From nek5000-users at lists.mcs.anl.gov Sun Jan 2 14:48:23 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 2 Jan 2011 14:48:23 -0600 (CST) Subject: [Nek5000-users] Question about running error In-Reply-To: References: Message-ID: Hi Albert, I'm just getting to that in the new manual www.mcs.anl.gov/~fischer/new.pdf It looks like you're already on your way. You can just fool around w/ postx - you won't break anything. The basic options are SET PLOT FORMAT SET QUANTITY SET TIME PLOT In 3D, it also become important to SET LOCATION which allows you to choose the surfaces on which the contour/color fill plots are drawn. Also, SET ATTRIBUTE SET RESOLUTION COLOR FILL 30 will give you higher resolution for the contour/color fill plots. If you want more contour lines: SET ATTRIBUTE SET RESOLUTION CONTOUR LINES 50 (say) will give you 50 lines. If you want to fix the range of the plot SET ATTRIBUTE SET RANGE n (no, not automatic) 0 100 (say, for range of 0 to 100) Note that for 3D stuff, you probably will find VisIt more useful. You can download VisIt by googling visit visualization software Paul On Sat, 1 Jan 2011, Albert S. Kim wrote: > Thank you so much. > So far I got this (see attached file) and saw this message: > > Hit left button for menu, right button for screen dump > > I tried to make movie but not very successful. > > Could you tell me in which part of your manual I can learn how to use postx? > > Happy New Year. > > Albert > > > On Fri, Dec 31, 2010 at 6:29 PM, Paul Fischer wrote: > >> >> Hi Albert, >> >> did you try: >> >> SET TIME >> 12 (type on keyboard) >> PLOT >> >> >> ? >> >> It looks like it read your .fld file correctly... >> >> If you type: >> >> ls -altr >> >> in your directory, do you see several .fld01 .fld02 ... files ? >> >> Paul >> >> >> >> On Fri, 31 Dec 2010, Albert S. Kim wrote: >> >> Probably you can download the zip file below and see it. >>> >>> postx works after I used "-X" option of my ssh to the server. >>> >>> But, it does not show any graphical results. >>> Values at the left bottom of postx show all zeros. >>> I do not know why. So I was asking whether you think the simulation was >>> done correct. >>> >>> Albert >>> >>> >>> On Fri, Dec 31, 2010 at 5:31 AM, Paul Fischer >>> wrote: >>> >>> >>>> Hi Albert, >>>> >>>> with your x-windows emulator in place, what happens >>>> when you type "postx" on your linux machine? >>>> >>>> What happens when you type, say, gnuplot or some other >>>> X-based software? >>>> >>>> Cheers, >>>> >>>> Paul >>>> >>>> >>>> >>>> On Thu, 30 Dec 2010, Albert S. Kim wrote: >>>> >>>> Dear Paul >>>> >>>>> >>>>> Thank you so much. >>>>> Reading your manual, I did the second simulation using "eddy" and got 12 >>>>> output files of "eddy_uv.fld01 -- eddy_uv.fld12". >>>>> I simply tried postx using >>>>> (1) X-win emulator from Linux to my Mac and >>>>> (2) VisIt installed on my Mac (by downloading .dmg file) >>>>> but did not figure out how to. >>>>> >>>>> Perhaps I need more reading, but if you can give me simple tips to make >>>>> my >>>>> first visualization using either of them, it will be a real end-of-year >>>>> gift! >>>>> >>>>> All the files are available to check at >>>>> http://heyum.eng.hawaii.edu/Downloads/eddy.zip >>>>> >>>>> Best wishes, >>>>> >>>>> Albert >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, Dec 29, 2010 at 10:59 AM, Paul Fischer >>>>> wrote: >>>>> >>>>> >>>>> Dear Albert, >>>>>> >>>>>> It looks like your case ran successfully. (grep tep *.out shows this) >>>>>> >>>>>> You can visualize the results using VisIt. >>>>>> >>>>>> There is also a way to visualize using postx -- please see the >>>>>> (under construction) manual: >>>>>> >>>>>> www.mcs.anl.gov/~fischer/new.pdf >>>>>> >>>>>> on how to build and run postx. At present, you would need to >>>>>> rerun the turbChannel case with >>>>>> >>>>>> subroutine userdat2 >>>>>> : >>>>>> : >>>>>> param(66)=4 >>>>>> param(67)=4 >>>>>> >>>>>> and with these parameters set to 4 in the .rea file. This requirement >>>>>> will go away within a couple of weeks once I convert postx to support >>>>>> the new default output file format (.f00000 vs .fld00). >>>>>> >>>>>> I'm hoping we'll soon have a similar "get started" section about using >>>>>> VisIt in the manual. VisIt it much better than postx for >>>>>> 3D analysis. >>>>>> >>>>>> Paul >>>>>> >>>>>> >>>>>> >>>>>> >>>>> -- >>>>> >>>>> ================================ >>>>> Albert S. Kim, Ph.D. >>>>> Editorial Board for ASCE Journal of Energy Engineering >>>>> Editorial Advisory Board for Recent Patents on Chemical Engineering >>>>> >>>>> Associate Professor >>>>> Department of Civil and Environmental Engineering >>>>> University of Hawaii at Manoa >>>>> 2540 Dole Street, Holmes 383 >>>>> Honolulu, HI 96822 >>>>> Office Telephone: (808) 956-3718 >>>>> Confidential Online Fax: (818) 301-7010 >>>>> Department Fax: (808) 956-5014 >>>>> URL: http://pam.eng.hawaii.edu >>>>> Department: http://www.cee.hawaii.edu/persons/kim/kim.htm >>>>> Facebook: http://www.facebook.com/albert.s.kim >>>>> Email: albertsk at hawaii.edu >>>>> ================================ >>>>> >>>>> >>>>> >>> >>> -- >>> >>> ================================ >>> Albert S. Kim, Ph.D. >>> Editorial Board for ASCE Journal of Energy Engineering >>> Editorial Advisory Board for Recent Patents on Chemical Engineering >>> >>> Associate Professor >>> Department of Civil and Environmental Engineering >>> University of Hawaii at Manoa >>> 2540 Dole Street, Holmes 383 >>> Honolulu, HI 96822 >>> Office Telephone: (808) 956-3718 >>> Confidential Online Fax: (818) 301-7010 >>> Department Fax: (808) 956-5014 >>> URL: http://pam.eng.hawaii.edu >>> Department: http://www.cee.hawaii.edu/persons/kim/kim.htm >>> Facebook: http://www.facebook.com/albert.s.kim >>> Email: albertsk at hawaii.edu >>> ================================ >>> >>> > > > -- > > ================================ > Albert S. Kim, Ph.D. > Editorial Board for ASCE Journal of Energy Engineering > Editorial Advisory Board for Recent Patents on Chemical Engineering > > Associate Professor > Department of Civil and Environmental Engineering > University of Hawaii at Manoa > 2540 Dole Street, Holmes 383 > Honolulu, HI 96822 > Office Telephone: (808) 956-3718 > Confidential Online Fax: (818) 301-7010 > Department Fax: (808) 956-5014 > URL: http://pam.eng.hawaii.edu > Department: http://www.cee.hawaii.edu/persons/kim/kim.htm > Facebook: http://www.facebook.com/albert.s.kim > Email: albertsk at hawaii.edu > ================================ > From nek5000-users at lists.mcs.anl.gov Mon Jan 3 10:34:34 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 03 Jan 2011 17:34:34 +0100 Subject: [Nek5000-users] Perturbation Mode Message-ID: <4D21FA9A.5070802@mech.kth.se> Hi Neks, We have been running the perturbation mode in order to study the linear evolution of disturbances in a couple of 2D boundary layer cases and are now setting up a 3D boundary layer case. Already for the 2D cases we experienced that the timestep needs to be decreased significantly compared to a corresponding nonlinear simulation in order to yield a numerically stable simulation. For the nonlinear simulations we put the disturbance with a small amplitude on top of the baseflow. Hence, running the perturbation mode for the 2D cases was more expensive than running a nonlinear simulation but still reasonable. However, the 3D case seems to become much more expensive. We first ran a nonlinear simulation as described above and compared the disturbance evolution to results of the parabolised stability equations which matched perfectly. Running then the perturbation mode for the same disturbance with the same base flow did not yield a stable simulation even when the timestep was reduced (divided by 5). The disturbance amplitude exploded very early. We then took a higher box and increased the resolution which made things a little better meaning that the simulation exploded much later. However, it is still not stable although the resolution is higher and the timestep is much smaller compared to the corresponding nonlinear simulation which worked fine. Also, the number of pressure iterations is around 20-30 times higher. Is there any reason why the linear stability equations in nekton should behave so much different than the full Navier-Stokes? Are there some parameters (filtering etc.) that have to be used differently in this case? Best regards, David -- David Tempelmann Linn? Flow Center, Mechanics KTH SE-100 44, Stockholm, Sweden Phone: +46 8 7907161 E-mail: david at mech.kth.se From nek5000-users at lists.mcs.anl.gov Mon Jan 3 11:26:33 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 3 Jan 2011 11:26:33 -0600 (CST) Subject: [Nek5000-users] Perturbation Mode In-Reply-To: <4D21FA9A.5070802@mech.kth.se> References: <4D21FA9A.5070802@mech.kth.se> Message-ID: Hi David, The perturbation solver was developed roughly 10 years back and hasn't been extensively exercised in recent years. As it is updated only when used (as you guys are doing now) there may be some maintenance that is overdue. There is no intrinsic reason why the perturbation solver should need a smaller timestep than the nonlinear one, so it sounds as though something is amiss; and most likely this is something that is fairly readily remedied. Some questions: .Are you using IFCHAR = true for your nonlinear solver? (I'm not certain of the status of IFCHAR + IFPERT at the moment.) Given that I'll be there next week we can look at this first-hand. I understand that you guys have already encountered (and perhaps resolved?) some issues with the perturbation solver, so hopefully we can get it all straightened out. If you'd like to send me the case files, I can take a quick look now. (You can email me off-list...) I look forward to meeting you next week! Best regards, Paul On Mon, 3 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > > We have been running the perturbation mode in order to study the linear > evolution of disturbances in a couple of 2D boundary layer cases and are > now setting up a 3D boundary layer case. > > Already for the 2D cases we experienced that the timestep needs to be > decreased significantly compared to a corresponding nonlinear simulation > in order to yield a numerically stable simulation. For the nonlinear > simulations we put the disturbance with a small amplitude on top of the > baseflow. Hence, running the perturbation mode for the 2D cases was more > expensive than running a nonlinear simulation but still reasonable. > > However, the 3D case seems to become much more expensive. We first ran a > nonlinear simulation as described above and compared the disturbance > evolution to results of the parabolised stability equations which > matched perfectly. > Running then the perturbation mode for the same disturbance with the > same base flow did not yield a stable simulation even when the timestep > was reduced (divided by 5). The disturbance amplitude exploded very > early. We then took a higher box and increased the resolution which made > things a little better meaning that the simulation exploded much later. > However, it is still not stable although the resolution is higher and > the timestep is much smaller compared to the corresponding nonlinear > simulation which worked fine. Also, the number of pressure iterations is > around 20-30 times higher. > > Is there any reason why the linear stability equations in nekton should > behave so much different than the full Navier-Stokes? Are there some > parameters (filtering etc.) that have to be used differently in this case? > > Best regards, > > David > > -- > David Tempelmann > Linn? Flow Center, Mechanics KTH > SE-100 44, Stockholm, Sweden > Phone: +46 8 7907161 > E-mail: david at mech.kth.se > > _______________________________________________ > 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 Jan 6 09:35:27 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 06 Jan 2011 10:35:27 -0500 Subject: [Nek5000-users] First Visit file In-Reply-To: Message-ID: <1294328127.2510.4.camel@alex-desktop> Hi, I am trying to open the binary example file in /nek5_svn/examples/vortex named r1492_n08.fld27 but i received the following error message: VisIt could not read from the file "/home/alex/Documents/nek5_svn/examples/vortex/r1492_n08.fld27". The generated error message was: There was an error opening /home/alex/Documents/nek5_svn/examples/vortex/r1492_n08.fld27. It may be an invalid file. VisIt tried using the following file format readers to open the file: Silo To check if visit was working fine I generated a bov ASCII file and open it with no problems. Thanks. From nek5000-users at lists.mcs.anl.gov Thu Jan 6 09:47:07 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 09:47:07 -0600 (CST) Subject: [Nek5000-users] First Visit file In-Reply-To: <1294328127.2510.4.camel@alex-desktop> References: <1294328127.2510.4.camel@alex-desktop> Message-ID: Hi, I'm not certain that r1492... has the requisite geometry in the .fld file. (nek5000 and postx do not require it) Also, it might be a good idea to start w/ .fld01, so I would suggest actually running the case and generating a sequence of a few .fld files (at least one). Nek5000 will put the geometry in .fld01 by default. Then, execute the following script: ----------------------------------------------------------------------------- #! /usr/bin/tcsh # set base = `head -1 SESSION.NAME` echo '\n Generating '$base'.nek3d file ...' set nfld = `ls $base.fld* | wc -l` #echo $base ' ' $nfld echo 'NEK3D' > $base.nek3d echo 'filetemplate: '$base'.fld%02d' >> $base.nek3d echo 'firsttimestep: 1' >> $base.nek3d echo 'numtimesteps: '$nfld >> $base.nek3d echo 'meshcoords: 1' >> $base.nek3d echo '\n Assuming that coordinates are in '$base'.fld01 -- otherwise edit $base.nek3d file ...' echo '\n Total : '$nfld' file(s) ... Done \n' # Extra lines? # # version: 1.0 # endian: big #ls `head -1 SESSION.NAME`0.f[0-9][0-9][0-9][0-9]* | wc -l ----------------------------------------------------------------------------- which will make a blah.nek3d file for session name "blah" (assuming blah is in your SESSION.NAME file). >From this you can run visit and load blah.nek3d Paul On Thu, 6 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > I am trying to open the binary example file in /nek5_svn/examples/vortex > named r1492_n08.fld27 but i received the following error message: > > VisIt could not read from the file > "/home/alex/Documents/nek5_svn/examples/vortex/r1492_n08.fld27". > > The generated error message was: > > There was an error > opening /home/alex/Documents/nek5_svn/examples/vortex/r1492_n08.fld27. > It may be an invalid file. VisIt tried using the following file format > readers to open the file: Silo > > To check if visit was working fine I generated a bov ASCII file and open > it with no problems. > > Thanks. > > > _______________________________________________ > 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 Jan 6 11:10:39 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 11:10:39 -0600 (CST) Subject: [Nek5000-users] First Visit file In-Reply-To: Message-ID: <183980396.32253.1294333839478.JavaMail.root@zimbra.anl.gov> Hello, If you run head -1 r1492_n08.fld27 | strings | head -1 you will see the output variable codes 'U P ' in the file header 140 8 8 8 5.0101000E+0250101 U P 4 NELT,NX,N which means there are only velocity and pressure fields in the file. As Paul suggested, in order to get coordinates for visit, you need to rerun the case with T COORDINATES and at least with NSTEPS=0 in .rea Best, Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, January 6, 2011 9:47:07 AM Subject: Re: [Nek5000-users] First Visit file Hi, I'm not certain that r1492... has the requisite geometry in the .fld file. (nek5000 and postx do not require it) Also, it might be a good idea to start w/ .fld01, so I would suggest actually running the case and generating a sequence of a few .fld files (at least one). Nek5000 will put the geometry in .fld01 by default. Then, execute the following script: ----------------------------------------------------------------------------- #! /usr/bin/tcsh # set base = `head -1 SESSION.NAME` echo '\n Generating '$base'.nek3d file ...' set nfld = `ls $base.fld* | wc -l` #echo $base ' ' $nfld echo 'NEK3D' > $base.nek3d echo 'filetemplate: '$base'.fld%02d' >> $base.nek3d echo 'firsttimestep: 1' >> $base.nek3d echo 'numtimesteps: '$nfld >> $base.nek3d echo 'meshcoords: 1' >> $base.nek3d echo '\n Assuming that coordinates are in '$base'.fld01 -- otherwise edit $base.nek3d file ...' echo '\n Total : '$nfld' file(s) ... Done \n' # Extra lines? # # version: 1.0 # endian: big #ls `head -1 SESSION.NAME`0.f[0-9][0-9][0-9][0-9]* | wc -l ----------------------------------------------------------------------------- which will make a blah.nek3d file for session name "blah" (assuming blah is in your SESSION.NAME file). >From this you can run visit and load blah.nek3d Paul On Thu, 6 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > I am trying to open the binary example file in /nek5_svn/examples/vortex > named r1492_n08.fld27 but i received the following error message: > > VisIt could not read from the file > "/home/alex/Documents/nek5_svn/examples/vortex/r1492_n08.fld27". > > The generated error message was: > > There was an error > opening /home/alex/Documents/nek5_svn/examples/vortex/r1492_n08.fld27. > It may be an invalid file. VisIt tried using the following file format > readers to open the file: Silo > > To check if visit was working fine I generated a bov ASCII file and open > it with no problems. > > Thanks. > > > _______________________________________________ > 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 Thu Jan 6 12:04:11 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 06 Jan 2011 13:04:11 -0500 Subject: [Nek5000-users] First Visit file In-Reply-To: <183980396.32253.1294333839478.JavaMail.root@zimbra.anl.gov> References: <183980396.32253.1294333839478.JavaMail.root@zimbra.anl.gov> Message-ID: <1294337051.2510.22.camel@alex-desktop> Hi, I used a test case (10 dump files from test1.fld01 to test1.fld10) which head sections look like this (test1.fld01): ------------------------------------------------------------------------ 100 12 12 1 2.0000000E-02 10 X Y U P NELT,NX,NY,N 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 1.154895E+01 2.755036E-03 0.000000E+00 0.000000E+00 0.000000E+00 1.080465E+01 9.036034E-03 0.000000E+00 0.000000E+00 0.000000E+00 9.776687E+00 ... ------------------------------------------------------------------------ the test1.nek3d file obtained after running the script contains: ------------------------------------------------------------------------ NEK3D filetemplate: test1.fld%02d firsttimestep: 1 numtimesteps: 10 meshcoords: 1 ------------------------------------------------------------------------ However Visit is unable to read it: ------------------------------------------------------------------------ The file format reader issued the following error message, which may (or may not) be indicative of the problem: VisIt believes this is a "Nek" file. Further, the reader for this format believes this is a non-compliant file of this type. Its description of non-compliance is: "A tag called filetemplate: must be specified" ------------------------------------------------------------------------ Thanks. From nek5000-users at lists.mcs.anl.gov Thu Jan 6 12:09:24 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 10:09:24 -0800 Subject: [Nek5000-users] First Visit file In-Reply-To: <1294337051.2510.22.camel@alex-desktop> References: <183980396.32253.1294333839478.JavaMail.root@zimbra.anl.gov> <1294337051.2510.22.camel@alex-desktop> Message-ID: Can you please send me a copy of the .nek3d file (hchilds at lbl.gov)? I know that you included it in your email, but sometimes stuff is lost in translation with cut-n-paste... Thx! -Hank On Thu, Jan 6, 2011 at 10:04 AM, wrote: > Hi, > > I used a test case (10 dump files from test1.fld01 to test1.fld10) which > head sections look like this (test1.fld01): > > ------------------------------------------------------------------------ > 100 12 12 1 2.0000000E-02 10 X Y U P > NELT,NX,NY,N > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 > 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 1.154895E+01 > 2.755036E-03 0.000000E+00 0.000000E+00 0.000000E+00 1.080465E+01 > 9.036034E-03 0.000000E+00 0.000000E+00 0.000000E+00 9.776687E+00 > ... > ------------------------------------------------------------------------ > > the test1.nek3d file obtained after running the script contains: > > ------------------------------------------------------------------------ > NEK3D > filetemplate: test1.fld%02d > firsttimestep: 1 > numtimesteps: 10 > meshcoords: 1 > ------------------------------------------------------------------------ > > However Visit is unable to read it: > > ------------------------------------------------------------------------ > The file format reader issued the following error message, which may (or > may not) be indicative of the problem: > > VisIt believes this is a "Nek" file. Further, the reader for this format > believes this is a non-compliant file of this type. Its description of > non-compliance is: "A tag called filetemplate: must be specified" > ------------------------------------------------------------------------ > > Thanks. > > _______________________________________________ > 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 Jan 6 12:14:56 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 12:14:56 -0600 (CST) Subject: [Nek5000-users] First Visit file In-Reply-To: <1294337051.2510.22.camel@alex-desktop> Message-ID: <1896091024.32713.1294337696049.JavaMail.root@zimbra.anl.gov> Hello, For some reason you have ASCII format which is usually triggered by param(66)<0 in .rea or an overwrite in .usr file with param(66)=0 instead of repo's param(66)=4 -- could you check you .usr file? Visit reader may not work with it since it's optimized to work with large datasets for which ASCII format is prohibitive. Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, January 6, 2011 12:04:11 PM Subject: Re: [Nek5000-users] First Visit file Hi, I used a test case (10 dump files from test1.fld01 to test1.fld10) which head sections look like this (test1.fld01): ------------------------------------------------------------------------ 100 12 12 1 2.0000000E-02 10 X Y U P NELT,NX,NY,N 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 1.154895E+01 2.755036E-03 0.000000E+00 0.000000E+00 0.000000E+00 1.080465E+01 9.036034E-03 0.000000E+00 0.000000E+00 0.000000E+00 9.776687E+00 ... ------------------------------------------------------------------------ the test1.nek3d file obtained after running the script contains: ------------------------------------------------------------------------ NEK3D filetemplate: test1.fld%02d firsttimestep: 1 numtimesteps: 10 meshcoords: 1 ------------------------------------------------------------------------ However Visit is unable to read it: ------------------------------------------------------------------------ The file format reader issued the following error message, which may (or may not) be indicative of the problem: VisIt believes this is a "Nek" file. Further, the reader for this format believes this is a non-compliant file of this type. Its description of non-compliance is: "A tag called filetemplate: must be specified" ------------------------------------------------------------------------ Thanks. _______________________________________________ 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 Jan 6 12:53:56 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 10:53:56 -0800 Subject: [Nek5000-users] First Visit file In-Reply-To: <1896091024.32713.1294337696049.JavaMail.root@zimbra.anl.gov> References: <1294337051.2510.22.camel@alex-desktop> <1896091024.32713.1294337696049.JavaMail.root@zimbra.anl.gov> Message-ID: Hi Everyone, I think the issue is the first line of the header. It needs to be "NEK5000", not "NEK3D". It looks like the parsing of the header looks for the form "TAG VALUE". The exception is the first line, which is "NEK5000". So it tried to read NEK3D as a tag and then ate the filetemplate as the tag "NEK3D"s value. When I switched it to NEK5000, VisIt was able to read the file and make a plot, no problem. (Aleks: looks like we can read ASCII! I wasn't sure myself ;) Best, Hank On Thu, Jan 6, 2011 at 10:14 AM, wrote: > Hello, > > For some reason you have ASCII format which is usually triggered by > param(66)<0 in .rea or an overwrite in .usr file with param(66)=0 instead of > repo's param(66)=4 -- could you check you .usr file? > > Visit reader may not work with it since it's optimized to work with large > datasets for which ASCII format is prohibitive. > > Aleks > > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Thursday, January 6, 2011 12:04:11 PM > Subject: Re: [Nek5000-users] First Visit file > > Hi, > > I used a test case (10 dump files from test1.fld01 to test1.fld10) which > head sections look like this (test1.fld01): > > ------------------------------------------------------------------------ > 100 12 12 1 2.0000000E-02 10 X Y U P > NELT,NX,NY,N > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 0.000 0.000 0.000 > 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 1.154895E+01 > 2.755036E-03 0.000000E+00 0.000000E+00 0.000000E+00 1.080465E+01 > 9.036034E-03 0.000000E+00 0.000000E+00 0.000000E+00 9.776687E+00 > ... > ------------------------------------------------------------------------ > > the test1.nek3d file obtained after running the script contains: > > ------------------------------------------------------------------------ > NEK3D > filetemplate: test1.fld%02d > firsttimestep: 1 > numtimesteps: 10 > meshcoords: 1 > ------------------------------------------------------------------------ > > However Visit is unable to read it: > > ------------------------------------------------------------------------ > The file format reader issued the following error message, which may (or > may not) be indicative of the problem: > > VisIt believes this is a "Nek" file. Further, the reader for this format > believes this is a non-compliant file of this type. Its description of > non-compliance is: "A tag called filetemplate: must be specified" > ------------------------------------------------------------------------ > > Thanks. > > _______________________________________________ > 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 Thu Jan 6 12:57:55 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 11:57:55 -0700 Subject: [Nek5000-users] NaN after velocity save Message-ID: Hello All. I'm try to run about the simplest problem possible in order to test some in-house post-processing code. So, I'm trying to run a 2-D simulation of planar couette flow and I'm doing so in serial on my mac. Once velocity solutions start being saved, param=94, I abruptly start getting NaN's. Any thoughts as to what's going wrong?? Attached are the relevant files. Thanks. --Mike -------------- next part -------------- A non-text attachment was scrubbed... Name: z2.map Type: application/octet-stream Size: 2131 bytes Desc: z2.map URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ATT00001..txt URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: z2.rea Type: application/octet-stream Size: 22621 bytes Desc: z2.rea URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ATT00002..txt URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: z2.usr Type: application/octet-stream Size: 2912 bytes Desc: z2.usr URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: ATT00003..txt URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: SIZE Type: application/octet-stream Size: 2950 bytes Desc: SIZE URL: From nek5000-users at lists.mcs.anl.gov Thu Jan 6 13:44:37 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 13:44:37 -0600 (CST) Subject: [Nek5000-users] First Visit file In-Reply-To: Message-ID: <1167903362.33364.1294343077219.JavaMail.root@zimbra.anl.gov> Great, Hank, thanks! I'll adjust the script. Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, January 6, 2011 12:53:56 PM Subject: Re: [Nek5000-users] First Visit file Hi Everyone, I think the issue is the first line of the header. It needs to be "NEK5000", not "NEK3D". It looks like the parsing of the header looks for the form "TAG VALUE". The exception is the first line, which is "NEK5000". So it tried to read NEK3D as a tag and then ate the filetemplate as the tag "NEK3D"s value. When I switched it to NEK5000, VisIt was able to read the file and make a plot, no problem. (Aleks: looks like we can read ASCII! I wasn't sure myself ;) Best, Hank On Thu, Jan 6, 2011 at 10:14 AM, < nek5000-users at lists.mcs.anl.gov > wrote: Hello, For some reason you have ASCII format which is usually triggered by param(66)<0 in .rea or an overwrite in .usr file with param(66)=0 instead of repo's param(66)=4 -- could you check you .usr file? Visit reader may not work with it since it's optimized to work with large datasets for which ASCII format is prohibitive. Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, January 6, 2011 12:04:11 PM Subject: Re: [Nek5000-users] First Visit file Hi, I used a test case (10 dump files from test1.fld01 to test1.fld10) which head sections look like this (test1.fld01): ------------------------------------------------------------------------ 100 12 12 1 2.0000000E-02 10 X Y U P NELT,NX,NY,N 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 1.154895E+01 2.755036E-03 0.000000E+00 0.000000E+00 0.000000E+00 1.080465E+01 9.036034E-03 0.000000E+00 0.000000E+00 0.000000E+00 9.776687E+00 ... ------------------------------------------------------------------------ the test1.nek3d file obtained after running the script contains: ------------------------------------------------------------------------ NEK3D filetemplate: test1.fld%02d firsttimestep: 1 numtimesteps: 10 meshcoords: 1 ------------------------------------------------------------------------ However Visit is unable to read it: ------------------------------------------------------------------------ The file format reader issued the following error message, which may (or may not) be indicative of the problem: VisIt believes this is a "Nek" file. Further, the reader for this format believes this is a non-compliant file of this type. Its description of non-compliance is: "A tag called filetemplate: must be specified" ------------------------------------------------------------------------ Thanks. _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu Jan 6 13:49:30 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 13:49:30 -0600 (CST) Subject: [Nek5000-users] NaN after velocity save In-Reply-To: References: Message-ID: Hi Mike, Before we look at the case, can you try it with p94=p95=0? Once a solution is close to steady state there can be a problem with projection... Thanks, Aleks On Thu, 6 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Hello All. > > I'm try to run about the simplest problem possible in order to test some in-house post-processing code. > > So, I'm trying to run a 2-D simulation of planar couette flow and I'm doing so in serial on my mac. Once velocity solutions start being saved, param=94, I abruptly start getting NaN's. > > Any thoughts as to what's going wrong?? > > Attached are the relevant files. > > Thanks. > --Mike > > From nek5000-users at lists.mcs.anl.gov Thu Jan 6 13:53:32 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 12:53:32 -0700 Subject: [Nek5000-users] NaN after velocity save In-Reply-To: References: Message-ID: Aleks, Thanks, that did it. Incidentally, I was starting it *with* the steady-state solution, so it couldn't have been closer! --Mike On Jan 6, 2011, at 12:49 PM, wrote: > Hi Mike, > > Before we look at the case, can you try it with p94=p95=0? Once a > solution is close to steady state there can be a problem with > projection... > > Thanks, > Aleks > > On Thu, 6 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > >> Hello All. >> >> I'm try to run about the simplest problem possible in order to test some in-house post-processing code. >> >> So, I'm trying to run a 2-D simulation of planar couette flow and I'm doing so in serial on my mac. Once velocity solutions start being saved, param=94, I abruptly start getting NaN's. >> >> Any thoughts as to what's going wrong?? >> >> Attached are the relevant files. >> >> Thanks. >> --Mike >> >> > _______________________________________________ > 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 Jan 6 14:04:06 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 06 Jan 2011 15:04:06 -0500 Subject: [Nek5000-users] First Visit file In-Reply-To: References: <1294328127.2510.4.camel@alex-desktop> Message-ID: <1294344246.2510.43.camel@alex-desktop> Hi, finally: should i assume that to have the same script for binary files the only thing to be done is to change the line echo 'filetemplate: '$base'.fld%02d' >> $base.nek3d in the previous script?. Thanks. From nek5000-users at lists.mcs.anl.gov Thu Jan 6 14:12:07 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 14:12:07 -0600 (CST) Subject: [Nek5000-users] First Visit file In-Reply-To: <1294344246.2510.43.camel@alex-desktop> References: <1294328127.2510.4.camel@alex-desktop> <1294344246.2510.43.camel@alex-desktop> Message-ID: Nek5000 header and extension will work for both including .f files. Aleks On Thu, 6 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > finally: should i assume that to have the same script for binary files > the only thing to be done is to change the line > > echo 'filetemplate: '$base'.fld%02d' >> $base.nek3d > > in the previous script?. > > Thanks. > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Thu Jan 6 14:20:34 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 14:20:34 -0600 (CST) Subject: [Nek5000-users] First Visit file In-Reply-To: References: <1294328127.2510.4.camel@alex-desktop> <1294344246.2510.43.camel@alex-desktop> Message-ID: Just to clarify - binary/ascii .fld files are the same w.r.t. VisIt (I believe). However, for ".f0000" files (the other binary format), you need a slightly different specification in the .nek3d file. (Correct guys?) Paul On Thu, 6 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Nek5000 header and extension will work for both including .f files. > > Aleks > > > > > On Thu, 6 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi, >> >> finally: should i assume that to have the same script for binary files >> the only thing to be done is to change the line >> >> echo 'filetemplate: '$base'.fld%02d' >> $base.nek3d >> >> in the previous script?. >> >> Thanks. >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Thu Jan 6 14:32:01 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 14:32:01 -0600 (CST) Subject: [Nek5000-users] First Visit file In-Reply-To: References: <1294328127.2510.4.camel@alex-desktop> <1294344246.2510.43.camel@alex-desktop> Message-ID: Right, Paul, but the difference is the line with the filename template while the rest of the visit metafile is the same -- skipping the header in .nek5000 works fine too. Here is the new script that should work for all cases: http://www.mcs.anl.gov/~obabko/visnek Best, Aleks On Thu, 6 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > > Just to clarify - > > binary/ascii .fld files are the same w.r.t. VisIt (I believe). > > However, for ".f0000" files (the other binary format), you > need a slightly different specification in the .nek3d file. > > (Correct guys?) > > Paul > > > > On Thu, 6 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > >> Nek5000 header and extension will work for both including .f files. >> >> Aleks >> >> >> >> >> On Thu, 6 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Hi, >>> >>> finally: should i assume that to have the same script for binary files >>> the only thing to be done is to change the line >>> >>> echo 'filetemplate: '$base'.fld%02d' >> $base.nek3d >>> >>> in the previous script?. >>> >>> Thanks. >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Thu Jan 6 14:37:27 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 6 Jan 2011 14:37:27 -0600 (CST) Subject: [Nek5000-users] Perturbation Mode In-Reply-To: <4D21FA9A.5070802@mech.kth.se> References: <4D21FA9A.5070802@mech.kth.se> Message-ID: On this topic, here are a couple of observations: 1. Perturbation solver was running slower than the nonlinear (std) solver because the perturbation solver did not use projection [Fischer1998] to accelerate the pressure solver. I've modified this so that pressure projection will be used for the perturbation solver if the following conditions are met: a. # perturbation modes = 1 b. baseflow is _not_ computed. These conditions could likely be relaxed, but for robustness I put them in since I don't have time to test all possible combinations at the moment. The rationale for these restrictions is that we (may or) may not want to mix the approximation spaces from the different pressure solves that are used to generate the initial guesses for each pressure solve. The above conditions ensure that pressure projection is used when there is only a single unknown pressure field and thus there will not be cross- population of the approximation space. [ Most likely, it would not hurt to have multiple source for the approximation space, but things get tricky when there are linear dependencies and my discriminators to identify these conditions are not robust.] 2. Linear solver was blowing up while nonlinear was not. The case in question is high Reynolds number (minimally dissipative) with TORDER=3 --- this case is in fact not guaranteed to be stable because the BDF3 timestepper is not A-stable, i.e., there are certain regions in the on the imaginary axis that are unstable. For some reason, this issue is cured for the nonlinear case with filtering [FischerMullen2001]. It appears, however, that the same fix does not cure these linear problems -- not certain why. The fix in this case seems to be to switch to TORDER=2, which has standard (i.e., CFL type) stability constraints and behavior. -- Please let me know if you have any further issues with this, and thanks to the KTH guys for providing a test case! Paul On Mon, 3 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > > We have been running the perturbation mode in order to study the linear > evolution of disturbances in a couple of 2D boundary layer cases and are > now setting up a 3D boundary layer case. > > Already for the 2D cases we experienced that the timestep needs to be > decreased significantly compared to a corresponding nonlinear simulation > in order to yield a numerically stable simulation. For the nonlinear > simulations we put the disturbance with a small amplitude on top of the > baseflow. Hence, running the perturbation mode for the 2D cases was more > expensive than running a nonlinear simulation but still reasonable. > > However, the 3D case seems to become much more expensive. We first ran a > nonlinear simulation as described above and compared the disturbance > evolution to results of the parabolised stability equations which > matched perfectly. > Running then the perturbation mode for the same disturbance with the > same base flow did not yield a stable simulation even when the timestep > was reduced (divided by 5). The disturbance amplitude exploded very > early. We then took a higher box and increased the resolution which made > things a little better meaning that the simulation exploded much later. > However, it is still not stable although the resolution is higher and > the timestep is much smaller compared to the corresponding nonlinear > simulation which worked fine. Also, the number of pressure iterations is > around 20-30 times higher. > > Is there any reason why the linear stability equations in nekton should > behave so much different than the full Navier-Stokes? Are there some > parameters (filtering etc.) that have to be used differently in this case? > > Best regards, > > David > > -- > David Tempelmann > Linn? Flow Center, Mechanics KTH > SE-100 44, Stockholm, Sweden > Phone: +46 8 7907161 > E-mail: david at mech.kth.se > > _______________________________________________ > 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 Jan 7 10:34:30 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 7 Jan 2011 17:34:30 +0100 Subject: [Nek5000-users] Compilation issue Message-ID: Dear all, this morning I checked out the latest revision of nek5000 (revision 620). I am trying right now to compile a new case and I have some compiling issues.Therefore I tried to compile the same case I compiled successfully this morning before the check out and I have the same issue. I send you the file with the compiler message. Best regards, Andrea. -------------- next part -------------- A non-text attachment was scrubbed... Name: compiler.out Type: application/octet-stream Size: 31215 bytes Desc: compiler.out URL: From nek5000-users at lists.mcs.anl.gov Tue Jan 11 10:07:35 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 11 Jan 2011 11:07:35 -0500 Subject: [Nek5000-users] Postx Message-ID: <20110111110735.243045c69jfpcm6f@webmail.vt.edu> Hello Neks, I am trying to post process the fld files using postx to generate a uniform xy grid of passive scalar data. During post processing the top half of the circular cross-section is cut-off (its a cylindrical domain with aspect ratio of 10 i.e radius to depth). The output file generated has only zeros in it. I have checked the input file and it has information of the entire domain. Any idea if i need to do something differently. Thanks, Himanshu From nek5000-users at lists.mcs.anl.gov Wed Jan 12 15:25:08 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 12 Jan 2011 16:25:08 -0500 Subject: [Nek5000-users] Compilation error In-Reply-To: <20110111110735.243045c69jfpcm6f@webmail.vt.edu> References: <20110111110735.243045c69jfpcm6f@webmail.vt.edu> Message-ID: <1294867508.19803.29.camel@alex-desktop> Hi, when compiling a medium size case, i obtained this error message: obj/prepost.o: In function `fill_tmp_': prepost.f:(.text+0x2e89): relocation truncated to fit: R_X86_64_32S against symbol `scrcg_' defined in COMMON section in obj/gmres.o obj/prepost.o: In function `outhis_': prepost.f:(.text+0x5571): relocation truncated to fit: R_X86_64_32S against symbol `scrcg_' defined in COMMON section in obj/gmres.o obj/prepost.o: In function `prepost_map_': prepost.f:(.text+0x6f34): relocation truncated to fit: R_X86_64_32S against symbol `scrcg_' defined in COMMON section in obj/gmres.o obj/ic.o: In function `mfi_': ic.f:(.text+0xa33): relocation truncated to fit: R_X86_64_32S against symbol `scrcg_' defined in COMMON section in obj/gmres.o obj/planx.o: In function `updrhsh2_': planx.f:(.text+0x22): relocation truncated to fit: R_X86_64_32S against symbol `vrthoi_' defined in COMMON section in obj/planx.o obj/planx.o: In function `updtseth2_': planx.f:(.text+0x3b0): relocation truncated to fit: R_X86_64_32S against symbol `vrthoi_' defined in COMMON section in obj/planx.o planx.f:(.text+0x3c1): relocation truncated to fit: R_X86_64_PC32 against symbol `vrthoi_' defined in COMMON section in obj/planx.o planx.f:(.text+0x3e2): relocation truncated to fit: R_X86_64_32S against symbol `vrthoi_' defined in COMMON section in obj/planx.o planx.f:(.text+0x42d): relocation truncated to fit: R_X86_64_32S against symbol `vrthoi_' defined in COMMON section in obj/planx.o planx.f:(.text+0x4b4): relocation truncated to fit: R_X86_64_32S against symbol `vrthoi_' defined in COMMON section in obj/planx.o obj/planx.o: In function `projh2_': planx.f:(.text+0x61d): additional relocation overflows omitted from the output collect2: ld returned 1 exit status make: *** [nek5000] Error 1 Any help?. Thanks in advance. From nek5000-users at lists.mcs.anl.gov Wed Jan 12 15:32:10 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 12 Jan 2011 15:32:10 -0600 (CST) Subject: [Nek5000-users] Compilation error In-Reply-To: <1294867508.19803.29.camel@alex-desktop> References: <20110111110735.243045c69jfpcm6f@webmail.vt.edu> <1294867508.19803.29.camel@alex-desktop> Message-ID: Hi, You don't have enough memory on your system for the per-processor resources required. Depending on compiler/processor, adding G="-mcmodel=medium" might resolve this, particularly if you are on a 64-bit architecture. If you are running in parallel it's certain that you can reduce LELT and then just use a correspondingly higher processor count. Note that per-node (per core) memory scales roughly as M*(lx1*ly1*lz1*lelt)*8 bytes where M ~ 300 As an example, if your problem requires 4000 elements and you have 16 processors, it is sufficient to set LELT > (4000/16 - 1) = 249. hth, Paul On Wed, 12 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > when compiling a medium size case, i obtained this error message: > > obj/prepost.o: In function `fill_tmp_': > prepost.f:(.text+0x2e89): relocation truncated to fit: R_X86_64_32S > against symbol `scrcg_' defined in COMMON section in obj/gmres.o > obj/prepost.o: In function `outhis_': > prepost.f:(.text+0x5571): relocation truncated to fit: R_X86_64_32S > against symbol `scrcg_' defined in COMMON section in obj/gmres.o > obj/prepost.o: In function `prepost_map_': > prepost.f:(.text+0x6f34): relocation truncated to fit: R_X86_64_32S > against symbol `scrcg_' defined in COMMON section in obj/gmres.o > obj/ic.o: In function `mfi_': > ic.f:(.text+0xa33): relocation truncated to fit: R_X86_64_32S against > symbol `scrcg_' defined in COMMON section in obj/gmres.o > obj/planx.o: In function `updrhsh2_': > planx.f:(.text+0x22): relocation truncated to fit: R_X86_64_32S against > symbol `vrthoi_' defined in COMMON section in obj/planx.o > obj/planx.o: In function `updtseth2_': > planx.f:(.text+0x3b0): relocation truncated to fit: R_X86_64_32S against > symbol `vrthoi_' defined in COMMON section in obj/planx.o > planx.f:(.text+0x3c1): relocation truncated to fit: R_X86_64_PC32 > against symbol `vrthoi_' defined in COMMON section in obj/planx.o > planx.f:(.text+0x3e2): relocation truncated to fit: R_X86_64_32S against > symbol `vrthoi_' defined in COMMON section in obj/planx.o > planx.f:(.text+0x42d): relocation truncated to fit: R_X86_64_32S against > symbol `vrthoi_' defined in COMMON section in obj/planx.o > planx.f:(.text+0x4b4): relocation truncated to fit: R_X86_64_32S against > symbol `vrthoi_' defined in COMMON section in obj/planx.o > obj/planx.o: In function `projh2_': > planx.f:(.text+0x61d): additional relocation overflows omitted from the > output > collect2: ld returned 1 exit status > make: *** [nek5000] Error 1 > > Any help?. > > Thanks in advance. > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > uuuuu #!/bin/bash # Nek5000 build config file # (c) 2008,2009,2010 UCHICAGO ARGONNE, LLC # source path SOURCE_ROOT="$HOME/nek5_svn/trunk/nek" # Fortran compiler F77="gfortran44" # C compiler CC="gcc44" # pre-processor symbol list # (set PPLIST=? to get a list of available symbols) #PPLIST="?" # plug-in list PLUGIN_LIST="" # OPTIONAL SETTINGS # ----------------- # enable MPI (default true) IFMPI="false" # auxilliary files to compile # NOTE: source files have to located in the same directory as makenek # a makefile_usr.inc has to be provided containing the build rules #USR="foo.o" # linking flags #USR_LFLAGS="-L/usr/lib -lfoo" # generic compiler flags #G="-g" # optimization flags #OPT_FLAGS_STD="" #OPT_FLAGS_MAG="" # enable AMG coarse grid solver (default XXT) #IFAMG="true" #IFAMG_DUMP="true" # CVODE path #CVODE_DIR=$HOME/cvode/lib # MOAB/iMESH path #MOAB_DIR="$HOME/moab" ############################################################################### # DONT'T TOUCH WHAT FOLLOWS !!! ############################################################################### # assign version tag mver=1 # overwrite source path with optional 2nd argument if [ -d $2 ] && [ $# -eq 2 ]; then SOURCE_ROOT="$2" echo "change source code directory to: ", $SOURCE_ROOT fi # do some checks and create makefile source $SOURCE_ROOT/makenek.inc # compile make -j4 -f makefile 2>&1 | tee compiler.out exit 0 From nek5000-users at lists.mcs.anl.gov Thu Jan 13 14:32:58 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 13 Jan 2011 15:32:58 -0500 Subject: [Nek5000-users] Postx In-Reply-To: <20110111110735.243045c69jfpcm6f@webmail.vt.edu> References: <20110111110735.243045c69jfpcm6f@webmail.vt.edu> Message-ID: Hello neks, I am trying to use postx to read some fld files that have passive scalar information. There are 3 passive scalars. The passive scalar options appear when I do "Set Quantity". But, when I try to set the plot format and read the input file, the passive scalar option is not shown in the Nekton menu. The velocity, co-ordinates, temperature options are present. Any idea why the passive scalar option does not appear? Thank you, Himanshu On Tue, Jan 11, 2011 at 11:07 AM, wrote: > Hello Neks, > > I am trying to post process the fld files using postx to generate a uniform > xy grid of passive scalar data. During post processing the top half of the > circular cross-section is cut-off (its a cylindrical domain with aspect > ratio of 10 i.e radius to depth). The output file generated has only zeros > in it. I have checked the input file and it has information of the entire > domain. Any idea if i need to do something differently. > > Thanks, > Himanshu > _______________________________________________ > 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 Jan 13 14:37:16 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 13 Jan 2011 14:37:16 -0600 (CST) Subject: [Nek5000-users] Postx In-Reply-To: References: <20110111110735.243045c69jfpcm6f@webmail.vt.edu> Message-ID: Hi Himanshu, Try to increase MAXFLD parameter in nek5_svn/trunk/tools/postnek (i.e., maximum total number of fields in .fld file) and recompile clean. Best, Aleks On Thu, 13 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Hello neks, > > I am trying to use postx to read some fld files that have passive scalar > information. There are 3 passive scalars. The passive scalar options appear > when I do "Set Quantity". But, when I try to set the plot format and read > the input file, the passive scalar option is not shown in the Nekton menu. > The velocity, co-ordinates, temperature options are present. Any idea why > the passive scalar option does not appear? > > Thank you, > Himanshu > > On Tue, Jan 11, 2011 at 11:07 AM, wrote: > >> Hello Neks, >> >> I am trying to post process the fld files using postx to generate a uniform >> xy grid of passive scalar data. During post processing the top half of the >> circular cross-section is cut-off (its a cylindrical domain with aspect >> ratio of 10 i.e radius to depth). The output file generated has only zeros >> in it. I have checked the input file and it has information of the entire >> domain. Any idea if i need to do something differently. >> >> Thanks, >> Himanshu >> _______________________________________________ >> 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 Jan 13 14:59:27 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 13 Jan 2011 15:59:27 -0500 Subject: [Nek5000-users] Postx In-Reply-To: References: <20110111110735.243045c69jfpcm6f@webmail.vt.edu> Message-ID: Hi Aleks, Thank you for the suggestion. In the postnek directory there are many .f files, do you know which one has the MAXFLD parameter? Thanks, Himanshu On Thu, Jan 13, 2011 at 3:37 PM, wrote: > Hi Himanshu, > > Try to increase MAXFLD parameter in nek5_svn/trunk/tools/postnek (i.e., > maximum total number of fields in .fld file) and recompile clean. > > Best, > Aleks > > > On Thu, 13 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > > Hello neks, >> >> I am trying to use postx to read some fld files that have passive scalar >> information. There are 3 passive scalars. The passive scalar options >> appear >> when I do "Set Quantity". But, when I try to set the plot format and read >> the input file, the passive scalar option is not shown in the Nekton menu. >> The velocity, co-ordinates, temperature options are present. Any idea why >> the passive scalar option does not appear? >> >> Thank you, >> Himanshu >> >> On Tue, Jan 11, 2011 at 11:07 AM, >> wrote: >> >> Hello Neks, >>> >>> I am trying to post process the fld files using postx to generate a >>> uniform >>> xy grid of passive scalar data. During post processing the top half of >>> the >>> circular cross-section is cut-off (its a cylindrical domain with aspect >>> ratio of 10 i.e radius to depth). The output file generated has only >>> zeros >>> in it. I have checked the input file and it has information of the entire >>> domain. Any idea if i need to do something differently. >>> >>> Thanks, >>> Himanshu >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >> _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Jan 14 19:19:32 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 14 Jan 2011 19:19:32 -0600 (CST) Subject: [Nek5000-users] Postx In-Reply-To: Message-ID: <951270688.66597.1295054372927.JavaMail.root@zimbra.anl.gov> Hi Himanshu, Sorry, I forgot the name of the file: nek5_svn/trunk/tools/postnek/basics.inc Best, Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, January 13, 2011 2:59:27 PM Subject: Re: [Nek5000-users] Postx Hi Aleks, Thank you for the suggestion. In the postnek directory there are many .f files, do you know which one has the MAXFLD parameter? Thanks, Himanshu On Thu, Jan 13, 2011 at 3:37 PM, < nek5000-users at lists.mcs.anl.gov > wrote: Hi Himanshu, Try to increase MAXFLD parameter in nek5_svn/trunk/tools/postnek (i.e., maximum total number of fields in .fld file) and recompile clean. Best, Aleks On Thu, 13 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: Hello neks, I am trying to use postx to read some fld files that have passive scalar information. There are 3 passive scalars. The passive scalar options appear when I do "Set Quantity". But, when I try to set the plot format and read the input file, the passive scalar option is not shown in the Nekton menu. The velocity, co-ordinates, temperature options are present. Any idea why the passive scalar option does not appear? Thank you, Himanshu On Tue, Jan 11, 2011 at 11:07 AM, < nek5000-users at lists.mcs.anl.gov > wrote: Hello Neks, I am trying to post process the fld files using postx to generate a uniform xy grid of passive scalar data. During post processing the top half of the circular cross-section is cut-off (its a cylindrical domain with aspect ratio of 10 i.e radius to depth). The output file generated has only zeros in it. I have checked the input file and it has information of the entire domain. Any idea if i need to do something differently. Thanks, Himanshu _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Mon Jan 17 09:40:24 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 17 Jan 2011 08:40:24 -0700 Subject: [Nek5000-users] Nek5000 and Non-Newtonian Fluids In-Reply-To: References: Message-ID: <2F8B4309-82A8-439A-9655-1DA591DDC383@nrel.gov> Paul, I switched this to the nek5000-users channel in case we discuss some thing relevant to others. For the Bingham model, it seems that all I need is to calculate the second invariant of the strain rate tensor, which is then used to calculate the time-varying apparent viscosity. I suspect the routine building-blocks for generating this tensor are already in the nek distribution. If so, could you point me in that direction? Once those routines are in order, all the calculation will be directed out of uservp, correct? Thanks. --Mike On Jan 14, 2011, at 7:27 AM, Paul Fischer wrote: > Hi Mike, > > [...] > The "peris" case uses the stress formulation, as do the "fs" > cases. These have the correct SiZE files (resp. for 3D and 2D) > and flags in the .rea file, save that you would set "IFMVBD" > to false, since you don't want moving boundaries. > > [...] > The code was used > for a lot of non-Newtonian stuff by Lee Ho and Einar, however, > so it has been exercised significantly in the past. > [...] From nek5000-users at lists.mcs.anl.gov Tue Jan 18 07:22:03 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Jan 2011 07:22:03 -0600 (CST) Subject: [Nek5000-users] Nek5000 and Non-Newtonian Fluids In-Reply-To: <2F8B4309-82A8-439A-9655-1DA591DDC383@nrel.gov> References: <2F8B4309-82A8-439A-9655-1DA591DDC383@nrel.gov> Message-ID: Hi Mike, Probably the best point to start is in the lambda2 routine, to be found in postpro.f, which reads in part as: do ie=1,nelv ! Compute velocity gradient tensor call comp_gije(gije,vx(1,1,1,ie),vy(1,1,1,ie),vz(1,1,1,ie),ie) do l=1,nxyz ! decompose into symm. and antisymm. part do j=1,ndim do i=1,ndim ss(i,j) = 0.5*(gije(l,i,j)+gije(l,j,i)) oo(i,j) = 0.5*(gije(l,i,j)-gije(l,j,i)) enddo enddo etc. I think from their you can see how to compute what you need. (Let me know if you have questions...) If you get such a routine (e.g., "compute_q") and are happy with it after a few trials, I'd be happy to insert it into the repo. Cheers, Paul On Mon, 17 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Paul, > > I switched this to the nek5000-users channel in case we discuss some thing relevant to others. > > For the Bingham model, it seems that all I need is to calculate the second invariant of the strain rate tensor, which is then used to calculate the time-varying apparent viscosity. I suspect the routine building-blocks for generating this tensor are already in the nek distribution. If so, could you point me in that direction? > > Once those routines are in order, all the calculation will be directed out of uservp, correct? > > Thanks. > --Mike > > > On Jan 14, 2011, at 7:27 AM, Paul Fischer wrote: > >> Hi Mike, >> >> [...] >> The "peris" case uses the stress formulation, as do the "fs" >> cases. These have the correct SiZE files (resp. for 3D and 2D) >> and flags in the .rea file, save that you would set "IFMVBD" >> to false, since you don't want moving boundaries. >> >> [...] >> The code was used >> for a lot of non-Newtonian stuff by Lee Ho and Einar, however, >> so it has been exercised significantly in the past. >> [...] > > _______________________________________________ > 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 Jan 18 09:18:46 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Jan 2011 20:48:46 +0530 Subject: [Nek5000-users] computing grad(T) in NEK5000 Message-ID: Dear Paul, I want to compute grad(Temp_field) for Rayleigh-Benard convection simulation. I found two functions in navier1.f, "opgrad" and "opgradt" which compute grad(scalar_field). Which one of these functions should I use? Please help. with regards, Supriyo -- Dr. Supriyo Paul Senior Project Scientist Department of Physics Indian Institute of Technology Kanpur 208 016 INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Jan 18 09:33:11 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Jan 2011 09:33:11 -0600 (CST) Subject: [Nek5000-users] computing grad(T) in NEK5000 In-Reply-To: References: Message-ID: gradm1() would be the recommend one... Cheers, Paul On Tue, 18 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Dear Paul, > > I want to compute grad(Temp_field) for Rayleigh-Benard convection > simulation. I found two functions in navier1.f, "opgrad" and "opgradt" which > compute grad(scalar_field). > > Which one of these functions should I use? Please help. > > with regards, > Supriyo > > -- > Dr. Supriyo Paul > Senior Project Scientist > Department of Physics > Indian Institute of Technology > Kanpur 208 016 > INDIA > From nek5000-users at lists.mcs.anl.gov Tue Jan 18 10:12:43 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Jan 2011 10:12:43 -0600 (CST) Subject: [Nek5000-users] computing grad(T) in NEK5000 In-Reply-To: References: Message-ID: PS - I think if you search the user discussion list, you'll find some additional information. Please post back to this list if you still have questions. On Tue, 18 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > > gradm1() > > would be the recommend one... > > Cheers, > > Paul > > > On Tue, 18 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > >> Dear Paul, >> >> I want to compute grad(Temp_field) for Rayleigh-Benard convection >> simulation. I found two functions in navier1.f, "opgrad" and "opgradt" >> which >> compute grad(scalar_field). >> >> Which one of these functions should I use? Please help. >> >> with regards, >> Supriyo >> >> -- >> Dr. Supriyo Paul >> Senior Project Scientist >> Department of Physics >> Indian Institute of Technology >> Kanpur 208 016 >> INDIA >> > _______________________________________________ > 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 Jan 18 13:00:39 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Jan 2011 12:00:39 -0700 Subject: [Nek5000-users] Nek5000 and Non-Newtonian Fluids In-Reply-To: References: <2F8B4309-82A8-439A-9655-1DA591DDC383@nrel.gov> Message-ID: <9E2FB37B-0524-4D45-990D-CC391D86F8A4@nrel.gov> Paul, That's got what I need, thanks. Also, are there any examples in the distribution that use the stress formulation and variable viscosity? Thanks. --Mike On Jan 18, 2011, at 6:22 AM, wrote: > > Hi Mike, > > Probably the best point to start is in the lambda2 routine, > to be found in postpro.f, which reads in part as: > > > do ie=1,nelv > ! Compute velocity gradient tensor > call comp_gije(gije,vx(1,1,1,ie),vy(1,1,1,ie),vz(1,1,1,ie),ie) > > do l=1,nxyz > ! decompose into symm. and antisymm. part > do j=1,ndim > do i=1,ndim > ss(i,j) = 0.5*(gije(l,i,j)+gije(l,j,i)) > oo(i,j) = 0.5*(gije(l,i,j)-gije(l,j,i)) > enddo > enddo > > etc. > > I think from their you can see how to compute what you need. > (Let me know if you have questions...) > > If you get such a routine (e.g., "compute_q") and are happy > with it after a few trials, I'd be happy to insert it into the repo. > > Cheers, > > Paul > > > > On Mon, 17 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > >> Paul, >> >> I switched this to the nek5000-users channel in case we discuss some thing relevant to others. >> >> For the Bingham model, it seems that all I need is to calculate the second invariant of the strain rate tensor, which is then used to calculate the time-varying apparent viscosity. I suspect the routine building-blocks for generating this tensor are already in the nek distribution. If so, could you point me in that direction? >> >> Once those routines are in order, all the calculation will be directed out of uservp, correct? >> >> Thanks. >> --Mike >> >> >> On Jan 14, 2011, at 7:27 AM, Paul Fischer wrote: >> >>> Hi Mike, >>> >>> [...] >>> The "peris" case uses the stress formulation, as do the "fs" >>> cases. These have the correct SiZE files (resp. for 3D and 2D) >>> and flags in the .rea file, save that you would set "IFMVBD" >>> to false, since you don't want moving boundaries. >>> >>> [...] >>> The code was used >>> for a lot of non-Newtonian stuff by Lee Ho and Einar, however, >>> so it has been exercised significantly in the past. >>> [...] >> >> _______________________________________________ >> 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 Jan 18 13:25:56 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 18 Jan 2011 13:25:56 -0600 (CST) Subject: [Nek5000-users] Nek5000 and Non-Newtonian Fluids In-Reply-To: <9E2FB37B-0524-4D45-990D-CC391D86F8A4@nrel.gov> References: <2F8B4309-82A8-439A-9655-1DA591DDC383@nrel.gov> <9E2FB37B-0524-4D45-990D-CC391D86F8A4@nrel.gov> Message-ID: Hi Mike, Just added "var_vis" to /examples --- it's a test case that I've tested in the past (no exact solution). So far, all exact solns I've found don't properly exercise the full stress tensor, whereas this particular example does - but I don't know the exact solution. In this case, I rely on the fact that the code is correct and convergent and thus trust that we are getting the right answer. If you happen to think of a case that is a better test (I'm certain they exist), please let me know. I believe that if you cd to /examples and say "svn update" that you will find this case deposited into your repo. Let me know if otherwise. Cheers, Paul On Tue, 18 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Paul, > > That's got what I need, thanks. > > Also, are there any examples in the distribution that use the stress formulation and variable viscosity? > > Thanks. > --Mike > > On Jan 18, 2011, at 6:22 AM, wrote: > >> >> Hi Mike, >> >> Probably the best point to start is in the lambda2 routine, >> to be found in postpro.f, which reads in part as: >> >> >> do ie=1,nelv >> ! Compute velocity gradient tensor >> call comp_gije(gije,vx(1,1,1,ie),vy(1,1,1,ie),vz(1,1,1,ie),ie) >> >> do l=1,nxyz >> ! decompose into symm. and antisymm. part >> do j=1,ndim >> do i=1,ndim >> ss(i,j) = 0.5*(gije(l,i,j)+gije(l,j,i)) >> oo(i,j) = 0.5*(gije(l,i,j)-gije(l,j,i)) >> enddo >> enddo >> >> etc. >> >> I think from their you can see how to compute what you need. >> (Let me know if you have questions...) >> >> If you get such a routine (e.g., "compute_q") and are happy >> with it after a few trials, I'd be happy to insert it into the repo. >> >> Cheers, >> >> Paul >> >> >> >> On Mon, 17 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Paul, >>> >>> I switched this to the nek5000-users channel in case we discuss some thing relevant to others. >>> >>> For the Bingham model, it seems that all I need is to calculate the second invariant of the strain rate tensor, which is then used to calculate the time-varying apparent viscosity. I suspect the routine building-blocks for generating this tensor are already in the nek distribution. If so, could you point me in that direction? >>> >>> Once those routines are in order, all the calculation will be directed out of uservp, correct? >>> >>> Thanks. >>> --Mike >>> >>> >>> On Jan 14, 2011, at 7:27 AM, Paul Fischer wrote: >>> >>>> Hi Mike, >>>> >>>> [...] >>>> The "peris" case uses the stress formulation, as do the "fs" >>>> cases. These have the correct SiZE files (resp. for 3D and 2D) >>>> and flags in the .rea file, save that you would set "IFMVBD" >>>> to false, since you don't want moving boundaries. >>>> >>>> [...] >>>> The code was used >>>> for a lot of non-Newtonian stuff by Lee Ho and Einar, however, >>>> so it has been exercised significantly in the past. >>>> [...] >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Wed Jan 19 10:49:45 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 19 Jan 2011 17:49:45 +0100 Subject: [Nek5000-users] viscous term Message-ID: <4D371629.1090906@lav.mavt.ethz.ch> Hi, In an simulation with the LowMach number formulation I need to compute the term : Laplacian(U) + 1/3 grad ( div(U) ) Is it stored somewhere ( BFX,BFY,BFZ ??? )? Moreover, since i need it anyway during postprocessing, which is the most efficient way to extract it? Thank you. francesco -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jan 20 15:14:50 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 20 Jan 2011 16:14:50 -0500 Subject: [Nek5000-users] Postx In-Reply-To: <951270688.66597.1295054372927.JavaMail.root@zimbra.anl.gov> References: <951270688.66597.1295054372927.JavaMail.root@zimbra.anl.gov> Message-ID: Hi Aleks, I made the changes you suggested and re-compiled postx. But, the passive scalar option still does not show up when I do "set plot format". Please let me know if i missed anything or I need to do something differently? Thank you, Himanshu On Fri, Jan 14, 2011 at 8:19 PM, wrote: > Hi Himanshu, > > Sorry, I forgot the name of the file: > > nek5_svn/trunk/tools/postnek/basics.inc > > Best, > Aleks > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Thursday, January 13, 2011 2:59:27 PM > Subject: Re: [Nek5000-users] Postx > > > Hi Aleks, > > > Thank you for the suggestion. In the postnek directory there are many .f > files, do you know which one has the MAXFLD parameter? > > > Thanks, > Himanshu > > > On Thu, Jan 13, 2011 at 3:37 PM, < nek5000-users at lists.mcs.anl.gov > > wrote: > > > Hi Himanshu, > > Try to increase MAXFLD parameter in nek5_svn/trunk/tools/postnek (i.e., > maximum total number of fields in .fld file) and recompile clean. > > Best, > Aleks > > > > > On Thu, 13 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > > > > Hello neks, > > I am trying to use postx to read some fld files that have passive scalar > information. There are 3 passive scalars. The passive scalar options appear > when I do "Set Quantity". But, when I try to set the plot format and read > the input file, the passive scalar option is not shown in the Nekton menu. > The velocity, co-ordinates, temperature options are present. Any idea why > the passive scalar option does not appear? > > Thank you, > Himanshu > > On Tue, Jan 11, 2011 at 11:07 AM, < nek5000-users at lists.mcs.anl.gov > > wrote: > > > > Hello Neks, > > I am trying to post process the fld files using postx to generate a uniform > xy grid of passive scalar data. During post processing the top half of the > circular cross-section is cut-off (its a cylindrical domain with aspect > ratio of 10 i.e radius to depth). The output file generated has only zeros > in it. I have checked the input file and it has information of the entire > domain. Any idea if i need to do something differently. > > Thanks, > Himanshu > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jan 20 16:30:13 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 20 Jan 2011 16:30:13 -0600 (CST) Subject: [Nek5000-users] Postx In-Reply-To: Message-ID: <1493826951.87017.1295562613356.JavaMail.root@zimbra.anl.gov> Hi Himanshu, I'll look into it. Best, Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, January 20, 2011 3:14:50 PM Subject: Re: [Nek5000-users] Postx Hi Aleks, I made the changes you suggested and re-compiled postx. But, the passive scalar option still does not show up when I do "set plot format". Please let me know if i missed anything or I need to do something differently? Thank you, Himanshu On Fri, Jan 14, 2011 at 8:19 PM, < nek5000-users at lists.mcs.anl.gov > wrote: Hi Himanshu, Sorry, I forgot the name of the file: nek5_svn/trunk/tools/postnek/basics.inc Best, Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, January 13, 2011 2:59:27 PM Subject: Re: [Nek5000-users] Postx Hi Aleks, Thank you for the suggestion. In the postnek directory there are many .f files, do you know which one has the MAXFLD parameter? Thanks, Himanshu On Thu, Jan 13, 2011 at 3:37 PM, < nek5000-users at lists.mcs.anl.gov > wrote: Hi Himanshu, Try to increase MAXFLD parameter in nek5_svn/trunk/tools/postnek (i.e., maximum total number of fields in .fld file) and recompile clean. Best, Aleks On Thu, 13 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: Hello neks, I am trying to use postx to read some fld files that have passive scalar information. There are 3 passive scalars. The passive scalar options appear when I do "Set Quantity". But, when I try to set the plot format and read the input file, the passive scalar option is not shown in the Nekton menu. The velocity, co-ordinates, temperature options are present. Any idea why the passive scalar option does not appear? Thank you, Himanshu On Tue, Jan 11, 2011 at 11:07 AM, < nek5000-users at lists.mcs.anl.gov > wrote: Hello Neks, I am trying to post process the fld files using postx to generate a uniform xy grid of passive scalar data. During post processing the top half of the circular cross-section is cut-off (its a cylindrical domain with aspect ratio of 10 i.e radius to depth). The output file generated has only zeros in it. I have checked the input file and it has information of the entire domain. Any idea if i need to do something differently. Thanks, Himanshu _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Jan 21 12:00:46 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 21 Jan 2011 12:00:46 -0600 (CST) Subject: [Nek5000-users] Postx In-Reply-To: Message-ID: <1692489571.89628.1295632846968.JavaMail.root@zimbra.anl.gov> Hi Himanshu, Make sure that your parameter(23)=3 in .rea which is your number of passive scalars or NPSCAL. If this does not help, can you tar up your .fld & .rea file and email me it offline (obabko at mcs.anl.gov) or send me the link to it on the web? Best, Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, January 20, 2011 3:14:50 PM Subject: Re: [Nek5000-users] Postx Hi Aleks, I made the changes you suggested and re-compiled postx. But, the passive scalar option still does not show up when I do "set plot format". Please let me know if i missed anything or I need to do something differently? Thank you, Himanshu On Fri, Jan 14, 2011 at 8:19 PM, < nek5000-users at lists.mcs.anl.gov > wrote: Hi Himanshu, Sorry, I forgot the name of the file: nek5_svn/trunk/tools/postnek/basics.inc Best, Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, January 13, 2011 2:59:27 PM Subject: Re: [Nek5000-users] Postx Hi Aleks, Thank you for the suggestion. In the postnek directory there are many .f files, do you know which one has the MAXFLD parameter? Thanks, Himanshu On Thu, Jan 13, 2011 at 3:37 PM, < nek5000-users at lists.mcs.anl.gov > wrote: Hi Himanshu, Try to increase MAXFLD parameter in nek5_svn/trunk/tools/postnek (i.e., maximum total number of fields in .fld file) and recompile clean. Best, Aleks On Thu, 13 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: Hello neks, I am trying to use postx to read some fld files that have passive scalar information. There are 3 passive scalars. The passive scalar options appear when I do "Set Quantity". But, when I try to set the plot format and read the input file, the passive scalar option is not shown in the Nekton menu. The velocity, co-ordinates, temperature options are present. Any idea why the passive scalar option does not appear? Thank you, Himanshu On Tue, Jan 11, 2011 at 11:07 AM, < nek5000-users at lists.mcs.anl.gov > wrote: Hello Neks, I am trying to post process the fld files using postx to generate a uniform xy grid of passive scalar data. During post processing the top half of the circular cross-section is cut-off (its a cylindrical domain with aspect ratio of 10 i.e radius to depth). The output file generated has only zeros in it. I have checked the input file and it has information of the entire domain. Any idea if i need to do something differently. Thanks, Himanshu _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Jan 28 10:49:16 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 28 Jan 2011 17:49:16 +0100 Subject: [Nek5000-users] lambda2 In-Reply-To: References: <4C4EB704.8050705@kit.edu> Message-ID: Hi Nek's, I have a few troubles using the lambda-2 subroutine. Here is my usrchk: subroutine userchk include 'SIZE' include 'TOTAL' include 'RESTART' character*80 filename(9999) parameter(lt = lx1*ly1*lz1*lelv) real L2(lx1,ly1,lz1,1) integer nfiles ntot = nx1*ny1*nz1*nelv ifreguo = .true. if (nid.eq.0) then open(unit=199,file='file.list',form='formatted',status='old') read(199,*) nfiles read(199,'(A80)') (filename(i),i=1,nfiles) close(199) endif call bcast(nfiles,isize) call bcast(filename,nfiles*80) do i = 1,nfiles call load_fld(filename(i)) call lambda2(L2) ifto = .true. call outpost(vx,vy,vz,pr,L2,'his') enddo call exitt return end The thing is that it actually outposts nothing (or at least it looks like to me that it doesn't outpost anything). I have tried switching from my l2 variable to the temperature t variable but it did not changed anything. Any clues? Regards, JC -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Jan 28 11:18:02 2011 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 28 Jan 2011 11:18:02 -0600 (CST) Subject: [Nek5000-users] lambda2 In-Reply-To: References: <4C4EB704.8050705@kit.edu> Message-ID: Hi JC, L2 does not look to be properly declared? Perhaps real l2(lx1,ly1,lz1,lelt) fixes this? (Let me know if otherwise...) Paul On Fri, 28 Jan 2011, nek5000-users at lists.mcs.anl.gov wrote: > Hi Nek's, > > I have a few troubles using the lambda-2 subroutine. Here is my usrchk: > > subroutine userchk > include 'SIZE' > include 'TOTAL' > include 'RESTART' > > character*80 filename(9999) > parameter(lt = lx1*ly1*lz1*lelv) > real L2(lx1,ly1,lz1,1) > integer nfiles > > ntot = nx1*ny1*nz1*nelv > > ifreguo = .true. > > if (nid.eq.0) then > open(unit=199,file='file.list',form='formatted',status='old') > read(199,*) nfiles > read(199,'(A80)') (filename(i),i=1,nfiles) > close(199) > endif > > call bcast(nfiles,isize) > call bcast(filename,nfiles*80) > > do i = 1,nfiles > call load_fld(filename(i)) > call lambda2(L2) > ifto = .true. > call outpost(vx,vy,vz,pr,L2,'his') > enddo > > call exitt > > return > end > > The thing is that it actually outposts nothing (or at least it looks like to > me that it doesn't outpost anything). I have tried switching from my l2 > variable to the temperature t variable but it did not changed anything. Any > clues? > > Regards, > JC >