September 2016 - 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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Problem reading binary .fld files into Postnek
by nek5000-users＠lists.mcs.anl.gov 27 Sep '16

27 Sep '16

Hello everyone, I am having some problem importing my bineary type data into postnek. When the files are imported, seems like many elements are missing and the error message that appears in the terminal is as follows - >>MAX_WINDOWW/H! -*-Helvetica-Medium-R-Normal--*-*-*-*-*-*-*-* NEKTON Version 2.6 Enter Session Name Beginning Session g40cond_as renaming SESSION.NAME SESSION.NAME~ Session name: g40cond_as >> LTRUNC: string: 28 >>LTRUNC: string: 80 >>this is iffmat: F -1.0000000 >>WARNING: Could not open file. >> ** ERROR ** Can't open file g40cond_as.his The same files can be read correctly by Visit though. Thanks for your help. Saikat. Saikat Mukherjee, Graduate Student, Engineering Science and Mechanics, BEAM, Virginia Tech.

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Pn-Pn and IFSTRS
by nek5000-users＠lists.mcs.anl.gov 24 Sep '16

24 Sep '16

Hi Neks, in the older version of the code when trying to set up Pn-Pn and IFSTRS the code returns "Stress formulation in Pn-Pn is not supported". Trying the channel flow with the new version, I do not get this line, however, NaN values appear in the solver output. Could you please help me out? Vlad Novosibirsk State University

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Error in Postnek for passive scalars.
by nek5000-users＠lists.mcs.anl.gov 23 Sep '16

23 Sep '16

Hello everyone, I am encountering an error when I am doing the SET QUANTITY in postnek. I have 3 passive scalars, and in the SET QUANTITY, I should get them as PS 1, PS 2 and PS 3. Instead I am getting I, E E E, E E E --- these kind of notations. When I try to set either one of them as my Quantity I end up with nothing. Also the Postnek window has E E E E E E...I on top of it, which I have never seen before. I think it's some sort of an error. Has anyone else encountered this? Thanks, Saikat. Saikat Mukherjee, Graduate Student, Engineering Science and Mechanics, BEAM, Virginia Tech.

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Definition of variables in the .usr file?
by nek5000-users＠lists.mcs.anl.gov 23 Sep '16

23 Sep '16

Dear All, Is there any documentation of all variables that I have available in the .usr file? For example, in the User Guide it is explained you to modify a mesh for a straight pipe into a pipe with a width that varies along it. You use then * The variable "ntot". Which I guess is the number of vertices, but i it? * The variable "ym1", which seems to be a 4D tensor. Here you change the element ym1(i,1,1,1) for i = 1,ntot. Is this the y-position of the verices? What alse does ym1 contain? These and other variables are variables that I would appreciate to know the definition of. Is it available somwhere? Best, Johan

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Re: [Nek5000-users] Drag calculation and mass flow rate with angled meshes
by nek5000-users＠lists.mcs.anl.gov 23 Sep '16

23 Sep '16

Hi Neks, I had recently clarified a few issues on the forum regarding the flow rate and the mean velocity parameters p54 and p55. There are still a few issues and therefore, for convenience, I am replying to the same thread. Paul, like you had suggested I ran a simulation with the p54 set to -1.0 and the p55 set to 1.0 (because I want the bulk mean velocity in the channel to be 1 , so as to make the viscosity \nu = 1 / Re). This I did with two domains at two different angles of 30 degrees and 60 degrees (a quick screenshot is attached in the mail. Note this is a 3D simulation, the image shows view perpendicular to the z-axis). The perpendicular distance between the walls normal to the y-axis are the same between these domains, as are all the other simulation parameters, except for the mesh points (of course, since the domains are different). The ffx variable in the userf sub-routine is set to zero, and as far as I can say, there is nothing else in the case files that could be affecting the mass flow rates or the velocity in this simulation. However when I run the simulation for the two different domains with the same p55, I am still ending up with different volume flow rates ( and therefore different turbulent Reynolds numbers, Re_\tau, which is my ultimate target). I could not understand, what it is that is causing this. Do you, or anybody else have any inputs on why this might be happening? Here are a few lines, of the last few time steps, from the logfile of the 30 degrees domain containing the volume flow rate: 161133 0.1099986E+04 4.03381E-03 9.43269E-05 5.39728E+00 5.39738E+00 volflow X 161134 0.1099994E+04 4.03312E-03 9.43107E-05 5.39728E+00 5.39738E+00 volflow X 161135 0.1100001E+04 4.03279E-03 7.99447E-05 5.39730E+00 5.39738E+00 volflow X Similar lines for the 60 degrees domain: 86405 0.1099983E+04 3.90944E-03 1.07987E-04 4.13041E+00 4.13052E+00 volflow X 86406 0.1099996E+04 3.91068E-03 1.08021E-04 4.13041E+00 4.13052E+00 volflow X 86407 0.1100005E+04 3.91126E-03 9.15895E-05 4.13043E+00 4.13052E+00 volflow X Thanks and regards, Pradyumna TU Delft, Student: Masters in Aerospace Engineering From: nek5000-users-bounces(a)lists.mcs.anl.gov [mailto:[email protected]] On Behalf Of nek5000-users(a)lists.mcs.anl.gov Sent: Tuesday, September 20, 2016 6:01 PM To: nek5000-users(a)lists.mcs.anl.gov Subject: Re: [Nek5000-users] Drag calculation and mass flow rate with angled meshes Paul, Thank you I will do that. Best regards, Pradyumna M K Prasad TU Delft, Student: Masters in Aerospace Engineering From: nek5000-users-bounces(a)lists.mcs.anl.gov<mailto:[email protected]> [mailto:[email protected]] On Behalf Of nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> Sent: Tuesday, September 20, 2016 5:48 PM To: nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> Subject: Re: [Nek5000-users] Drag calculation and mass flow rate with angled meshes Hi Pradyumna, If you are using p54/p55, you should set ffx (ffy,ffz) to 0. Nek will adjust the mean pressure drop to sustain your requested flow rate. You can find what this is, as a function of time, by: grep volf logfile Column 1 is step number Column 2 is time Column 3 is ffx (unless you prescribed ffx, then c2 will be ffx - what you prescribed). Paul ________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov<mailto:[email protected]> [nek5000-users-bounces(a)lists.mcs.anl.gov] on behalf of nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> [nek5000-users(a)lists.mcs.anl.gov] Sent: Tuesday, September 20, 2016 9:55 AM To: nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> Subject: Re: [Nek5000-users] Drag calculation and mass flow rate with angled meshes Paul, I am not using the usrdat2 sub-routine for now. But in any case, I will set p59 = 1. I am only using the function ffx in the sub-routine userf. But I checked the vol_flow routine and could not find anything that should affect ffx in the angled domain. So I will keep it. Do you agree? Best regards, c From: nek5000-users-bounces(a)lists.mcs.anl.gov<mailto:[email protected]> [mailto:[email protected]] On Behalf Of nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> Sent: Tuesday, September 20, 2016 4:43 PM To: nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> Subject: Re: [Nek5000-users] Drag calculation and mass flow rate with angled meshes Hi Pradyumna, Periodicity is pretty robust in nek. As long as the pair of periodic faces has the same normal vector and are of the same area, then it should work. Yes - I believe that using the correct Ubar will work for you. Another point, which I discovered just last week: If you are applying a shear in usrdat2 (which would be a normal thing to do), you need to make certain you set param(59)=1 in the .usr file. This turns off the "fast" operator evaluation that is valid only for element that are proper rectilinear bricks. The code detects such bricks when they are read from the .rea file, but the mechanism uses information that is not touched by standard morphing procedures. I'm working on a fix for this, but for now you should set param(59)=1, which will turn off the fast mode. Paul ________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov<mailto:[email protected]> [nek5000-users-bounces(a)lists.mcs.anl.gov] on behalf of nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> [nek5000-users(a)lists.mcs.anl.gov] Sent: Tuesday, September 20, 2016 9:32 AM To: nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> Subject: Re: [Nek5000-users] Drag calculation and mass flow rate with angled meshes Hi Paul, Thank you for your reply. I am indeed using the flow rate parameter, that is p54 > 0. From your reply, then can I assume that prescribing the mean velocity should lead to reliable results? Also it struck me when reading your reply, so I am directly asking you. If the Lx =xmax - xmin is incorrect for an angled domain, then will it in anyway affect the periodic boundary conditions. I still want the same periodic conditions, as they were in the orthogonal turbulent channel flow case (periodic about the x-axis direction). That is the velocity profile in the right-most elements should be implanted onto the left-most profile. Will this happen reliably or could there be any factors that might cause a problem? Thanks and regards, Pradyumna M K Prasad TU Delft, Student: Masters in Aerospace Engineering From: nek5000-users-bounces(a)lists.mcs.anl.gov<mailto:[email protected]> [mailto:[email protected]] On Behalf Of nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> Sent: Tuesday, September 20, 2016 4:04 PM To: nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> Subject: Re: [Nek5000-users] Drag calculation and mass flow rate with angled meshes Hi Pardyumna, Nek supports two fixed flow-rate modes: .prescribed flow rate .prescribed average velocity. You toggle between these modes according to the sign of parameter 54. If p54 < 0, you are prescribing mean velocity If p54 > 0, you are prescribing flow rate. The flow rate may not work in your case because of the fact that your domain "length" ( := xmax - xmin) is not the same as your periodic pitch. The mean velocity is computed is: \int u dV / \int dV and I believe that should work OK. Flow rate needs an estimate of the length of the domain Q(x) = \int_A u dA = constant (by mass conservation) Q := (1/Lx) \int_0^Lx Q(x) dx = (1/Lx) * \int_Omega u dV In your case, Lx is the periodic pitch, and not equal to (xmax-xmin). However, Nek does not know how to find the periodic pitch. It is using Lx = xmax-xmin, which is incorrect for your geometry. Which one are your using? Best, Paul ________________________________ From: nek5000-users-bounces(a)lists.mcs.anl.gov<mailto:[email protected]> [nek5000-users-bounces(a)lists.mcs.anl.gov] on behalf of nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> [nek5000-users(a)lists.mcs.anl.gov] Sent: Tuesday, September 20, 2016 7:24 AM To: nek5000-users(a)lists.mcs.anl.gov<mailto:[email protected]> Subject: [Nek5000-users] Drag calculation and mass flow rate with angled meshes Hi Neks, I am trying to run a simulation case similar to the turbulent channel flow case. I initially ran a simulation on the normal turbulent channel flow domain (with the geometry like the fig on the left). I used the parameter p55 in the rea file to ensure that the bulk velocity of the flow is 1 in the domain, and used the parameter p02 to set the turbulent Reynolds number, Re_tau to my required value of 180. I used the sub-routine drag_calc to find the mean shear on the wall, from which I calculated the shear stress and then the Re_tau and u_tau values. However, recently I was trying the same thing on a slightly different domain (fig to the right). --------------------------------------------------------------------- --------------------------------------------------------------------- | | / / ^ Y | | / / | | | / / |_____> X | | / / | | / / --------------------------------------------------------------------- --------------------------------------------------------------------- This domain is almost the same as the first except now there is an angle of 30 degrees in the mesh grid about the z-axis. Please note that the perpendicular distance between the walls normal to the y-direction remains the same for both the domains. In this domain if I use the same p55 and p02 parameters that I use for the orthogonal domain, then Re_tau, calculated as described above, is increasing to higher values (~220). If I reduce the parameter p55 to lesser values, then the Re_tau value is restored to 180. I could not figure out why exactly this was happening, and whether this difference is now because my way of calculating the Re_tau is not valid anymore in the angled domain. Or is the change because the mass flow rate is actually higher in the angled domain? If the case is latter, then why is the mass flow rate increasing just due to the angling of the mesh? I went through the sub-routines drag_calc, vol_flow and set_obj (to see if the integral object needs to be changed) in moderate detail, but could not figure out the reasons for this. Any help in this might be appreciated, as I want to establish the reason, so that I can trust the accuracy of the results of this simulation. Thanks and regards, Pradyumna M K Prasad TU Delft, Student: Masters in Aerospace Engineering

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Drag calculation and mass flow rate with angled meshes
by nek5000-users＠lists.mcs.anl.gov 20 Sep '16

20 Sep '16

Hi Neks, I am trying to run a simulation case similar to the turbulent channel flow case. I initially ran a simulation on the normal turbulent channel flow domain (with the geometry like the fig on the left). I used the parameter p55 in the rea file to ensure that the bulk velocity of the flow is 1 in the domain, and used the parameter p02 to set the turbulent Reynolds number, Re_tau to my required value of 180. I used the sub-routine drag_calc to find the mean shear on the wall, from which I calculated the shear stress and then the Re_tau and u_tau values. However, recently I was trying the same thing on a slightly different domain (fig to the right). --------------------------------------------------------------------- --------------------------------------------------------------------- | | / / ^ Y | | / / | | | / / |_____> X | | / / | | / / --------------------------------------------------------------------- --------------------------------------------------------------------- This domain is almost the same as the first except now there is an angle of 30 degrees in the mesh grid about the z-axis. Please note that the perpendicular distance between the walls normal to the y-direction remains the same for both the domains. In this domain if I use the same p55 and p02 parameters that I use for the orthogonal domain, then Re_tau, calculated as described above, is increasing to higher values (~220). If I reduce the parameter p55 to lesser values, then the Re_tau value is restored to 180. I could not figure out why exactly this was happening, and whether this difference is now because my way of calculating the Re_tau is not valid anymore in the angled domain. Or is the change because the mass flow rate is actually higher in the angled domain? If the case is latter, then why is the mass flow rate increasing just due to the angling of the mesh? I went through the sub-routines drag_calc, vol_flow and set_obj (to see if the integral object needs to be changed) in moderate detail, but could not figure out the reasons for this. Any help in this might be appreciated, as I want to establish the reason, so that I can trust the accuracy of the results of this simulation. Thanks and regards, Pradyumna M K Prasad TU Delft, Student: Masters in Aerospace Engineering

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IFMGRID and IFMVBD
by nek5000-users＠lists.mcs.anl.gov 19 Sep '16

19 Sep '16

Dear Nek users, In *.rea file, there are two logical switches for free surface flow, i.e. IFMGRID and IFMVBD. Should both of them be set to true in simulating free surface flow? Thank you, Peng

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Profile points in Postnek
by nek5000-users＠lists.mcs.anl.gov 16 Sep '16

16 Sep '16

Hello all, How do you change the default maximum number of profile points in Postnek? I have the maximum set at 4000. Thanks, Saikat. Saikat Mukherjee, Graduate Student, Engineering Science and Mechanics, BEAM, Virginia Tech.

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recycling BC
by nek5000-users＠lists.mcs.anl.gov 13 Sep '16

13 Sep '16

I'm trying to setup a problem with recycling BC and am getting a series of errors. First in 'get_shift' I hit the check : npmax = iglmax(npts,1) ! max RBC pts/core if (npmax.gt.lpart) call exitti( $ 'set_inflow err: increase lpart in SIZE$',npmax) After I increased lpart in SIZE to satisfy the above, the code aborted complaining that the problem is too large and is suggesting to recompile with lelt = total number of elements. What is the role of this check? Thanks for looking into this. -emilian

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