From nek5000-users at lists.mcs.anl.gov Mon Aug 4 06:15:57 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 4 Aug 2014 16:45:57 +0530 Subject: [Nek5000-users] Magnetoconvection setup Message-ID: Dear NEK developers, We are trying to set up a magneto-convection case with NEK. Can you kindly give us pointers on how to do that? Also we would like to know the form of equations that are implemented in case of magneto-convection. with best wishes and regards, Supriyo Paul *********************************************************** *Dr. Supriyo Paul* CFD/CAE Centre for Development of Advanced Computing (C-DAC) Pune University Campus, Ganeshkhind, Pune - 411007 INDIA Phone:+91-202-570-4175 Mobile:+91-860-596-5538 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Aug 5 23:56:54 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 6 Aug 2014 10:26:54 +0530 Subject: [Nek5000-users] SFD error message from p66 In-Reply-To: References: Message-ID: Hello I implemented an SFD for a 2d cylinder https://bitbucket.org/cpraveen/nek5000/src/master/ext_cyl/ It seems to work but the residuals reduce by about 5 orders of magnitude only. Maybe I am not choosing the parameters correctly. I would like to see how others do it and compare with my own implementation. Best praveen On Mon, Jun 30, 2014 at 1:21 PM, wrote: > Hi SL > > We have implemented SFD some time ago and we can share the code if you > wish. It is probably good to have single tested version of the code than > develop number of variations. We've already shared the code with Elia. > Regards > Adam > > > > On 27/06/14 17:28, nek5000-users at lists.mcs.anl.gov wrote: > >> Dear Nek's, >> >> I'm trying to program a Selective Frequency Damping following the article >> of Akervik et. al (Physics of Fluids, 2006) and some Nek5000 posts. >> >> I'm able to compile the code, however, when I try to run my simulation, I >> find the following error message: >> >> 0 0.0000E+00 Write checkpoint: >> >> 0 0.0000E+00 OPEN: >> At line 335 of file User/nek5_svn/trunk/nek/prepost.f (unit = 24, file = >> '') >> Fortran runtime error: File '' does not exist >> >> It seems to be something related to param 66. I've tried with p66=6, 0, >> 1, -1, but I always get the same error. >> >> Do you know what happens? >> >> Thanks >> SL >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Aug 5 23:56:54 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 6 Aug 2014 10:26:54 +0530 Subject: [Nek5000-users] SFD error message from p66 In-Reply-To: References: Message-ID: Hello I implemented an SFD for a 2d cylinder https://bitbucket.org/cpraveen/nek5000/src/master/ext_cyl/ It seems to work but the residuals reduce by about 5 orders of magnitude only. Maybe I am not choosing the parameters correctly. I would like to see how others do it and compare with my own implementation. Best praveen On Mon, Jun 30, 2014 at 1:21 PM, wrote: > Hi SL > > We have implemented SFD some time ago and we can share the code if you > wish. It is probably good to have single tested version of the code than > develop number of variations. We've already shared the code with Elia. > Regards > Adam > > > > On 27/06/14 17:28, nek5000-users at lists.mcs.anl.gov wrote: > >> Dear Nek's, >> >> I'm trying to program a Selective Frequency Damping following the article >> of Akervik et. al (Physics of Fluids, 2006) and some Nek5000 posts. >> >> I'm able to compile the code, however, when I try to run my simulation, I >> find the following error message: >> >> 0 0.0000E+00 Write checkpoint: >> >> 0 0.0000E+00 OPEN: >> At line 335 of file User/nek5_svn/trunk/nek/prepost.f (unit = 24, file = >> '') >> Fortran runtime error: File '' does not exist >> >> It seems to be something related to param 66. I've tried with p66=6, 0, >> 1, -1, but I always get the same error. >> >> Do you know what happens? >> >> Thanks >> SL >> _______________________________________________ >> 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 Wed Aug 6 06:03:04 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 6 Aug 2014 11:03:04 +0000 Subject: [Nek5000-users] Mesh Files Message-ID: Dear Nekz, I am wondering whether there is any support for .msh or any of the other ANSYS compatible files? As ANSYS have stopped supporting GAMBIT I can no longer create .cub files, thus gambit2nek is not viable. I have seen in message titled "Convert Mesh to Moab" - Thu Aug 29 14:38:31 CDT 2013, our friend Amirezza has a method of converting .msh to .h5m. If there were any further infomation on this or tips on how best to convert files to .h5m or .neu I would be most grateful! On another note I feel the community would be better served with either a forum or contact details being left in the e-mails in the archives. This is as I sometimes see a post to which I may have a crud of advice to offer, but cannot leave a quick response. But this is just my humble opinion feel free to ignore. Thanks in advance for any response, Friedrich. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Aug 6 16:01:21 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 7 Aug 2014 01:01:21 +0400 Subject: [Nek5000-users] common variables In-Reply-To: References: Message-ID: I have a number of parameters, which I use in several subroutines in *usr files, namely userchk, userbc and userf. I am still not very familiar with code of nek5000 and fortan, so my question is what is the best way to define only once the whole set of parameters, which would be visible for all subroutines. I saw here in that it is recommended to define local variables as common. Is it better to define your own common block or to user preexisting in nek like common /scrns/ ? and in which subroutine it is better to initialize them? Thank you in advance -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Aug 7 15:52:43 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 8 Aug 2014 00:52:43 +0400 Subject: [Nek5000-users] common variables Message-ID: I have a number of parameters, which I use in several subroutines in *usr files, namely userchk, userbc and userf. I am still not very familiar with code of nek5000 and fortan, so my question is what is the best way to define only once the whole set of parameters, which would be visible for all subroutines. I saw here in that it is recommended to define local variables as common. Is it better to define your own common block or to user preexisting in nek like common /scrns/ ? and in which subroutine it is better to initialize them? Thank you in advance, Van From nek5000-users at lists.mcs.anl.gov Thu Aug 7 15:54:32 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 8 Aug 2014 00:54:32 +0400 Subject: [Nek5000-users] common variables In-Reply-To: References: Message-ID: Sorry, a have put the question in this thread, please delete it. Van 07.08.2014, 1:01:34 ???????????? (nek5000-users at lists.mcs.anl.gov) ???????: I have a number of parameters, which I use in several subroutines in *usr files, namely userchk, userbc and userf. I am still not very familiar with code of nek5000 and fortan, so my question is what is the best way to define only once the whole set of parameters, which would be visible for all subroutines. I saw here in that it is recommended to define local variables as common. Is it better to define your own common block or to user preexisting in nek like common /scrns/ ? and in which subroutine it is better to initialize them? Thank you in advance -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Aug 7 16:09:58 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 7 Aug 2014 21:09:58 +0000 Subject: [Nek5000-users] common variables In-Reply-To: References: Message-ID: I would normally define my own common block, that is common between the routines in the .usr file, e.g. common /mystuffi/ i1,i2 common /mystuffr/ a(lx1*ly1*lz1*lelt) Note that it's important to segregate declared variables by type (i.e., integers in the first case and reals in the second) in order to assure proper byte alignment. Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, August 07, 2014 3:52 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] common variables I have a number of parameters, which I use in several subroutines in *usr files, namely userchk, userbc and userf. I am still not very familiar with code of nek5000 and fortan, so my question is what is the best way to define only once the whole set of parameters, which would be visible for all subroutines. I saw here in that it is recommended to define local variables as common. Is it better to define your own common block or to user preexisting in nek like common /scrns/ ? and in which subroutine it is better to initialize them? Thank you in advance, Van _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu Aug 7 16:42:47 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 7 Aug 2014 21:42:47 +0000 Subject: [Nek5000-users] common variables In-Reply-To: References: , Message-ID: Hi Van, If your variables are not already defined in the code, either in the existing common blocks or as parameters, you can either define them in a routine or inside a new common block with a name of your choice. However to reduce memory overhead it is good to check whether these new variables already exist and if so re-use the internal ones (work arrays etc.). But be aware of side effects! Usually it is good practice to not change anything in the main part of the code, as these files are overwritten with every code update. So confine your changes to the user file (as Paul just wrote). It is also a question of what you want to do with them. I guess you already know about user parameters which already are in common blocks. Oana ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, August 07, 2014 4:09 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] common variables I would normally define my own common block, that is common between the routines in the .usr file, e.g. common /mystuffi/ i1,i2 common /mystuffr/ a(lx1*ly1*lz1*lelt) Note that it's important to segregate declared variables by type (i.e., integers in the first case and reals in the second) in order to assure proper byte alignment. Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Thursday, August 07, 2014 3:52 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] common variables I have a number of parameters, which I use in several subroutines in *usr files, namely userchk, userbc and userf. I am still not very familiar with code of nek5000 and fortan, so my question is what is the best way to define only once the whole set of parameters, which would be visible for all subroutines. I saw here in that it is recommended to define local variables as common. Is it better to define your own common block or to user preexisting in nek like common /scrns/ ? and in which subroutine it is better to initialize them? Thank you in advance, Van _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Aug 8 01:40:54 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 8 Aug 2014 12:10:54 +0530 Subject: [Nek5000-users] Computing RHS for linearized NS Message-ID: Dear neks I want to compute the rhs of the linearized Navier-Stokes equation which would be of the form M du/dt = A(us) u + Bp 0 = B^T u where us is the stationary solution about which the equations are linearized. I want to use ARPACK to compute eigenvalues for which I need to be able to compute the above matrix-vector products. Is this already available in some part of nek. I have tried to read perturb.f but have not succeeded in clearly understanding the code. Thanks praveen -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Aug 11 09:50:28 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 11 Aug 2014 15:50:28 +0100 Subject: [Nek5000-users] Restarting a Nek5000 job (Fault Tolerance study) In-Reply-To: References: Message-ID: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Neks, We are undertaking a FT study in HPC and we would like to use Nek5000 as the application to run. So far I've failed to find out how to create checkpoints on Nek5000 so we can restart the jobs at a later time. Is there any documentation of how to do it? Can someone point me into the right direction? Best regards, L -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux) iQEcBAEBAgAGBQJT6Ng0AAoJEIhcgrtekvd+d4MH/i02cDeOFKfsBZwVwy0q9O06 mAIxow6xCHk+GpoIips6hYPPftEWLdogtq749mmuOFogp4rnBqgQnsrKi/G3RVll KUwYHrOqzHxwrxlXFntuN0AX9XFOdu4mlhjWHWy1xJcRFSkM8B52sHUPQuESYPv0 HVKVndHSt+i+HJojBXNCL/H1VnUiYS8Vhkj7cO8ZzJa9FG0ancsxlPcmxNOX5zv3 RVvfEuyZXNBdUzU+d4EBBL6Tv8QB/08FpbCMkUpyhyJld5jnWXXXvukGkA+4HTKa VkaxoXLg++4tYUlasmHXN4nqrAYZuWmIRCPLy9IsIKBatC5IRDhH4KMQR37b1M0= =d/4i -----END PGP SIGNATURE----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From nek5000-users at lists.mcs.anl.gov Mon Aug 11 11:03:59 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 11 Aug 2014 16:03:59 +0000 Subject: [Nek5000-users] Restarting a Nek5000 job (Fault Tolerance study) In-Reply-To: References: , Message-ID: Dear L, Have you looked at p. 8 of the users manual? Best, Paul ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Monday, August 11, 2014 9:50 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Restarting a Nek5000 job (Fault Tolerance study) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Neks, We are undertaking a FT study in HPC and we would like to use Nek5000 as the application to run. So far I've failed to find out how to create checkpoints on Nek5000 so we can restart the jobs at a later time. Is there any documentation of how to do it? Can someone point me into the right direction? Best regards, L -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux) iQEcBAEBAgAGBQJT6Ng0AAoJEIhcgrtekvd+d4MH/i02cDeOFKfsBZwVwy0q9O06 mAIxow6xCHk+GpoIips6hYPPftEWLdogtq749mmuOFogp4rnBqgQnsrKi/G3RVll KUwYHrOqzHxwrxlXFntuN0AX9XFOdu4mlhjWHWy1xJcRFSkM8B52sHUPQuESYPv0 HVKVndHSt+i+HJojBXNCL/H1VnUiYS8Vhkj7cO8ZzJa9FG0ancsxlPcmxNOX5zv3 RVvfEuyZXNBdUzU+d4EBBL6Tv8QB/08FpbCMkUpyhyJld5jnWXXXvukGkA+4HTKa VkaxoXLg++4tYUlasmHXN4nqrAYZuWmIRCPLy9IsIKBatC5IRDhH4KMQR37b1M0= =d/4i -----END PGP SIGNATURE----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________ 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 Aug 12 02:11:33 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 12 Aug 2014 09:11:33 +0200 Subject: [Nek5000-users] Computing RHS for linearized NS In-Reply-To: References: Message-ID: Hi Praveen We have implemented arpack to calculate spectra of the linearised direct and adjoint Navier-Stokes equations for relatively complex flow configurations. Some results you can find at http://www.sciencedirect.com/science/article/pii/S0997754614001009 (Global stability and optimal perturbation for a jet in cross-flow). We are going to talk about ot the aspects on the nek user meeting in Greece? Are you going to participate? Regards Adam On 08/08/14 08:40, nek5000-users at lists.mcs.anl.gov wrote: > Dear neks > > I want to compute the rhs of the linearized Navier-Stokes equation > which would be of the form > > M du/dt = A(us) u + Bp > 0 = B^T u > > where us is the stationary solution about which the equations are > linearized. I want to use ARPACK to compute eigenvalues for which I > need to be able to compute the above matrix-vector products. Is this > already available in some part of nek. I have tried to read perturb.f > but have not succeeded in clearly understanding the code. > > Thanks > praveen > > > _______________________________________________ > 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 Aug 12 03:00:58 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 12 Aug 2014 10:00:58 +0200 Subject: [Nek5000-users] SFD error message from p66 In-Reply-To: References: Message-ID: Hi We had similar problem. Check tolerance fro pressure and velocity solver (parameters 21, 22 in .rea). They can limit your convergence. Regards Adam On 06/08/14 06:56, nek5000-users at lists.mcs.anl.gov wrote: > Hello > > I implemented an SFD for a 2d cylinder > > https://bitbucket.org/cpraveen/nek5000/src/master/ext_cyl/ > > It seems to work but the residuals reduce by about 5 orders of > magnitude only. Maybe I am not choosing the parameters correctly. I > would like to see how others do it and compare with my own implementation. > > Best > praveen > > > On Mon, Jun 30, 2014 at 1:21 PM, > wrote: > > Hi SL > > We have implemented SFD some time ago and we can share the code if > you wish. It is probably good to have single tested version of the > code than develop number of variations. We've already shared the > code with Elia. > Regards > Adam > > > > On 27/06/14 17:28, nek5000-users at lists.mcs.anl.gov > wrote: > > Dear Nek's, > > I'm trying to program a Selective Frequency Damping following > the article of Akervik et. al (Physics of Fluids, 2006) and > some Nek5000 posts. > > I'm able to compile the code, however, when I try to run my > simulation, I find the following error message: > > 0 0.0000E+00 Write checkpoint: > > 0 0.0000E+00 OPEN: > At line 335 of file User/nek5_svn/trunk/nek/prepost.f (unit = > 24, file = '') > Fortran runtime error: File '' does not exist > > It seems to be something related to param 66. I've tried with > p66=6, 0, 1, -1, but I always get the same error. > > Do you know what happens? > > Thanks > SL > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Aug 12 04:24:00 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 12 Aug 2014 10:24:00 +0100 Subject: [Nek5000-users] Restarting a Nek5000 job (Fault Tolerance study) In-Reply-To: References: , Message-ID: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Paul, Thanks for your help, just one thing. In order to restart a job we need to have a .fld file. Working on the pipe example, we should edit stenosis.rea to create .fld files every desired step "p68 iastep: freq for avg_all". My understanding was that if we change: 0. p68 iastep: freq for avg_all to 2. p68 iastep: freq for avg_all we would obtain a .fld file every 2 time steps. However, we only obtain one... are we missing something? Regards, L. On 11/08/14 17:03, nek5000-users at lists.mcs.anl.gov wrote: > > Dear L, > > Have you looked at p. 8 of the users manual? > > Best, > > > Paul > > ________________________________________ From: > nek5000-users-bounces at lists.mcs.anl.gov > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > Sent: Monday, August 11, 2014 9:50 AM To: > nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Restarting > a Nek5000 job (Fault Tolerance study) > > Hi Neks, > > We are undertaking a FT study in HPC and we would like to use > Nek5000 as the application to run. So far I've failed to find out > how to create checkpoints on Nek5000 so we can restart the jobs at > a later time. Is there any documentation of how to do it? Can > someone point me into the right direction? > > Best regards, L > > -- The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ 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 > -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux) iQEcBAEBAgAGBQJT6d0vAAoJEIhcgrtekvd+4IgH/1S76/JZGfGsbK6lTDSrxGsZ CAE8strelnDjPIE7G8A1dJq5XRoiHfPQyJ/IoXFXzR+EHJPGzmuDrMUS7cRNqOLN 9inYIAYOdrJhm7xNfX0Nh5E7FPKd7we3Hg8rBsK719YVLYkAncJVYvynYIFAMw4c htpL/FmmuDmt057zc9qK9u9ayfgxHk/q/7kmseQ/TlODgKhdK6jUf5VJbRqZCb6N kP43sF6Rfrg8xY3FPWlYtn7Ti+EcIjOX3sdkbZ7qzY2zz2egMJg6mtYzZZDXHprR nOci5PZpWWY+KNE0P57hY+tecRB58mkEm3Ksqwb+jS1Wf7R3C9H8rW9gGwBkN00= =8IZe -----END PGP SIGNATURE----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From nek5000-users at lists.mcs.anl.gov Tue Aug 12 11:33:06 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 12 Aug 2014 11:33:06 -0500 Subject: [Nek5000-users] Restarting a Nek5000 job (Fault Tolerance study) In-Reply-To: References: Message-ID: Hi, p68 is for the frequency of the average_all routine, often used in post-processing results. If you just want .fld files for restarts, you can change parameter 15 (IOSTEP). This will then set Nek to dump out fld files every X steps as set by this parameter. hth, Katherine On Tue, Aug 12, 2014 at 4:24 AM, wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear Paul, > > Thanks for your help, just one thing. In order to restart a job we > need to have a .fld file. Working on the pipe example, we should edit > stenosis.rea to create .fld files every desired step "p68 iastep: freq > for avg_all". My understanding was that if we change: > > 0. p68 iastep: freq for avg_all > > to > > 2. p68 iastep: freq for avg_all > > we would obtain a .fld file every 2 time steps. However, we only > obtain one... are we missing something? > > Regards, > > L. > On 11/08/14 17:03, nek5000-users at lists.mcs.anl.gov wrote: > > > > Dear L, > > > > Have you looked at p. 8 of the users manual? > > > > Best, > > > > > > Paul > > > > ________________________________________ From: > > nek5000-users-bounces at lists.mcs.anl.gov > > [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of > > nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] > > Sent: Monday, August 11, 2014 9:50 AM To: > > nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Restarting > > a Nek5000 job (Fault Tolerance study) > > > > Hi Neks, > > > > We are undertaking a FT study in HPC and we would like to use > > Nek5000 as the application to run. So far I've failed to find out > > how to create checkpoints on Nek5000 so we can restart the jobs at > > a later time. Is there any documentation of how to do it? Can > > someone point me into the right direction? > > > > Best regards, L > > > > -- The University of Edinburgh is a charitable body, registered in > > Scotland, with registration number SC005336. > > > > _______________________________________________ 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 > > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v2.0.14 (GNU/Linux) > > iQEcBAEBAgAGBQJT6d0vAAoJEIhcgrtekvd+4IgH/1S76/JZGfGsbK6lTDSrxGsZ > CAE8strelnDjPIE7G8A1dJq5XRoiHfPQyJ/IoXFXzR+EHJPGzmuDrMUS7cRNqOLN > 9inYIAYOdrJhm7xNfX0Nh5E7FPKd7we3Hg8rBsK719YVLYkAncJVYvynYIFAMw4c > htpL/FmmuDmt057zc9qK9u9ayfgxHk/q/7kmseQ/TlODgKhdK6jUf5VJbRqZCb6N > kP43sF6Rfrg8xY3FPWlYtn7Ti+EcIjOX3sdkbZ7qzY2zz2egMJg6mtYzZZDXHprR > nOci5PZpWWY+KNE0P57hY+tecRB58mkEm3Ksqwb+jS1Wf7R3C9H8rW9gGwBkN00= > =8IZe > -----END PGP SIGNATURE----- > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > 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 Aug 13 08:56:09 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 13 Aug 2014 19:26:09 +0530 Subject: [Nek5000-users] Computing RHS for linearized NS In-Reply-To: References: Message-ID: On Tue, Aug 12, 2014 at 12:41 PM, wrote: > Hi Praveen > > We have implemented arpack to calculate spectra of the linearised direct > and adjoint Navier-Stokes equations for relatively complex flow > configurations. Some results you can find at > http://www.sciencedirect.com/science/article/pii/S0997754614001009 > (Global stability and optimal perturbation for a jet in cross-flow). We are > going to talk about ot the aspects on the nek user meeting in Greece? Are > you going to participate? > Regards > Adam > Hello Adam I do not have access to this journal. Is it possible to send a preprint of the paper to cpraveen @ gmail.com No, I am not attending the nek user meet. Best regards praveen -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Aug 13 11:56:36 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 13 Aug 2014 16:56:36 +0000 Subject: [Nek5000-users] Compressible version of NEK5000 Message-ID: Hi guys, Is there any compressible/variable density version of NEK5000? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Aug 13 13:02:31 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 13 Aug 2014 18:02:31 +0000 Subject: [Nek5000-users] Compressible version of NEK5000 In-Reply-To: References: Message-ID: There is a Low Mach variable density formulation used mainly for combustion cases, see http://www.researchgate.net/publication/226667135_Numerical_Simulation_of_Low_Mach_Number_Reactive_Flows But there is no fully compressible NS in Nek5000. Oana ________________________________ 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: Wednesday, August 13, 2014 11:56 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Compressible version of NEK5000 Hi guys, Is there any compressible/variable density version of NEK5000? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Aug 13 14:37:20 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 13 Aug 2014 19:37:20 +0000 Subject: [Nek5000-users] Compressible version of NEK5000 In-Reply-To: References: , Message-ID: Thank you so much Oana, Is this method included in the code, or should I download it separately? Arash ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, August 13, 2014 2:02 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Compressible version of NEK5000 There is a Low Mach variable density formulation used mainly for combustion cases, see http://www.researchgate.net/publication/226667135_Numerical_Simulation_of_Low_Mach_Number_Reactive_Flows But there is no fully compressible NS in Nek5000. Oana ________________________________ 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: Wednesday, August 13, 2014 11:56 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Compressible version of NEK5000 Hi guys, Is there any compressible/variable density version of NEK5000? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Aug 13 14:45:25 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 13 Aug 2014 19:45:25 +0000 Subject: [Nek5000-users] Compressible version of NEK5000 In-Reply-To: References: , , Message-ID: It is included in the code. You need to turn on a few switches. Best is to insipire yourself from the example lowMach_test under examples. Try to run that one and then study the .rea file Oana ________________________________ 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: Wednesday, August 13, 2014 2:37 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Compressible version of NEK5000 Thank you so much Oana, Is this method included in the code, or should I download it separately? Arash ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: Wednesday, August 13, 2014 2:02 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Compressible version of NEK5000 There is a Low Mach variable density formulation used mainly for combustion cases, see http://www.researchgate.net/publication/226667135_Numerical_Simulation_of_Low_Mach_Number_Reactive_Flows But there is no fully compressible NS in Nek5000. Oana ________________________________ 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: Wednesday, August 13, 2014 11:56 AM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Compressible version of NEK5000 Hi guys, Is there any compressible/variable density version of NEK5000? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Aug 15 03:34:51 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 15 Aug 2014 10:34:51 +0200 Subject: [Nek5000-users] Outpost question Message-ID: Howdy Nek's, I have a couple questions regarding the ouput of files: 1. How can force, within the code (say in usrchk), some files to be output in 64 bits for high-accuracy checkpointing and other in regular 8 bits for simple visualisation? 2. Say, during the first 1000 iterations, the code outpost a file every single iteration so that I have blah0.f00001 to blah0.f01000. How can I then force the code to outpost my new files (from istep = 1001 to 2000 say) rewriting on blah0.f00001 to blah0.f01000? Thanks a lot. Regards, JC -- Jean-Christophe Loiseau Homepage -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Aug 15 09:53:49 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 15 Aug 2014 09:53:49 -0500 Subject: [Nek5000-users] Outpost question In-Reply-To: References: Message-ID: Hi JC, You should be able to control the outpost frequency and precision using the parameters parameter 15 (IOSTEP) and parameter 63, respectively. So, if you wanted the first 100 steps to output every step, you would set something like: if(istep.le.100) param(15)=1 To set the precision to 64bit, set param(63)=8, as well. Setting param(63) to anything else should default it to 8 byte precision. As far as overwriting previous fld files, you should be able to reset a parameter used in prepost.f that increments the file counter. I haven't had a chance to test this, but I can take a look at it last this weekend. hth. Katherine On Fri, Aug 15, 2014 at 3:34 AM, wrote: > Howdy Nek's, > > I have a couple questions regarding the ouput of files: > > 1. How can force, within the code (say in usrchk), some files to be > output in 64 bits for high-accuracy checkpointing and other in regular 8 > bits for simple visualisation? > 2. Say, during the first 1000 iterations, the code outpost a file > every single iteration so that I have blah0.f00001 to blah0.f01000. How can > I then force the code to outpost my new files (from istep = 1001 to 2000 > say) rewriting on blah0.f00001 to blah0.f01000? > > Thanks a lot. > Regards, > > JC > > -- > Jean-Christophe Loiseau > Homepage > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Aug 15 09:57:55 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 15 Aug 2014 16:57:55 +0200 Subject: [Nek5000-users] Outpost question In-Reply-To: References: Message-ID: Hi Katherine, Thanks for the answer. I knew about the parameter 15 and was not sure about the 64 bits precision. This is now more clear. Regarding the overwriting, I had guessed that prepost has a parameter that needs to be reset, but I haven't been able to figure out which one so far. That would be very helpful if you can take a quick look at it. Thanks a lot and enjoy the end of the summer ++ JC 2014-08-15 16:53 GMT+02:00 : > Hi JC, > > You should be able to control the outpost frequency and precision using > the parameters parameter 15 (IOSTEP) and parameter 63, respectively. > > So, if you wanted the first 100 steps to output every step, you would set > something like: > > if(istep.le.100) param(15)=1 > > To set the precision to 64bit, set param(63)=8, as well. Setting > param(63) to anything else should default it to 8 byte precision. > > As far as overwriting previous fld files, you should be able to reset a > parameter used in prepost.f that increments the file counter. I haven't > had a chance to test this, but I can take a look at it last this weekend. > > hth. > Katherine > > > On Fri, Aug 15, 2014 at 3:34 AM, wrote: > >> Howdy Nek's, >> >> I have a couple questions regarding the ouput of files: >> >> 1. How can force, within the code (say in usrchk), some files to be >> output in 64 bits for high-accuracy checkpointing and other in regular 8 >> bits for simple visualisation? >> 2. Say, during the first 1000 iterations, the code outpost a file >> every single iteration so that I have blah0.f00001 to blah0.f01000. How can >> I then force the code to outpost my new files (from istep = 1001 to 2000 >> say) rewriting on blah0.f00001 to blah0.f01000? >> >> Thanks a lot. >> Regards, >> >> JC >> >> -- >> Jean-Christophe Loiseau >> Homepage >> >> _______________________________________________ >> 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 > > -- Jean-Christophe Loiseau Homepage -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Aug 20 06:44:10 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Aug 2014 12:44:10 +0100 Subject: [Nek5000-users] IFSCHCLOB In-Reply-To: References: Message-ID: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Neks, I am interested in running multiple jobs sequentially in an automatic process. However I've noticed problems with .sch file (.sch file already exists. Use IFSCHCLOB=F to $disable this check BUT BEWARE!!!!!!). I have tried to remove it before and after a job, but I can still see problems for some of the jobs. Is there a way of disable this check? If so, how can I do it? The message says set IFSCHLOB=F, however I can see that IFSCHCLOB = .false. in connect2.f Any ideas? Regards, Luis -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.14 (GNU/Linux) iQEcBAEBAgAGBQJT9IoKAAoJEIhcgrtekvd+pF8IAKtuI2drqlOJEAGVKguH4BT2 KMXQx2R7LLNkgSt/GGUbJvybI0oDnFIMO9cJk3r/qJP6m0UhixcWv0SIic+O+0ww e61lTuELcXSL03yVrWdlx3zUffbIvSG7NQ8yjjSXXa3YyWNnZ09HHduB/cQP9hE8 nYFkwHWbcFkqbWadLn328Qyx3VRUWwrPNB6wQsQep731i45FrC8J6jRuulh612jD B0dK0dPiAH0SA5smDl46xjYV6GPpShYyOiB+VtbstzeI6SRtpHe4xqMwE0pmoxZO pUKcHbqxv3CCwOp/Xww6+HTPgfoXeHRnYNefSh8/b4AWBYY7Z7cI39rTEnQmyms= =KPe0 -----END PGP SIGNATURE----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From nek5000-users at lists.mcs.anl.gov Wed Aug 20 10:12:33 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Aug 2014 11:12:33 -0400 Subject: [Nek5000-users] emergency exit because of number of processors Message-ID: Hello Neks, I am running pipe flow with nek5000, however, once I increase the number of processors, after few iterations CFL dramatically goes up immediately and it breaks out my simulation (Emergency Exit). Does any one has any idea what is wrong with that?! Thanks, Ami -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Aug 27 10:10:28 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 27 Aug 2014 15:10:28 +0000 Subject: [Nek5000-users] Lagrangian Particle Tracking In-Reply-To: References: Message-ID: Hi, I searched about Lagrangian Particle Tracking subject in history texts and I found that "hemi" example relates to it. After a review of this example, some questions are: - How can I have a constant number of particles in the domain? It needs that the number of particles which come to the domain should be equal to the number of particles exit the domain. - How about the particles which contact to the wall? How do they come back? - How can I attach some information (for example Temperature) to any particle and change it each time step according to the flow properties and then have ensemble average of the magnitude of these information particles? Thank you Arash From nek5000-users at lists.mcs.anl.gov Thu Aug 28 03:02:55 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 28 Aug 2014 10:02:55 +0200 Subject: [Nek5000-users] Lagrangian Particle Tracking In-Reply-To: References: Message-ID: Hi Arash, I guess you are looking for an LPT module to track inertial particles with wall-collision and so on. At the moment we are working on a more unified implementation of such routine to be added to the nek trunk. A version of that will be finalised soon. Cheers Azad Quoting nek5000-users-request at lists.mcs.anl.gov: > 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. Lagrangian Particle Tracking (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 27 Aug 2014 15:10:28 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: [Nek5000-users] Lagrangian Particle Tracking > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I searched about Lagrangian Particle Tracking subject in history > texts and I found that "hemi" example relates to it. > After a review of this example, some questions are: > - How can I have a constant number of particles in the domain? It > needs that the number of particles which come to the domain should > be equal to the number of particles exit the domain. > - How about the particles which contact to the wall? How do they come back? > - How can I attach some information (for example Temperature) to any > particle and change it each time step according to the flow > properties and then have ensemble average of the magnitude of these > information particles? > > Thank you > Arash > > > ------------------------------ > > _______________________________________________ > 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 66, Issue 11 > ********************************************* From nek5000-users at lists.mcs.anl.gov Thu Aug 28 15:09:28 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 28 Aug 2014 20:09:28 +0000 Subject: [Nek5000-users] Lagrangian Particle Tracking In-Reply-To: References: , Message-ID: Dear Azad, Yes, you are right. Can I ask about your time estimation for commence of this module? How can I know when we can use it? regards, Arash ________________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov on behalf of nek5000-users at lists.mcs.anl.gov Sent: Thursday, August 28, 2014 4:02 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Lagrangian Particle Tracking Hi Arash, I guess you are looking for an LPT module to track inertial particles with wall-collision and so on. At the moment we are working on a more unified implementation of such routine to be added to the nek trunk. A version of that will be finalised soon. Cheers Azad Quoting nek5000-users-request at lists.mcs.anl.gov: > 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. Lagrangian Particle Tracking (nek5000-users at lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 27 Aug 2014 15:10:28 +0000 > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000-users at lists.mcs.anl.gov" > > Subject: [Nek5000-users] Lagrangian Particle Tracking > Message-ID: > > Content-Type: text/plain; charset="us-ascii" > > Hi, > > I searched about Lagrangian Particle Tracking subject in history > texts and I found that "hemi" example relates to it. > After a review of this example, some questions are: > - How can I have a constant number of particles in the domain? It > needs that the number of particles which come to the domain should > be equal to the number of particles exit the domain. > - How about the particles which contact to the wall? How do they come back? > - How can I attach some information (for example Temperature) to any > particle and change it each time step according to the flow > properties and then have ensemble average of the magnitude of these > information particles? > > Thank you > Arash > > > ------------------------------ > > _______________________________________________ > 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 66, Issue 11 > ********************************************* _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu Aug 28 15:55:54 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 28 Aug 2014 13:55:54 -0700 Subject: [Nek5000-users] boyd filtering in dyn. Smagorinsky model Message-ID: Hello Neks, In *turbChannel* example, explicit modal filtering has been used in the dynamaic Smagorinsky case in the eddy_visc(eddif,e) routines. This routine calls the setup filtering routine *set_ds_filt(fh,fht,nt,diag,nx)*, where coefficients for diag() are defined manually. Cases for nt = nx1-1 and nt = nx1-2 are mentioned in the routines. I am wondering if anybody could tell me how to set up the routines for nt = nx1-3 and nt = nx1-4, where nt is the filtered grids. Thanks in advance, Sincerely, Tanmoy -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Aug 29 13:15:49 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 29 Aug 2014 18:15:49 +0000 Subject: [Nek5000-users] Linking other libs to Nek, e.g. ESSL in Blue Gene Message-ID: Dear Neks, I have a short technical question. For our post processing analysis of turbulent convection we want to use routines from ESSL Library. Where is the best place to include the link command to this library into the makefile or makenek? Thanks in advance, Joerg. ==================================================== Joerg Schumacher Professor for Fluid Mechanics Institute of Thermodynamics and Fluid Mechanics Technische Universit?t Ilmenau P.O. Box 100565 D-98684 Ilmenau Germany E-mail: joerg.schumacher at tu-ilmenau.de http://www.tu-ilmenau.de/tsm Phone: +49-3677-69-2428 Fax: +49-3677-69-2411 ==================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Aug 29 14:12:44 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 29 Aug 2014 19:12:44 +0000 Subject: [Nek5000-users] Linking other libs to Nek, e.g. ESSL in Blue Gene In-Reply-To: References: Message-ID: Hi Joerg, The easiest place to call your routines will be in userchk since it is called by every rank every time step including istep=0 Best. 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, August 29, 2014 1:15 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Linking other libs to Nek, e.g. ESSL in Blue Gene Dear Neks, I have a short technical question. For our post processing analysis of turbulent convection we want to use routines from ESSL Library. Where is the best place to include the link command to this library into the makefile or makenek? Thanks in advance, Joerg. ==================================================== Joerg Schumacher Professor for Fluid Mechanics Institute of Thermodynamics and Fluid Mechanics Technische Universit?t Ilmenau P.O. Box 100565 D-98684 Ilmenau Germany E-mail: joerg.schumacher at tu-ilmenau.de http://www.tu-ilmenau.de/tsm Phone: +49-3677-69-2428 Fax: +49-3677-69-2411 ==================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Aug 29 14:18:11 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 29 Aug 2014 19:18:11 +0000 Subject: [Nek5000-users] Linking other libs to Nek, e.g. ESSL in Blue Gene In-Reply-To: References: , Message-ID: P.S. Sorry -- missed the question -- as far as the makenek is concerned -- you could use USR_LFLAGS= like USR_LFLAGS="-L/usr/lib -lfoo" ________________________________ 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, August 29, 2014 2:12 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] Linking other libs to Nek, e.g. ESSL in Blue Gene Hi Joerg, The easiest place to call your routines will be in userchk since it is called by every rank every time step including istep=0 Best. 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, August 29, 2014 1:15 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Linking other libs to Nek, e.g. ESSL in Blue Gene Dear Neks, I have a short technical question. For our post processing analysis of turbulent convection we want to use routines from ESSL Library. Where is the best place to include the link command to this library into the makefile or makenek? Thanks in advance, Joerg. ==================================================== Joerg Schumacher Professor for Fluid Mechanics Institute of Thermodynamics and Fluid Mechanics Technische Universit?t Ilmenau P.O. Box 100565 D-98684 Ilmenau Germany E-mail: joerg.schumacher at tu-ilmenau.de http://www.tu-ilmenau.de/tsm Phone: +49-3677-69-2428 Fax: +49-3677-69-2411 ==================================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Aug 29 14:18:27 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 29 Aug 2014 19:18:27 +0000 Subject: [Nek5000-users] Linking other libs to Nek, e.g. ESSL in Blue Gene In-Reply-To: References: Message-ID: Hi Aleks, I agree, but that does unfortunately not answer my question. Let me give an example: I want to call the routine call dgeev (..,..,..) in usrchk. But where do I have to link the ESSL lib? Something like -lessl needs to be added somewhere in the makefiles? Thanks a lot, Joerg. Am 29.08.2014 um 21:12 schrieb > >: Hi Joerg, The easiest place to call your routines will be in userchk since it is called by every rank every time step including istep=0 Best. 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, August 29, 2014 1:15 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Linking other libs to Nek, e.g. ESSL in Blue Gene Dear Neks, I have a short technical question. For our post processing analysis of turbulent convection we want to use routines from ESSL Library. Where is the best place to include the link command to this library into the makefile or makenek? Thanks in advance, Joerg. ==================================================== Joerg Schumacher Professor for Fluid Mechanics Institute of Thermodynamics and Fluid Mechanics Technische Universit?t Ilmenau P.O. Box 100565 D-98684 Ilmenau Germany E-mail: joerg.schumacher at tu-ilmenau.de http://www.tu-ilmenau.de/tsm Phone: +49-3677-69-2428 Fax: +49-3677-69-2411 ==================================================== _______________________________________________ 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 Aug 31 13:17:18 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 31 Aug 2014 20:17:18 +0200 Subject: [Nek5000-users] Outpost question In-Reply-To: References: Message-ID: Hi Katherine, I was wondering if you had time to check on the parameter to be reset so that I can overwrite previous files? Bonne soir?e, JC 2014-08-15 16:57 GMT+02:00 : > Hi Katherine, > > Thanks for the answer. I knew about the parameter 15 and was not sure > about the 64 bits precision. This is now more clear. > Regarding the overwriting, I had guessed that prepost has a parameter that > needs to be reset, but I haven't been able to figure out which one so far. > That would be very helpful if you can take a quick look at it. > > Thanks a lot and enjoy the end of the summer > ++ > > JC > > > 2014-08-15 16:53 GMT+02:00 : > >> Hi JC, >> >> You should be able to control the outpost frequency and precision using >> the parameters parameter 15 (IOSTEP) and parameter 63, respectively. >> >> So, if you wanted the first 100 steps to output every step, you would set >> something like: >> >> if(istep.le.100) param(15)=1 >> >> To set the precision to 64bit, set param(63)=8, as well. Setting >> param(63) to anything else should default it to 8 byte precision. >> >> As far as overwriting previous fld files, you should be able to reset a >> parameter used in prepost.f that increments the file counter. I haven't >> had a chance to test this, but I can take a look at it last this weekend. >> >> hth. >> Katherine >> >> >> On Fri, Aug 15, 2014 at 3:34 AM, wrote: >> >>> Howdy Nek's, >>> >>> I have a couple questions regarding the ouput of files: >>> >>> 1. How can force, within the code (say in usrchk), some files to be >>> output in 64 bits for high-accuracy checkpointing and other in regular 8 >>> bits for simple visualisation? >>> 2. Say, during the first 1000 iterations, the code outpost a file >>> every single iteration so that I have blah0.f00001 to blah0.f01000. How can >>> I then force the code to outpost my new files (from istep = 1001 to 2000 >>> say) rewriting on blah0.f00001 to blah0.f01000? >>> >>> Thanks a lot. >>> Regards, >>> >>> JC >>> >>> -- >>> Jean-Christophe Loiseau >>> Homepage >>> >>> _______________________________________________ >>> 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 >> >> > > > -- > Jean-Christophe Loiseau > Homepage > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Jean-Christophe Loiseau Homepage -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Aug 31 17:57:27 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 31 Aug 2014 22:57:27 +0000 Subject: [Nek5000-users] Constant mass flow rate in simulation Message-ID: Dear Neks, Recently I've been struggling with constant mass flow rate in my turbulent channel flow simulation. Based on the userchk subroutine in 'turbChannel' tutorial case, I also used torque_calc(1.0,x0,.false.,.false.) to calculate the wall shear and then got the mean wall shear. After that I set mean pressure gradient 'ffx' equal to the mean wall shear in order to keep constant mass flow rate. In this case, the flow rate started from 1 (nondimensionalised case, bulk mean equal to 1) and kept increasing. Although the increment was very small at each time step, it never stopped and the bulk mean velocity has increased to 1.002. Is it appropriate to set constant mass flow rate by updating mean pressure gradient based on mean wall shear in Nek5000 or am I using the wrong calculation? Since the bulk mean is still increasing, the simulation is like acceleration channel flow. Does anyone has any clue about how to set constant mass flow rate for turbulent channel flow in Nek5000? Any idea is appreciated and many thanks in advance. Thanks and regards, Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Aug 31 18:58:32 2014 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 31 Aug 2014 23:58:32 +0000 Subject: [Nek5000-users] Constant mass flow rate in simulation In-Reply-To: References: Message-ID: Hi Tony, I would just set p55=1.0; p54=-1.0 This will fix < u_x > == 1.0 If you are using variable viscosity, this might be problematic, but for the constant viscosity case this is the best way. Be certain to also set ffx=ffy=ffz=0 in the .usr file, the the p54/p55 combination sets the x-body force as needed to ensure the prescribed mass flux is realized. Paul ________________________________ From: nek5000-users-bounces at lists.mcs.anl.gov [nek5000-users-bounces at lists.mcs.anl.gov] on behalf of nek5000-users at lists.mcs.anl.gov [nek5000-users at lists.mcs.anl.gov] Sent: Sunday, August 31, 2014 5:57 PM To: nek5000-users at lists.mcs.anl.gov Subject: [Nek5000-users] Constant mass flow rate in simulation Dear Neks, Recently I've been struggling with constant mass flow rate in my turbulent channel flow simulation. Based on the userchk subroutine in 'turbChannel' tutorial case, I also used torque_calc(1.0,x0,.false.,.false.) to calculate the wall shear and then got the mean wall shear. After that I set mean pressure gradient 'ffx' equal to the mean wall shear in order to keep constant mass flow rate. In this case, the flow rate started from 1 (nondimensionalised case, bulk mean equal to 1) and kept increasing. Although the increment was very small at each time step, it never stopped and the bulk mean velocity has increased to 1.002. Is it appropriate to set constant mass flow rate by updating mean pressure gradient based on mean wall shear in Nek5000 or am I using the wrong calculation? Since the bulk mean is still increasing, the simulation is like acceleration channel flow. Does anyone has any clue about how to set constant mass flow rate for turbulent channel flow in Nek5000? Any idea is appreciated and many thanks in advance. Thanks and regards, Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: