(trim(filen)) return end However, I the program crashes. This is how it looks in the logfile: nsteps=0 -> skip time loop running solver in post processing mode call userchk set initial conditions Checking restart options: cha0.f000274^@^@^@^@start nekuic (1) for ifld 1 nekuic (1) for ifld 2 nekuic (1) for ifld 3 nekuic (1) for ifld 4 Reading checkpoint data 0 0 OPEN: cha0.f000274^@^@^@^@start cha0.f000274 byte_read() :: fopen failure2! ERROR: Error reading restart header in mfi_prepare ierr= 1 Why does this error appear, and how can Ifix it? Best, Johan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 20 09:19:42 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Oct 2017 16:19:42 +0200 Subject: [Nek5000-users] Error when loading file Message-ID: load_fld() expects a character*132 on input! Cheers, Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 20th October 2017 16:11 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Error when loading file > > Hi, > > I load a file in userchk for postprocessing like this: > > ????? subroutine userchk > ????? include 'SIZE' > ????? include 'TOTAL' > ????? character(64)::filen > ????? filen="cha0.f00027" > > ????? call load_fld(trim(filen)) > > ????? return > ????? end > > However, I the program crashes. This is how it looks in the logfile: > > ?nsteps=0 -> skip time loop > ?running solver in post processing mode > > ?call userchk > > ?set initial conditions > ?Checking restart options: cha0.f000274^@^@^@^@start > ?nekuic (1) for ifld??????????? 1 > ?nekuic (1) for ifld??????????? 2 > ?nekuic (1) for ifld??????????? 3 > ?nekuic (1) for ifld??????????? 4 > ?Reading checkpoint data > ?????? 0?????? 0 OPEN: cha0.f000274^@^@^@^@start > cha0.f000274 > byte_read() :: fopen failure2! > ERROR: Error reading restart header in mfi_prepare? ierr=? 1 > > Why does this error appear, and how can Ifix it? > > Best, > > Johan > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Oct 20 10:06:43 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Oct 2017 15:06:43 +0000 Subject: [Nek5000-users] Error when loading file In-Reply-To: References: Message-ID: Hi Johan, There's also an example in navier5.f in the subroutine autoaverager(). Usage is (say): ls -C1 case0.f* > list.in then add this to a blank .usr file and run it c----------------------------------------------------------------------- subroutine usrdat2 ! This routine to modify mesh coordinates include 'SIZE' include 'TOTAL' character*127 fname127 call blank(fname127,127) fname127='list.in' call auto_averager(fname127) ! simple average of files call outpost(vx,vy,vz,pr,t,' ') call exitti('quit after autoaverager$',nelv) return end c----------------------------------------------------------------------- Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Friday, October 20, 2017 9:19:42 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Error when loading file load_fld() expects a character*132 on input! Cheers, Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 20th October 2017 16:11 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Error when loading file > > Hi, > > I load a file in userchk for postprocessing like this: > > subroutine userchk > include 'SIZE' > include 'TOTAL' > character(64)::filen > filen="cha0.f00027" > > call load_fld(trim(filen)) > > return > end > > However, I the program crashes. This is how it looks in the logfile: > > nsteps=0 -> skip time loop > running solver in post processing mode > > call userchk > > set initial conditions > Checking restart options: cha0.f000274^@^@^@^@start > nekuic (1) for ifld 1 > nekuic (1) for ifld 2 > nekuic (1) for ifld 3 > nekuic (1) for ifld 4 > Reading checkpoint data > 0 0 OPEN: cha0.f000274^@^@^@^@start > cha0.f000274 > byte_read() :: fopen failure2! > ERROR: Error reading restart header in mfi_prepare ierr= 1 > > Why does this error appear, and how can Ifix it? > > Best, > > Johan > > > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 20 10:25:30 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Oct 2017 15:25:30 +0000 Subject: [Nek5000-users] Error when loading file In-Reply-To: References: , Message-ID: This solved the problem, thank you! By the way: Is is OK to load files from outside the current directory using the full path to the file? Best, Johan ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Friday, October 20, 2017 5:06:43 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Error when loading file Hi Johan, There's also an example in navier5.f in the subroutine autoaverager(). Usage is (say): ls -C1 case0.f* > list.in then add this to a blank .usr file and run it c----------------------------------------------------------------------- subroutine usrdat2 ! This routine to modify mesh coordinates include 'SIZE' include 'TOTAL' character*127 fname127 call blank(fname127,127) fname127='list.in' call auto_averager(fname127) ! simple average of files call outpost(vx,vy,vz,pr,t,' ') call exitti('quit after autoaverager$',nelv) return end c----------------------------------------------------------------------- Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Friday, October 20, 2017 9:19:42 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Error when loading file load_fld() expects a character*132 on input! Cheers, Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 20th October 2017 16:11 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Error when loading file > > Hi, > > I load a file in userchk for postprocessing like this: > > subroutine userchk > include 'SIZE' > include 'TOTAL' > character(64)::filen > filen="cha0.f00027" > > call load_fld(trim(filen)) > > return > end > > However, I the program crashes. This is how it looks in the logfile: > > nsteps=0 -> skip time loop > running solver in post processing mode > > call userchk > > set initial conditions > Checking restart options: cha0.f000274^@^@^@^@start > nekuic (1) for ifld 1 > nekuic (1) for ifld 2 > nekuic (1) for ifld 3 > nekuic (1) for ifld 4 > Reading checkpoint data > 0 0 OPEN: cha0.f000274^@^@^@^@start > cha0.f000274 > byte_read() :: fopen failure2! > ERROR: Error reading restart header in mfi_prepare ierr= 1 > > Why does this error appear, and how can Ifix it? > > Best, > > Johan > > > > > _______________________________________________ > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 20 10:27:35 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 20 Oct 2017 17:27:35 +0200 Subject: [Nek5000-users] Error when loading file In-Reply-To: References: Message-ID: Yes, as long as the string does not exceed 132 characters. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 20th October 2017 17:25 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Error when loading file > > This solved the problem, thank you! > > By the way: Is is OK to load files from outside the current directory?using the full path to the file? > > Best, > > Johan > ----------- > From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Friday, October 20, 2017 5:06:43 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Error when loading file > > Hi Johan, > > There's also an example in navier5.f in the subroutine autoaverager(). > > Usage is (say): > > ls -C1 case0.f* > list.in > > then add this to a blank .usr file and run it > > c----------------------------------------------------------------------- > ? ? ? subroutine usrdat2? > ! This routine to modify mesh coordinates > ? ? ? include 'SIZE' > ? ? ? include 'TOTAL' > ? ? ? character*127 fname127 > > ? ? ? call blank(fname127,127) > > ? ? ? fname127='list.in' > ? ? ? call auto_averager(fname127) ! simple average of files > ? ? ? call outpost(vx,vy,vz,pr,t,' > ? ') > ? ? ? call exitti('quit after autoaverager$',nelv) > > ? ? ? return > ? ? ? end > c----------------------------------------------------------------------- > Paul > > ----------- > From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov > Sent: Friday, October 20, 2017 9:19:42 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Error when loading file > load_fld() expects a character*132 on input! > > Cheers, > Stefan > > -----Original message----- > > From:nek5000-users at lists.mcs.anl.gov > > Sent: Friday 20th October 2017 16:11 > > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] Error when loading file > > > > Hi, > > > > I load a file in userchk for postprocessing like this: > > > > ????? subroutine userchk > > ????? include 'SIZE' > > ????? include 'TOTAL' > > ????? character(64)::filen > > ????? filen="cha0.f00027" > > > > ????? call load_fld(trim(filen)) > > > > ????? return > > ????? end > > > > However, I the program crashes. This is how it looks in the logfile: > > > > ?nsteps=0 -> skip time loop > > ?running solver in post processing mode > > > > ?call userchk > > > > ?set initial conditions > > ?Checking restart options: cha0.f000274^@^@^@^@start > > ?nekuic (1) for ifld??????????? 1 > > ?nekuic (1) for ifld??????????? 2 > > ?nekuic (1) for ifld??????????? 3 > > ?nekuic (1) for ifld??????????? 4 > > ?Reading checkpoint data > > ?????? 0?????? 0 OPEN: cha0.f000274^@^@^@^@start > > cha0.f000274 > > byte_read() :: fopen failure2! > > ERROR: Error reading restart header in mfi_prepare? ierr=? 1 > > > > Why does this error appear, and how can Ifix it? > > > > Best, > > > > Johan > > > > > > > > > > _______________________________________________ > > 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 From nek5000-users at lists.mcs.anl.gov Mon Oct 23 04:31:48 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Oct 2017 11:31:48 +0200 Subject: [Nek5000-users] Accessing variables Message-ID: I am trying to access local velocity to do some post-processing during execution. If I take as output vy on a given point, I have a result. The same value of vy is given in my output ascii field file. The vy changes the sign but the mangitude is exactly the same when I see the field files on visit. Finally, if I export the field file to tecplot formula, the vy has the same value I see on visit. The problem is that the post-processing works well on tecplot, while on my subroutine in the usr file doesn't work, since not only the vy value is wrong, but it affects also the vorticity computation, that I need. Thanks Mario Ostieri Ph.D. Student University of Naples Federico II Department of Industrial Engineering Piazzale V. Tecchio 80 80125 Napoli, Italy tel. +390817682184 email: mario.ostieri at unina.it From nek5000-users at lists.mcs.anl.gov Mon Oct 23 04:38:07 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Oct 2017 11:38:07 +0200 Subject: [Nek5000-users] Accessing variables In-Reply-To: References: Message-ID: I consider the values in vy as the "truth", not the values you see in VisIt or Tecplot. What's the magnitude of the values switching their sign? -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Monday 23rd October 2017 11:32 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Accessing variables > > I am trying to access local velocity to do some post-processing during > execution. > If I take as output vy on a given point, I have a result. The same > value of vy is given in my output ascii field file. > The vy changes the sign but the mangitude is exactly the same when I > see the field files on visit. > Finally, if I export the field file to tecplot formula, the vy has the > same value I see on visit. > The problem is that the post-processing works well on tecplot, while > on my subroutine in the usr file doesn't work, since not only the vy > value is wrong, but it affects also the vorticity computation, that I > need. > > Thanks > > Mario Ostieri > > Ph.D. Student > University of Naples Federico II > Department of Industrial Engineering > Piazzale V. Tecchio 80 > 80125 Napoli, Italy > tel. +390817682184 > email: mario.ostieri at unina.it > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Mon Oct 23 04:57:51 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Oct 2017 11:57:51 +0200 Subject: [Nek5000-users] Accessing variables In-Reply-To: References: Message-ID: The value is 0.0242. I simulated a plunging flat plate in the body reference frame. So if uy it was the ''real'' body velocity, I set the opposite on the v bcs and wall bc on the body. The ic I set was -uy at t=0. The vy valuss along the flow field are basically set by the boundary condition since the plunging frequency is low, so I would expect little differences from the magnitude but not a change of the sign. Furthermore, what I don't understand is the fact that the post processing with the visit values (I'm computing volume integrals of the vorticity multiplied vy) is right, while the same integrals on my subroutine go wrong. Mario Quoting nek5000-users at lists.mcs.anl.gov: > I consider the values in vy as the "truth", not the values you see > in VisIt or Tecplot. What's the magnitude of the values switching > their sign? > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Monday 23rd October 2017 11:32 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: [Nek5000-users] Accessing variables >> >> I am trying to access local velocity to do some post-processing during >> execution. >> If I take as output vy on a given point, I have a result. The same >> value of vy is given in my output ascii field file. >> The vy changes the sign but the mangitude is exactly the same when I >> see the field files on visit. >> Finally, if I export the field file to tecplot formula, the vy has the >> same value I see on visit. >> The problem is that the post-processing works well on tecplot, while >> on my subroutine in the usr file doesn't work, since not only the vy >> value is wrong, but it affects also the vorticity computation, that I >> need. >> >> Thanks >> >> Mario Ostieri >> >> Ph.D. Student >> University of Naples Federico II >> Department of Industrial Engineering >> Piazzale V. Tecchio 80 >> 80125 Napoli, Italy >> tel. +390817682184 >> email: mario.ostieri at unina.it >> >> _______________________________________________ >> 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 > > Mario Ostieri Ph.D. Student University of Naples Federico II Department of Industrial Engineering Piazzale V. Tecchio 80 80125 Napoli, Italy tel. +390817682184 email: mario.ostieri at unina.it From nek5000-users at lists.mcs.anl.gov Mon Oct 23 08:19:52 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Oct 2017 15:19:52 +0200 Subject: [Nek5000-users] Monitor points In-Reply-To: <07d9c63f18562f417c187df4ce221889@vki.ac.be> References: <07d9c63f18562f417c187df4ce221889@vki.ac.be> Message-ID: Dear Nek experts, I would like to record different quantities such as the temperature or the velocity over the time. I tried to use the subroutine "hpts()" in userchk. So I created a file hpts.in as said in http://www.mcs.anl.gov/~oanam/old_page/index.php/Data_processing_example. The problem is that I had the error "Cannot open history file in subroutine hpts()" I also tried to rename my file to case.hpts_in but I still got the same error. Does anyone have a suggestion ? Thanks, Samuel From nek5000-users at lists.mcs.anl.gov Mon Oct 23 08:29:46 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Oct 2017 15:29:46 +0200 Subject: [Nek5000-users] Monitor points In-Reply-To: References: <07d9c63f18562f417c187df4ce221889@vki.ac.be> Message-ID: This section of the documentation is outdated (see issues on GitHub). You have to provide a file called casename.his instead of hpts.in. Please help us to fix the documentation! -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Monday 23rd October 2017 15:20 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Monitor points > > Dear Nek experts, > > I would like to record different quantities such as the temperature or > the velocity over the time. > I tried to use the subroutine "hpts()" in userchk. So I created a file > hpts.in as said in > http://www.mcs.anl.gov/~oanam/old_page/index.php/Data_processing_example. > > The problem is that I had the error "Cannot open history file in > subroutine hpts()" > > I also tried to rename my file to case.hpts_in but I still got the same > error. > > Does anyone have a suggestion ? > > Thanks, > Samuel > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Mon Oct 23 10:56:04 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Oct 2017 15:56:04 +0000 Subject: [Nek5000-users] Monitor points In-Reply-To: References: <07d9c63f18562f417c187df4ce221889@vki.ac.be> Message-ID: Samuel, With some recent updates to the history points routines, the default file name is 'case.his'. Also note that Nek will no longer create a new file, it will append the history point data to the end of case.his. -Dillon -----Original Message----- From: Nek5000-users [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users at lists.mcs.anl.gov Sent: Monday, October 23, 2017 8:20 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Monitor points Dear Nek experts, I would like to record different quantities such as the temperature or the velocity over the time. I tried to use the subroutine "hpts()" in userchk. So I created a file hpts.in as said in http://www.mcs.anl.gov/~oanam/old_page/index.php/Data_processing_example. The problem is that I had the error "Cannot open history file in subroutine hpts()" I also tried to rename my file to case.hpts_in but I still got the same error. Does anyone have a suggestion ? Thanks, Samuel _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Mon Oct 23 11:43:39 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Oct 2017 18:43:39 +0200 Subject: [Nek5000-users] Monitor points In-Reply-To: References: <07d9c63f18562f417c187df4ce221889@vki.ac.be> Message-ID: Thanks for your advices, I will do that. Samuel From nek5000-users at lists.mcs.anl.gov Mon Oct 23 15:14:11 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 23 Oct 2017 20:14:11 +0000 Subject: [Nek5000-users] par file and moving mesh In-Reply-To: References: Message-ID: Hi all, I have an update on this issue. The mesh I am using was generated in Cubit and then converted to the Nek5000 re2 format using the exo2nek script. I call the function ?gen_rea? to make Nek5000 write the mesh in a rea file. My mesh has a moving boundary condition, and the mesh motion is computed by the ALE solver. I then do the following: 1) I run my session using the mesh read from the re2 file that comes from the exo2nek script. 2) I run my session using the rea file that was generated by the function call ?gen_rea'. In the first case, the output file does not show the mesh motion even though the velocity profile seems correct. In the second case, the mesh motion shows in the output file when I visualize the solution with Visit. Is this a bug, or simply a misuse of the exo2nek script? Marco > On Oct 19, 2017, at 8:51 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi all, > > I am trying to switch from a rea file to a par file and I am having difficulties with the moving mesh capabilities. When visualizing the numerical solution, the mesh is not moving, whereas it was moving with a previous version of Nek5000. > > I copied the par file from the my_cyl examples as a start point. The main different between my session and the mv_cyl session is the way the mesh motion is handled. I believe the mesh velocity is provided by the user through a function, whereas in my session the mesh velocity is solved for. > > Below is the par file I am currently using: > > # > # nek parameter file > # > [GENERAL] > #startFrom = restart.fld > stopAt = numSteps > endTime = 0 > numSteps = 1000 > > dt = 1e-03 > timeStepper = bdf #bdf #char #steady > tOrder = 3 > variableDt = no > maxCFL = 2.0 > > writeControl = timeStep #runTime > writeInterval = 50 > > dealiasing = yes > userParam01 = 1.16 > userParam02 = 1.8550800E-05 > > [PROBLEMTYPE] > lowMachNumber = no > variableProperties = yes > dp0dt = no > > [MESH] > motion = yes > meshVelocity = no > > [PRESSURE] > residualTol = 1e-10 > residualProj = no > #preconditioner = amg > > [VELOCITY] > residualTol = 1e-12 > residualProj = no > > > Any help will be appreciated. > > Thanks, > > Marco > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Tue Oct 24 10:52:05 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 24 Oct 2017 15:52:05 +0000 Subject: [Nek5000-users] Turbulent heat flux calculation Message-ID: I need to calculate turbulent heat fluxes, u'T', v'T', w'T'. Where u'T' = avg(uT) - avg(u)*avg(T) The avg_all() function should give me the avg(u) and avg(T) but is there another function that I can call to get avg(uT) ? Or is there a simpler way to calculate the turbulent heat fluxes? Thank you Andrew -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 24 10:59:10 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 24 Oct 2017 17:59:10 +0200 Subject: [Nek5000-users] par file and moving mesh Message-ID: Marco, please note that the .par file is still experimental and not as robust as the good old .rea. It looks like I forgot to support the viscosity and tolerance for the mesh elasticity solver - so the default values 0.4 and 0.02 will be used. Anyway, your mesh should be moving unless there is something wrong with the BC in the exo case. Cheers, Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Monday 23rd October 2017 22:15 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] par file and moving mesh > > Hi all, > > I have an update on this issue. > > The mesh I am using was generated in Cubit and then converted to the Nek5000 re2 format using the exo2nek script. I call the function ?gen_rea? to make Nek5000 write the mesh in a rea file. My mesh has a moving boundary condition, and the mesh motion is computed by the ALE solver. I then do the following: > 1) I run my session using the mesh read from the re2 file that comes from the exo2nek script. > 2) I run my session using the rea file that was generated by the function call ?gen_rea'. > > In the first case, the output file does not show the mesh motion even though the velocity profile seems correct. In the second case, the mesh motion shows in the output file when I visualize the solution with Visit. > > Is this a bug, or simply a misuse of the exo2nek script? > > Marco > > > On Oct 19, 2017, at 8:51 AM, nek5000-users at lists.mcs.anl.gov wrote: > > > > Hi all, > > > > I am trying to switch from a rea file to a par file and I am having difficulties with the moving mesh capabilities. When visualizing the numerical solution, the mesh is not moving, whereas it was moving with a previous version of Nek5000. > > > > I copied the par file from the my_cyl examples as a start point. The main different between my session and the mv_cyl session is the way the mesh motion is handled. I believe the mesh velocity is provided by the user through a function, whereas in my session the mesh velocity is solved for. > > > > Below is the par file I am currently using: > > > > # > > # nek parameter file > > # > > [GENERAL] > > #startFrom = restart.fld > > stopAt = numSteps > > endTime = 0 > > numSteps = 1000 > > > > dt = 1e-03 > > timeStepper = bdf #bdf #char #steady > > tOrder = 3 > > variableDt = no > > maxCFL = 2.0 > > > > writeControl = timeStep #runTime > > writeInterval = 50 > > > > dealiasing = yes > > userParam01 = 1.16 > > userParam02 = 1.8550800E-05 > > > > [PROBLEMTYPE] > > lowMachNumber = no > > variableProperties = yes > > dp0dt = no > > > > [MESH] > > motion = yes > > meshVelocity = no > > > > [PRESSURE] > > residualTol = 1e-10 > > residualProj = no > > #preconditioner = amg > > > > [VELOCITY] > > residualTol = 1e-12 > > residualProj = no > > > > > > Any help will be appreciated. > > > > Thanks, > > > > Marco > > > > _______________________________________________ > > 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 > From nek5000-users at lists.mcs.anl.gov Tue Oct 24 11:01:22 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 24 Oct 2017 16:01:22 +0000 Subject: [Nek5000-users] par file and moving mesh In-Reply-To: References: Message-ID: Stefan, thank for your reply. My mesh moves if I write the mesh in a rea file. If I use the mesh generated from exo2nek script, the mesh does not move. Marco > On Oct 24, 2017, at 11:59 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Marco, > > please note that the .par file is still experimental and not as robust as the good old .rea. > It looks like I forgot to support the viscosity and tolerance for the mesh elasticity solver - so the default values 0.4 and 0.02 will be used. Anyway, your mesh should be moving unless there is something wrong with the BC in the exo case. > > Cheers, > Stefan > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Monday 23rd October 2017 22:15 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] par file and moving mesh >> >> Hi all, >> >> I have an update on this issue. >> >> The mesh I am using was generated in Cubit and then converted to the Nek5000 re2 format using the exo2nek script. I call the function ?gen_rea? to make Nek5000 write the mesh in a rea file. My mesh has a moving boundary condition, and the mesh motion is computed by the ALE solver. I then do the following: >> 1) I run my session using the mesh read from the re2 file that comes from the exo2nek script. >> 2) I run my session using the rea file that was generated by the function call ?gen_rea'. >> >> In the first case, the output file does not show the mesh motion even though the velocity profile seems correct. In the second case, the mesh motion shows in the output file when I visualize the solution with Visit. >> >> Is this a bug, or simply a misuse of the exo2nek script? >> >> Marco >> >>> On Oct 19, 2017, at 8:51 AM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>> Hi all, >>> >>> I am trying to switch from a rea file to a par file and I am having difficulties with the moving mesh capabilities. When visualizing the numerical solution, the mesh is not moving, whereas it was moving with a previous version of Nek5000. >>> >>> I copied the par file from the my_cyl examples as a start point. The main different between my session and the mv_cyl session is the way the mesh motion is handled. I believe the mesh velocity is provided by the user through a function, whereas in my session the mesh velocity is solved for. >>> >>> Below is the par file I am currently using: >>> >>> # >>> # nek parameter file >>> # >>> [GENERAL] >>> #startFrom = restart.fld >>> stopAt = numSteps >>> endTime = 0 >>> numSteps = 1000 >>> >>> dt = 1e-03 >>> timeStepper = bdf #bdf #char #steady >>> tOrder = 3 >>> variableDt = no >>> maxCFL = 2.0 >>> >>> writeControl = timeStep #runTime >>> writeInterval = 50 >>> >>> dealiasing = yes >>> userParam01 = 1.16 >>> userParam02 = 1.8550800E-05 >>> >>> [PROBLEMTYPE] >>> lowMachNumber = no >>> variableProperties = yes >>> dp0dt = no >>> >>> [MESH] >>> motion = yes >>> meshVelocity = no >>> >>> [PRESSURE] >>> residualTol = 1e-10 >>> residualProj = no >>> #preconditioner = amg >>> >>> [VELOCITY] >>> residualTol = 1e-12 >>> residualProj = no >>> >>> >>> Any help will be appreciated. >>> >>> Thanks, >>> >>> Marco >>> >>> _______________________________________________ >>> 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 From nek5000-users at lists.mcs.anl.gov Tue Oct 24 11:23:36 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 24 Oct 2017 16:23:36 +0000 Subject: [Nek5000-users] Turbulent heat flux calculation In-Reply-To: References: Message-ID: Hi Andrew, In the past, I have been copying avg_all in my .usr as a modified version with avg3's calls for avg(uT), etc. and its own outpost file sequence. Aleks ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 24, 2017 10:52:05 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Turbulent heat flux calculation I need to calculate turbulent heat fluxes, u?T?, v?T?, w?T?. Where u?T? = avg(uT) ? avg(u)*avg(T) The avg_all() function should give me the avg(u) and avg(T) but is there another function that I can call to get avg(uT) ? Or is there a simpler way to calculate the turbulent heat fluxes? Thank you Andrew -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 24 11:39:19 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 24 Oct 2017 18:39:19 +0200 Subject: [Nek5000-users] par file and moving mesh In-Reply-To: References: Message-ID: How do you specify the BC in the exo case? On 24 Oct 2017, at 18:05, "nek5000-users at lists.mcs.anl.gov " > wrote: Stefan, thank for your reply. My mesh moves if I write the mesh in a rea file. If I use the mesh generated from exo2nek script, the mesh does not move. Marco > On Oct 24, 2017, at 11:59 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Marco, > > please note that the .par file is still experimental and not as robust as the good old .rea. > It looks like I forgot to support the viscosity and tolerance for the mesh elasticity solver - so the default values 0.4 and 0.02 will be used. Anyway, your mesh should be moving unless there is something wrong with the BC in the exo case. > > Cheers, > Stefan > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Monday 23rd October 2017 22:15 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] par file and moving mesh >> >> Hi all, >> >> I have an update on this issue. >> >> The mesh I am using was generated in Cubit and then converted to the Nek5000 re2 format using the exo2nek script. I call the function ?gen_rea? to make Nek5000 write the mesh in a rea file. My mesh has a moving boundary condition, and the mesh motion is computed by the ALE solver. I then do the following: >> ??? 1) I run my session using the mesh read from the re2 file that comes from the exo2nek script. >> ??? 2) I run my session using the rea file that was generated by the function call ?gen_rea'. >> >> In the first case, the output file does not show the mesh motion even though the velocity profile seems correct. In the second case, the mesh motion shows in the output file when I visualize the solution with Visit. >> >> Is this a bug, or simply a misuse of the exo2nek script? >> >> Marco >> >>> On Oct 19, 2017, at 8:51 AM, nek5000-users at lists.mcs.anl.gov > wrote: >>> >>> Hi all, >>> >>> I am trying to switch from a rea file to a par file and I am having difficulties with the moving mesh capabilities. When visualizing the numerical solution, the mesh is not moving, whereas it was moving with a previous version of Nek5000. >>> >>> I copied the par file from the my_cyl examples as a start point. The main different between my session and the mv_cyl session is the way the mesh motion is handled. I believe the mesh velocity is provided by the user through a function, whereas in my session the mesh velocity is solved for. >>> >>> Below is the par file I am currently using: >>> >>> # >>> # nek parameter file >>> # >>> [GENERAL] >>> #start>From = restart.fld >>> stopAt = numSteps >>> endTime = 0 >>> numSteps = 1000 >>> >>> dt = 1e-03 >>> timeStepper = bdf #bdf #char #steady >>> tOrder = 3 >>> variableDt = no >>> maxCFL = 2.0 >>> >>> writeControl = timeStep #runTime >>> writeInterval = 50 >>> >>> dealiasing = yes >>> userParam01 = 1.16 >>> userParam02 = 1.8550800E-05 >>> >>> [PROBLEMTYPE] >>> lowMachNumber = no >>> variableProperties = yes >>> dp0dt = no >>> >>> [MESH] >>> motion = yes >>> meshVelocity = no >>> >>> [PRESSURE] >>> residualTol = 1e-10 >>> residualProj = no >>> #preconditioner = amg >>> >>> [VELOCITY] >>> residualTol = 1e-12 >>> residualProj = no >>> >>> >>> Any help will be appreciated. >>> >>> Thanks, >>> >>> Marco >>> >>> _______________________________________________ >>> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 24 11:55:04 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 24 Oct 2017 16:55:04 +0000 Subject: [Nek5000-users] par file and moving mesh In-Reply-To: References: Message-ID: I specify the boundary conditions in the usr file using the following piece of code: do i=1,nelt do j=1,2*ndim if(bc(5,j,i,1).eq.1) then cbc(j,i,1)='mv ' elseif(bc(5,j,i,1).eq.2) then cbc(j,i,1)='W ' elseif(bc(5,j,i,1).eq.3) then cbc(j,i,1)='W ' elseif(bc(5,j,i,1).eq.4) then cbc(j,i,1)='W ' else cbc(j,i,1)='E ' endif enddo enddo Marco On Oct 24, 2017, at 12:39 PM, nek5000-users at lists.mcs.anl.gov wrote: How do you specify the BC in the exo case? On 24 Oct 2017, at 18:05, "nek5000-users at lists.mcs.anl.gov" > wrote: Stefan, thank for your reply. My mesh moves if I write the mesh in a rea file. If I use the mesh generated from exo2nek script, the mesh does not move. Marco > On Oct 24, 2017, at 11:59 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Marco, > > please note that the .par file is still experimental and not as robust as the good old .rea. > It looks like I forgot to support the viscosity and tolerance for the mesh elasticity solver - so the default values 0.4 and 0.02 will be used. Anyway, your mesh should be moving unless there is something wrong with the BC in the exo case. > > Cheers, > Stefan > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Monday 23rd October 2017 22:15 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] par file and moving mesh >> >> Hi all, >> >> I have an update on this issue. >> >> The mesh I am using was generated in Cubit and then converted to the Nek5000 re2 format using the exo2nek script. I call the function ?gen_rea? to make Nek5000 write the mesh in a rea file. My mesh has a moving boundary condition, and the mesh motion is computed by the ALE solver. I then do the following: >> 1) I run my session using the mesh read from the re2 file that comes from the exo2nek script. >> 2) I run my session using the rea file that was generated by the function call ?gen_rea'. >> >> In the first case, the output file does not show the mesh motion even though the velocity profile seems correct. In the second case, the mesh motion shows in the output file when I visualize the solution with Visit. >> >> Is this a bug, or simply a misuse of the exo2nek script? >> >> Marco >> >>> On Oct 19, 2017, at 8:51 AM, nek5000-users at lists.mcs.anl.gov > wrote: >>> >>> Hi all, >>> >>> I am trying to switch from a rea file to a par file and I am having difficulties with the moving mesh capabilities. When visualizing the numerical solution, the mesh is not moving, whereas it was moving with a previous version of Nek5000. >>> >>> I copied the par file from the my_cyl examples as a start point. The main different between my session and the mv_cyl session is the way the mesh motion is handled. I believe the mesh velocity is provided by the user through a function, whereas in my session the mesh velocity is solved for. >>> >>> Below is the par file I am currently using: >>> >>> # >>> # nek parameter file >>> # >>> [GENERAL] >>> #startFrom = restart.fld >>> stopAt = numSteps >>> endTime = 0 >>> numSteps = 1000 >>> >>> dt = 1e-03 >>> timeStepper = bdf #bdf #char #steady >>> tOrder = 3 >>> variableDt = no >>> maxCFL = 2.0 >>> >>> writeControl = timeStep #runTime >>> writeInterval = 50 >>> >>> dealiasing = yes >>> userParam01 = 1.16 >>> userParam02 = 1.8550800E-05 >>> >>> [PROBLEMTYPE] >>> lowMachNumber = no >>> variableProperties = yes >>> dp0dt = no >>> >>> [MESH] >>> motion = yes >>> meshVelocity = no >>> >>> [PRESSURE] >>> residualTol = 1e-10 >>> residualProj = no >>> #preconditioner = amg >>> >>> [VELOCITY] >>> residualTol = 1e-12 >>> residualProj = no >>> >>> >>> Any help will be appreciated. >>> >>> Thanks, >>> >>> Marco >>> >>> _______________________________________________ >>> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 24 16:43:44 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 24 Oct 2017 17:43:44 -0400 Subject: [Nek5000-users] Restarting with Periodic boundary Condition Message-ID: Hello Neks, I have a small (4x4x1) cubic domain, which is periodic in Y. No slip boundaries in X and Z. This is to generate a Rayleigh Benard convection flowfield with Z being the convective direction. The flow is driven by hot sidewalls in X. My problem is when I restart the flowfiled from a particular flowfiled file using the same .rea, .usr files and everything, the periodicity in the Y direction seems to be gone. My originial flowfileds are periodic in Y and have the same value of Velocity Magnitude through all the Y slices ( as can be seen with VisIt). But my restarted files have different values of velocity magnitude in different slices of Y, which should not be the case. This seems to suggest something going wrong during restarting for the periodic bc side. I haven't noticed any change in the Velocity if I have no-slip in Y instead of Periodic. I would appreciate any input on this problem. Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 25 08:50:38 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 25 Oct 2017 13:50:38 +0000 Subject: [Nek5000-users] Restarting with Periodic boundary Condition In-Reply-To: References: Message-ID: Saikat, Send me a tar file of your case files off list and I'll take a look. Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Tuesday, October 24, 2017 4:43:44 PM To: nek5000-users Subject: [Nek5000-users] Restarting with Periodic boundary Condition Hello Neks, I have a small (4x4x1) cubic domain, which is periodic in Y. No slip boundaries in X and Z. This is to generate a Rayleigh Benard convection flowfield with Z being the convective direction. The flow is driven by hot sidewalls in X. My problem is when I restart the flowfiled from a particular flowfiled file using the same .rea, .usr files and everything, the periodicity in the Y direction seems to be gone. My originial flowfileds are periodic in Y and have the same value of Velocity Magnitude through all the Y slices ( as can be seen with VisIt). But my restarted files have different values of velocity magnitude in different slices of Y, which should not be the case. This seems to suggest something going wrong during restarting for the periodic bc side. I haven't noticed any change in the Velocity if I have no-slip in Y instead of Periodic. I would appreciate any input on this problem. Thanks, Saikat Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 25 08:58:49 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 25 Oct 2017 13:58:49 +0000 Subject: [Nek5000-users] Nek5000 Hackathon, November 12-14, 2017 In-Reply-To: References: Message-ID: Dear All, Please register at the following site if you plan to attend the upcoming Nek5000 Hackathon, November 12-14 at UIUC. https://doodle.com/poll/yxxtw49ewxtzzruk [https://doodle.com/graphics/static/facebookSharingThumbnail.png] Doodle: Nek5000 Hackathon, November 12-14, 2017 doodle.com Doodle radically simplifies the process of scheduling events, meetings, appointments, etc. Herding cats gets 2x faster with Doodle. For free! There will be two group dinners at nearby restaurants. Looking forward to seeing you there! The Nek5000 Team ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Saturday, October 14, 2017 10:40:09 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Nek5000 Hackathon, November 12-14, 2017 Dear Nek Developers and Users, We are excited to announce the first-ever Nek5000 Hackathon. When: Nov. 12 (1 PM, Sunday) -- Nov. 14 (5pm, Tuesday), 2017 Where: NCSA Building, University of Illinois, Urbana-Champaign (UIUC), IL, USA Hackathon Goal: The event will bring together users and developers with the intent to help new and current users bring their applications into production mode. It will also give users a chance to provide the development team with feedback on what features or enhancements they would like to see in future releases. Format: We are asking each of the participants (or as a team) to develop a small example demonstrating the phenomena of interest that could be shared with the rest of the user community through the NekExamples Suite. There will not be a formal presentation agenda. We anticipate, however, several rounds of short presentations describing the problems of interest, the features that make the problem interesting and challenging, and the anticipated ways in which the Nek team can help. Please bring your laptops and come prepared to access your usual work sites remotely, from UIUC. Cost: There is no formal registration fee. Lunches will be covered. We may collect a nominal fee for group dinners on Sunday and Monday. Registration: In order to anticipate the number of attendees, we will post a registration site in the coming week. Please stay tuned for details. Hotels: There are several hotels in the area that are a short walk from the workshop site (Siebel Center, Day 1; NCSA Days 2 & 3). Hampton Inn on University ~ 5 minute walk. Illini Union ~ 10 minute walk. Towne Place Suites by Marriott, Champaign 15 minutes I Hotel - 2 miles Sylvia's Irish Inn B&B 10 minutes We look forward to seeing you next month! Sincerely, The Nek Development Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Oct 25 14:23:19 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 26 Oct 2017 00:53:19 +0530 Subject: [Nek5000-users] variable viscosity formulation Message-ID: Hi Nek Forum, I am using a variable viscosity formulation for a Rayleigh-Benard problem. I get the following error after some time : ERROR: Non-positive diffusivity ( -0.481 ) specified for field 1, group 0 element Please let me know what might be wrong. Thank you Swarandeep From nek5000-users at lists.mcs.anl.gov Wed Oct 25 14:30:22 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 25 Oct 2017 19:30:22 +0000 Subject: [Nek5000-users] variable viscosity formulation In-Reply-To: References: Message-ID: It means that the viscosity coefficient for the velocity field is negative. What is the expression for your viscosity coefficient? > On Oct 25, 2017, at 3:23 PM, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Nek Forum, > > I am using a variable viscosity formulation for a Rayleigh-Benard > problem. I get the following error after some time : > > ERROR: Non-positive diffusivity ( -0.481 ) specified for field 1, > group 0 element > > Please let me know what might be wrong. > > Thank you > Swarandeep > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Thu Oct 26 07:57:57 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 26 Oct 2017 13:57:57 +0100 Subject: [Nek5000-users] Reynolds for pipe Message-ID: Hi, May I know for shear Reynolds number (Re_t) equals to 361, whether setting p02 VISCOS in rea file to be -11700 and the pipe radius equals to 1 in the mesh part is correct. Kind regards, ZJ -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 26 09:33:53 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 26 Oct 2017 14:33:53 +0000 Subject: [Nek5000-users] Reynolds for pipe In-Reply-To: References: Message-ID: Hi ZJ, rho = p01 = rho mu = p02 (or, if p02 < 0, then mu = 1/| p02 | ) and your Reynolds number will be Re_D = rho Ubar / (D mu) How this translates into shear Re depends on the Reynolds number you are running. An approximate formula: Re_? = 0.123 Re_D^ 0.875 hth Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, October 26, 2017 7:57 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Reynolds for pipe Hi, May I know for shear Reynolds number (Re_t) equals to 361, whether setting p02 VISCOS in rea file to be -11700 and the pipe radius equals to 1 in the mesh part is correct. Kind regards, ZJ -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Oct 26 11:09:39 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 26 Oct 2017 18:09:39 +0200 Subject: [Nek5000-users] Reynolds for pipe In-Reply-To: References: Message-ID: Hi, Re_tau=360 corresponds approximately to Re_D=11700, that means that your diameter should be 1 (i.e. the radius 0.5), and the bulk speed should be 1. This is achieved by: - setting p02 to -11700 - having a pipe radius of 0.5 - setting p54 to the (negative) direction of the pressure gradient (-1=x, -2=y, -3=z) - setting p55 to 1 Best regards, Philipp and Jacopo On 2017-10-26 14:57, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > May I know for shear Reynolds number (Re_t) equals to 361, whether > setting p02 VISCOS in rea file to be -11700 and the pipe radius equals > to 1 in the mesh part is correct. > > Kind regards, > > ZJ > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Oct 27 05:11:55 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 27 Oct 2017 17:11:55 +0700 Subject: [Nek5000-users] amg solver Message-ID: Dear Neks, Recently I decide to use the amg solver. I had done all preparations from github documentation, but it did not work for the first time. After this I look throw the forum and catch up the topic about amg dump. It was said that p40 in rea file is bound with amg solver, although official manual says that p40 "NOT IN USE". Since I set the p40 to 1 the amg solver starts to work (amg dump and after amg solver). So I want to clarify, what exactly does this p40 parameter ? And perhaps is there any additional flag or parameters (except ifamg and ifamg_dump) that I need to do for make amg solver works correctly in my simulation? All Regards, Vatslav. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 27 05:58:27 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 27 Oct 2017 12:58:27 +0200 Subject: [Nek5000-users] amg solver Message-ID: Note, the AMG section of the documentation is outdated (see issues on NekDoc). To use the AMG solver set p40=1 (for .rea) or solver=semg_amg (in pressure section for .par file). This will dump all required AMG setup files. Then run amg_hypre (part of our tools) in your case directory. Now just run Nek5000 again. Cheers, Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 27th October 2017 12:19 > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] amg solver > > Dear Neks, > > Recently I decide to use the amg solver. > I had done all preparations from github documentation, but it did not work for the first time. > After this I look throw the forum and catch up the topic about amg dump. > It was said that p40 in rea file is bound with amg solver, although official manual says that p40 "NOT IN USE". > Since I set the p40 to 1 the amg solver starts to work (amg dump and after amg solver). > So I want to clarify, what exactly does this p40 parameter ? > And perhaps is there any additional flag or parameters (except ifamg and ifamg_dump) that I need to do for make amg solver works correctly in my simulation? >
All Regards, Vatslav. > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Oct 27 08:11:14 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 27 Oct 2017 13:11:14 +0000 Subject: [Nek5000-users] par file and moving mesh In-Reply-To: <5FAE18FE-EC89-4A9E-8A48-29129EE37E51@ornl.gov> References: <5FAE18FE-EC89-4A9E-8A48-29129EE37E51@ornl.gov> Message-ID: One more update on this matter. I generated a mesh with cubit that I exported in a exodus format and in a msh format. I then did the following: - in the first case, I used the exo2nek script to generate the re2 file, and run Nek5000 to get a rea file by calling ?gen_rea?. - I used the msh2nek python script to generate a rea file. My geometry has a moving boundary conditions and the mesh motion is solved by Nek5000 in my current setting. I observe the following when running all above rea files with the same Nek5000 compiled usr file: - when running the Nek5000 session with the re2 file generated from the exo2nek script, the mesh is static when visualized with Visit. The log file shows that Nek5000 is solving for the mesh motion, though. - when running the Nek5000 session with the rea file generated with the gen_rea call, the mesh moves when visualized with Visit, but Nek5000 exits the run and writes a file named ?xyz***?. - when running the Nek5000 session with the rea file generated with the python script, the mesh moves, the solution looks good and Nek5000 runs all the way to the final time specified in the rea file. When running the Nek5000 session with the re2 file generated with the exo2nek script, I set the boundary condition in the usrdat subroutine. At first glance, it seems to be the right approach since the boundary conditions are correctly labeled in the rea file that is generated with gen_rea. But because Nek5000 exits with an error message when I run the rea file coming from the gen_rea call, I am not so sure. Should I be setting the boundary conditions at a different initialization stage? Note that I used the exo2nek script for other geometries that have more common boundary conditions (v and O), and I did not run into any issue. This problem seems to be specific to the moving mesh and boundary conditions capabilities, I think. Once again, I would appreciate any help on this matter. Thanks, Marco On Oct 24, 2017, at 12:55 PM, Delchini, Marc-Olivier G. > wrote: I specify the boundary conditions in the usr file using the following piece of code: do i=1,nelt do j=1,2*ndim if(bc(5,j,i,1).eq.1) then cbc(j,i,1)='mv ' elseif(bc(5,j,i,1).eq.2) then cbc(j,i,1)='W ' elseif(bc(5,j,i,1).eq.3) then cbc(j,i,1)='W ' elseif(bc(5,j,i,1).eq.4) then cbc(j,i,1)='W ' else cbc(j,i,1)='E ' endif enddo enddo Marco On Oct 24, 2017, at 12:39 PM, nek5000-users at lists.mcs.anl.gov wrote: How do you specify the BC in the exo case? On 24 Oct 2017, at 18:05, "nek5000-users at lists.mcs.anl.gov" > wrote: Stefan, thank for your reply. My mesh moves if I write the mesh in a rea file. If I use the mesh generated from exo2nek script, the mesh does not move. Marco > On Oct 24, 2017, at 11:59 AM, nek5000-users at lists.mcs.anl.gov wrote: > > Marco, > > please note that the .par file is still experimental and not as robust as the good old .rea. > It looks like I forgot to support the viscosity and tolerance for the mesh elasticity solver - so the default values 0.4 and 0.02 will be used. Anyway, your mesh should be moving unless there is something wrong with the BC in the exo case. > > Cheers, > Stefan > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Monday 23rd October 2017 22:15 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] par file and moving mesh >> >> Hi all, >> >> I have an update on this issue. >> >> The mesh I am using was generated in Cubit and then converted to the Nek5000 re2 format using the exo2nek script. I call the function ?gen_rea? to make Nek5000 write the mesh in a rea file. My mesh has a moving boundary condition, and the mesh motion is computed by the ALE solver. I then do the following: >> 1) I run my session using the mesh read from the re2 file that comes from the exo2nek script. >> 2) I run my session using the rea file that was generated by the function call ?gen_rea'. >> >> In the first case, the output file does not show the mesh motion even though the velocity profile seems correct. In the second case, the mesh motion shows in the output file when I visualize the solution with Visit. >> >> Is this a bug, or simply a misuse of the exo2nek script? >> >> Marco >> >>> On Oct 19, 2017, at 8:51 AM, nek5000-users at lists.mcs.anl.gov > wrote: >>> >>> Hi all, >>> >>> I am trying to switch from a rea file to a par file and I am having difficulties with the moving mesh capabilities. When visualizing the numerical solution, the mesh is not moving, whereas it was moving with a previous version of Nek5000. >>> >>> I copied the par file from the my_cyl examples as a start point. The main different between my session and the mv_cyl session is the way the mesh motion is handled. I believe the mesh velocity is provided by the user through a function, whereas in my session the mesh velocity is solved for. >>> >>> Below is the par file I am currently using: >>> >>> # >>> # nek parameter file >>> # >>> [GENERAL] >>> #startFrom = restart.fld >>> stopAt = numSteps >>> endTime = 0 >>> numSteps = 1000 >>> >>> dt = 1e-03 >>> timeStepper = bdf #bdf #char #steady >>> tOrder = 3 >>> variableDt = no >>> maxCFL = 2.0 >>> >>> writeControl = timeStep #runTime >>> writeInterval = 50 >>> >>> dealiasing = yes >>> userParam01 = 1.16 >>> userParam02 = 1.8550800E-05 >>> >>> [PROBLEMTYPE] >>> lowMachNumber = no >>> variableProperties = yes >>> dp0dt = no >>> >>> [MESH] >>> motion = yes >>> meshVelocity = no >>> >>> [PRESSURE] >>> residualTol = 1e-10 >>> residualProj = no >>> #preconditioner = amg >>> >>> [VELOCITY] >>> residualTol = 1e-12 >>> residualProj = no >>> >>> >>> Any help will be appreciated. >>> >>> Thanks, >>> >>> Marco >>> >>> _______________________________________________ >>> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 27 08:18:41 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 27 Oct 2017 15:18:41 +0200 Subject: [Nek5000-users] par file and moving mesh In-Reply-To: References: <5FAE18FE-EC89-4A9E-8A48-29129EE37E51@ornl.gov> Message-ID: If you provide a link to download your case I can have a look. Cheers, Stefan -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 27th October 2017 15:13 > To: nek5000-users at lists.mcs.anl.gov > Cc: Merzari, Elia > Subject: Re: [Nek5000-users] par file and moving mesh > > One more update on this matter. I generated a mesh with cubit that I exported in a exodus format and in a msh format. I then did the following:? > - in the first case, I used the exo2nek script to generate the re2 file, and run Nek5000 to get a rea file by calling ?gen_rea?. > -?I used the msh2nek python script to generate a rea file. >
> My geometry has a moving boundary conditions and the mesh motion is solved by Nek5000 in my current setting. >
> I observe the following when running all above rea files with the same Nek5000 compiled usr file: > - when running the Nek5000 session with the re2 file generated from the exo2nek script, the mesh is static when visualized with Visit. The log file shows that Nek5000 is solving for the > mesh motion, though. > - when running the Nek5000 session with the rea file generated with the gen_rea call, the mesh moves when visualized with Visit, but Nek5000 exits the run and writes a file named ?xyz***?. > - when running the Nek5000 session with the rea file generated with the python script, the mesh moves, the solution looks good and Nek5000 runs all the way to the final time specified > in the rea file. >
> When running the Nek5000 session with the re2 file generated with the exo2nek script, I set the boundary condition in the usrdat subroutine. At first glance, it seems to be the right approach since the boundary conditions are correctly labeled > in the rea file that is generated with gen_rea. But because Nek5000 exits with an error message when I run the rea file coming from the gen_rea call, I am not so sure. Should I be setting the boundary conditions at a different initialization stage? >
> Note that I used the exo2nek script for other geometries that have more common boundary conditions (v and O), and I did not run into any issue. This problem seems to be specific to the moving mesh and boundary conditions capabilities, I think. >
> Once again, I would appreciate any help on this matter.? >
> Thanks, >
> Marco >
> On Oct 24, 2017, at 12:55 PM, Delchini, Marc-Olivier G. > wrote: >
> I specify the boundary conditions in the usr file using the following piece of code: >
> ? ? ? do i=1,nelt > ? ? ? ? do j=1,2*ndim > ? ? ? ? ? if(bc(5,j,i,1).eq.1) then > ? ? ? ? ? ? cbc(j,i,1)='mv ?' > ? ? ? ? ? elseif(bc(5,j,i,1).eq.2) then > ? ? ? ? ? ? cbc(j,i,1)='W ?' > ? ? ? ? ? elseif(bc(5,j,i,1).eq.3) then > ? ? ? ? ? ? cbc(j,i,1)='W ?' > ? ? ? ? ? elseif(bc(5,j,i,1).eq.4) then > ? ? ? ? ? ? cbc(j,i,1)='W ?' > ? ? ? ? ? else > ? ? ? ? ? ? cbc(j,i,1)='E ?' > ? ? ? ? ? endif > ? ? ? ? enddo > ? ? ? enddo >
> Marco >
> On Oct 24, 2017, at 12:39 PM, > nek5000-users at lists.mcs.anl.gov wrote: >
> How do you specify the BC in the exo case? >
> On 24 Oct 2017, at 18:05, "nek5000-users at lists.mcs.anl.gov " > wrote:
>
> Stefan,
>
> thank for your reply.
>
> My mesh moves if I write the mesh in a rea file. If I use the mesh generated from exo2nek script, the mesh does not move.
>
> Marco
>
> > On Oct 24, 2017, at 11:59 AM, > nek5000-users at lists.mcs.anl.gov wrote:
> >
> > Marco,
> >
> > please note that the .par file is still experimental and not as robust as the good old .rea.
> > It looks like I forgot to support the viscosity and tolerance for the mesh elasticity solver - so the default values 0.4 and 0.02 will be used. Anyway, your mesh should be moving unless there is something wrong with the BC in the exo case.
> >
> > Cheers,
> > Stefan
> >
> > -----Original message-----
> >> From:nek5000-users at lists.mcs.anl.gov >
> >> Sent: Monday 23rd October 2017 22:15
> >> To: nek5000-users at lists.mcs.anl.gov
> >> Subject: Re: [Nek5000-users] par file and moving mesh
> >>
> >> Hi all,
> >>
> >> I have an update on this issue.
> >>
> >> The mesh I am using was generated in Cubit and then converted to the Nek5000 re2 format using the exo2nek script. I call the function ?gen_rea? to make Nek5000 write the mesh in a rea file. My mesh has a moving boundary condition, and the mesh motion is > computed by the ALE solver. I then do the following:
> >> ??? 1) I run my session using the mesh read from the re2 file that comes from the exo2nek script.
> >> ??? 2) I run my session using the rea file that was generated by the function call ?gen_rea'.
> >>
> >> In the first case, the output file does not show the mesh motion even though the velocity profile seems correct. In the second case, the mesh motion shows in the output file when I visualize the solution with Visit.
> >>
> >> Is this a bug, or simply a misuse of the exo2nek script?
> >>
> >> Marco
> >>
> >>> On Oct 19, 2017, at 8:51 AM, > nek5000-users at lists.mcs.anl.gov > wrote:
> >>>
> >>> Hi all,
> >>>
> >>> I am trying to switch from a rea file to a par file and I am having difficulties with the moving mesh capabilities. When visualizing the numerical solution, the mesh is not moving, whereas it was moving with a previous version of Nek5000.
> >>>
> >>> I copied the par file from the my_cyl examples as a start point. The main different between my session and the mv_cyl session is the way the mesh motion is handled. I believe the mesh velocity is provided by the user through a function, whereas in my session > the mesh velocity is solved for.
> >>>
> >>> Below is the par file I am currently using:
> >>>
> >>> #
> >>> # nek parameter file
> >>> #
> >>> [GENERAL]
> >>> #startFrom = restart.fld
> >>> stopAt = numSteps
> >>> endTime = 0
> >>> numSteps = 1000
> >>>
> >>> dt = 1e-03
> >>> timeStepper = bdf #bdf #char #steady
> >>> tOrder = 3
> >>> variableDt = no
> >>> maxCFL = 2.0
> >>>
> >>> writeControl = timeStep #runTime
> >>> writeInterval = 50
> >>>
> >>> dealiasing = yes
> >>> userParam01 = 1.16
> >>> userParam02 = 1.8550800E-05
> >>>
> >>> [PROBLEMTYPE]
> >>> lowMachNumber = no
> >>> variableProperties = yes
> >>> dp0dt = no
> >>>
> >>> [MESH]
> >>> motion = yes
> >>> meshVelocity = no
> >>>
> >>> [PRESSURE]
> >>> residualTol = 1e-10
> >>> residualProj = no
> >>> #preconditioner = amg
> >>>
> >>> [VELOCITY]
> >>> residualTol = 1e-12
> >>> residualProj = no
> >>>
> >>>
> >>> Any help will be appreciated.
> >>>
> >>> Thanks,
> >>>
> >>> Marco
> >>>
> >>> _______________________________________________
> >>> 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 From nek5000-users at lists.mcs.anl.gov Fri Oct 27 09:05:43 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 27 Oct 2017 14:05:43 +0000 Subject: [Nek5000-users] par file and moving mesh In-Reply-To: References: <5FAE18FE-EC89-4A9E-8A48-29129EE37E51@ornl.gov> Message-ID: Stefan, thanks for taking the time to look into this. Is it ok if I use your work email to send you a dropbox link for the case? Marco > On Oct 27, 2017, at 9:18 AM, nek5000-users at lists.mcs.anl.gov wrote: > > If you provide a link to download your case I can have a look. > > Cheers, > Stefan > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Friday 27th October 2017 15:13 >> To: nek5000-users at lists.mcs.anl.gov >> Cc: Merzari, Elia >> Subject: Re: [Nek5000-users] par file and moving mesh >> >> One more update on this matter. I generated a mesh with cubit that I exported in a exodus format and in a msh format. I then did the following: >> - in the first case, I used the exo2nek script to generate the re2 file, and run Nek5000 to get a rea file by calling ?gen_rea?. >> - I used the msh2nek python script to generate a rea file. >>
>> My geometry has a moving boundary conditions and the mesh motion is solved by Nek5000 in my current setting. >>
>> I observe the following when running all above rea files with the same Nek5000 compiled usr file: >> - when running the Nek5000 session with the re2 file generated from the exo2nek script, the mesh is static when visualized with Visit. The log file shows that Nek5000 is solving for the >> mesh motion, though. >> - when running the Nek5000 session with the rea file generated with the gen_rea call, the mesh moves when visualized with Visit, but Nek5000 exits the run and writes a file named ?xyz***?. >> - when running the Nek5000 session with the rea file generated with the python script, the mesh moves, the solution looks good and Nek5000 runs all the way to the final time specified >> in the rea file. >>
>> When running the Nek5000 session with the re2 file generated with the exo2nek script, I set the boundary condition in the usrdat subroutine. At first glance, it seems to be the right approach since the boundary conditions are correctly labeled >> in the rea file that is generated with gen_rea. But because Nek5000 exits with an error message when I run the rea file coming from the gen_rea call, I am not so sure. Should I be setting the boundary conditions at a different initialization stage? >>
>> Note that I used the exo2nek script for other geometries that have more common boundary conditions (v and O), and I did not run into any issue. This problem seems to be specific to the moving mesh and boundary conditions capabilities, I think. >>
>> Once again, I would appreciate any help on this matter. >>
>> Thanks, >>
>> Marco >>
>> On Oct 24, 2017, at 12:55 PM, Delchini, Marc-Olivier G. > wrote: >>
>> I specify the boundary conditions in the usr file using the following piece of code: >>
>> do i=1,nelt >> do j=1,2*ndim >> if(bc(5,j,i,1).eq.1) then >> cbc(j,i,1)='mv ' >> elseif(bc(5,j,i,1).eq.2) then >> cbc(j,i,1)='W ' >> elseif(bc(5,j,i,1).eq.3) then >> cbc(j,i,1)='W ' >> elseif(bc(5,j,i,1).eq.4) then >> cbc(j,i,1)='W ' >> else >> cbc(j,i,1)='E ' >> endif >> enddo >> enddo >>
>> Marco >>
>> On Oct 24, 2017, at 12:39 PM, >> nek5000-users at lists.mcs.anl.gov wrote: >>
>> How do you specify the BC in the exo case? >>
>> On 24 Oct 2017, at 18:05, "nek5000-users at lists.mcs.anl.gov " > wrote:
>>
>> Stefan,
>>
>> thank for your reply.
>>
>> My mesh moves if I write the mesh in a rea file. If I use the mesh generated from exo2nek script, the mesh does not move.
>>
>> Marco
>>
>>> On Oct 24, 2017, at 11:59 AM, >> nek5000-users at lists.mcs.anl.gov wrote:
>>>
>>> Marco,
>>>
>>> please note that the .par file is still experimental and not as robust as the good old .rea.
>>> It looks like I forgot to support the viscosity and tolerance for the mesh elasticity solver - so the default values 0.4 and 0.02 will be used. Anyway, your mesh should be moving unless there is something wrong with the BC in the exo case.
>>>
>>> Cheers,
>>> Stefan
>>>
>>> -----Original message-----
>>>> From:nek5000-users at lists.mcs.anl.gov >
>>>> Sent: Monday 23rd October 2017 22:15
>>>> To: nek5000-users at lists.mcs.anl.gov
>>>> Subject: Re: [Nek5000-users] par file and moving mesh
>>>>
>>>> Hi all,
>>>>
>>>> I have an update on this issue.
>>>>
>>>> The mesh I am using was generated in Cubit and then converted to the Nek5000 re2 format using the exo2nek script. I call the function ?gen_rea? to make Nek5000 write the mesh in a rea file. My mesh has a moving boundary condition, and the mesh motion is >> computed by the ALE solver. I then do the following:
>>>> 1) I run my session using the mesh read from the re2 file that comes from the exo2nek script.
>>>> 2) I run my session using the rea file that was generated by the function call ?gen_rea'.
>>>>
>>>> In the first case, the output file does not show the mesh motion even though the velocity profile seems correct. In the second case, the mesh motion shows in the output file when I visualize the solution with Visit.
>>>>
>>>> Is this a bug, or simply a misuse of the exo2nek script?
>>>>
>>>> Marco
>>>>
>>>>> On Oct 19, 2017, at 8:51 AM, >> nek5000-users at lists.mcs.anl.gov > wrote:
>>>>>
>>>>> Hi all,
>>>>>
>>>>> I am trying to switch from a rea file to a par file and I am having difficulties with the moving mesh capabilities. When visualizing the numerical solution, the mesh is not moving, whereas it was moving with a previous version of Nek5000.
>>>>>
>>>>> I copied the par file from the my_cyl examples as a start point. The main different between my session and the mv_cyl session is the way the mesh motion is handled. I believe the mesh velocity is provided by the user through a function, whereas in my session >> the mesh velocity is solved for.
>>>>>
>>>>> Below is the par file I am currently using:
>>>>>
>>>>> #
>>>>> # nek parameter file
>>>>> #
>>>>> [GENERAL]
>>>>> #startFrom = restart.fld
>>>>> stopAt = numSteps
>>>>> endTime = 0
>>>>> numSteps = 1000
>>>>>
>>>>> dt = 1e-03
>>>>> timeStepper = bdf #bdf #char #steady
>>>>> tOrder = 3
>>>>> variableDt = no
>>>>> maxCFL = 2.0
>>>>>
>>>>> writeControl = timeStep #runTime
>>>>> writeInterval = 50
>>>>>
>>>>> dealiasing = yes
>>>>> userParam01 = 1.16
>>>>> userParam02 = 1.8550800E-05
>>>>>
>>>>> [PROBLEMTYPE]
>>>>> lowMachNumber = no
>>>>> variableProperties = yes
>>>>> dp0dt = no
>>>>>
>>>>> [MESH]
>>>>> motion = yes
>>>>> meshVelocity = no
>>>>>
>>>>> [PRESSURE]
>>>>> residualTol = 1e-10
>>>>> residualProj = no
>>>>> #preconditioner = amg
>>>>>
>>>>> [VELOCITY]
>>>>> residualTol = 1e-12
>>>>> residualProj = no
>>>>>
>>>>>
>>>>> Any help will be appreciated.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Marco
>>>>>
>>>>> _______________________________________________
>>>>> 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 From nek5000-users at lists.mcs.anl.gov Fri Oct 27 09:09:06 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 27 Oct 2017 16:09:06 +0200 Subject: [Nek5000-users] par file and moving mesh In-Reply-To: References: <5FAE18FE-EC89-4A9E-8A48-29129EE37E51@ornl.gov> Message-ID: You'll find my email on the Nek5000 webpage. -----Original message----- > From:nek5000-users at lists.mcs.anl.gov > Sent: Friday 27th October 2017 16:07 > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] par file and moving mesh > > Stefan, > > thanks for taking the time to look into this. Is it ok if I use your work email to send you a dropbox link for the case? > > Marco > > > On Oct 27, 2017, at 9:18 AM, nek5000-users at lists.mcs.anl.gov wrote: > > > > If you provide a link to download your case I can have a look. > > > > Cheers, > > Stefan > > > > -----Original message----- > >> From:nek5000-users at lists.mcs.anl.gov > >> Sent: Friday 27th October 2017 15:13 > >> To: nek5000-users at lists.mcs.anl.gov > >> Cc: Merzari, Elia > >> Subject: Re: [Nek5000-users] par file and moving mesh > >> > >> One more update on this matter. I generated a mesh with cubit that I exported in a exodus format and in a msh format. I then did the following: > >> - in the first case, I used the exo2nek script to generate the re2 file, and run Nek5000 to get a rea file by calling ?gen_rea?. > >> - I used the msh2nek python script to generate a rea file. > >>
> >> My geometry has a moving boundary conditions and the mesh motion is solved by Nek5000 in my current setting. > >>
> >> I observe the following when running all above rea files with the same Nek5000 compiled usr file: > >> - when running the Nek5000 session with the re2 file generated from the exo2nek script, the mesh is static when visualized with Visit. The log file shows that Nek5000 is solving for the > >> mesh motion, though. > >> - when running the Nek5000 session with the rea file generated with the gen_rea call, the mesh moves when visualized with Visit, but Nek5000 exits the run and writes a file named ?xyz***?. > >> - when running the Nek5000 session with the rea file generated with the python script, the mesh moves, the solution looks good and Nek5000 runs all the way to the final time specified > >> in the rea file. > >>
> >> When running the Nek5000 session with the re2 file generated with the exo2nek script, I set the boundary condition in the usrdat subroutine. At first glance, it seems to be the right approach since the boundary conditions are correctly labeled > >> in the rea file that is generated with gen_rea. But because Nek5000 exits with an error message when I run the rea file coming from the gen_rea call, I am not so sure. Should I be setting the boundary conditions at a different initialization stage? > >>
> >> Note that I used the exo2nek script for other geometries that have more common boundary conditions (v and O), and I did not run into any issue. This problem seems to be specific to the moving mesh and boundary conditions capabilities, I think. > >>
> >> Once again, I would appreciate any help on this matter. > >>
> >> Thanks, > >>
> >> Marco > >>
> >> On Oct 24, 2017, at 12:55 PM, Delchini, Marc-Olivier G. > wrote: > >>
> >> I specify the boundary conditions in the usr file using the following piece of code: > >>
> >> do i=1,nelt > >> do j=1,2*ndim > >> if(bc(5,j,i,1).eq.1) then > >> cbc(j,i,1)='mv ' > >> elseif(bc(5,j,i,1).eq.2) then > >> cbc(j,i,1)='W ' > >> elseif(bc(5,j,i,1).eq.3) then > >> cbc(j,i,1)='W ' > >> elseif(bc(5,j,i,1).eq.4) then > >> cbc(j,i,1)='W ' > >> else > >> cbc(j,i,1)='E ' > >> endif > >> enddo > >> enddo > >>
> >> Marco > >>
> >> On Oct 24, 2017, at 12:39 PM, > >> nek5000-users at lists.mcs.anl.gov wrote: > >>
> >> How do you specify the BC in the exo case? > >>
> >> On 24 Oct 2017, at 18:05, "nek5000-users at lists.mcs.anl.gov " > wrote:
> >>
> >> Stefan,
> >>
> >> thank for your reply.
> >>
> >> My mesh moves if I write the mesh in a rea file. If I use the mesh generated from exo2nek script, the mesh does not move.
> >>
> >> Marco
> >>
> >>> On Oct 24, 2017, at 11:59 AM, > >> nek5000-users at lists.mcs.anl.gov wrote:
> >>>
> >>> Marco,
> >>>
> >>> please note that the .par file is still experimental and not as robust as the good old .rea.
> >>> It looks like I forgot to support the viscosity and tolerance for the mesh elasticity solver - so the default values 0.4 and 0.02 will be used. Anyway, your mesh should be moving unless there is something wrong with the BC in the exo case.
> >>>
> >>> Cheers,
> >>> Stefan
> >>>
> >>> -----Original message-----
> >>>> From:nek5000-users at lists.mcs.anl.gov >
> >>>> Sent: Monday 23rd October 2017 22:15
> >>>> To: nek5000-users at lists.mcs.anl.gov
> >>>> Subject: Re: [Nek5000-users] par file and moving mesh
> >>>>
> >>>> Hi all,
> >>>>
> >>>> I have an update on this issue.
> >>>>
> >>>> The mesh I am using was generated in Cubit and then converted to the Nek5000 re2 format using the exo2nek script. I call the function ?gen_rea? to make Nek5000 write the mesh in a rea file. My mesh has a moving boundary condition, and the mesh motion is > >> computed by the ALE solver. I then do the following:
> >>>> 1) I run my session using the mesh read from the re2 file that comes from the exo2nek script.
> >>>> 2) I run my session using the rea file that was generated by the function call ?gen_rea'.
> >>>>
> >>>> In the first case, the output file does not show the mesh motion even though the velocity profile seems correct. In the second case, the mesh motion shows in the output file when I visualize the solution with Visit.
> >>>>
> >>>> Is this a bug, or simply a misuse of the exo2nek script?
> >>>>
> >>>> Marco
> >>>>
> >>>>> On Oct 19, 2017, at 8:51 AM, > >> nek5000-users at lists.mcs.anl.gov > wrote:
> >>>>>
> >>>>> Hi all,
> >>>>>
> >>>>> I am trying to switch from a rea file to a par file and I am having difficulties with the moving mesh capabilities. When visualizing the numerical solution, the mesh is not moving, whereas it was moving with a previous version of Nek5000.
> >>>>>
> >>>>> I copied the par file from the my_cyl examples as a start point. The main different between my session and the mv_cyl session is the way the mesh motion is handled. I believe the mesh velocity is provided by the user through a function, whereas in my session > >> the mesh velocity is solved for.
> >>>>>
> >>>>> Below is the par file I am currently using:
> >>>>>
> >>>>> #
> >>>>> # nek parameter file
> >>>>> #
> >>>>> [GENERAL]
> >>>>> #startFrom = restart.fld
> >>>>> stopAt = numSteps
> >>>>> endTime = 0
> >>>>> numSteps = 1000
> >>>>>
> >>>>> dt = 1e-03
> >>>>> timeStepper = bdf #bdf #char #steady
> >>>>> tOrder = 3
> >>>>> variableDt = no
> >>>>> maxCFL = 2.0
> >>>>>
> >>>>> writeControl = timeStep #runTime
> >>>>> writeInterval = 50
> >>>>>
> >>>>> dealiasing = yes
> >>>>> userParam01 = 1.16
> >>>>> userParam02 = 1.8550800E-05
> >>>>>
> >>>>> [PROBLEMTYPE]
> >>>>> lowMachNumber = no
> >>>>> variableProperties = yes
> >>>>> dp0dt = no
> >>>>>
> >>>>> [MESH]
> >>>>> motion = yes
> >>>>> meshVelocity = no
> >>>>>
> >>>>> [PRESSURE]
> >>>>> residualTol = 1e-10
> >>>>> residualProj = no
> >>>>> #preconditioner = amg
> >>>>>
> >>>>> [VELOCITY]
> >>>>> residualTol = 1e-12
> >>>>> residualProj = no
> >>>>>
> >>>>>
> >>>>> Any help will be appreciated.
> >>>>>
> >>>>> Thanks,
> >>>>>
> >>>>> Marco
> >>>>>
> >>>>> _______________________________________________
> >>>>> 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 > From nek5000-users at lists.mcs.anl.gov Fri Oct 27 10:34:32 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 27 Oct 2017 22:34:32 +0700 Subject: [Nek5000-users] amg solver Message-ID: Thanks a lot, Stefan, for your reply. But I use the amg_matlab2/run script instead of amg_hypre, and it seems to produce the same files: amg.dat, amg_Af*, amg_W.dat What is the difference between these approaches? Regards, Vatslav. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Oct 27 11:13:20 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 27 Oct 2017 16:13:20 +0000 Subject: [Nek5000-users] par file and moving mesh In-Reply-To: References: <5FAE18FE-EC89-4A9E-8A48-29129EE37E51@ornl.gov> Message-ID: I emailed it to your gmail address. > On Oct 27, 2017, at 10:09 AM, nek5000-users at lists.mcs.anl.gov wrote: > > You'll find my email on the Nek5000 webpage. > > -----Original message----- >> From:nek5000-users at lists.mcs.anl.gov >> Sent: Friday 27th October 2017 16:07 >> To: nek5000-users at lists.mcs.anl.gov >> Subject: Re: [Nek5000-users] par file and moving mesh >> >> Stefan, >> >> thanks for taking the time to look into this. Is it ok if I use your work email to send you a dropbox link for the case? >> >> Marco >> >>> On Oct 27, 2017, at 9:18 AM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>> If you provide a link to download your case I can have a look. >>> >>> Cheers, >>> Stefan >>> >>> -----Original message----- >>>> From:nek5000-users at lists.mcs.anl.gov >>>> Sent: Friday 27th October 2017 15:13 >>>> To: nek5000-users at lists.mcs.anl.gov >>>> Cc: Merzari, Elia >>>> Subject: Re: [Nek5000-users] par file and moving mesh >>>> >>>> One more update on this matter. I generated a mesh with cubit that I exported in a exodus format and in a msh format. I then did the following: >>>> - in the first case, I used the exo2nek script to generate the re2 file, and run Nek5000 to get a rea file by calling ?gen_rea?. >>>> - I used the msh2nek python script to generate a rea file. >>>>
>>>> My geometry has a moving boundary conditions and the mesh motion is solved by Nek5000 in my current setting. >>>>
>>>> I observe the following when running all above rea files with the same Nek5000 compiled usr file: >>>> - when running the Nek5000 session with the re2 file generated from the exo2nek script, the mesh is static when visualized with Visit. The log file shows that Nek5000 is solving for the >>>> mesh motion, though. >>>> - when running the Nek5000 session with the rea file generated with the gen_rea call, the mesh moves when visualized with Visit, but Nek5000 exits the run and writes a file named ?xyz***?. >>>> - when running the Nek5000 session with the rea file generated with the python script, the mesh moves, the solution looks good and Nek5000 runs all the way to the final time specified >>>> in the rea file. >>>>
>>>> When running the Nek5000 session with the re2 file generated with the exo2nek script, I set the boundary condition in the usrdat subroutine. At first glance, it seems to be the right approach since the boundary conditions are correctly labeled >>>> in the rea file that is generated with gen_rea. But because Nek5000 exits with an error message when I run the rea file coming from the gen_rea call, I am not so sure. Should I be setting the boundary conditions at a different initialization stage? >>>>
>>>> Note that I used the exo2nek script for other geometries that have more common boundary conditions (v and O), and I did not run into any issue. This problem seems to be specific to the moving mesh and boundary conditions capabilities, I think. >>>>
>>>> Once again, I would appreciate any help on this matter. >>>>
>>>> Thanks, >>>>
>>>> Marco >>>>
>>>> On Oct 24, 2017, at 12:55 PM, Delchini, Marc-Olivier G. > wrote: >>>>
>>>> I specify the boundary conditions in the usr file using the following piece of code: >>>>
>>>> do i=1,nelt >>>> do j=1,2*ndim >>>> if(bc(5,j,i,1).eq.1) then >>>> cbc(j,i,1)='mv ' >>>> elseif(bc(5,j,i,1).eq.2) then >>>> cbc(j,i,1)='W ' >>>> elseif(bc(5,j,i,1).eq.3) then >>>> cbc(j,i,1)='W ' >>>> elseif(bc(5,j,i,1).eq.4) then >>>> cbc(j,i,1)='W ' >>>> else >>>> cbc(j,i,1)='E ' >>>> endif >>>> enddo >>>> enddo >>>>
>>>> Marco >>>>
>>>> On Oct 24, 2017, at 12:39 PM, >>>> nek5000-users at lists.mcs.anl.gov wrote: >>>>
>>>> How do you specify the BC in the exo case? >>>>
>>>> On 24 Oct 2017, at 18:05, "nek5000-users at lists.mcs.anl.gov " > wrote:
>>>>
>>>> Stefan,
>>>>
>>>> thank for your reply.
>>>>
>>>> My mesh moves if I write the mesh in a rea file. If I use the mesh generated from exo2nek script, the mesh does not move.
>>>>
>>>> Marco
>>>>
>>>>> On Oct 24, 2017, at 11:59 AM, >>>> nek5000-users at lists.mcs.anl.gov wrote:
>>>>>
>>>>> Marco,
>>>>>
>>>>> please note that the .par file is still experimental and not as robust as the good old .rea.
>>>>> It looks like I forgot to support the viscosity and tolerance for the mesh elasticity solver - so the default values 0.4 and 0.02 will be used. Anyway, your mesh should be moving unless there is something wrong with the BC in the exo case.
>>>>>
>>>>> Cheers,
>>>>> Stefan
>>>>>
>>>>> -----Original message-----
>>>>>> From:nek5000-users at lists.mcs.anl.gov >
>>>>>> Sent: Monday 23rd October 2017 22:15
>>>>>> To: nek5000-users at lists.mcs.anl.gov
>>>>>> Subject: Re: [Nek5000-users] par file and moving mesh
>>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I have an update on this issue.
>>>>>>
>>>>>> The mesh I am using was generated in Cubit and then converted to the Nek5000 re2 format using the exo2nek script. I call the function ?gen_rea? to make Nek5000 write the mesh in a rea file. My mesh has a moving boundary condition, and the mesh motion is >>>> computed by the ALE solver. I then do the following:
>>>>>> 1) I run my session using the mesh read from the re2 file that comes from the exo2nek script.
>>>>>> 2) I run my session using the rea file that was generated by the function call ?gen_rea'.
>>>>>>
>>>>>> In the first case, the output file does not show the mesh motion even though the velocity profile seems correct. In the second case, the mesh motion shows in the output file when I visualize the solution with Visit.
>>>>>>
>>>>>> Is this a bug, or simply a misuse of the exo2nek script?
>>>>>>
>>>>>> Marco
>>>>>>
>>>>>>> On Oct 19, 2017, at 8:51 AM, >>>> nek5000-users at lists.mcs.anl.gov > wrote:
>>>>>>>
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I am trying to switch from a rea file to a par file and I am having difficulties with the moving mesh capabilities. When visualizing the numerical solution, the mesh is not moving, whereas it was moving with a previous version of Nek5000.
>>>>>>>
>>>>>>> I copied the par file from the my_cyl examples as a start point. The main different between my session and the mv_cyl session is the way the mesh motion is handled. I believe the mesh velocity is provided by the user through a function, whereas in my session >>>> the mesh velocity is solved for.
>>>>>>>
>>>>>>> Below is the par file I am currently using:
>>>>>>>
>>>>>>> #
>>>>>>> # nek parameter file
>>>>>>> #
>>>>>>> [GENERAL]
>>>>>>> #startFrom = restart.fld
>>>>>>> stopAt = numSteps
>>>>>>> endTime = 0
>>>>>>> numSteps = 1000
>>>>>>>
>>>>>>> dt = 1e-03
>>>>>>> timeStepper = bdf #bdf #char #steady
>>>>>>> tOrder = 3
>>>>>>> variableDt = no
>>>>>>> maxCFL = 2.0
>>>>>>>
>>>>>>> writeControl = timeStep #runTime
>>>>>>> writeInterval = 50
>>>>>>>
>>>>>>> dealiasing = yes
>>>>>>> userParam01 = 1.16
>>>>>>> userParam02 = 1.8550800E-05
>>>>>>>
>>>>>>> [PROBLEMTYPE]
>>>>>>> lowMachNumber = no
>>>>>>> variableProperties = yes
>>>>>>> dp0dt = no
>>>>>>>
>>>>>>> [MESH]
>>>>>>> motion = yes
>>>>>>> meshVelocity = no
>>>>>>>
>>>>>>> [PRESSURE]
>>>>>>> residualTol = 1e-10
>>>>>>> residualProj = no
>>>>>>> #preconditioner = amg
>>>>>>>
>>>>>>> [VELOCITY]
>>>>>>> residualTol = 1e-12
>>>>>>> residualProj = no
>>>>>>>
>>>>>>>
>>>>>>> Any help will be appreciated.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Marco
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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 From nek5000-users at lists.mcs.anl.gov Fri Oct 27 14:34:02 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 27 Oct 2017 15:34:02 -0400 Subject: [Nek5000-users] wavelet decomposition Message-ID: Dear all, I would like to perform a wavelet decomposition on my DNS data of stratified turbulence generated using Nek5000. The details of the decomposition to extract coherent vorticies is explained in this paper: Farge, M., Schneider, K., Pellegrino, G., Wray, A. A., & Rogallo, R. S. (2003). Coherent vortex extraction in three-dimensional homogeneous turbulence: Comparison between CVS-wavelet and POD-Fourier decompositions. *Physics of Fluids*, *15*(10), 2886-2896. I am wondering if anyone in our community has had any experience with integrating the wavelet analysis with Nek5000 in the post-processing mode? If not, would you suggest performing such a decomposition in the VisIt Python Interface using a python package like PyWavelets for example? Thanks a lot for the help, Regards, Hesam -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Oct 31 07:07:52 2017 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 31 Oct 2017 12:07:52 +0000 Subject: [Nek5000-users] wavelet decomposition In-Reply-To: References: Message-ID: Hi Hesam, I've not looked in detail at this paper, but my guess is that you're trying to do some convolution sums. (How many?) One option is just to do them. For n points, the cost for each is O(n). Another option (perhaps), is to map all your data onto a uniform grid and use an FFT-based convolution (provided your method can be written this way, as I've seen in at least one paper on the topic). Here, a parallel FFT might be of value (but there might be other ways as well). hth, Paul ________________________________ From: Nek5000-users on behalf of nek5000-users at lists.mcs.anl.gov Sent: Friday, October 27, 2017 2:34:02 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] wavelet decomposition Dear all, I would like to perform a wavelet decomposition on my DNS data of stratified turbulence generated using Nek5000. The details of the decomposition to extract coherent vorticies is explained in this paper: Farge, M., Schneider, K., Pellegrino, G., Wray, A. A., & Rogallo, R. S. (2003). Coherent vortex extraction in three-dimensional homogeneous turbulence: Comparison between CVS-wavelet and POD-Fourier decompositions. Physics of Fluids, 15(10), 2886-2896. I am wondering if anyone in our community has had any experience with integrating the wavelet analysis with Nek5000 in the post-processing mode? If not, would you suggest performing such a decomposition in the VisIt Python Interface using a python package like PyWavelets for example? Thanks a lot for the help, Regards, Hesam -------------- next part -------------- An HTML attachment was scrubbed... URL: