June 2014 - Nek5000-users - mailman3.cels.anl.gov

Re: [Nek5000-users] Vorticity
by nek5000-users＠lists.mcs.anl.gov 11 Oct '16

11 Oct '16

Hi, Thanks for your quick reply. Just I wanna know if I can use the interpolated values of velocity at some arbitrary points in the domain (not necessarily the grid points) as the input arguments to theses subroutines. Regards, Alireza Quoting nek5000-users-request(a)lists.mcs.anl.gov: > Send Nek5000-users mailing list submissions to > nek5000-users(a)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(a)lists.mcs.anl.gov > > You can reach the person managing the list at > nek5000-users-owner(a)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. Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > 3. Re: Vorticity (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 13 Jul 2011 17:55:35 -0400 > From: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <20110713175535.1042430oct81vz2v(a)webmail.vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Hi, > > I need to calculate the vorticity vector and the rate of strain tensor > at any arbitrary point in the domain. I wonder if these values are > computed somewhere in the code or if I should interpolate them in the > usr file. I appreciate any kind of help. > > Thanks in advance, > > > Regards, > Alireza Karimi > > > > ------------------------------ > > Message: 2 > Date: Wed, 13 Jul 2011 17:09:48 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: <Pine.LNX.4.64.1107131704140.26989(a)jacobi.mcs.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > Message: 3 > Date: Wed, 13 Jul 2011 23:59:08 -0500 (CDT) > From: nek5000-users(a)lists.mcs.anl.gov > Subject: Re: [Nek5000-users] Vorticity > To: nek5000-users(a)lists.mcs.anl.gov > Message-ID: > <600285192.94128.1310619548370.JavaMail.root(a)zimbra.anl.gov> > Content-Type: text/plain; charset=utf-8 > > Hi Alireza, > > > For a strain stress computation you can call subroutine comp_sij > > call comp_sij(sij,nij,vx,vy,vz > $ ,ur,us,ut,vr,vs,vt,wr,ws,wt) > > > (navier5.f:2225) with nij=6 for 3D somewhere from userchk once you > declare the stress component array sij and arrays with local > coordinate r-s-t derivatives of velocity components > > common /csij/ > $ sij(lx1*ly1*lz1,6,lelv) ! 6 components > $ ,ur (lx1*ly1*lz1) > ... > $ ,wt (lx1*ly1*lz1) > > > Best, > Aleks > > > > > > > ----- Original Message ----- > From: nek5000-users(a)lists.mcs.anl.gov > To: nek5000-users(a)lists.mcs.anl.gov > Sent: Wednesday, July 13, 2011 5:09:48 PM > Subject: Re: [Nek5000-users] Vorticity > > Hi Alireza, > > For vorticity computation, you can call > > call comp_vort3(vort,work1,work2,vx,vy,vz) > > from userchk with the appropriate definitions of vorticity and work arrays > like > > common /scren/ vort (lx1,ly1,lz1,lelv,3) ! x y z components > $ , work1(lx1,ly1,lz1,lelv) > $ , work2(lx1,ly1,lz1,lelv) > > Let me check what we have for the calculation of strain tensor. > Best, > Aleks > > > On Wed, 13 Jul 2011, nek5000-users(a)lists.mcs.anl.gov wrote: > >> Hi, >> >> I need to calculate the vorticity vector and the rate of strain >> tensor at any >> arbitrary point in the domain. I wonder if these values are computed >> somewhere in the code or if I should interpolate them in the usr file. I >> appreciate any kind of help. >> >> Thanks in advance, >> >> >> Regards, >> Alireza Karimi >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users(a)lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > End of Nek5000-users Digest, Vol 29, Issue 2 > ******************************************** > -- Alireza Karimi PhD Candidate Department of Engineering Science and Mechanics Virginia Polytechnic Institute and State University Blacksburg, VA 24061

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SFD error message from p66
by nek5000-users＠lists.mcs.anl.gov 12 Aug '14

12 Aug '14

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

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Error in generalev
by nek5000-users＠lists.mcs.anl.gov 02 Jul '14

02 Jul '14

Hello Neks, I've recently come across an error I haven't seen before. It occurs in the routine "generalev" at the beginning of my run. It looks like the matrix "a" and "b" being fed to the routine have an Infinity or NaN at position (0,0). Are there any ideas of what could cause this type of error? I have attached the logfile to this email. Thanks, -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke

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non-physical temp. at walls
by nek5000-users＠lists.mcs.anl.gov 30 Jun '14

30 Jun '14

Hello all, I wondered if anyone have ever experienced high/low nonphysical temperature field for a configuration in which there is a volumetric heat source. I have such hot/cold spots very close to a few insulated walls as boundary conditions in my configuration. In fact, such temperatures have been observed in the elements adjacent to the wall. The heat source is uniform for part of the domain and zero for the rest of it. It might be due to non-monotonicity of advection scheme and insufficient resolution. The minimum temperature can be clipped, but there is no way to limit the maximum temperature. Any help would be appreciated. Thanks, Mohsen

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running NEK5000 on a cluster with fast/slow storage subsystems. Relative paths instead of absolute
by nek5000-users＠lists.mcs.anl.gov 29 Jun '14

29 Jun '14

I am trying to use nek5000 on the cluster Lomonosov. What is special in the configuration is that it has two levels of storage. The basic storage of a user (i.e. his home directory) is not seen by computational nodes. Computational nodes have their own file system which can be accessed by user through "~/_scratch" subdirectory of the user's home directory. So "~/_scratch" is the home directory for programs running on computational nodes. This is why I can't run nek5000 on this very cluster. I have the following message in the log file: ... read .rea file forrtl: No such file or directory forrtl: severe (29): file not found, unit 9, file /mnt/data/users/dm4/vol12/vanvan/_scratch/stw/stw32x32.rea ... You can see that the program tries to look for an absolute path of the file: it expanded home directory to "/mnt/data/users/dm4/vol12/vanvan" and tries to find the file in the "_scratch" subdirectory which does not exist on computational nodes. For the program on computational nodes the path is simply "~/stw/stw32x32.rea" or "/home/users/vanvan/stw/stw32x32.rea" Can you tell me what I have to change for a relative path instead of absolute or give the absolute path manually. Suppose this situation can happen on other clusters. Thank you, Van

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Small diffusivity. How heat/diffusion equations are solved?
by nek5000-users＠lists.mcs.anl.gov 27 Jun '14

27 Jun '14

I am trying to model inner waves in a salinity-stratified solution, for which kinematic viscosity is 10^-6, diffusivity is 10^-9, so Schmidt number is about 10^-3. If I set viscosity=diffusivity=10^-6, the program works fine, but I get too great effect of diffusion. If I set diffusivity to be less than 10^-6, solution blows up. In this connection I have two questions: Is there a description how heat/diffusion equations are solved in nek5000? Is it possible to change transport/diffusion equation just to transport equation, i.e. without diffusion at all? Thanks.

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Output problem
by nek5000-users＠lists.mcs.anl.gov 26 Jun '14

26 Jun '14

Hi, Neks I want to frequently output my data. Every run will generate over 10000 files. However the maximum value for fld file is fld9999. Is there any way to solve this problem? Thank you. Mu Xu

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perturbation mode question
by nek5000-users＠lists.mcs.anl.gov 25 Jun '14

25 Jun '14

Hi Neks, I'm trying to solve the linearized Navier Stokes equations. Following different posts, I've seen that it maight be possible if I activate the perturbation mode. What I'm doing is the following: 1) I set param 31 to -1.00000 p031 NPERT: #perturbation modes 2) I have introduced the base flow in the presolve/restart options in the following way: 1 PRESOLVE/RESTART OPTIONS ***** BASE0.f00011 Should it be enough to solve this problem? I don't know how to introduce the perturbation in the equations and how to set in Nek5000 the file BASE0.f00011 as base flow. Thanks SL

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Re: [Nek5000-users] test of the time average of turbChannel--what's wrong?
by nek5000-users＠lists.mcs.anl.gov 23 Jun '14

23 Jun '14

I think at the end of 'userchk' the 'timel = time' just needed to come after the 'endif' rather than before. Otherwise things seems to be fine, I guess. Thanks Azad ________________________________________ Thanks Azad -- so is it currently messed up? Or was it messed up before? (i.e., do I need to undo my recent change?) Thanks! 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, June 23, 2014 8:20 AM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] test of the time average of turbChannel--what's wrong? Hi Paul, I just wanted to come back to this point as it seems the correction regarding the turbchannel case in the new version of nek is quite sound; though, the command "timel = time" seems to sit in a wrong position. To what I understand it must appear after the 'if' statement with regards the 'write' block to make sure the timel is saved correctly per timestep. Cheers Azad ________________________________ Hi Xianbei, You are correct that dtime should be equal to DT. If you look at avg_all() in navier5.f in the main nek source directory, this is what happens because timel is updated after the averaging. In the turbchannel case, this was not done - so I've now modified the .usr file to reflect this. I would suggest to simply use the avg_all code to do the time averaging and then to use those average fields to generate profiles. Thanks for pointing out the problem with the turbChannel example. 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: Saturday, May 31, 2014 10:38 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] test of the time average of turbChannel--what's wrong? Hi Xianbei, The usr files are meant to be modified by the users, so you can adjust it to suit your needs. 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: Saturday, May 31, 2014 9:58 PM To: Nek5000 Subject: [Nek5000-users] test of the time average of turbChannel--what's wrong? Hi, all: I read about the time average method in the turbChannel.usr/userchk,here is the origin codes: if(icalld.eq.0) then call rzero(uavg,n) call rzero(urms,n) call rzero(vrms,n) call rzero(wrms,n) call rzero(uvms,n) atime = 0. timel = time call planar_average_s(yy ,ym1 ,w1,w2) icalld = 1 endif dtime = time - timel atime = atime + dtime if (atime.ne.0. .and. dtime.ne.0.) then beta = dtime/atime alpha = 1.-beta ifverbose = .false. call avg1(uavg,vx ,alpha,beta,n,'uavg',ifverbose) As seen , atime and timel is initialized by 0 and time, so when time=time+DT, dtime=DT, atime=DT, so the first average value is vx(t=DT), when time=time+2*DT, dtime=2*DT(timel is not changed, just equal to the initial value ),atime=3*DT, here question comes: this will lead to vxmean(t=2*DT)=2/3*vx(t=DT)+1/3*vx(t=2*DT), this is not what we respect. The right one is make sure that dtime=DT all the time. Also, I do a test to verify this.In order to be more reliable, the velocity isn't nomorlized by u_tau. First, calculate by 1 step and output the means.dat, so the value equal to the time=DT's #time = 2.0000000E-02 # y uup_tau Umean 0.000000000E+00 2.031155153E-02 0.000000000E+00 2.565198406E-03 2.031155153E-02 1.285886819E-02 then restart with the field from previous calculation and output the means.dat, this will output the value of time=2*DT's, #time = 4.0000000E-02 # y uup_tau Umean 0.000000000E+00 2.072569248E-02 0.000000000E+00 2.565205097E-03 2.072569248E-02 1.288671376E-02 At last, restart the calculation and run 2 steps to calculate the average of vx(time=DT) and vx(time=2*DT) #time = 4.0000000E-02 # y uup_tau Umean 0.000000000E+00 2.061649552E-02 0.000000000E+00 2.565198406E-03 2.061649552E-02 1.287524390E-02 As can be seen, the 2 step average is almost equal to the average of step 1 and step 2. So what's wrong with my understanding? Is timel alway updated to the previous time and make sure that dtime=constant? How? Can anyone help? Xianbei

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Re: [Nek5000-users] test of the time average of turbChannel--what's wrong?
by nek5000-users＠lists.mcs.anl.gov 23 Jun '14

23 Jun '14

Hi Paul, I just wanted to come back to this point as it seems the correction regarding the turbchannel case in the new version of nek is quite sound; though, the command "timel = time" seems to sit in a wrong position. To what I understand it must appear after the 'if' statement with regards the 'write' block to make sure the timel is saved correctly per timestep. Cheers Azad ________________________________ Hi Xianbei, You are correct that dtime should be equal to DT. If you look at avg_all() in navier5.f in the main nek source directory, this is what happens because timel is updated after the averaging. In the turbchannel case, this was not done - so I've now modified the .usr file to reflect this. I would suggest to simply use the avg_all code to do the time averaging and then to use those average fields to generate profiles. Thanks for pointing out the problem with the turbChannel example. 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: Saturday, May 31, 2014 10:38 PM To: nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] test of the time average of turbChannel--what's wrong? Hi Xianbei, The usr files are meant to be modified by the users, so you can adjust it to suit your needs. 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: Saturday, May 31, 2014 9:58 PM To: Nek5000 Subject: [Nek5000-users] test of the time average of turbChannel--what's wrong? Hi, all: I read about the time average method in the turbChannel.usr/userchk,here is the origin codes: if(icalld.eq.0) then call rzero(uavg,n) call rzero(urms,n) call rzero(vrms,n) call rzero(wrms,n) call rzero(uvms,n) atime = 0. timel = time call planar_average_s(yy ,ym1 ,w1,w2) icalld = 1 endif dtime = time - timel atime = atime + dtime if (atime.ne.0. .and. dtime.ne.0.) then beta = dtime/atime alpha = 1.-beta ifverbose = .false. call avg1(uavg,vx ,alpha,beta,n,'uavg',ifverbose) As seen , atime and timel is initialized by 0 and time, so when time=time+DT, dtime=DT, atime=DT, so the first average value is vx(t=DT), when time=time+2*DT, dtime=2*DT(timel is not changed, just equal to the initial value ),atime=3*DT, here question comes: this will lead to vxmean(t=2*DT)=2/3*vx(t=DT)+1/3*vx(t=2*DT), this is not what we respect. The right one is make sure that dtime=DT all the time. Also, I do a test to verify this.In order to be more reliable, the velocity isn't nomorlized by u_tau. First, calculate by 1 step and output the means.dat, so the value equal to the time=DT's #time = 2.0000000E-02 # y uup_tau Umean 0.000000000E+00 2.031155153E-02 0.000000000E+00 2.565198406E-03 2.031155153E-02 1.285886819E-02 then restart with the field from previous calculation and output the means.dat, this will output the value of time=2*DT's, #time = 4.0000000E-02 # y uup_tau Umean 0.000000000E+00 2.072569248E-02 0.000000000E+00 2.565205097E-03 2.072569248E-02 1.288671376E-02 At last, restart the calculation and run 2 steps to calculate the average of vx(time=DT) and vx(time=2*DT) #time = 4.0000000E-02 # y uup_tau Umean 0.000000000E+00 2.061649552E-02 0.000000000E+00 2.565198406E-03 2.061649552E-02 1.287524390E-02 As can be seen, the 2 step average is almost equal to the average of step 1 and step 2. So what's wrong with my understanding? Is timel alway updated to the previous time and make sure that dtime=constant? How? Can anyone help? Xianbei

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