November 2016 - Nek5000-users - mailman3.cels.anl.gov

Questions on turbChannel
by nek5000-users＠lists.mcs.anl.gov 02 Dec '16

02 Dec '16

Hello, I have a few questions on the turbChannel example. 1) the ‘eddy viscosity ‘ is computed in the function eddy_visc and called in a loop over the elements of mesh 1. Inside the function eddy_visc there is the following piece of code: if (e.eq.nelv) then ! planar avg and define nu_tau … ntot = nx1*ny1*nz1*nelv do i=1,ntot cdyn = 0 if (den(i,1).gt.0) cdyn = 0.5*num(i,1)/den(i,1) cdyn = 0.16*0.16 ! max(cdyn,0.) ! AS ALTERNATIVE, could clip ediff ediff(i,1) = param(2)+cdyn*dg2(i,1)*snrm(i,1) enddo endif eddy that stores the eddy viscosity is updated when the last element of mesh 1 is called. Is there any reason why it should be done in this manner? 2) I am still confused over the differences between ‘ifsplit’, ‘ifexplvis’ and ‘ifstrs’. From the archive and the documentation I understand the following (please correct me if I am wrong): * ‘ifexplvis’ is set to true when the user specified the viscosity coefficient in uservp. It does not required, however, the stress formation meaning the the diffusive term in the NS equations looks like \mu(x,t) \nabla^2 \vec{u}. * when ‘ifsplit’ is set to true, the viscosity is split in a explicit part and an implicit part. If this correct, how and where are defined the explicit and implicit parts? * ‘ifstrs’: when set to true, ‘ifexplvis’ and ‘if split’ do not have any effect. 3) could someone shed some light on the subroutine ‘set_ds_filt’ in turbChannel.usr, please? It seems to compute some sort of filter that is then used to compute M_{i,j} and L_{i,j} Thanks, Marco

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Error reading domains with 3072 elements in Postnek
by nek5000-users＠lists.mcs.anl.gov 30 Nov '16

30 Nov '16

Hi Neks, I have been having trouble reading my domain with 3 Scalars, having 3072 elements in Postnek. The same domain can be however read without the Scalars. Also the same domain with lesser elements, like 768, can be read fine with/without scalars. I am getting this kind of an error in the terminal. postx window width and/or height > MAX_WINDOWW/H! -*-Helvetica-Medium-R-Normal--*-*-*-*-*-*-*-* NEKTON Version 2.6 Enter Session Name --Default= g40cond_as Beginning Session g40cond_as renaming SESSION.NAME <http://session.name/> SESSION.NAME <http://session.name/>~ Session name: g40cond_as renaming g40cond_as.plt01 g40cond_as.plt01~ LTRUNC: string: 28 Tue Oct 11 15:13:33 PDT 2016 Reading geometry from g40cond_as .rea XYZ Min,Max: -40.0000 40.0000 -40.0000 40.0000 0.00000 1.00000 3072 3017 1 TRYING TO READ BC 3072 3072 2 TRYING TO READ BC 3072 3072 3 TRYING TO READ BC 3072 3072 4 TRYING TO READ BC 3072 3072 5 TRYING TO READ BC LTRUNC: string: 80 E E I E E I E E I E E E E I E E E E E E E E E E E E E LTRUNC: string: 80 E E I E E I E E I E E E E I E E E E E E E E E E E E E LTRUNC: string: 80 E E I E E I E E I E E E E I E E E E E E E E E E E E E this is iffmat: F 6.0000000 E E I E E I E E I E E E E I E E E E E E E E E E E E E E E I E E I E E I E E E E I E E E E E E E E E E E E E opening file: 80 E E I E E I E E I E E E E I E E E E E E E E E E E E E this is param(66): 6.0000000 LTRUNC: string: 80 E E I E E I E E I E E E E I E E E E E E E E E E E E E WARNING: Could not open file. E E I E E I E E I E E E E I E E E E E E E E E E E E E ** ERROR ** Can't open file g40cond_as.his Any help is appreciated. Thanks, Saikat. Saikat Mukherjee, PhD Student, Paul Research Group - http://www.me.vt.edu/mpaul/ Engineering Science and Mechanics, Virginia Tech.

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srun error
by nek5000-users＠lists.mcs.anl.gov 29 Nov '16

29 Nov '16

Hi Neks, I am trying to run a job using SLURM Job script. The batch script job suggested for MPI uses the srun command. My job submission failed and I got the following error: ………………………………………………………………………… srun: error: Application launch failed: Job credential revoked ………………………………………………………………………… Has anybody faced similar difficulties? SP

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Re: [Nek5000-users] postx black window
by nek5000-users＠lists.mcs.anl.gov 23 Nov '16

23 Nov '16

Hi Mateus, This post might help: http://lists.mcs.anl.gov/pipermail/nek5000-users/2016-November/004007.html Ketan

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postx black window
by nek5000-users＠lists.mcs.anl.gov 23 Nov '16

23 Nov '16

Hi neks, After enter "postx" at terminal I got a black window with any sidebar. At terminal I got: ------------------------------------------------------------------------ Beginning Session renaming SESSION.NAME SESSION.NAME~ Session name: ** ERROR ** Can't open file .rea Enter Session Name ------------------------------------------------------------------------ What I have to do for plot the results? Thanks, Mateus. -- Mateus Peixoto Avanci Engenheiro Mecânico Aluno do Programa de Pós-Graduação em Engenharia Mecânica Universidade Federal Fluminense *http://lattes.cnpq.br/1773896725783894 <http://lattes.cnpq.br/1773896725783894>*

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Laminar Flow Poiseuille
by nek5000-users＠lists.mcs.anl.gov 22 Nov '16

22 Nov '16

Hi neks! I just want to simulate a laminar flow case like a Poiseuille flow. What case example I can use? Sorry for the question, I'm very new at nek. Thanks. Mateus. -- Mateus Peixoto Avanci Engenheiro Mecânico Aluno do Programa de Pós-Graduação em Engenharia Mecânica Universidade Federal Fluminense *http://lattes.cnpq.br/1773896725783894 <http://lattes.cnpq.br/1773896725783894>*

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Mantle convection (infinite Prandtl, variable viscosity) with Nek5000
by nek5000-users＠lists.mcs.anl.gov 22 Nov '16

22 Nov '16

Hi Neks, I'm trying to use Nek to simulate convection in planetary mantles (infinite Prandtl-number, variable viscosity...) in the way Jan has requested a few months ago: >> Hi all, >> I was wondering if it is possible to use Nek5000 for simulations in >> the infinite Prandtlnumber regime (e.g. planetary mantles). This >> would require to solve the NS Stokes equation without the time >> derivative and advection term and the heat equation for T: >> >> 1) Solve visc * laplace u - grad p + buoyancy = 0 and div u = 0, >> where bouyancy depends on a given T field and a Rayleigh number >> 2) Update T by solving dT/dt + u grad T = diff * laplace T (+ other >> sources) >> 3) go back to 1 with the new T field, repeat >> >> More realistic models would then use a varying viscosity. >> I looked at the steady state example (kov_st_state), but this is >> missing the time depencence via the Temperature. Any hints on the >> possibility would be much appreciated. >> >> Thanks, >> Jan Initially I tried the whole thing with a simple 2D rectangular geometry and a fluid with temperature-dependent viscosity ([udiff=param(2)*exp(-log(param(70))*temp)] were param(70) is the viscosity contrast between temp=1 and temp=0) cooled from above (T=0) and heated from below (T=1) . At first I tried the way Paul suggested: >> Hi Jan, >> I just saw this and the follow-on posts. (Apologies - have been on the road for >> several weeks.) >> >> I've not tried this, but it appears to me that you simply will set IFNAV = F in the .rea >> file and can set param(1) [ rho ] to be a very small number. Param(2) is the dynamic >> viscosity, so you can set that independently of param(1). This will have the affect >> of forcing the velocity to relax very quickly (its inertia is negligible compared to the >> other terms in the momentum equation). So, you could conceivably set param(1) >> to be 1.e-30, say. >> >> Note that, on the same line where IFNAV is set, you would set IFADV to be "T" for >> the second field. It should look something like: >> >> F T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) >> Also, you might find it of value in this scenario to try the Pn-Pn-2 formulation with >> plan1 ... In this case, you would indeed want to edit the source --- specifically: >> change the call to plan3() to call plan1() in drive2.f ... As I say, I've not experimented >> with this flow regime so am only making suggestions to try, rather than firm >> recommendations based on experience. >> Paul but I got the problem that Nek worked well only for one condition, either for an infinite Prandtlnumber (i.e. density=1.e-30) or variable viscosity. As I wanted Nek to solve both, I got some strange results... for a sufficient resolution very thin boundary layers evolve (they should be much thicker with for instance Rayleigh numbers like 10^4 and a viscosity contrast of 1000) and the boundary layers had a rough structure, but they should be quite smooth. For lower resolution I got no or completely wrong results, either the temperature was oscillating very strong (with values higher than the maximum temperature of 1) or Nek crashed at all. Maybe someone has an idea how to fix it?! However, after that I also tried the way lailai suggested: > Hello, Jan, > > We have in fact solved a similar problem as you face now. In our case, > we have steady Stokes equation at each time step, > in the absence of time derivative and convection term. However we have > time-dependent volume forcing and boundary > conditions, as we solve for fluid-structure interactions in the Stokes > regime. > > You only need to change the source code for one thing. By changing the > flags in the .rea file, you can easily turn > off the two terms. However, the code only runs for 1 time step even if > you specify for example 10 total time steps, which makes sense > as NEK realizes this is a steady problem. NEK5000 does not see that > the next time step, BCs and forcing will be changed, and so > as the flow. > > So I remember I only commented two lines of the source code to achieve > this, in the file 'connect2.f', subroutine 'rdparam', > this is what I have done (i am using a quite old version of the NEK, > so...) > > IF (.NOT.IFTRAN) THEN > c PARAM(11) = 1.0 !lailai comment for steady stokes > c PARAM(12) = 1.0 !lailai comment for steady stokes > PARAM(19) = 0.0 > ENDIF > > Of course you need to set the flags right in .rea file, which you can > find the details on the webpage. You also need to > solve for heat equations to get T. Then in the userchk subroutine, you > calculate the T-dependent buoyancy forcing at each time step. > Solve the flow with new forcing terms. This should be all manageable. > > cheers and good luck, > > lailai where I've included Jan's advice as well: > Hi, > thanks for the advice. I found that one also has to comment the line > IF (.NOT.IFTRAN) NSTEPS=1 > in setvar in drive2.f and use a fixed timestep so that the timeloop does > not stop too soon. > > Thanks again, > Jan Using this method I got more satisfying results, at least for the tested parameters (Ra=10^4, viscosity contrast of 1000), but to achieve a statistically steady state it took a very long time (non-dimensional) of t>1 (independent of the maximum stepsize dt) and therefore very much iteration steps (~10^6) and CPU-time. For comparison other mantle convection codes need a non-dimensional time of t<0.1 and less than 10000 steps (with a comparable maximum stepsize). Unfortunately I've no idea why it takes that much time using Nek... I would be vary grateful for any hints or suggestions to make at least one method work (either Paul's or lailai's way). Thanks, Philipp ---------------------- Philipp Hellenkamp Institut für Geophysik Corrensstr. 24 D-48149 Münster

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Impose/change velocity in userchk
by nek5000-users＠lists.mcs.anl.gov 21 Nov '16

21 Nov '16

Dear Neks, I am using the MHD example for kinematic Dynamo. In the example gpf, the force is added as f=-Nabla^2 u - partial u/partial t, where u is ux = -sys uy = -cxc uz = sxc + cys I want to do it the straight forward approach i.e. directly imposing the velocity in userchk and switching off the iteration Navier-Stokes equation. For this I set the IFNAV to False F T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F F T T T T T T T T T IFTMSH (IF mesh for this field is T mesh) IC being the same as imposed velocity and in userchk added the following if (ifield.eq.1) then ! velocity omega = 1. do i=1,nx1*ny1*nz1*nelv x = xm1(i,1,1,1); y = ym1(i,1,1,1); z = zm1(i,1,1,1) st = sin(omega*time) ct = cos(omega*time) c argxc = x + ct argyc = y + ct argxs = x + st argys = y + st c visc = param(2) s = 3./2. s = sqrt(s) c cxc = s*cos(argxc) cys = s*cos(argys) sxc = s*sin(argxc) sys = s*sin(argys) c vx(i,1,1,1) = -sys vy(i,1,1,1) = -cxc vz(i,1,1,1) = sxc + cys enddo endif ibstep = iostep if (istep.gt.0.and.mod(istep,ibstep).eq.0) $ call outpost(bx,by,bz,pm,t,' ') ! odd blah.fld/.f for B-field c $ call outpost(bx,by,bz,pm,t,'mag') ! magblah.fld/.f for B-field if (ifxyo.and.istep.gt.istep) ifxyo = .false. kinerg2 = 0.5*(glsc3(vx,bm1,vx,m) $ +glsc3(vy,bm1,vy,m) $ +glsc3(vz,bm1,vz,m))/volvm1 n = nx1*ny1*nz1*nelfld(ifldmhd) ! Magnetic energy !?nelb energy0 = energy energy = glsc3(bx,bm1,bx,n) $ + glsc3(by,bm1,by,n) $ + glsc3(bz,bm1,bz,n) energy = 0.5*energy/volfld(ifldmhd) if (istep.gt.1) then ratio = energy/energy0 growth = 0.5*log(ratio)/dt ! 1/2 of magnetic energy growth rate if (nid.eq.0) write(6,1) istep,time,growth,energy, $ kinerg1,kinerg2 1 format(i8,1p5e15.6,' growth') nstepag = param(120) ! p121 < t_avg < p120 nstepsa = param(121) if (istep.lt.nstepag) call $ runtimeavg(Emga,growth,1,nstepsa,1,'gr_Em') ! avg. growth endif When I calculate the energy of the system, it is decaying. Is there anyway I can tamper with / change the velocity field array in nek5000 from userchk? Thanking you in advance. Cheers, Sandeep PS: Attached are the .usr and .rea files

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Mantle Convection (infinite Prandtl, variable viscosity) with Nek5000
by nek5000-users＠lists.mcs.anl.gov 21 Nov '16

21 Nov '16

Hi Neks, I'm trying to use Nek to simulate convection in planetary mantles (infinite Prandtl-number, variable viscosity...) in the way Jan has requested a few months ago: >> Hi all, >> I was wondering if it is possible to use Nek5000 for simulations in >> the infinite Prandtlnumber regime (e.g. planetary mantles). This >> would require to solve the NS Stokes equation without the time >> derivative and advection term and the heat equation for T: >> >> 1) Solve visc * laplace u - grad p + buoyancy = 0 and div u = 0, >> where bouyancy depends on a given T field and a Rayleigh number >> 2) Update T by solving dT/dt + u grad T = diff * laplace T (+ other >> sources) >> 3) go back to 1 with the new T field, repeat >> >> More realistic models would then use a varying viscosity. >> I looked at the steady state example (kov_st_state), but this is >> missing the time depencence via the Temperature. Any hints on the >> possibility would be much appreciated. >> >> Thanks, >> Jan Initially I tried the whole thing with a simple 2D rectangular geometry and a fluid with temperature-dependent viscosity ([udiff=param(2)*exp(-log(param(70))*temp)] were param(70) is the viscosity contrast between temp=1 and temp=0) cooled from above (T=0) and heated from below (T=1) . At first I tried the way Paul suggested: >> Hi Jan, >> I just saw this and the follow-on posts. (Apologies - have been on the road for >> several weeks.) >> >> I've not tried this, but it appears to me that you simply will set IFNAV = F in the .rea >> file and can set param(1) [ rho ] to be a very small number. Param(2) is the dynamic >> viscosity, so you can set that independently of param(1). This will have the affect >> of forcing the velocity to relax very quickly (its inertia is negligible compared to the >> other terms in the momentum equation). So, you could conceivably set param(1) >> to be 1.e-30, say. >> >> Note that, on the same line where IFNAV is set, you would set IFADV to be "T" for >> the second field. It should look something like: >> >> F T F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) >> Also, you might find it of value in this scenario to try the Pn-Pn-2 formulation with >> plan1 ... In this case, you would indeed want to edit the source --- specifically: >> change the call to plan3() to call plan1() in drive2.f ... As I say, I've not experimented >> with this flow regime so am only making suggestions to try, rather than firm >> recommendations based on experience. >> Paul but I got the problem that Nek worked well only for one condition, either for an infinite Prandtlnumber (i.e. density=1.e-30) or variable viscosity. As I wanted Nek to solve both, I got some strange results... for a sufficient resolution very thin boundary layers evolve (they should be much thicker with for instance Rayleigh numbers like 10^4 and a viscosity contrast of 1000) and the boundary layers had a rough structure, but they should be quite smooth. For lower resolution I got no or completely wrong results, either the temperature was oscillating very strong (with values higher than the maximum temperature of 1) or Nek crashed at all. Maybe someone has an idea how to fix it?! However, after that I also tried the way lailai suggested: > Hello, Jan, > > We have in fact solved a similar problem as you face now. In our case, > we have steady Stokes equation at each time step, > in the absence of time derivative and convection term. However we have > time-dependent volume forcing and boundary > conditions, as we solve for fluid-structure interactions in the Stokes > regime. > > You only need to change the source code for one thing. By changing the > flags in the .rea file, you can easily turn > off the two terms. However, the code only runs for 1 time step even if > you specify for example 10 total time steps, which makes sense > as NEK realizes this is a steady problem. NEK5000 does not see that > the next time step, BCs and forcing will be changed, and so > as the flow. > > So I remember I only commented two lines of the source code to achieve > this, in the file 'connect2.f', subroutine 'rdparam', > this is what I have done (i am using a quite old version of the NEK, > so...) > > IF (.NOT.IFTRAN) THEN > c PARAM(11) = 1.0 !lailai comment for steady stokes > c PARAM(12) = 1.0 !lailai comment for steady stokes > PARAM(19) = 0.0 > ENDIF > > Of course you need to set the flags right in .rea file, which you can > find the details on the webpage. You also need to > solve for heat equations to get T. Then in the userchk subroutine, you > calculate the T-dependent buoyancy forcing at each time step. > Solve the flow with new forcing terms. This should be all manageable. > > cheers and good luck, > > lailai where I've included Jan's advice as well: > Hi, > thanks for the advice. I found that one also has to comment the line > IF (.NOT.IFTRAN) NSTEPS=1 > in setvar in drive2.f and use a fixed timestep so that the timeloop does > not stop too soon. > > Thanks again, > Jan Using this method I got more satisfying results, at least for the tested parameters (Ra=10^4, viscosity contrast of 1000), but to achieve a statistically steady state it took a very long time (non-dimensional) of t>1 (independent of the maximum stepsize dt) and therefore very much iteration steps (~10^6) and CPU-time. For comparison other mantle convection codes need a non-dimensional time of t<0.1 and less than 10000 steps (with a comparable maximum stepsize). Unfortunately I've no idea why it takes that much time using Nek... I would be vary grateful for any hints or suggestions to make at least one method work (either Paul's or lailai's way). Thanks, Philipp ---------------------- Philipp Hellenkamp Institut für Geophysik Corrensstr. 24 D-48149 Münster

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Re: [Nek5000-users] Nek5000-users Digest, Vol 93, Issue 6
by nek5000-users＠lists.mcs.anl.gov 21 Nov '16

21 Nov '16

HI, all I would like to make a supplementary that for an inner circle (or other curved boundary) the 'radius' in your commend should be a minus value, say, -0.5. ---------------------------------------------------------------- Bolun Xu University of Science and Technology of China Hefei, Anhui, China -----邮件原件----- 发件人: Xu Bolun [mailto:[email protected]] 发送时间: 2016年11月10日 10:12 收件人: 'nek5000-users(a)lists.mcs.anl.gov' 主题: 答复: Nek5000-users Digest, Vol 93, Issue 6 Hello, Nicolas I read the documentation again carefully and very happy that my problem has been solved. Thank you very much for advice. I would like to share the curve definition parts in my mesh converting commands for a ring below: Curves={4:{'type':'C','depth':4,'circle_center':(0,0), 'radius':1},3:{'type':'C','depth':4,'circle_center':(0,0),'radius':0.5}} For 4 and 3 are outer and inner circle. ---------------------------------------------------------------- Bolun Xu University of Science and Technology of China Hefei, Anhui, China -----邮件原件----- 发件人: nek5000-users-bounces(a)lists.mcs.anl.gov [mailto:[email protected]] 代表 nek5000-users-request(a)lists.mcs.anl.gov 发送时间: 2016年11月9日 23:27 收件人: nek5000-users(a)lists.mcs.anl.gov 主题: Nek5000-users Digest, Vol 93, Issue 6 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. Re: A problem in Prenek (nek5000-users(a)lists.mcs.anl.gov) 2. 2D circular ring mesh converting by mshconvert.py (nek5000-users(a)lists.mcs.anl.gov) 3. Re: 2D circular ring mesh converting by mshconvert.py (nek5000-users(a)lists.mcs.anl.gov) 4. Re: Read Nek output in Matlab (nek5000-users(a)lists.mcs.anl.gov) 5. Name of the variable in userf and userq (nek5000-users(a)lists.mcs.anl.gov) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Nov 2016 21:32:25 +0000 From: nek5000-users(a)lists.mcs.anl.gov To: "nek5000-users(a)lists.mcs.anl.gov" <nek5000-users(a)lists.mcs.anl.gov> Subject: Re: [Nek5000-users] A problem in Prenek Message-ID: <mailman.5887.1478640760.3602.nek5000-users(a)lists.mcs.anl.gov> Content-Type: text/plain; charset="utf-8" Hi Saikat, I think this is what is expected. If we look at postpro.f in nek?s source code (subroutine gen_rea_bc), there are 4 different formats in which the boundary conditions will be written depending on the element count. In your case, since the element count is greater than 1000 but less than 100,000, we expect the format to be: first 4 character spaces for boundary condition, next 5 characters for element number, 1 character for edge/face number depending on 2d/3d and so on. As a result, your boundary condition line shows as: E 30724 2731.00 2.00000 0.00000 0.00000 0.00000 Thanks, Ketan

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