From nek5000-users at lists.mcs.anl.gov Wed Jun 1 10:02:42 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 1 Jun 2016 17:02:42 +0200 Subject: [Nek5000-users] Spectral coefficients for velocity In-Reply-To: References: Message-ID: Hi Nicolas, Thanks a lot for your help. I wanted to compute spectral coefficients in NEK5000. Andrey 2016-05-25 17:06 GMT+02:00 : > Hi Andrey, > > I don't know if you got an answer yet but here are my suggestions. > > If you are asking about the theory behind spectral transforms, I suggest > that you look at appendix B in the book "High-Order Methods for > Incompressible Fluid Flow" by Fischer, Deville and Mund. In particular, > Section B.3.1 gives the formula for the spectral coefficients uh_k > > uh_k = 1/gamma_k \int_-1^1 w(x) u(x) p_k(x) dx > > where gamma_k=||p_k||^2 is the discrete norm and w(x) is the weight > function, both of them associated to polynomial p_k. > > If you want to compute these coefficients in Nek5000, then you can look at > the routine "local_err_est" in the file navier5.f. There, one goes to the > Legendre space by using > > call tensr3(uh,nx,u,nx,Lj,Ljt,Ljt,w) > > where uh is the array of spectral elements and the operators Lj and Ljt > are computed in the routine "build_legend_transform" (also in navier5.f) > from the GLL points. > > I hope that helps. > > Best regards, > Nicolas Offermans > > > Quoting nek5000-users at lists.mcs.anl.gov: > > Hi Neks, >> >> Priviously, the parameters p101 and p103 have been discussed: >> >> "In each direction, on each element, the solution is represented as a >> polynomial of degree N in the reference element (i.e., on the interval >> [-1,1]). >> >> For any Nth-order polynomial there is a modal expansion of the form: >> >> u(x) = \sum_k=0^N uh_k phi_k(x) >> >> where phi_0 = 1, phi_1 = x, and phi_k(x)=L_k(x) - L_{k-1} (x) for k > 1, >> where L_k(x)=kth Legendre polynomial." >> >> How can I obtain these coefficients "uh_k" on the several elements? >> >> Thanks in advance for any suggestion, >> >> Andrey >> > > > _______________________________________________ > 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 Jun 1 22:46:42 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 2 Jun 2016 03:46:42 +0000 Subject: [Nek5000-users] postx black window In-Reply-To: References: Message-ID: Hello, I have successfully compiled the eddy tutorial, but when I a run the postx command, I just get a black Nekton window. I have attached a screen shot of my terminal. I did get two "errors" (don't know if they are errors) : mv: cannot stat 'eddy_uv.log': No such file or directory mv: cannot stat 'eddy_uv.sch': No such file or directory It seems that the simulation still ran fine despite of these "errors" since when I run the grep commands I receive the same outputs as the tutorials. So I do not know what is causing the black window once I run postx. Thank you, Virgilio A. Gomez -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2016-06-01 22-41-02.png Type: image/png Size: 221637 bytes Desc: Screenshot from 2016-06-01 22-41-02.png URL: From nek5000-users at lists.mcs.anl.gov Thu Jun 2 12:12:11 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 2 Jun 2016 17:12:11 +0000 Subject: [Nek5000-users] problems in generating .rea file Message-ID: Hello all, I want to ask what type of mesh does Nek5000 accept? tetrahedral, hexahedral,etc? Because I am using ICEM CFD for generating mesh which has extension .msh and for that I used python code given for mshconvert to convert into .rea file but I am getting error. the error image is attached. Please let me know following questions 1)what should I do to solve error? 2)what are mesh types that we can use? 3) I there any other easy way to convert .msh file to .rea? Thanks, any help would be appreciated. Thanks, Mansi Patel -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: error.png Type: image/png Size: 91392 bytes Desc: error.png URL: From nek5000-users at lists.mcs.anl.gov Thu Jun 2 16:21:13 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 2 Jun 2016 21:21:13 +0000 Subject: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 3 In-Reply-To: References: Message-ID: Hi Mansi, 1)what should I do to solve error? Right now mshconvert can only deal with single zone's case. So you should have to manually merge the multi-zone to single-zone in the .msh file. Also we found that there are few bugs in the file. Could you please send us your .msh file to test and then we will get back to you with the corrected version? 2)what are mesh types that we can use? Quadrant for 2D- and hexahedral for 3D-cases. 3) I there any other easy way to convert .msh file to .rea? I leave this question to other users. Thanks. Regards, Jing ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: Thursday, June 2, 2016 19:17 To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 3 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. problems in generating .rea file (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 2 Jun 2016 17:12:11 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" Subject: [Nek5000-users] problems in generating .rea file Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hello all, I want to ask what type of mesh does Nek5000 accept? tetrahedral, hexahedral,etc? Because I am using ICEM CFD for generating mesh which has extension .msh and for that I used python code given for mshconvert to convert into .rea file but I am getting error. the error image is attached. Please let me know following questions 1)what should I do to solve error? 2)what are mesh types that we can use? 3) I there any other easy way to convert .msh file to .rea? Thanks, any help would be appreciated. Thanks, Mansi Patel -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: error.png Type: image/png Size: 91392 bytes Desc: error.png URL: ------------------------------ _______________________________________________ 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 88, Issue 3 ******************************************** From nek5000-users at lists.mcs.anl.gov Mon Jun 6 14:58:31 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 6 Jun 2016 19:58:31 +0000 Subject: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 4, Problem creating .rea file In-Reply-To: References: Message-ID: Hello all, Thanks jing, that was a lot helpful to me. I have generated the .msh file for the hexahedral mesh for my geometry. File is attached to this mail. I have given boundary condition in this file only let me know if there are any changes to be made and file has only one zone( if by one zone you mean only 1 type of mesh through out whole geometry). Questions: 1) Users, what are other ways to convert (Icem cfd) .msh file to .rea file? 2) is there any way to smooth hexahedral mesh for unstructured geometry? Thanks, Mansi Patel ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: Friday, June 3, 2016 1:00 PM To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 4 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. Re: Nek5000-users Digest, Vol 88, Issue 3 (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 2 Jun 2016 21:21:13 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 3 Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi Mansi, 1)what should I do to solve error? Right now mshconvert can only deal with single zone's case. So you should have to manually merge the multi-zone to single-zone in the .msh file. Also we found that there are few bugs in the file. Could you please send us your .msh file to test and then we will get back to you with the corrected version? 2)what are mesh types that we can use? Quadrant for 2D- and hexahedral for 3D-cases. 3) I there any other easy way to convert .msh file to .rea? I leave this question to other users. Thanks. Regards, Jing ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: Thursday, June 2, 2016 19:17 To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 3 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. problems in generating .rea file (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 2 Jun 2016 17:12:11 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" Subject: [Nek5000-users] problems in generating .rea file Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hello all, I want to ask what type of mesh does Nek5000 accept? tetrahedral, hexahedral,etc? Because I am using ICEM CFD for generating mesh which has extension .msh and for that I used python code given for mshconvert to convert into .rea file but I am getting error. the error image is attached. Please let me know following questions 1)what should I do to solve error? 2)what are mesh types that we can use? 3) I there any other easy way to convert .msh file to .rea? Thanks, any help would be appreciated. Thanks, Mansi Patel -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: error.png Type: image/png Size: 91392 bytes Desc: error.png URL: ------------------------------ _______________________________________________ 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 88, Issue 3 ******************************************** ------------------------------ _______________________________________________ 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 88, Issue 4 ******************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh_hexa_final.msh Type: application/octet-stream Size: 24802571 bytes Desc: mesh_hexa_final.msh URL: From nek5000-users at lists.mcs.anl.gov Mon Jun 6 15:34:56 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 6 Jun 2016 22:34:56 +0200 Subject: [Nek5000-users] Problem creating .rea file In-Reply-To: References: Message-ID: Hi Mansi, an exodus-to-nek converter is currently under development and will be soon committed to the repo. This will allow the user to convert an exodusII mesh consisting of quad9/hex27 elements to a nek readable format, with curved edges/faces and the capability of accommodating the SideSets/bc?s set by the user in the meshing software (that is, any meshing software that supports exodusII format, including icemcfd). Best, George > On 06 Jun 2016, at 22:09, nek5000-users-request at lists.mcs.anl.gov 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. Re: Nek5000-users Digest, Vol 88, Issue 4, Problem creating > .rea file (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 6 Jun 2016 19:58:31 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 4, > Problem creating .rea file > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > > > Thanks jing, that was a lot helpful to me. > > I have generated the .msh file for the hexahedral mesh for my geometry. File is attached to this mail. > > > I have given boundary condition in this file only let me know if there are any changes to be made and file has only one zone( if by one zone you mean only 1 type of mesh through out whole geometry). > > > Questions: > > 1) Users, what are other ways to convert (Icem cfd) .msh file to .rea file? > > 2) is there any way to smooth hexahedral mesh for unstructured geometry? > > > Thanks, > > Mansi Patel > > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users-request at lists.mcs.anl.gov > Sent: Friday, June 3, 2016 1:00 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 4 > > 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. Re: Nek5000-users Digest, Vol 88, Issue 3 > (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Jun 2016 21:21:13 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 3 > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Mansi, > > 1)what should I do to solve error? > > Right now mshconvert can only deal with single zone's case. So you should have to manually merge the multi-zone to single-zone in the .msh file. > > Also we found that there are few bugs in the file. Could you please send us your .msh file to test and then we will get back to you with the corrected version? > > 2)what are mesh types that we can use? > Quadrant for 2D- and hexahedral for 3D-cases. > > 3) I there any other easy way to convert .msh file to .rea? > I leave this question to other users. > > Thanks. > > Regards, Jing > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users-request at lists.mcs.anl.gov > Sent: Thursday, June 2, 2016 19:17 > To: nek5000-users at lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 3 > > 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. problems in generating .rea file (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Jun 2016 17:12:11 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: [Nek5000-users] problems in generating .rea file > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > > I want to ask what type of mesh does Nek5000 accept? tetrahedral, hexahedral,etc? > > Because I am using ICEM CFD for generating mesh which has extension .msh and for that I used python code given for mshconvert to convert into .rea file but I am getting error. the error image is attached. > > Please let me know following questions > > 1)what should I do to solve error? > > 2)what are mesh types that we can use? > > 3) I there any other easy way to convert .msh file to .rea? > > > Thanks, any help would be appreciated. > > > Thanks, > > Mansi Patel > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: error.png > Type: image/png > Size: 91392 bytes > Desc: error.png > URL: > > ------------------------------ > > _______________________________________________ > 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 88, Issue 3 > ******************************************** > > > ------------------------------ > > _______________________________________________ > 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 88, Issue 4 > ******************************************** > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: mesh_hexa_final.msh > Type: application/octet-stream > Size: 24802571 bytes > Desc: mesh_hexa_final.msh > URL: > > ------------------------------ > > _______________________________________________ > 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 88, Issue 5 > ******************************************** From nek5000-users at lists.mcs.anl.gov Wed Jun 8 08:46:13 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 8 Jun 2016 13:46:13 +0000 Subject: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 5 In-Reply-To: References: Message-ID: Hi Mansi, You can find the updated "mshconvert.py" in the attachment. You can run the script for your case likes ### $ ipython In [1]: from mshconvert import * Converting from ANSYS Fluent format (.msh) to Nek5000, semtex or FEniCS format In [2]: convert('mesh_hexa_final.msh', bcs={10:'W',11:'v',12:'v',13:'O'}) ... ### Here I assume that BC "W" is on zone 10, "v" is on zones 11 and 12, and 'O' on zone 13. The snapshot for the Nek5000 mesh using visit is also attached in the email. /Jing ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: Monday, June 6, 2016 22:09 To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 5 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. Re: Nek5000-users Digest, Vol 88, Issue 4, Problem creating .rea file (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2016 19:58:31 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 4, Problem creating .rea file Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hello all, Thanks jing, that was a lot helpful to me. I have generated the .msh file for the hexahedral mesh for my geometry. File is attached to this mail. I have given boundary condition in this file only let me know if there are any changes to be made and file has only one zone( if by one zone you mean only 1 type of mesh through out whole geometry). Questions: 1) Users, what are other ways to convert (Icem cfd) .msh file to .rea file? 2) is there any way to smooth hexahedral mesh for unstructured geometry? Thanks, Mansi Patel ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: Friday, June 3, 2016 1:00 PM To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 4 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. Re: Nek5000-users Digest, Vol 88, Issue 3 (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 2 Jun 2016 21:21:13 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 3 Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi Mansi, 1)what should I do to solve error? Right now mshconvert can only deal with single zone's case. So you should have to manually merge the multi-zone to single-zone in the .msh file. Also we found that there are few bugs in the file. Could you please send us your .msh file to test and then we will get back to you with the corrected version? 2)what are mesh types that we can use? Quadrant for 2D- and hexahedral for 3D-cases. 3) I there any other easy way to convert .msh file to .rea? I leave this question to other users. Thanks. Regards, Jing ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: Thursday, June 2, 2016 19:17 To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 3 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. problems in generating .rea file (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Thu, 2 Jun 2016 17:12:11 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" Subject: [Nek5000-users] problems in generating .rea file Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hello all, I want to ask what type of mesh does Nek5000 accept? tetrahedral, hexahedral,etc? Because I am using ICEM CFD for generating mesh which has extension .msh and for that I used python code given for mshconvert to convert into .rea file but I am getting error. the error image is attached. Please let me know following questions 1)what should I do to solve error? 2)what are mesh types that we can use? 3) I there any other easy way to convert .msh file to .rea? Thanks, any help would be appreciated. Thanks, Mansi Patel -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: error.png Type: image/png Size: 91392 bytes Desc: error.png URL: ------------------------------ _______________________________________________ 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 88, Issue 3 ******************************************** ------------------------------ _______________________________________________ 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 88, Issue 4 ******************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh_hexa_final.msh Type: application/octet-stream Size: 24802571 bytes Desc: mesh_hexa_final.msh URL: ------------------------------ _______________________________________________ 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 88, Issue 5 ******************************************** -------------- next part -------------- A non-text attachment was scrubbed... Name: mshconvert.py Type: text/x-python Size: 62532 bytes Desc: mshconvert.py URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh_fine.pdf Type: application/pdf Size: 44347 bytes Desc: mesh_fine.pdf URL: From nek5000-users at lists.mcs.anl.gov Wed Jun 8 11:15:42 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 8 Jun 2016 18:15:42 +0200 Subject: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 5 In-Reply-To: References: Message-ID: Hello Jing, Recently I am also working on converting fluent mesh to nek5000. I have generated the *msh from gambit, then using the mshconvert.py tool to convert a simple mesh with a circular cylinder inside a square. simply, I can get the *rea file with circle of the "W", "v" and "O". but I have met two problems; 1. to impose the periodic boundary conditons: in the script, it strongly recommend to impose "P" through the script, then how to setup it in mshconvert.py? the way convert('mesh.msh', bcs={1:'W',2:'v',3:'O',4:'P', 5:'P'}) can generate the rea field but failed in the step of genmap. so how to treat boundary 4 and 5 as periodic BCs? 2. about the curved wall. there is no problem to define a circle by "Circle" command, but if I want to using "m" to define a spline curve, how to seed middle points? I know in Gambit I can mesh the line using 3 node, I defined 3 node mode to mesh a circle, and using "m" instead of "circle", however, it failed to generate the rea file. the circle merged into a point, then what should I do to active the spline curve? Thanks! Wei 2016-06-08 15:46 GMT+02:00 : > Hi Mansi, > > You can find the updated "mshconvert.py" in the attachment. You can run > the script for your case likes > > ### > $ ipython > > In [1]: from mshconvert import * > Converting from ANSYS Fluent format (.msh) to Nek5000, semtex or FEniCS > format > > In [2]: convert('mesh_hexa_final.msh', bcs={10:'W',11:'v',12:'v',13:'O'}) > ... > ### > > Here I assume that BC "W" is on zone 10, "v" is on zones 11 and 12, and > 'O' on zone 13. > > The snapshot for the Nek5000 mesh using visit is also attached in the > email. > > /Jing > > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov < > nek5000-users-bounces at lists.mcs.anl.gov> on behalf of > nek5000-users-request at lists.mcs.anl.gov < > nek5000-users-request at lists.mcs.anl.gov> > Sent: Monday, June 6, 2016 22:09 > To: nek5000-users at lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 5 > > 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. Re: Nek5000-users Digest, Vol 88, Issue 4, Problem creating > .rea file (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 6 Jun 2016 19:58:31 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 4, > Problem creating .rea file > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > > > Thanks jing, that was a lot helpful to me. > > I have generated the .msh file for the hexahedral mesh for my geometry. > File is attached to this mail. > > > I have given boundary condition in this file only let me know if there are > any changes to be made and file has only one zone( if by one zone you mean > only 1 type of mesh through out whole geometry). > > > Questions: > > 1) Users, what are other ways to convert (Icem cfd) .msh file to .rea > file? > > 2) is there any way to smooth hexahedral mesh for unstructured geometry? > > > Thanks, > > Mansi Patel > > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov < > nek5000-users-bounces at lists.mcs.anl.gov> on behalf of > nek5000-users-request at lists.mcs.anl.gov < > nek5000-users-request at lists.mcs.anl.gov> > Sent: Friday, June 3, 2016 1:00 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 4 > > 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. Re: Nek5000-users Digest, Vol 88, Issue 3 > (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Jun 2016 21:21:13 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 3 > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Mansi, > > 1)what should I do to solve error? > > Right now mshconvert can only deal with single zone's case. So you should > have to manually merge the multi-zone to single-zone in the .msh file. > > Also we found that there are few bugs in the file. Could you please send > us your .msh file to test and then we will get back to you with the > corrected version? > > 2)what are mesh types that we can use? > Quadrant for 2D- and hexahedral for 3D-cases. > > 3) I there any other easy way to convert .msh file to .rea? > I leave this question to other users. > > Thanks. > > Regards, Jing > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov < > nek5000-users-bounces at lists.mcs.anl.gov> on behalf of > nek5000-users-request at lists.mcs.anl.gov < > nek5000-users-request at lists.mcs.anl.gov> > Sent: Thursday, June 2, 2016 19:17 > To: nek5000-users at lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 3 > > 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. problems in generating .rea file (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Jun 2016 17:12:11 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: [Nek5000-users] problems in generating .rea file > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > > I want to ask what type of mesh does Nek5000 accept? tetrahedral, > hexahedral,etc? > > Because I am using ICEM CFD for generating mesh which has extension .msh > and for that I used python code given for mshconvert to convert into .rea > file but I am getting error. the error image is attached. > > Please let me know following questions > > 1)what should I do to solve error? > > 2)what are mesh types that we can use? > > 3) I there any other easy way to convert .msh file to .rea? > > > Thanks, any help would be appreciated. > > > Thanks, > > Mansi Patel > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160602/aaf91e41/attachment.html > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: error.png > Type: image/png > Size: 91392 bytes > Desc: error.png > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160602/aaf91e41/attachment.png > > > > ------------------------------ > > _______________________________________________ > 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 88, Issue 3 > ******************************************** > > > ------------------------------ > > _______________________________________________ > 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 88, Issue 4 > ******************************************** > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160606/e07ab762/attachment.html > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: mesh_hexa_final.msh > Type: application/octet-stream > Size: 24802571 bytes > Desc: mesh_hexa_final.msh > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160606/e07ab762/attachment.obj > > > > ------------------------------ > > _______________________________________________ > 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 88, Issue 5 > ******************************************** > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Wei HE ?? School of Aeronautics Universidad Polit?cnica de Madrid http://www.cfm.upm.es/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Jun 8 13:18:12 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 8 Jun 2016 18:18:12 +0000 Subject: [Nek5000-users] problems in good quality of hexahedral mesh Message-ID: Hello all, I am creating my mesh in ICEM CFD. My geometry is unstructured as it has arteries and veins so I know how to create Tetrahedral mesh so to get hexahedral mesh I have used icon to convert tetra to hexa in ICEM CFD but it is not of good quality. Does any one know good method to get good quality of hexahedral mesh on unstructured geometry like arteries and veins in ICEM CFD? If you have any tutorial or anythig please send a link. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jun 9 06:33:08 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 09 Jun 2016 13:33:08 +0200 Subject: [Nek5000-users] grid2grid interpolation Message-ID: Hello Neks, I am trying to refine my current mesh using Prenek and interpolating my current data from the current grid to the refined one. I kept following the instructions for the function g2gi() and was able to run makenek successful. But using nek or nekmpi keeps giving me following error messages. For nek: /----------------------------------------------------------\\ | _ __ ______ __ __ ______ ____ ____ ____ | | / | / // ____// //_/ / ____/ / __ \\ / __ \\ / __ \\ | | / |/ // __/ / ,< /___ \\ / / / // / / // / / / | | / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / | | /_/ |_//_____//_/ |_|/_____/ \\____/ \\____/ \\____/ | | | |----------------------------------------------------------| | | | NEK5000: Open Source Spectral Element Solver | | COPYRIGHT (c) 2008-2010 UCHICAGO ARGONNE, LLC | | Version: 1.0rc1 / SVN r1061 | | Web: http://nek5000.mcs.anl.gov | | | \\----------------------------------------------------------/ Number of processors: 1 REAL wdsize : 8 INTEGER wdsize : 4 [satyajit-All-Series:17818] *** An error occurred in MPI_Bcast [satyajit-All-Series:17818] *** on communicator MPI COMMUNICATOR 3 DUP FROM 0 [satyajit-All-Series:17818] *** MPI_ERR_TYPE: invalid datatype [satyajit-All-Series:17818] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort real 0m0.029s user 0m0.005s sys 0m0.010s and for nekmpi: /----------------------------------------------------------\\ | _ __ ______ __ __ ______ ____ ____ ____ | | / | / // ____// //_/ / ____/ / __ \\ / __ \\ / __ \\ | | / |/ // __/ / ,< /___ \\ / / / // / / // / / / | | / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / | | /_/ |_//_____//_/ |_|/_____/ \\____/ \\____/ \\____/ | | | |----------------------------------------------------------| | | | NEK5000: Open Source Spectral Element Solver | | COPYRIGHT (c) 2008-2010 UCHICAGO ARGONNE, LLC | | Version: 1.0rc1 / SVN r1061 | | Web: http://nek5000.mcs.anl.gov | | | \\----------------------------------------------------------/ Number of processors: 2 REAL wdsize : 8 INTEGER wdsize : 4 ERROR (proc 0000, /home/michaelr/nek5_svn/trunk/nek/jl/fcrystal.c:94): comm_init_check: passed P=2, but not compiled with -DMPI call exitt: dying ... ERROR (proc 0000, /home/michaelr/nek5_svn/trunk/nek/jl/fcrystal.c:94): comm_init_check: passed P=2, but not compiled with -DMPI backtrace(): obtained 11 stack frames. ./nek5000() [0x4e6b0a] ./nek5000() [0x5a55e9] ./nek5000() [0x5dfe25] ./nek5000() [0x5dfeba] ./nek5000() [0x5e0053] ./nek5000() [0x5a7b96] ./nek5000() [0x5a8a28] ./nek5000() [0x402c5f] ./nek5000() [0x4022d4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f95d20b3ec5] ./nek5000() [0x402319] total elapsed time : 1.46547E+09 sec total solver time incl. I/O : 0.00000E+00 sec time/timestep : 0.00000E+00 sec CPU seconds/timestep/gridpt : 0.00000E+00 sec Any suggestions? Br, Michael From nek5000-users at lists.mcs.anl.gov Thu Jun 9 09:15:37 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 9 Jun 2016 14:15:37 +0000 Subject: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 8 In-Reply-To: References: Message-ID: Hi Wei, >1. to impose the periodic boundary conditons: in the script, it strongly >recommend to impose "P" through the script, then how to setup it in >mshconvert.py? the way >convert('mesh.msh', bcs={1:'W',2:'v',3:'O',4:'P', 5:'P'}) > can generate the rea field but failed in the step of genmap. so how to > treat boundary 4 and 5 as periodic BCs? Probably you should have to do likes convert('mesh.msh', periodic_dx={(4,5) : [0, 0, 2]}, bcs={1:'W',2:'v',3:'O'}) Where the "periodic_dx" is to specify which pair-zone is periodic and what is the orientation of zones. in the example, zones 4,5 are the periodic boundaries and on the z-direction with distance of 2. >2. about the curved wall. there is no problem to define a circle by >"Circle" command, but if I want to using "m" to define a spline curve, how t>o seed middle points? I know in Gambit I can mesh the line using 3 node, I >defined 3 node mode to mesh a circle, and using "m" instead of "circle", >however, it failed to generate the rea file. the circle merged into a >point, then what should I do to active the spline curve? Yes, it seems to be bugs in the python script with "m" method. In the python script, the midpoints is (somehow) defined by ... x_m = (x_1+x_2)/2; y_m = (y_1+y_2)/2; ... However, in the nek5000 (tools/prenek/zipper2.f) it read the values of (x_q, y_q) instead of (x_m,y_m) !? .... ! subroutine xyzquad(xl,yl,zl,nxl,nyl,nzl,e) ... do k=1,nedge if (ccurve(k,e).eq.'m') then j = eindx(k) xq(j) = curve(1,k,e) yq(j) = curve(2,k,e) zq(j) = curve(3,k,e) endif enddo ... This should be confirmed by nek5000 developers. Thanks. /Jing ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: Wednesday, June 8, 2016 18:18 To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 8 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. Re: Nek5000-users Digest, Vol 88, Issue 5 (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Jun 2016 18:15:42 +0200 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 5 Message-ID: Content-Type: text/plain; charset="utf-8" Hello Jing, Recently I am also working on converting fluent mesh to nek5000. I have generated the *msh from gambit, then using the mshconvert.py tool to convert a simple mesh with a circular cylinder inside a square. simply, I can get the *rea file with circle of the "W", "v" and "O". but I have met two problems; 1. to impose the periodic boundary conditons: in the script, it strongly recommend to impose "P" through the script, then how to setup it in mshconvert.py? the way convert('mesh.msh', bcs={1:'W',2:'v',3:'O',4:'P', 5:'P'}) can generate the rea field but failed in the step of genmap. so how to treat boundary 4 and 5 as periodic BCs? 2. about the curved wall. there is no problem to define a circle by "Circle" command, but if I want to using "m" to define a spline curve, how to seed middle points? I know in Gambit I can mesh the line using 3 node, I defined 3 node mode to mesh a circle, and using "m" instead of "circle", however, it failed to generate the rea file. the circle merged into a point, then what should I do to active the spline curve? Thanks! Wei 2016-06-08 15:46 GMT+02:00 : > Hi Mansi, > > You can find the updated "mshconvert.py" in the attachment. You can run > the script for your case likes > > ### > $ ipython > > In [1]: from mshconvert import * > Converting from ANSYS Fluent format (.msh) to Nek5000, semtex or FEniCS > format > > In [2]: convert('mesh_hexa_final.msh', bcs={10:'W',11:'v',12:'v',13:'O'}) > ... > ### > > Here I assume that BC "W" is on zone 10, "v" is on zones 11 and 12, and > 'O' on zone 13. > > The snapshot for the Nek5000 mesh using visit is also attached in the > email. > > /Jing > > From nek5000-users at lists.mcs.anl.gov Thu Jun 9 19:09:08 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 10 Jun 2016 00:09:08 +0000 Subject: [Nek5000-users] rms in turbChannel Message-ID: Hello, In the userchk subroutine in the .usr file for the turbChannel example, what line of code can I add so rms values can be written in a .dat file such as it is done for umean and reystresses values. ! write statistics to file iostep_avg = param(68) if (nid.eq.0 .and. istep.gt.0 .and. & mod(istep,iostep_avg).eq.0) then write(6,*) 'Dumping statistics ...' open(unit=56,file='reystresses.dat') write(56,'(A,1pe14.7)') '#time = ', time write(56,'(A)') & '# y y+ R_uu R_vv R_ww R_uv' open(unit=57,file='means.dat') write(57,'(A,1pe14.7)') '#time = ', time write(57,'(A)') & '# y y+ Umean' m = ny1*nely/2 do i=1,m write(56,3) yy(i)+1 & ,(yy(i)+1)*Re_tau & , (urms_pl(i)-(uavg_pl(i))**2)/u_tau**2 & , vrms_pl(i)/u_tau**2 & , wrms_pl(i)/u_tau**2 & , uvms_pl(i)/u_tau**2 write(57,3) yy(i) + 1. & , (yy(i)+1.)*Re_tau & , uavg_pl(i)/u_tau 3 format(1p15e17.9) enddo close(56) close(57) timel = time endif return end Thank you, Virgilio A. Gomez -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jun 9 19:13:14 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 10 Jun 2016 00:13:14 +0000 Subject: [Nek5000-users] lambda2 in turbChannel Message-ID: Hello, In the userchk subroutine for the turbChannel example, lambda2 was computed. How can I visualize the isosurfaces (streamwise structures) in visit? if(mod(istep,iostep).eq.0 .and. istep.gt.0) then ! compute lambda2 vortex call lambda2(t(1,1,1,1,2)) ! compute vorticity --- 3 components returned in t(...) if(ldimt.ge.5) call comp_vort3(t(1,1,1,1,3),wo1,wo2,vx,vy,vz) endif Thank you, Virgilio A. Gomez -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jun 9 22:12:29 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 10 Jun 2016 03:12:29 +0000 Subject: [Nek5000-users] Nek5000 Users Meeting, Aug. 10-12, 2016, Cambridge, MA Message-ID: Dear Neks, Registration is now open for the 5th Nek5000 Users Meeting, to be held August 10-12, 2016, on the M.I.T. campus in Cambridge, Massachussets. As this year marks the 30th anniversary of Nek5000, which started as Nekton 2.0 in 1986, we have planned a special format for this meeting. The first day will feature several invited speakers who made significant contributions to the theory and development of high-order methods, as well as some of the principal user/developers who have pushed these methods to the limit in important application areas on the world's fastest computers. The second and third day will feature our standard User/Developer Meeting format, with 10 minute talks by each participant along with a handful of more extended presentations. We anticipate 40-60 participants. Invited speakers include Michel Deville (EPFL), Yvon Maday (Paris VI), Anthony Patera (MIT), Alfio Quarteroni(EPFL), Philipp Schlatter (KTH), and Ananias Tomboulides (AUT/ANL). There will be a conference dinner at Legal Seafood near the M.I.T. campus (walking distance from the meeting venue). We hope you will sign up for this opportunity to enjoy a collegial evening at a classic New England institution. We note that August is a busy tourist time in Boston and so encourage you to book your travel plans, hotel especially, early. Registration and instructions for submitting a presentation can be found at the following URL: https://www.regonline.com/builder/site/Default.aspx?EventID=1823410 We look forward to seeing you in August! Your local Nek development team. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jun 9 18:10:56 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 9 Jun 2016 19:10:56 -0400 Subject: [Nek5000-users] getting velocity profile for laminar and turbulent re Message-ID: dear NEKS I am trying a simple case of flow through a 2d antisymmetric pipe for laminar and turbulent Re. The pipe is vertical and the flow is upward with an initial velocity. I want to match the velocity curve with the analytical velocity curves. Any ideas how i should go about it?please help Apoorva -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Jun 12 14:20:45 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 12 Jun 2016 21:20:45 +0200 Subject: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 8 In-Reply-To: References: Message-ID: Hi Jing, Following your instructions, I re-generate a new 2D cylinder mesh (see attachment, plz), set the upper (4) and bottom (3) as the periodics, the distance in y is 30, the setting as followed: convert('cyl.msh', curves={7:{'type':'C', 'radius':-0.5, 'depth': 3, 'circle_center': (0, 0)}}, periodic_dx={(3,4) : [0, 30.0, 0]}, bcs={ 5: 'O', 6: 'v', 7: 'W'}) as fas as fine, while it failed to convert , error informations are *Traceback (most recent call last): File "mshconvert_new.py", line 15, in convert('cyl.msh', curves={7:{'type':'C', 'radius':-0.5, 'depth': 3, 'circle_center': (0, 0)}}, periodic_dx={(3,4) : [0, -30.0, 0]}, bcs={ 5: 'O', 6: 'v', 7: 'W'}) File "/home/wei/Workstation/CFD/mshconvert/mshconvert.py", line 1458, in convert create_periodic_face_map(periodic_dx) File "/home/wei/Workstation/CFD/mshconvert/mshconvert.py", line 304, in create_periodic_face_map - abs(dx)) < 1.e-7*norm(dx)):ValueError: operands could not be broadcast together with shapes (2,) (3,) * would you like to help me? thanks! regards Wei 2016-06-09 16:15 GMT+02:00 : > Hi Wei, > > >1. to impose the periodic boundary conditons: in the script, it strongly > >recommend to impose "P" through the script, then how to setup it in > >mshconvert.py? the way > >convert('mesh.msh', bcs={1:'W',2:'v',3:'O',4:'P', 5:'P'}) > > can generate the rea field but failed in the step of genmap. so how to > > treat boundary 4 and 5 as periodic BCs? > > Probably you should have to do likes > > convert('mesh.msh', periodic_dx={(4,5) : [0, 0, 2]}, > bcs={1:'W',2:'v',3:'O'}) > > Where the "periodic_dx" is to specify which pair-zone is periodic and what > is the orientation of zones. in the example, zones 4,5 are the periodic > boundaries and on the z-direction with distance of 2. > > >2. about the curved wall. there is no problem to define a circle by > >"Circle" command, but if I want to using "m" to define a spline curve, how > t>o seed middle points? I know in Gambit I can mesh the line using 3 node, > I > >defined 3 node mode to mesh a circle, and using "m" instead of "circle", > >however, it failed to generate the rea file. the circle merged into a > >point, then what should I do to active the spline curve? > > Yes, it seems to be bugs in the python script with "m" method. In the > python script, the midpoints is (somehow) defined by > ... > x_m = (x_1+x_2)/2; > y_m = (y_1+y_2)/2; > ... > However, in the nek5000 (tools/prenek/zipper2.f) it read the values of > (x_q, y_q) instead of (x_m,y_m) !? > .... > ! subroutine xyzquad(xl,yl,zl,nxl,nyl,nzl,e) > ... > do k=1,nedge > if (ccurve(k,e).eq.'m') then > j = eindx(k) > xq(j) = curve(1,k,e) > yq(j) = curve(2,k,e) > zq(j) = curve(3,k,e) > endif > enddo > ... > This should be confirmed by nek5000 developers. > > Thanks. > > /Jing > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov < > nek5000-users-bounces at lists.mcs.anl.gov> on behalf of > nek5000-users-request at lists.mcs.anl.gov < > nek5000-users-request at lists.mcs.anl.gov> > Sent: Wednesday, June 8, 2016 18:18 > To: nek5000-users at lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 8 > > 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. Re: Nek5000-users Digest, Vol 88, Issue 5 > (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 8 Jun 2016 18:15:42 +0200 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 5 > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hello Jing, > > Recently I am also working on converting fluent mesh to nek5000. I have > generated the *msh from gambit, then using the mshconvert.py tool to > convert a simple mesh with a circular cylinder inside a square. > > simply, I can get the *rea file with circle of the "W", "v" and "O". but I > have met two problems; > > 1. to impose the periodic boundary conditons: in the script, it strongly > recommend to impose "P" through the script, then how to setup it in > mshconvert.py? the way > > convert('mesh.msh', bcs={1:'W',2:'v',3:'O',4:'P', 5:'P'}) > > can generate the rea field but failed in the step of genmap. so how to > treat boundary 4 and 5 as periodic BCs? > > 2. about the curved wall. there is no problem to define a circle by > "Circle" command, but if I want to using "m" to define a spline curve, how > to seed middle points? I know in Gambit I can mesh the line using 3 node, I > defined 3 node mode to mesh a circle, and using "m" instead of "circle", > however, it failed to generate the rea file. the circle merged into a > point, then what should I do to active the spline curve? > > Thanks! > > Wei > > 2016-06-08 15:46 GMT+02:00 : > > > Hi Mansi, > > > > You can find the updated "mshconvert.py" in the attachment. You can run > > the script for your case likes > > > > ### > > $ ipython > > > > In [1]: from mshconvert import * > > Converting from ANSYS Fluent format (.msh) to Nek5000, semtex or FEniCS > > format > > > > In [2]: convert('mesh_hexa_final.msh', bcs={10:'W',11:'v',12:'v',13:'O'}) > > ... > > ### > > > > Here I assume that BC "W" is on zone 10, "v" is on zones 11 and 12, and > > 'O' on zone 13. > > > > The snapshot for the Nek5000 mesh using visit is also attached in the > > email. > > > > /Jing > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- Wei HE ?? School of Aeronautics Universidad Polit?cnica de Madrid http://www.cfm.upm.es/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: cyl.msh Type: model/mesh Size: 43196 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Mon Jun 13 10:01:36 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 13 Jun 2016 08:01:36 -0700 Subject: [Nek5000-users] lambda2 in turbChannel In-Reply-To: References: Message-ID: You can run nek5000 in postprocessing mode (set NSTEPS = 0). Then in userchk, you can do the following INCLUDE ?SIZE? INCLUDE ?TOTAL? INCLUDE ?RESTART? character*80 filename(9999) real l2(lx1,ly1,lz1,lelv) ntot = nx1*ny1*nz1*nelv call load_ fld(filename) ! select a filename fld file of your choice. call lambdat2(l2) call outpost(.vx,vy,vz,pr,l2,'lam') enddo If your file is say turbChannel.fld015, the postprocessing will generate, lamturbChannel.fld01. You can type in visnek lamturbChannel in the terminal and then open visit and visualize the temperature variable. That will your l2. Best Regards, Tanmoy On Thu, Jun 9, 2016 at 5:13 PM, wrote: > Hello, > > > In the userchk subroutine for the turbChannel example, lambda2 was > computed. How can I visualize the isosurfaces (streamwise structures) in > visit? > > > if(mod(istep,iostep).eq.0 .and. istep.gt.0) then > ! compute lambda2 vortex > call lambda2(t(1,1,1,1,2)) > ! compute vorticity --- 3 components returned in t(...) > if(ldimt.ge.5) call comp_vort3(t(1,1,1,1,3),wo1,wo2,vx,vy,vz) > endif > > > Thank you, > > Virgilio A. Gomez > > > > _______________________________________________ > 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 Mon Jun 13 10:40:42 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 13 Jun 2016 17:40:42 +0200 Subject: [Nek5000-users] lambda2 in turbChannel In-Reply-To: References: Message-ID: Hi Tannoy, Is there an exist subroutine to compute Q-criterion? Thanks! Wei 2016-06-13 17:01 GMT+02:00 : > You can run nek5000 in postprocessing mode (set NSTEPS = 0). Then in > userchk, you can do the following > > INCLUDE ?SIZE? > INCLUDE ?TOTAL? > INCLUDE ?RESTART? > > character*80 filename(9999) > real l2(lx1,ly1,lz1,lelv) > > ntot = nx1*ny1*nz1*nelv > > call load_ fld(filename) ! select a filename fld file of your > choice. > call lambdat2(l2) > > call outpost(.vx,vy,vz,pr,l2,'lam') > enddo > > If your file is say turbChannel.fld015, the postprocessing will generate, > lamturbChannel.fld01. You can type in visnek lamturbChannel in the terminal > and then open visit and visualize the temperature variable. That will your > l2. > > Best Regards, > Tanmoy > > On Thu, Jun 9, 2016 at 5:13 PM, wrote: > >> Hello, >> >> >> In the userchk subroutine for the turbChannel example, lambda2 was >> computed. How can I visualize the isosurfaces (streamwise structures) in >> visit? >> >> >> if(mod(istep,iostep).eq.0 .and. istep.gt.0) then >> ! compute lambda2 vortex >> call lambda2(t(1,1,1,1,2)) >> ! compute vorticity --- 3 components returned in t(...) >> if(ldimt.ge.5) call comp_vort3(t(1,1,1,1,3),wo1,wo2,vx,vy,vz) >> endif >> >> >> Thank you, >> >> Virgilio A. Gomez >> >> >> >> _______________________________________________ >> 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 Mon Jun 13 11:50:49 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 13 Jun 2016 16:50:49 +0000 Subject: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 8 In-Reply-To: References: Message-ID: Hello Jing, I tried your new python code for msh convert. I was able to read file successfully but not able to get .rea file. For my geometry I have following zones: (0 "Zone Sections") (39 (8 fluid CREATED_MATERIAL_6)()) (39 (9 interior int_CREATED_MATERIAL_6)()) (39 (10 wall W)()) (39 (11 velocity-inlet PA)()) (39 (12 velocity-inlet VEIN)()) (39 (13 pressure-outlet DA)()) I have attached error file with this mail(error file name = error(1).png and msh file is mesh_hexa_final.msh). what other changes should I make to convert .msh file to .rea. Thanks, Mansi Patel ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users-request at lists.mcs.anl.gov Sent: Wednesday, June 8, 2016 12:18 PM To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 8 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. Re: Nek5000-users Digest, Vol 88, Issue 5 (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 8 Jun 2016 18:15:42 +0200 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 5 Message-ID: Content-Type: text/plain; charset="utf-8" Hello Jing, Recently I am also working on converting fluent mesh to nek5000. I have generated the *msh from gambit, then using the mshconvert.py tool to convert a simple mesh with a circular cylinder inside a square. simply, I can get the *rea file with circle of the "W", "v" and "O". but I have met two problems; 1. to impose the periodic boundary conditons: in the script, it strongly recommend to impose "P" through the script, then how to setup it in mshconvert.py? the way convert('mesh.msh', bcs={1:'W',2:'v',3:'O',4:'P', 5:'P'}) can generate the rea field but failed in the step of genmap. so how to treat boundary 4 and 5 as periodic BCs? 2. about the curved wall. there is no problem to define a circle by "Circle" command, but if I want to using "m" to define a spline curve, how to seed middle points? I know in Gambit I can mesh the line using 3 node, I defined 3 node mode to mesh a circle, and using "m" instead of "circle", however, it failed to generate the rea file. the circle merged into a point, then what should I do to active the spline curve? Thanks! Wei 2016-06-08 15:46 GMT+02:00 : > Hi Mansi, > > You can find the updated "mshconvert.py" in the attachment. You can run > the script for your case likes > > ### > $ ipython > > In [1]: from mshconvert import * > Converting from ANSYS Fluent format (.msh) to Nek5000, semtex or FEniCS > format > > In [2]: convert('mesh_hexa_final.msh', bcs={10:'W',11:'v',12:'v',13:'O'}) > ... > ### > > Here I assume that BC "W" is on zone 10, "v" is on zones 11 and 12, and > 'O' on zone 13. > > The snapshot for the Nek5000 mesh using visit is also attached in the > email. > > /Jing > > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov < > nek5000-users-bounces at lists.mcs.anl.gov> on behalf of > nek5000-users-request at lists.mcs.anl.gov < > nek5000-users-request at lists.mcs.anl.gov> > Sent: Monday, June 6, 2016 22:09 > To: nek5000-users at lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 5 > > 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. Re: Nek5000-users Digest, Vol 88, Issue 4, Problem creating > .rea file (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 6 Jun 2016 19:58:31 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 4, > Problem creating .rea file > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > > > Thanks jing, that was a lot helpful to me. > > I have generated the .msh file for the hexahedral mesh for my geometry. > File is attached to this mail. > > > I have given boundary condition in this file only let me know if there are > any changes to be made and file has only one zone( if by one zone you mean > only 1 type of mesh through out whole geometry). > > > Questions: > > 1) Users, what are other ways to convert (Icem cfd) .msh file to .rea > file? > > 2) is there any way to smooth hexahedral mesh for unstructured geometry? > > > Thanks, > > Mansi Patel > > > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov < > nek5000-users-bounces at lists.mcs.anl.gov> on behalf of > nek5000-users-request at lists.mcs.anl.gov < > nek5000-users-request at lists.mcs.anl.gov> > Sent: Friday, June 3, 2016 1:00 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 4 > > 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. Re: Nek5000-users Digest, Vol 88, Issue 3 > (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Jun 2016 21:21:13 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Nek5000-users Digest, Vol 88, Issue 3 > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Mansi, > > 1)what should I do to solve error? > > Right now mshconvert can only deal with single zone's case. So you should > have to manually merge the multi-zone to single-zone in the .msh file. > > Also we found that there are few bugs in the file. Could you please send > us your .msh file to test and then we will get back to you with the > corrected version? > > 2)what are mesh types that we can use? > Quadrant for 2D- and hexahedral for 3D-cases. > > 3) I there any other easy way to convert .msh file to .rea? > I leave this question to other users. > > Thanks. > > Regards, Jing > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov < > nek5000-users-bounces at lists.mcs.anl.gov> on behalf of > nek5000-users-request at lists.mcs.anl.gov < > nek5000-users-request at lists.mcs.anl.gov> > Sent: Thursday, June 2, 2016 19:17 > To: nek5000-users at lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 3 > > 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. problems in generating .rea file (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Jun 2016 17:12:11 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: [Nek5000-users] problems in generating .rea file > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello all, > > I want to ask what type of mesh does Nek5000 accept? tetrahedral, > hexahedral,etc? > > Because I am using ICEM CFD for generating mesh which has extension .msh > and for that I used python code given for mshconvert to convert into .rea > file but I am getting error. the error image is attached. > > Please let me know following questions > > 1)what should I do to solve error? > > 2)what are mesh types that we can use? > > 3) I there any other easy way to convert .msh file to .rea? > > > Thanks, any help would be appreciated. > > > Thanks, > > Mansi Patel > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160602/aaf91e41/attachment.html > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: error.png > Type: image/png > Size: 91392 bytes > Desc: error.png > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160602/aaf91e41/attachment.png > > > > ------------------------------ > > _______________________________________________ > 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 88, Issue 3 > ******************************************** > > > ------------------------------ > > _______________________________________________ > 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 88, Issue 4 > ******************************************** > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160606/e07ab762/attachment.html > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: mesh_hexa_final.msh > Type: application/octet-stream > Size: 24802571 bytes > Desc: mesh_hexa_final.msh > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160606/e07ab762/attachment.obj > > > > ------------------------------ > > _______________________________________________ > 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 88, Issue 5 > ******************************************** > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Wei HE ?? School of Aeronautics Universidad Polit?cnica de Madrid http://www.cfm.upm.es/ -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ 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 88, Issue 8 ******************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: error (1).png Type: image/png Size: 106163 bytes Desc: error (1).png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mesh_hexa_final.msh Type: application/octet-stream Size: 14680064 bytes Desc: mesh_hexa_final.msh URL: From nek5000-users at lists.mcs.anl.gov Mon Jun 13 14:09:05 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 13 Jun 2016 13:09:05 -0600 Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results Message-ID: Hello neks, I have a DNS simulation that I was running as PNPN-2 and I would like to run it as PNPN without starting back at the initial conditions. I am curious if anyone has experience running a PNPN case with initial conditions from a PNPN-2 simulation? I have tried this and the simulation runs okay, except the pressure term never seems to converge when running the PNPN simulation. This dramatically increases runtime and makes the results questionable. It seems to me that restarting with PNPN-2 results should be doable, and that it should only take a few iterations for the pressure term to start converging. However, my simulation is still not converging after 100+ iterations, but it was converging fine when I was running PNPN-2. Any suggestions for things I should look for that might cause the problem, or potential fixes? Thanks -- Phil Sakievich PhD Candidate - Mechanical Engineering Arizona State University - Ira A. Fulton School for Engineering of Matter Transport and Energy Tempe, Arizona -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jun 13 14:15:32 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 13 Jun 2016 19:15:32 +0000 Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results In-Reply-To: References: Message-ID: Hi Phil, The regularity of the pressure field is much larger for Pn-Pn as compared to Pn-Pn-2 so it should take some time to readjust to the larger resolution. Aleks ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, June 13, 2016 2:09 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results Hello neks, I have a DNS simulation that I was running as PNPN-2 and I would like to run it as PNPN without starting back at the initial conditions. I am curious if anyone has experience running a PNPN case with initial conditions from a PNPN-2 simulation? I have tried this and the simulation runs okay, except the pressure term never seems to converge when running the PNPN simulation. This dramatically increases runtime and makes the results questionable. It seems to me that restarting with PNPN-2 results should be doable, and that it should only take a few iterations for the pressure term to start converging. However, my simulation is still not converging after 100+ iterations, but it was converging fine when I was running PNPN-2. Any suggestions for things I should look for that might cause the problem, or potential fixes? Thanks -- Phil Sakievich PhD Candidate - Mechanical Engineering Arizona State University - Ira A. Fulton School for Engineering of Matter Transport and Energy Tempe, Arizona -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jun 13 14:31:08 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 13 Jun 2016 21:31:08 +0200 Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results In-Reply-To: References: Message-ID: Hi, In principle, you can do a Navier-Stokes restart without pressure field. For PnPn-2 you can for instance do one step with Uzawa (nested iterations) to have a good pressure. So usually, when we do a restart of a solution wi thout pressure (e.g. when doing Arnoldi or Newton) then one Uzawa step fixes everything. I am not too familiar with PnPn, but I guess that there is a flavour that is not dependent on a previous pressure solution. Perhaps a PnPn-expert has some opinion on a Uzawa-like method? Best regards, Philipp On 2016-06-13 21:15, nek5000-users at lists.mcs.anl.gov wrote: > Hi Phil, > > The regularity of the pressure field is much larger for Pn-Pn as > compared to Pn-Pn-2 so it should take some time to readjust to the > larger resolution. > > Aleks > ------------------------------------------------------------------------ > *From:* nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > *Sent:* Monday, June 13, 2016 2:09 PM > *To:* nek5000-users at lists.mcs.anl.gov > *Subject:* [Nek5000-users] Restarting with PNPN using PNPN-2 results > > Hello neks, > > I have a DNS simulation that I was running as PNPN-2 and I would like to > run it as PNPN without starting back at the initial conditions. > I am curious if anyone has experience running a PNPN case with initial > conditions from a PNPN-2 simulation? I have tried this and the > simulation runs okay, except the pressure term never seems to converge > when running the PNPN simulation. This dramatically increases runtime > and makes the results questionable. It seems to me that restarting with > PNPN-2 results should be doable, and that it should only take a few > iterations for the pressure term to start converging. However, my > simulation is still not converging after 100+ iterations, but it was > converging fine when I was running PNPN-2. > > Any suggestions for things I should look for that might cause the > problem, or potential fixes? > > Thanks > -- > Phil Sakievich > > PhD Candidate - Mechanical Engineering > Arizona State University - Ira A. Fulton School for Engineering of > Matter Transport and Energy > Tempe, Arizona > > > _______________________________________________ > 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 Jun 13 18:11:14 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 13 Jun 2016 16:11:14 -0700 Subject: [Nek5000-users] lambda2 in turbChannel In-Reply-To: References: Message-ID: Hi Wei, I do not think so. But you can definitely, modify the lambda2() routine to generate the Q criterion. It is quite straightforward. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Jun 14 04:21:16 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 14 Jun 2016 11:21:16 +0200 Subject: [Nek5000-users] g2gi() no geometry found In-Reply-To: References: Message-ID: Hello Neks, I am trying to use the g2gi subroutine, but keep getting the error massage ABORT: No geometry found in: call userchk grid-to-grid interpolation 140 8 8 8 2.0010000E+03 4002 U P 4 NELT,NX,N ?a?@ NONSTD HDR, parse_hdr, abort. ABORT: No geometry found in newgeom.fld call exitt: dying ... Anybody familiar with this error? Do I give him the wrong files? I assumed Nek wants a .fld. Any help or working case as an example would be highly appreciated. Br Michael e1429308 at student.tuwien.ac.at From nek5000-users at lists.mcs.anl.gov Tue Jun 14 06:40:05 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 14 Jun 2016 11:40:05 +0000 Subject: [Nek5000-users] g2gi() no geometry found In-Reply-To: References: , Message-ID: Hi Michael, You need to compile with the ifmpiio flag set in makenek: # (set PPLIST=? to get a list of available symbols) PPLIST="MPIIO" All files should be .f00000 files, which is the current default. (Make certain that your current .usr file does not reset param(66) to 4.) [ You can convert a .fld file to a .f0000 file by running a 0 step, 0 FINTIME job and setting p66=6, p67=4 in the .usr file, say, in subroutine usrdat(). ] When running g2gi, make certain that the new file has the geometry in it. The old file does not need the geometry, only the data to be interpolated. hth Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Tuesday, June 14, 2016 4:21 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] g2gi() no geometry found Hello Neks, I am trying to use the g2gi subroutine, but keep getting the error massage ABORT: No geometry found in: call userchk grid-to-grid interpolation 140 8 8 8 2.0010000E+03 4002 U P 4 NELT,NX,N ?a?@ NONSTD HDR, parse_hdr, abort. ABORT: No geometry found in newgeom.fld call exitt: dying ... Anybody familiar with this error? Do I give him the wrong files? I assumed Nek wants a .fld. Any help or working case as an example would be highly appreciated. Br Michael e1429308 at student.tuwien.ac.at _______________________________________________ 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 Jun 14 15:14:51 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 14 Jun 2016 22:14:51 +0200 Subject: [Nek5000-users] g2gi() no geometry found In-Reply-To: References: , Message-ID: Hi Paul, First of all: Thanks for your help, it is highly appreciated. Second: Following your guidance, the previews error has changed into a new one: call userchk grid-to-grid interpolation ABORT: nelr>lelr on rank 0 This one I was able to solve, by using nekmpi instead of nek, leading to this error: call userchk grid-to-grid interpolation set initial conditions Checking restart options: base0.f00004 nekuic (1) for ifld 1 Reading checkpoint data ** ERROR ** ** ERROR ** Could not open restart file: base0.f00004 I tried different approaches, but I don?t really have a clue, why Nek isn?t able to open the restart file. Any suggestions on this point? Br, Michael -----Urspr?ngliche Nachricht----- Von: nek5000-users-bounces at lists.mcs.anl.gov [mailto:nek5000-users-bounces at lists.mcs.anl.gov] Im Auftrag von nek5000-users at lists.mcs.anl.gov Gesendet: Dienstag, 14. Juni 2016 13:40 An: nek5000-users at lists.mcs.anl.gov Betreff: Re: [Nek5000-users] g2gi() no geometry found Hi Michael, You need to compile with the ifmpiio flag set in makenek: # (set PPLIST=? to get a list of available symbols) PPLIST="MPIIO" All files should be .f00000 files, which is the current default. (Make certain that your current .usr file does not reset param(66) to 4.) [ You can convert a .fld file to a .f0000 file by running a 0 step, 0 FINTIME job and setting p66=6, p67=4 in the .usr file, say, in subroutine usrdat(). ] When running g2gi, make certain that the new file has the geometry in it. The old file does not need the geometry, only the data to be interpolated. hth Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Tuesday, June 14, 2016 4:21 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] g2gi() no geometry found Hello Neks, I am trying to use the g2gi subroutine, but keep getting the error massage ABORT: No geometry found in: call userchk grid-to-grid interpolation 140 8 8 8 2.0010000E+03 4002 U P 4 NELT,NX,N ?a?@ NONSTD HDR, parse_hdr, abort. ABORT: No geometry found in newgeom.fld call exitt: dying ... Anybody familiar with this error? Do I give him the wrong files? I assumed Nek wants a .fld. Any help or working case as an example would be highly appreciated. Br Michael e1429308 at student.tuwien.ac.at _______________________________________________ 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 Jun 14 17:44:38 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 14 Jun 2016 16:44:38 -0600 Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results Message-ID: Philipp and Aleks, Thanks for the replies. The Uzawa method sounds exactly like what I am looking for. I would like to pay a penalty upfront to converge to a good pressure solution without taking too many (or really any) timesteps and then move forward with a resolved pressure solution. I am hoping there is a way to do this since a pressure projection method is being used. My solution is already well resolved temporally and I don't want to perturbe it with a long time series of unresolved pressure fields/slightly divergent velocity fields. Can anyone comment on the use of Uzawa with PNPN? Also, Philipp is there a specific routine you call to perform just one of these iterations? I haven't used this method before. Kind regards, Phil On Tue, Jun 14, 2016 at 11:00 AM, 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. Restarting with PNPN using PNPN-2 results > (nek5000-users at lists.mcs.anl.gov) > 2. Re: Restarting with PNPN using PNPN-2 results > (nek5000-users at lists.mcs.anl.gov) > 3. Re: Restarting with PNPN using PNPN-2 results > (nek5000-users at lists.mcs.anl.gov) > 4. Re: lambda2 in turbChannel (nek5000-users at lists.mcs.anl.gov) > 5. g2gi() no geometry found (nek5000-users at lists.mcs.anl.gov) > 6. Re: g2gi() no geometry found (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Jun 2016 13:09:05 -0600 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hello neks, > > I have a DNS simulation that I was running as PNPN-2 and I would like to > run it as PNPN without starting back at the initial conditions. > I am curious if anyone has experience running a PNPN case with initial > conditions from a PNPN-2 simulation? I have tried this and the simulation > runs okay, except the pressure term never seems to converge when running > the PNPN simulation. This dramatically increases runtime and makes the > results questionable. It seems to me that restarting with PNPN-2 results > should be doable, and that it should only take a few iterations for the > pressure term to start converging. However, my simulation is still not > converging after 100+ iterations, but it was converging fine when I was > running PNPN-2. > > Any suggestions for things I should look for that might cause the problem, > or potential fixes? > > Thanks > -- > Phil Sakievich > > PhD Candidate - Mechanical Engineering > Arizona State University - Ira A. Fulton School for Engineering of Matter > Transport and Energy > Tempe, Arizona > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160613/790d807b/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Jun 2016 19:15:32 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Restarting with PNPN using PNPN-2 results > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Phil, > > The regularity of the pressure field is much larger for Pn-Pn as compared > to Pn-Pn-2 so it should take some time to readjust to the larger resolution. > > Aleks > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [ > nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Monday, June 13, 2016 2:09 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results > > Hello neks, > > I have a DNS simulation that I was running as PNPN-2 and I would like to > run it as PNPN without starting back at the initial conditions. > I am curious if anyone has experience running a PNPN case with initial > conditions from a PNPN-2 simulation? I have tried this and the simulation > runs okay, except the pressure term never seems to converge when running > the PNPN simulation. This dramatically increases runtime and makes the > results questionable. It seems to me that restarting with PNPN-2 results > should be doable, and that it should only take a few iterations for the > pressure term to start converging. However, my simulation is still not > converging after 100+ iterations, but it was converging fine when I was > running PNPN-2. > > Any suggestions for things I should look for that might cause the problem, > or potential fixes? > > Thanks > -- > Phil Sakievich > > PhD Candidate - Mechanical Engineering > Arizona State University - Ira A. Fulton School for Engineering of Matter > Transport and Energy > Tempe, Arizona > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160613/09bbb78b/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Mon, 13 Jun 2016 21:31:08 +0200 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Restarting with PNPN using PNPN-2 results > Message-ID: > > Content-Type: text/plain; charset=windows-1252; format=flowed > > Hi, > > In principle, you can do a Navier-Stokes restart without pressure field. > For PnPn-2 you can for instance do one step with Uzawa (nested > iterations) to have a good pressure. So usually, when we do a restart of > a solution wi > thout pressure (e.g. when doing Arnoldi or Newton) then one Uzawa step > fixes everything. I am not too familiar with PnPn, but I guess that > there is a flavour that is not dependent on a previous pressure > solution. Perhaps a PnPn-expert has some opinion on a Uzawa-like method? > > Best regards, > Philipp > > On 2016-06-13 21:15, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Phil, > > > > The regularity of the pressure field is much larger for Pn-Pn as > > compared to Pn-Pn-2 so it should take some time to readjust to the > > larger resolution. > > > > Aleks > > ------------------------------------------------------------------------ > > *From:* nek5000-users-bounces at lists.mcs.anl.gov > > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > > *Sent:* Monday, June 13, 2016 2:09 PM > > *To:* nek5000-users at lists.mcs.anl.gov > > *Subject:* [Nek5000-users] Restarting with PNPN using PNPN-2 results > > > > Hello neks, > > > > I have a DNS simulation that I was running as PNPN-2 and I would like to > > run it as PNPN without starting back at the initial conditions. > > I am curious if anyone has experience running a PNPN case with initial > > conditions from a PNPN-2 simulation? I have tried this and the > > simulation runs okay, except the pressure term never seems to converge > > when running the PNPN simulation. This dramatically increases runtime > > and makes the results questionable. It seems to me that restarting with > > PNPN-2 results should be doable, and that it should only take a few > > iterations for the pressure term to start converging. However, my > > simulation is still not converging after 100+ iterations, but it was > > converging fine when I was running PNPN-2. > > > > Any suggestions for things I should look for that might cause the > > problem, or potential fixes? > > > > Thanks > > -- > > Phil Sakievich > > > > PhD Candidate - Mechanical Engineering > > Arizona State University - Ira A. Fulton School for Engineering of > > Matter Transport and Energy > > Tempe, Arizona > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > ------------------------------ > > Message: 4 > Date: Mon, 13 Jun 2016 16:11:14 -0700 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] lambda2 in turbChannel > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Hi Wei, > > I do not think so. But you can definitely, modify the lambda2() routine to > generate the Q criterion. It is quite straightforward. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160613/40eedaf9/attachment-0001.html > > > > ------------------------------ > > Message: 5 > Date: Tue, 14 Jun 2016 11:21:16 +0200 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] g2gi() no geometry found > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hello Neks, > > I am trying to use the g2gi subroutine, but keep getting the error > massage ABORT: No geometry found in: > > call userchk > grid-to-grid interpolation > 140 8 8 8 2.0010000E+03 4002 U P 4 > NELT,NX,N ?a?@ > > NONSTD HDR, parse_hdr, abort. > ABORT: No geometry found in newgeom.fld > > call exitt: dying ... > > Anybody familiar with this error? Do I give him the wrong files? I > assumed Nek wants a .fld. Any help or working case as an example would > be highly appreciated. > > Br > Michael > e1429308 at student.tuwien.ac.at > > > > > > > ------------------------------ > > Message: 6 > Date: Tue, 14 Jun 2016 11:40:05 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] g2gi() no geometry found > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > > Hi Michael, > > You need to compile with the ifmpiio flag set in makenek: > > > # (set PPLIST=? to get a list of available symbols) > PPLIST="MPIIO" > > All files should be .f00000 files, which is the current default. (Make > certain that your > current .usr file does not reset param(66) to 4.) [ You can convert a > .fld file to a .f0000 > file by running a 0 step, 0 FINTIME job and setting p66=6, p67=4 in the > .usr file, say, in > subroutine usrdat(). ] > > When running g2gi, make certain that the new file has the geometry in it. > The old file does not need the > geometry, only the data to be interpolated. > > hth > > Paul > > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [ > nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Tuesday, June 14, 2016 4:21 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] g2gi() no geometry found > > Hello Neks, > > I am trying to use the g2gi subroutine, but keep getting the error > massage ABORT: No geometry found in: > > call userchk > grid-to-grid interpolation > 140 8 8 8 2.0010000E+03 4002 U P 4 > NELT,NX,N ?a?@ > > NONSTD HDR, parse_hdr, abort. > ABORT: No geometry found in newgeom.fld > > call exitt: dying ... > > Anybody familiar with this error? Do I give him the wrong files? I > assumed Nek wants a .fld. Any help or working case as an example would > be highly appreciated. > > Br > Michael > e1429308 at student.tuwien.ac.at > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > End of Nek5000-users Digest, Vol 88, Issue 13 > ********************************************* > -- Phil Sakievich PhD Candidate - Mechanical Engineering Arizona State University - Ira A. Fulton School for Engineering of Matter Transport and Energy Tempe, Arizona -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Jun 15 03:44:04 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 15 Jun 2016 10:44:04 +0200 Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results In-Reply-To: References: Message-ID: Hi, I guess the question is whether there is a similar type of Uzawa iteration also for Pnpn, this I don't know and I have not looked into the theory. I can only say that for PnPn-2, with the nested iterations you can get a perfect pressure (i.e. not proportional to Delta p) in one time step. I guess one needs a PnPn user to answer that question. Just as a side question; why do you want to go from PnPn-2 to PnPn? Out of curiosity... Best regards, PHilipp On 2016-06-15 00:44, nek5000-users at lists.mcs.anl.gov wrote: > Philipp and Aleks, > > Thanks for the replies. The Uzawa method sounds exactly like what I am > looking for. I would like to pay a penalty upfront to converge to a > good pressure solution without taking too many (or really any) timesteps > and then move forward with a resolved pressure solution. I am hoping > there is a way to do this since a pressure projection method is being used. > > My solution is already well resolved temporally and I don't want to > perturbe it with a long time series of unresolved pressure > fields/slightly divergent velocity fields. Can anyone comment on the use > of Uzawa with PNPN? Also, Philipp is there a specific routine you call > to perform just one of these iterations? I haven't used this method before. > > Kind regards, > > Phil > > On Tue, Jun 14, 2016 at 11:00 AM, > > 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. Restarting with PNPN using PNPN-2 results > (nek5000-users at lists.mcs.anl.gov > ) > 2. Re: Restarting with PNPN using PNPN-2 results > (nek5000-users at lists.mcs.anl.gov > ) > 3. Re: Restarting with PNPN using PNPN-2 results > (nek5000-users at lists.mcs.anl.gov > ) > 4. Re: lambda2 in turbChannel (nek5000-users at lists.mcs.anl.gov > ) > 5. g2gi() no geometry found (nek5000-users at lists.mcs.anl.gov > ) > 6. Re: g2gi() no geometry found (nek5000-users at lists.mcs.anl.gov > ) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Jun 2016 13:09:05 -0600 > From: nek5000-users at lists.mcs.anl.gov > > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hello neks, > > I have a DNS simulation that I was running as PNPN-2 and I would like to > run it as PNPN without starting back at the initial conditions. > I am curious if anyone has experience running a PNPN case with initial > conditions from a PNPN-2 simulation? I have tried this and the > simulation > runs okay, except the pressure term never seems to converge when running > the PNPN simulation. This dramatically increases runtime and makes the > results questionable. It seems to me that restarting with PNPN-2 > results > should be doable, and that it should only take a few iterations for the > pressure term to start converging. However, my simulation is still not > converging after 100+ iterations, but it was converging fine when I was > running PNPN-2. > > Any suggestions for things I should look for that might cause the > problem, > or potential fixes? > > Thanks > -- > Phil Sakievich > > PhD Candidate - Mechanical Engineering > Arizona State University - Ira A. Fulton School for Engineering of > Matter > Transport and Energy > Tempe, Arizona > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Jun 2016 19:15:32 +0000 > From: nek5000-users at lists.mcs.anl.gov > > To: "nek5000-users at lists.mcs.anl.gov > " > > > Subject: Re: [Nek5000-users] Restarting with PNPN using PNPN-2 results > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Phil, > > The regularity of the pressure field is much larger for Pn-Pn as > compared to Pn-Pn-2 so it should take some time to readjust to the > larger resolution. > > Aleks > ________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > > [nek5000-users-bounces at lists.mcs.anl.gov > ] on behalf of > nek5000-users at lists.mcs.anl.gov > > [nek5000-users at lists.mcs.anl.gov > ] > Sent: Monday, June 13, 2016 2:09 PM > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results > > Hello neks, > > I have a DNS simulation that I was running as PNPN-2 and I would > like to run it as PNPN without starting back at the initial conditions. > I am curious if anyone has experience running a PNPN case with > initial conditions from a PNPN-2 simulation? I have tried this and > the simulation runs okay, except the pressure term never seems to > converge when running the PNPN simulation. This dramatically > increases runtime and makes the results questionable. It seems to > me that restarting with PNPN-2 results should be doable, and that it > should only take a few iterations for the pressure term to start > converging. However, my simulation is still not converging after > 100+ iterations, but it was converging fine when I was running PNPN-2. > > Any suggestions for things I should look for that might cause the > problem, or potential fixes? > > Thanks > -- > Phil Sakievich > > PhD Candidate - Mechanical Engineering > Arizona State University - Ira A. Fulton School for Engineering of > Matter Transport and Energy > Tempe, Arizona > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 3 > Date: Mon, 13 Jun 2016 21:31:08 +0200 > From: nek5000-users at lists.mcs.anl.gov > > To: nek5000-users at lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] Restarting with PNPN using PNPN-2 results > Message-ID: > > > > Content-Type: text/plain; charset=windows-1252; format=flowed > > Hi, > > In principle, you can do a Navier-Stokes restart without pressure field. > For PnPn-2 you can for instance do one step with Uzawa (nested > iterations) to have a good pressure. So usually, when we do a restart of > a solution wi > thout pressure (e.g. when doing Arnoldi or Newton) then one Uzawa step > fixes everything. I am not too familiar with PnPn, but I guess that > there is a flavour that is not dependent on a previous pressure > solution. Perhaps a PnPn-expert has some opinion on a Uzawa-like method? > > Best regards, > Philipp > > On 2016-06-13 21:15, nek5000-users at lists.mcs.anl.gov > wrote: > > Hi Phil, > > > > The regularity of the pressure field is much larger for Pn-Pn as > > compared to Pn-Pn-2 so it should take some time to readjust to the > > larger resolution. > > > > Aleks > > > ------------------------------------------------------------------------ > > *From:* nek5000-users-bounces at lists.mcs.anl.gov > > > [nek5000-users-bounces at lists.mcs.anl.gov > ] on behalf of > > nek5000-users at lists.mcs.anl.gov > > [nek5000-users at lists.mcs.anl.gov > ] > > *Sent:* Monday, June 13, 2016 2:09 PM > > *To:* nek5000-users at lists.mcs.anl.gov > > > *Subject:* [Nek5000-users] Restarting with PNPN using PNPN-2 results > > > > Hello neks, > > > > I have a DNS simulation that I was running as PNPN-2 and I would > like to > > run it as PNPN without starting back at the initial conditions. > > I am curious if anyone has experience running a PNPN case with initial > > conditions from a PNPN-2 simulation? I have tried this and the > > simulation runs okay, except the pressure term never seems to converge > > when running the PNPN simulation. This dramatically increases runtime > > and makes the results questionable. It seems to me that > restarting with > > PNPN-2 results should be doable, and that it should only take a few > > iterations for the pressure term to start converging. However, my > > simulation is still not converging after 100+ iterations, but it was > > converging fine when I was running PNPN-2. > > > > Any suggestions for things I should look for that might cause the > > problem, or potential fixes? > > > > Thanks > > -- > > Phil Sakievich > > > > PhD Candidate - Mechanical Engineering > > Arizona State University - Ira A. Fulton School for Engineering of > > Matter Transport and Energy > > Tempe, Arizona > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > ------------------------------ > > Message: 4 > Date: Mon, 13 Jun 2016 16:11:14 -0700 > From: nek5000-users at lists.mcs.anl.gov > > To: nek5000-users at lists.mcs.anl.gov > > Subject: Re: [Nek5000-users] lambda2 in turbChannel > Message-ID: > > > > Content-Type: text/plain; charset="utf-8" > > Hi Wei, > > I do not think so. But you can definitely, modify the lambda2() > routine to > generate the Q criterion. It is quite straightforward. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > Message: 5 > Date: Tue, 14 Jun 2016 11:21:16 +0200 > From: nek5000-users at lists.mcs.anl.gov > > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] g2gi() no geometry found > Message-ID: > > > > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hello Neks, > > I am trying to use the g2gi subroutine, but keep getting the error > massage ABORT: No geometry found in: > > call userchk > grid-to-grid interpolation > 140 8 8 8 2.0010000E+03 4002 U P 4 > NELT,NX,N ?a?@ > > NONSTD HDR, parse_hdr, abort. > ABORT: No geometry found in newgeom.fld > > call exitt: dying ... > > Anybody familiar with this error? Do I give him the wrong files? I > assumed Nek wants a .fld. Any help or working case as an example would > be highly appreciated. > > Br > Michael > e1429308 at student.tuwien.ac.at > > > > > > > ------------------------------ > > Message: 6 > Date: Tue, 14 Jun 2016 11:40:05 +0000 > From: nek5000-users at lists.mcs.anl.gov > > To: "nek5000-users at lists.mcs.anl.gov > " > > > Subject: Re: [Nek5000-users] g2gi() no geometry found > Message-ID: > > > > Content-Type: text/plain; charset="us-ascii" > > > Hi Michael, > > You need to compile with the ifmpiio flag set in makenek: > > > # (set PPLIST=? to get a list of available symbols) > PPLIST="MPIIO" > > All files should be .f00000 files, which is the current default. > (Make certain that your > current .usr file does not reset param(66) to 4.) [ You can > convert a .fld file to a .f0000 > file by running a 0 step, 0 FINTIME job and setting p66=6, p67=4 in > the .usr file, say, in > subroutine usrdat(). ] > > When running g2gi, make certain that the new file has the geometry > in it. The old file does not need the > geometry, only the data to be interpolated. > > hth > > Paul > > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov > > [nek5000-users-bounces at lists.mcs.anl.gov > ] on behalf of > nek5000-users at lists.mcs.anl.gov > > [nek5000-users at lists.mcs.anl.gov > ] > Sent: Tuesday, June 14, 2016 4:21 AM > To: nek5000-users at lists.mcs.anl.gov > > Subject: [Nek5000-users] g2gi() no geometry found > > Hello Neks, > > I am trying to use the g2gi subroutine, but keep getting the error > massage ABORT: No geometry found in: > > call userchk > grid-to-grid interpolation > 140 8 8 8 2.0010000E+03 4002 U P 4 > NELT,NX,N ?a?@ > > NONSTD HDR, parse_hdr, abort. > ABORT: No geometry found in newgeom.fld > > call exitt: dying ... > > Anybody familiar with this error? Do I give him the wrong files? I > assumed Nek wants a .fld. Any help or working case as an example would > be highly appreciated. > > Br > Michael > e1429308 at student.tuwien.ac.at > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > End of Nek5000-users Digest, Vol 88, Issue 13 > ********************************************* > > > > > -- > Phil Sakievich > > PhD Candidate - Mechanical Engineering > Arizona State University - Ira A. Fulton School for Engineering of > Matter Transport and Energy > Tempe, Arizona > > > _______________________________________________ > 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 Jun 15 22:22:52 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 15 Jun 2016 21:22:52 -0600 Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results Message-ID: Philipp, I am investigating a switch for two reasons: 1) to see how it affects my results. This is why I want to converge pressure right away before performing more timesteps. I will be running several more simulations that are similar to this one, and I am interested in how PNPN will perform for the same flow. I have already put in a significant amount of compute time into my current case and so I don't want to start it over to perform this simple investigation. 2) I have an additional interest in post processing and analyzing the pressure fluctuation field. Using PNPN over PNPN-2 makes sense in this case since the pressure field is better resolved and enforces C0 continuity across element boundaries. Thanks, Phil On Wed, Jun 15, 2016 at 11:00 AM, 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. Re: Restarting with PNPN using PNPN-2 results > (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 15 Jun 2016 10:44:04 +0200 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Restarting with PNPN using PNPN-2 results > Message-ID: > > Content-Type: text/plain; charset=windows-1252; format=flowed > > Hi, > I guess the question is whether there is a similar type of Uzawa > iteration also for Pnpn, this I don't know and I have not looked into > the theory. I can only say that for PnPn-2, with the nested iterations > you can get a perfect pressure (i.e. not proportional to Delta p) in one > time step. I guess one needs a PnPn user to answer that question. > > Just as a side question; why do you want to go from PnPn-2 to PnPn? Out > of curiosity... > > Best regards, > PHilipp > > On 2016-06-15 00:44, nek5000-users at lists.mcs.anl.gov wrote: > > Philipp and Aleks, > > > > Thanks for the replies. The Uzawa method sounds exactly like what I am > > looking for. I would like to pay a penalty upfront to converge to a > > good pressure solution without taking too many (or really any) timesteps > > and then move forward with a resolved pressure solution. I am hoping > > there is a way to do this since a pressure projection method is being > used. > > > > My solution is already well resolved temporally and I don't want to > > perturbe it with a long time series of unresolved pressure > > fields/slightly divergent velocity fields. Can anyone comment on the use > > of Uzawa with PNPN? Also, Philipp is there a specific routine you call > > to perform just one of these iterations? I haven't used this method > before. > > > > Kind regards, > > > > Phil > > > > On Tue, Jun 14, 2016 at 11:00 AM, > > > > 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. Restarting with PNPN using PNPN-2 results > > (nek5000-users at lists.mcs.anl.gov > > ) > > 2. Re: Restarting with PNPN using PNPN-2 results > > (nek5000-users at lists.mcs.anl.gov > > ) > > 3. Re: Restarting with PNPN using PNPN-2 results > > (nek5000-users at lists.mcs.anl.gov > > ) > > 4. Re: lambda2 in turbChannel (nek5000-users at lists.mcs.anl.gov > > ) > > 5. g2gi() no geometry found (nek5000-users at lists.mcs.anl.gov > > ) > > 6. Re: g2gi() no geometry found (nek5000-users at lists.mcs.anl.gov > > ) > > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 13 Jun 2016 13:09:05 -0600 > > From: nek5000-users at lists.mcs.anl.gov > > > > To: nek5000-users at lists.mcs.anl.gov > > > > Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results > > Message-ID: > > > > > mailman.23731.1465844987.24727.nek5000-users at lists.mcs.anl.gov>> > > Content-Type: text/plain; charset="utf-8" > > > > Hello neks, > > > > I have a DNS simulation that I was running as PNPN-2 and I would > like to > > run it as PNPN without starting back at the initial conditions. > > I am curious if anyone has experience running a PNPN case with > initial > > conditions from a PNPN-2 simulation? I have tried this and the > > simulation > > runs okay, except the pressure term never seems to converge when > running > > the PNPN simulation. This dramatically increases runtime and makes > the > > results questionable. It seems to me that restarting with PNPN-2 > > results > > should be doable, and that it should only take a few iterations for > the > > pressure term to start converging. However, my simulation is still > not > > converging after 100+ iterations, but it was converging fine when I > was > > running PNPN-2. > > > > Any suggestions for things I should look for that might cause the > > problem, > > or potential fixes? > > > > Thanks > > -- > > Phil Sakievich > > > > PhD Candidate - Mechanical Engineering > > Arizona State University - Ira A. Fulton School for Engineering of > > Matter > > Transport and Energy > > Tempe, Arizona > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160613/790d807b/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 2 > > Date: Mon, 13 Jun 2016 19:15:32 +0000 > > From: nek5000-users at lists.mcs.anl.gov > > > > To: "nek5000-users at lists.mcs.anl.gov > > " > > > > > > Subject: Re: [Nek5000-users] Restarting with PNPN using PNPN-2 > results > > Message-ID: > > > > > mailman.23735.1465845499.24727.nek5000-users at lists.mcs.anl.gov>> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Hi Phil, > > > > The regularity of the pressure field is much larger for Pn-Pn as > > compared to Pn-Pn-2 so it should take some time to readjust to the > > larger resolution. > > > > Aleks > > ________________________________ > > From: nek5000-users-bounces at lists.mcs.anl.gov > > > > [nek5000-users-bounces at lists.mcs.anl.gov > > ] on behalf of > > nek5000-users at lists.mcs.anl.gov > > > > [nek5000-users at lists.mcs.anl.gov > > ] > > Sent: Monday, June 13, 2016 2:09 PM > > To: nek5000-users at lists.mcs.anl.gov > > > > Subject: [Nek5000-users] Restarting with PNPN using PNPN-2 results > > > > Hello neks, > > > > I have a DNS simulation that I was running as PNPN-2 and I would > > like to run it as PNPN without starting back at the initial > conditions. > > I am curious if anyone has experience running a PNPN case with > > initial conditions from a PNPN-2 simulation? I have tried this and > > the simulation runs okay, except the pressure term never seems to > > converge when running the PNPN simulation. This dramatically > > increases runtime and makes the results questionable. It seems to > > me that restarting with PNPN-2 results should be doable, and that it > > should only take a few iterations for the pressure term to start > > converging. However, my simulation is still not converging after > > 100+ iterations, but it was converging fine when I was running > PNPN-2. > > > > Any suggestions for things I should look for that might cause the > > problem, or potential fixes? > > > > Thanks > > -- > > Phil Sakievich > > > > PhD Candidate - Mechanical Engineering > > Arizona State University - Ira A. Fulton School for Engineering of > > Matter Transport and Energy > > Tempe, Arizona > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160613/09bbb78b/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 3 > > Date: Mon, 13 Jun 2016 21:31:08 +0200 > > From: nek5000-users at lists.mcs.anl.gov > > > > To: nek5000-users at lists.mcs.anl.gov > > > > Subject: Re: [Nek5000-users] Restarting with PNPN using PNPN-2 > results > > Message-ID: > > > > > mailman.23743.1465847039.24727.nek5000-users at lists.mcs.anl.gov>> > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > Hi, > > > > In principle, you can do a Navier-Stokes restart without pressure > field. > > For PnPn-2 you can for instance do one step with Uzawa (nested > > iterations) to have a good pressure. So usually, when we do a > restart of > > a solution wi > > thout pressure (e.g. when doing Arnoldi or Newton) then one Uzawa > step > > fixes everything. I am not too familiar with PnPn, but I guess that > > there is a flavour that is not dependent on a previous pressure > > solution. Perhaps a PnPn-expert has some opinion on a Uzawa-like > method? > > > > Best regards, > > Philipp > > > > On 2016-06-13 21:15, nek5000-users at lists.mcs.anl.gov > > wrote: > > > Hi Phil, > > > > > > The regularity of the pressure field is much larger for Pn-Pn as > > > compared to Pn-Pn-2 so it should take some time to readjust to the > > > larger resolution. > > > > > > Aleks > > > > > > ------------------------------------------------------------------------ > > > *From:* nek5000-users-bounces at lists.mcs.anl.gov > > > > > [nek5000-users-bounces at lists.mcs.anl.gov > > ] on behalf of > > > nek5000-users at lists.mcs.anl.gov > > > > [nek5000-users at lists.mcs.anl.gov > > ] > > > *Sent:* Monday, June 13, 2016 2:09 PM > > > *To:* nek5000-users at lists.mcs.anl.gov > > > > > *Subject:* [Nek5000-users] Restarting with PNPN using PNPN-2 > results > > > > > > Hello neks, > > > > > > I have a DNS simulation that I was running as PNPN-2 and I would > > like to > > > run it as PNPN without starting back at the initial conditions. > > > I am curious if anyone has experience running a PNPN case with > initial > > > conditions from a PNPN-2 simulation? I have tried this and the > > > simulation runs okay, except the pressure term never seems to > converge > > > when running the PNPN simulation. This dramatically increases > runtime > > > and makes the results questionable. It seems to me that > > restarting with > > > PNPN-2 results should be doable, and that it should only take a few > > > iterations for the pressure term to start converging. However, my > > > simulation is still not converging after 100+ iterations, but it > was > > > converging fine when I was running PNPN-2. > > > > > > Any suggestions for things I should look for that might cause the > > > problem, or potential fixes? > > > > > > Thanks > > > -- > > > Phil Sakievich > > > > > > PhD Candidate - Mechanical Engineering > > > Arizona State University - Ira A. Fulton School for Engineering of > > > Matter Transport and Energy > > > Tempe, Arizona > > > > > > > > > _______________________________________________ > > > Nek5000-users mailing list > > > Nek5000-users at lists.mcs.anl.gov > > > > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > > > > > ------------------------------ > > > > Message: 4 > > Date: Mon, 13 Jun 2016 16:11:14 -0700 > > From: nek5000-users at lists.mcs.anl.gov > > > > To: nek5000-users at lists.mcs.anl.gov > > > > Subject: Re: [Nek5000-users] lambda2 in turbChannel > > Message-ID: > > > > > mailman.23757.1465860244.24727.nek5000-users at lists.mcs.anl.gov>> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Wei, > > > > I do not think so. But you can definitely, modify the lambda2() > > routine to > > generate the Q criterion. It is quite straightforward. > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160613/40eedaf9/attachment-0001.html > > > > > > ------------------------------ > > > > Message: 5 > > Date: Tue, 14 Jun 2016 11:21:16 +0200 > > From: nek5000-users at lists.mcs.anl.gov > > > > To: nek5000-users at lists.mcs.anl.gov > > > > Subject: [Nek5000-users] g2gi() no geometry found > > Message-ID: > > > > > mailman.23773.1465903728.24727.nek5000-users at lists.mcs.anl.gov>> > > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > > format="flowed" > > > > Hello Neks, > > > > I am trying to use the g2gi subroutine, but keep getting the error > > massage ABORT: No geometry found in: > > > > call userchk > > grid-to-grid interpolation > > 140 8 8 8 2.0010000E+03 4002 U P > 4 > > NELT,NX,N ?a?@ > > > > NONSTD HDR, parse_hdr, abort. > > ABORT: No geometry found in newgeom.fld > > > > call exitt: dying ... > > > > Anybody familiar with this error? Do I give him the wrong files? I > > assumed Nek wants a .fld. Any help or working case as an example > would > > be highly appreciated. > > > > Br > > Michael > > e1429308 at student.tuwien.ac.at > > > > > > > > > > > > > > ------------------------------ > > > > Message: 6 > > Date: Tue, 14 Jun 2016 11:40:05 +0000 > > From: nek5000-users at lists.mcs.anl.gov > > > > To: "nek5000-users at lists.mcs.anl.gov > > " > > > > > > Subject: Re: [Nek5000-users] g2gi() no geometry found > > Message-ID: > > > > > mailman.23774.1465904407.24727.nek5000-users at lists.mcs.anl.gov>> > > Content-Type: text/plain; charset="us-ascii" > > > > > > Hi Michael, > > > > You need to compile with the ifmpiio flag set in makenek: > > > > > > # (set PPLIST=? to get a list of available symbols) > > PPLIST="MPIIO" > > > > All files should be .f00000 files, which is the current default. > > (Make certain that your > > current .usr file does not reset param(66) to 4.) [ You can > > convert a .fld file to a .f0000 > > file by running a 0 step, 0 FINTIME job and setting p66=6, p67=4 in > > the .usr file, say, in > > subroutine usrdat(). ] > > > > When running g2gi, make certain that the new file has the geometry > > in it. The old file does not need the > > geometry, only the data to be interpolated. > > > > hth > > > > Paul > > > > > > ________________________________________ > > From: nek5000-users-bounces at lists.mcs.anl.gov > > > > [nek5000-users-bounces at lists.mcs.anl.gov > > ] on behalf of > > nek5000-users at lists.mcs.anl.gov > > > > [nek5000-users at lists.mcs.anl.gov > > ] > > Sent: Tuesday, June 14, 2016 4:21 AM > > To: nek5000-users at lists.mcs.anl.gov > > > > Subject: [Nek5000-users] g2gi() no geometry found > > > > Hello Neks, > > > > I am trying to use the g2gi subroutine, but keep getting the error > > massage ABORT: No geometry found in: > > > > call userchk > > grid-to-grid interpolation > > 140 8 8 8 2.0010000E+03 4002 U P > 4 > > NELT,NX,N ?a?@ > > > > NONSTD HDR, parse_hdr, abort. > > ABORT: No geometry found in newgeom.fld > > > > call exitt: dying ... > > > > Anybody familiar with this error? Do I give him the wrong files? I > > assumed Nek wants a .fld. Any help or working case as an example > would > > be highly appreciated. > > > > Br > > Michael > > e1429308 at student.tuwien.ac.at > > > > > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov 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 Nek5000-users at lists.mcs.anl.gov> > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > > End of Nek5000-users Digest, Vol 88, Issue 13 > > ********************************************* > > > > > > > > > > -- > > Phil Sakievich > > > > PhD Candidate - Mechanical Engineering > > Arizona State University - Ira A. Fulton School for Engineering of > > Matter Transport and Energy > > Tempe, Arizona > > > > > > _______________________________________________ > > Nek5000-users mailing list > > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > End of Nek5000-users Digest, Vol 88, Issue 15 > ********************************************* > -- Phil Sakievich PhD Candidate - Mechanical Engineering Arizona State University - Ira A. Fulton School for Engineering of Matter Transport and Energy Tempe, Arizona -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Jun 17 09:33:22 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 17 Jun 2016 14:33:22 +0000 Subject: [Nek5000-users] Configure a stress at boundary Message-ID: Dear Neks, I am simulating a water flow in the 3dbox example. In order to simulate the wind blowing over the water, I hope to add a wind stress at the top boundary. The wind stress (tau) formulation is given as tau = rho*C_d*U*U where tau is the wind stress, rho is the air density, C_d is the drag coefficient, and U is the wind speed. I guess the wind stress should be configured in ?userbc?, but how to do it? Can anyone help? Thank you! Peng ************************* Peng Wang, Ph.D. Postdoctoral Associate Department of Ocean Sciences Rosenstiel School of Marine and Atmospheric Science University of Miami 4600 Rickenbacker Causeway Miami, Florida 33149-1098, USA From nek5000-users at lists.mcs.anl.gov Fri Jun 17 11:31:38 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 17 Jun 2016 16:31:38 +0000 Subject: [Nek5000-users] Configure a stress at boundary In-Reply-To: References: Message-ID: Hi Peng, We have looked a bit into this type of boundary condition of Nek5000 stress-formulation -- you need to set boundary condition character in .box file (or choose prenek' option) to 'shl' (which probably stands for stress-horizontal-local) and set NEKUSE's the horizontal stress components to tr1 and tr2 in userbc. Aleks ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Friday, June 17, 2016 9:33 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Configure a stress at boundary Dear Neks, I am simulating a water flow in the 3dbox example. In order to simulate the wind blowing over the water, I hope to add a wind stress at the top boundary. The wind stress (tau) formulation is given as tau = rho*C_d*U*U where tau is the wind stress, rho is the air density, C_d is the drag coefficient, and U is the wind speed. I guess the wind stress should be configured in ?userbc?, but how to do it? Can anyone help? Thank you! Peng ************************* Peng Wang, Ph.D. Postdoctoral Associate Department of Ocean Sciences Rosenstiel School of Marine and Atmospheric Science University of Miami 4600 Rickenbacker Causeway Miami, Florida 33149-1098, USA _______________________________________________ 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 Jun 17 17:12:40 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 17 Jun 2016 22:12:40 +0000 Subject: [Nek5000-users] Configure a stress at boundary In-Reply-To: References: Message-ID: Thank you Aleks! It works. Peng > On Jun 17, 2016, at 1:00 PM, nek5000-users-request at lists.mcs.anl.gov 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://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mailman_listinfo_nek5000-2Dusers&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=QEl5evD27KmYmPJRHh_RJPXwtG0VKYwu68jKU6Xd1hw&m=Gqhwz-z3hpV1tYrJPqLsRElKdrWNR-RpyM47qRxfaig&s=I_CZEf3_IDG5xpCIRze6X4TkEA3zClPlwIl2i7-7cH0&e= > 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. Configure a stress at boundary (nek5000-users at lists.mcs.anl.gov) > 2. Re: Configure a stress at boundary > (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Jun 2016 14:33:22 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: [Nek5000-users] Configure a stress at boundary > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Neks, > > I am simulating a water flow in the 3dbox example. > In order to simulate the wind blowing over the water, I hope to add a wind stress at the top boundary. > The wind stress (tau) formulation is given as > tau = rho*C_d*U*U > where tau is the wind stress, rho is the air density, C_d is the drag coefficient, and U is the wind speed. > I guess the wind stress should be configured in ?userbc?, but how to do it? Can anyone help? > > Thank you! > Peng > > > > ************************* > Peng Wang, Ph.D. > > Postdoctoral Associate > Department of Ocean Sciences > Rosenstiel School of Marine and Atmospheric Science > University of Miami > 4600 Rickenbacker Causeway > Miami, Florida 33149-1098, USA > > > > ------------------------------ > > Message: 2 > Date: Fri, 17 Jun 2016 16:31:38 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: Re: [Nek5000-users] Configure a stress at boundary > Message-ID: > > Content-Type: text/plain; charset="Windows-1252" > > Hi Peng, > > We have looked a bit into this type of boundary condition of Nek5000 stress-formulation -- you need to set boundary condition character in .box file (or choose prenek' option) to > > 'shl' > > (which probably stands for stress-horizontal-local) and set NEKUSE's the horizontal stress components to tr1 and tr2 in userbc. > > Aleks > > ________________________________________ > From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Friday, June 17, 2016 9:33 AM > To: nek5000-users at lists.mcs.anl.gov > Subject: [Nek5000-users] Configure a stress at boundary > > Dear Neks, > > I am simulating a water flow in the 3dbox example. > In order to simulate the wind blowing over the water, I hope to add a wind stress at the top boundary. > The wind stress (tau) formulation is given as > tau = rho*C_d*U*U > where tau is the wind stress, rho is the air density, C_d is the drag coefficient, and U is the wind speed. > I guess the wind stress should be configured in ?userbc?, but how to do it? Can anyone help? > > Thank you! > Peng > > > > ************************* > Peng Wang, Ph.D. > > Postdoctoral Associate > Department of Ocean Sciences > Rosenstiel School of Marine and Atmospheric Science > University of Miami > 4600 Rickenbacker Causeway > Miami, Florida 33149-1098, USA > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mailman_listinfo_nek5000-2Dusers&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=QEl5evD27KmYmPJRHh_RJPXwtG0VKYwu68jKU6Xd1hw&m=Gqhwz-z3hpV1tYrJPqLsRElKdrWNR-RpyM47qRxfaig&s=I_CZEf3_IDG5xpCIRze6X4TkEA3zClPlwIl2i7-7cH0&e= > > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mailman_listinfo_nek5000-2Dusers&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=QEl5evD27KmYmPJRHh_RJPXwtG0VKYwu68jKU6Xd1hw&m=Gqhwz-z3hpV1tYrJPqLsRElKdrWNR-RpyM47qRxfaig&s=I_CZEf3_IDG5xpCIRze6X4TkEA3zClPlwIl2i7-7cH0&e= > > > End of Nek5000-users Digest, Vol 88, Issue 17 > ********************************************* From nek5000-users at lists.mcs.anl.gov Wed Jun 22 09:03:33 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 22 Jun 2016 14:03:33 +0000 Subject: [Nek5000-users] Re : CYCLIC BC for bend pipe Message-ID: Hello, I have a script that uses Pretex to generate a circle that is then extruded in a pipe. I think the script has some option that do not match my current version of Pretex. Here is the script (only the part for generating and meshing the circle): pretex << EOF inlet2d 1 READ PREVIOUS PARAMETERS one2d 1 BUILD FROM FILE one2d 5 DELETE ELEMENT 4 CURVE SIDES 5 Autosphere 4 3 Enter number of elements in core and shell: .65 Enter ratio in outer shell: 8 Convert Midside to Circle 2. Input maxium radius: 1 BUILD MENU 3 GLOBAL REFINE 13 Clean up vertices 7 REPLICATE/ROTATE 3 Rep. (1), Rot. (2), Rep/Rot (3) Template (4)? (0=abort) 90 Input rotation angle (deg): 1 Input number of reps (e.g., 1 --> double mesh size) 13 Clean up vertices 1 END GLOBAL REFINE 1 END ELEMENTS 1 ACCEPT MATL,QVOL 1 ACCEPT B.C.'s 1 ACCEPT B.C.'s 1 EXIT EOF The line that is causing the error message is '8 Convert Midside to Circle?. In my pretex version I have ?8 RENUMBER ELEMENTS?. Could you please let me know what I can do to fix the script? Thanks, marco -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Jun 22 09:37:15 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 22 Jun 2016 14:37:15 +0000 Subject: [Nek5000-users] Pretex script Message-ID: Hello, I have a script that uses Pretex to generate a circle that is then extruded in a pipe. I think the script has some option that do not match my current version of Pretex. Here is the script (only the part for generating and meshing the circle): pretex << EOF inlet2d 1 READ PREVIOUS PARAMETERS one2d 1 BUILD FROM FILE one2d 5 DELETE ELEMENT 4 CURVE SIDES 5 Autosphere 4 3 Enter number of elements in core and shell: .65 Enter ratio in outer shell: 8 Convert Midside to Circle 2. Input maxium radius: 1 BUILD MENU 3 GLOBAL REFINE 13 Clean up vertices 7 REPLICATE/ROTATE 3 Rep. (1), Rot. (2), Rep/Rot (3) Template (4)? (0=abort) 90 Input rotation angle (deg): 1 Input number of reps (e.g., 1 --> double mesh size) 13 Clean up vertices 1 END GLOBAL REFINE 1 END ELEMENTS 1 ACCEPT MATL,QVOL 1 ACCEPT B.C.'s 1 ACCEPT B.C.'s 1 EXIT EOF The line that is causing the error message is '8 Convert Midside to Circle?. In my pretex version I have ?8 RENUMBER ELEMENTS?. Could you please let me know what I can do to fix the script? Thanks, marco -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Jun 24 10:02:14 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 24 Jun 2016 15:02:14 +0000 Subject: [Nek5000-users] Pretex and Prex Message-ID: Hello, My question is related to the use of Pretex and Prex: according to the user?s manual, Pretex is the command line version of Prex. When I open Pretex, however, the GUI opens as well, causing Pretex to crash when running on the cluster. I need to call Pretex through a script that is ?qsub' to perform a sensitivity analysis. Because Pretex looks for an interface to open the GUI, my script fails to run. Has anybody else experienced such a behavior when using Pretex? If someone has, is there a work around this problem? Thanks, Marco From nek5000-users at lists.mcs.anl.gov Fri Jun 24 16:45:00 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 24 Jun 2016 21:45:00 +0000 Subject: [Nek5000-users] Refining Mesh for turbChannel Message-ID: Hello, I want to refine the mesh for the example turbChannel to resolve the Kolmogrov scale by modifying the given example files. How can I do that? Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Jun 25 10:35:06 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 25 Jun 2016 08:35:06 -0700 Subject: [Nek5000-users] Refining Mesh for turbChannel In-Reply-To: References: Message-ID: You can do so by modifying the box file, turbChannel.box file. For more details, you can refer to the nek5000 document from the ANL website. https://nek5000.mcs.anl.gov/files/2015/09/NEK_doc.pdf Best Regards, Tanmoy On Fri, Jun 24, 2016 at 2:45 PM, wrote: > Hello, > > > I want to refine the mesh for the example turbChannel to resolve the > Kolmogrov scale by modifying the given example files. How can I do that? > > > Thank you. > > > > _______________________________________________ > 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 Sun Jun 26 13:22:32 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 26 Jun 2016 18:22:32 +0000 Subject: [Nek5000-users] Refining Mesh for turbChannel Message-ID: Modifying just the .box file is sufficient? I know the .rea file also contains geometry information. Do I leave that alone? Thanks, Virgilio A. Gomez -----Original Message----- From: nek5000-users-bounces at lists.mcs.anl.gov [mailto:nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of nek5000-users-request at lists.mcs.anl.gov Sent: Saturday, June 25, 2016 12:00 PM To: nek5000-users at lists.mcs.anl.gov Subject: Nek5000-users Digest, Vol 88, Issue 21 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. Refining Mesh for turbChannel (nek5000-users at lists.mcs.anl.gov) 2. Re: Refining Mesh for turbChannel (nek5000-users at lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Fri, 24 Jun 2016 21:45:00 +0000 From: nek5000-users at lists.mcs.anl.gov To: "nek5000-users at lists.mcs.anl.gov" Subject: [Nek5000-users] Refining Mesh for turbChannel Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hello, I want to refine the mesh for the example turbChannel to resolve the Kolmogrov scale by modifying the given example files. How can I do that? Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Sat, 25 Jun 2016 08:35:06 -0700 From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Refining Mesh for turbChannel Message-ID: Content-Type: text/plain; charset="utf-8" You can do so by modifying the box file, turbChannel.box file. For more details, you can refer to the nek5000 document from the ANL website. https://nek5000.mcs.anl.gov/files/2015/09/NEK_doc.pdf Best Regards, Tanmoy On Fri, Jun 24, 2016 at 2:45 PM, wrote: > Hello, > > > I want to refine the mesh for the example turbChannel to resolve the > Kolmogrov scale by modifying the given example files. How can I do that? > > > Thank you. > > > > _______________________________________________ > 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: ------------------------------ _______________________________________________ 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 88, Issue 21 ********************************************* From nek5000-users at lists.mcs.anl.gov Mon Jun 27 03:17:31 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 27 Jun 2016 10:17:31 +0200 Subject: [Nek5000-users] Projection technique's parameters Message-ID: Hi Neks, My question is about the parameters which manage the projection method in the NEK5000: p93, p94 and p95. How can the correct values be selected for these parameters to obtain the better performance depending on the nature of simulation: laminar / turbulent, convection / diffusion, time step? Thank you for any suggestion, Andrew -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jun 27 07:55:27 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 27 Jun 2016 12:55:27 +0000 Subject: [Nek5000-users] Projection technique's parameters In-Reply-To: References: Message-ID: Hi Andrew, The projection routines are currently being overhauled, but the general strategy is: Number of projections controlled by p93 and mxprev in SIZE. p94 > 0: start projecting velocity/temp after step p94 p95 > 0: start projecting pressure after step 95 I typically set p94 and p95 to 5 I set mxprev and p93 to 20, but sometimes to a higher value. I used to occasionally to to much higher than 20 (say, 80), but in a recent rewrite and effort to make projection more robust I slowed the projection step down with too much work, so another rewrite is due soon. Paul PS - note that certain combinations of run parameters don't support projection or potentially blow up. Set p94=0 in this case and retry. There was a bug that was fixed about 6 weeks back---it may have cured some of the cases that users were running into. ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, June 27, 2016 3:17 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Projection technique's parameters Hi Neks, My question is about the parameters which manage the projection method in the NEK5000: p93, p94 and p95. How can the correct values be selected for these parameters to obtain the better performance depending on the nature of simulation: laminar / turbulent, convection / diffusion, time step? Thank you for any suggestion, Andrew -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jun 27 08:01:08 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 27 Jun 2016 13:01:08 +0000 Subject: [Nek5000-users] Projection technique's parameters In-Reply-To: References: Message-ID: Paul, is there a paper/report we can have access to that goes in the details of the implementation, please? Also, are the typical values based on your personal experience? Thanks, Marco On Jun 27, 2016, at 8:55 AM, nek5000-users at lists.mcs.anl.gov wrote: Hi Andrew, The projection routines are currently being overhauled, but the general strategy is: Number of projections controlled by p93 and mxprev in SIZE. p94 > 0: start projecting velocity/temp after step p94 p95 > 0: start projecting pressure after step 95 I typically set p94 and p95 to 5 I set mxprev and p93 to 20, but sometimes to a higher value. I used to occasionally to to much higher than 20 (say, 80), but in a recent rewrite and effort to make projection more robust I slowed the projection step down with too much work, so another rewrite is due soon. Paul PS - note that certain combinations of run parameters don't support projection or potentially blow up. Set p94=0 in this case and retry. There was a bug that was fixed about 6 weeks back---it may have cured some of the cases that users were running into. ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, June 27, 2016 3:17 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Projection technique's parameters Hi Neks, My question is about the parameters which manage the projection method in the NEK5000: p93, p94 and p95. How can the correct values be selected for these parameters to obtain the better performance depending on the nature of simulation: laminar / turbulent, convection / diffusion, time step? Thank you for any suggestion, Andrew _______________________________________________ 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 Mon Jun 27 08:44:35 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 27 Jun 2016 13:44:35 +0000 Subject: [Nek5000-users] Projection technique's parameters In-Reply-To: References: , Message-ID: Hi Marco, Here is the reference: 1. Fischer, P.F., "Projection techniques for iterative solution of Ax=b with successive right-hand sides." Comp. Meth. in Appl. Mech 163 (1998). There is also a 1993 ICASE Report, but it's mostly a subset of this paper. Paul PS - these typical values are based on my experience... but, it's easy to try a run for a few hundred steps and see which parameters make things run faster. ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, June 27, 2016 8:01 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Projection technique's parameters Paul, is there a paper/report we can have access to that goes in the details of the implementation, please? Also, are the typical values based on your personal experience? Thanks, Marco On Jun 27, 2016, at 8:55 AM, nek5000-users at lists.mcs.anl.gov wrote: Hi Andrew, The projection routines are currently being overhauled, but the general strategy is: Number of projections controlled by p93 and mxprev in SIZE. p94 > 0: start projecting velocity/temp after step p94 p95 > 0: start projecting pressure after step 95 I typically set p94 and p95 to 5 I set mxprev and p93 to 20, but sometimes to a higher value. I used to occasionally to to much higher than 20 (say, 80), but in a recent rewrite and effort to make projection more robust I slowed the projection step down with too much work, so another rewrite is due soon. Paul PS - note that certain combinations of run parameters don't support projection or potentially blow up. Set p94=0 in this case and retry. There was a bug that was fixed about 6 weeks back---it may have cured some of the cases that users were running into. ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, June 27, 2016 3:17 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Projection technique's parameters Hi Neks, My question is about the parameters which manage the projection method in the NEK5000: p93, p94 and p95. How can the correct values be selected for these parameters to obtain the better performance depending on the nature of simulation: laminar / turbulent, convection / diffusion, time step? Thank you for any suggestion, Andrew _______________________________________________ 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 Jun 28 08:01:56 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 28 Jun 2016 06:01:56 -0700 Subject: [Nek5000-users] Refining Mesh for turbChannel In-Reply-To: References: Message-ID: After modifying the .box file you have to run genbox, and from that you can generate the .rea file, which contains the geometry information. On Sun, Jun 26, 2016 at 11:22 AM, wrote: > Modifying just the .box file is sufficient? I know the .rea file also > contains geometry information. Do I leave that alone? > > Thanks, > > Virgilio A. Gomez > > -----Original Message----- > From: nek5000-users-bounces at lists.mcs.anl.gov [mailto: > nek5000-users-bounces at lists.mcs.anl.gov] On Behalf Of > nek5000-users-request at lists.mcs.anl.gov > Sent: Saturday, June 25, 2016 12:00 PM > To: nek5000-users at lists.mcs.anl.gov > Subject: Nek5000-users Digest, Vol 88, Issue 21 > > 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. Refining Mesh for turbChannel (nek5000-users at lists.mcs.anl.gov) > 2. Re: Refining Mesh for turbChannel > (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 24 Jun 2016 21:45:00 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: [Nek5000-users] Refining Mesh for turbChannel > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > > I want to refine the mesh for the example turbChannel to resolve the > Kolmogrov scale by modifying the given example files. How can I do that? > > > Thank you. > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160624/649e986e/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Sat, 25 Jun 2016 08:35:06 -0700 > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Refining Mesh for turbChannel > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > You can do so by modifying the box file, turbChannel.box file. > > For more details, you can refer to the nek5000 document from the ANL > website. > > https://nek5000.mcs.anl.gov/files/2015/09/NEK_doc.pdf > > Best Regards, > Tanmoy > > On Fri, Jun 24, 2016 at 2:45 PM, wrote: > > > Hello, > > > > > > I want to refine the mesh for the example turbChannel to resolve the > > Kolmogrov scale by modifying the given example files. How can I do that? > > > > > > Thank you. > > > > > > > > _______________________________________________ > > 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: < > http://lists.mcs.anl.gov/pipermail/nek5000-users/attachments/20160625/1ff5539c/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > 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 88, Issue 21 > ********************************************* > _______________________________________________ > 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 Jun 30 07:46:39 2016 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 30 Jun 2016 12:46:39 +0000 Subject: [Nek5000-users] symmetry boundary conditions and genmap Message-ID: Hello, I have two rea files that are exactly identical but for the boundary conditions: one has ?W? and the other one has ?SYM?. If I am not mistaken, the ?SYM? boundary type is supported by Nek5000 but is causing problem when I try to generate a map file with genmap. It returns the following error message: reading .rea file data ... ERROR: error reading 1 79200 299357 aborting 530 in routine rdbdry. 1 quit The rea file with ?W? boundary type successfully goes through the genmap script. Is there anything I should be aware when setting SYM bc type in the rea file? I could not find any related post in the archive of the mailing list. Thanks, Marco