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

Re: [Nek5000-users] Time of restart
by nek5000-users＠lists.mcs.anl.gov 09 Sep '16

09 Sep '16

Thanks Paul! Peng > On Sep 9, 2016, at 1:00 PM, nek5000-users-request(a)lists.mcs.anl.gov wrote: > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mail… > 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. Time of restart (nek5000-users(a)lists.mcs.anl.gov) > 2. Re: Time of restart (nek5000-users(a)lists.mcs.anl.gov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 9 Sep 2016 14:51:02 +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: [Nek5000-users] Time of restart > Message-ID: > <mailman.2528.1473436553.3602.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="utf-8" > > Dear Nek users, > > I?m using the restart option in *.rea. > How can I force the restart time to 0, instead of the time in restarting file. > The file to restart has format of *.f0000 > > Thank you, > Peng > > > ------------------------------ > > Message: 2 > Date: Fri, 9 Sep 2016 16:13:30 +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] Time of restart > Message-ID: > <mailman.2531.1473437612.3602.nek5000-users(a)lists.mcs.anl.gov> > Content-Type: text/plain; charset="Windows-1252" > > > Hi Peng, > > I usually do the following in the .usr file: > > in userchk .... > > > if (step.eq.0) time=0 > > ...You do have to remember to comment this out for subsequent restarts, however. > > Paul > > ________________________________________ > From: nek5000-users-bounces(a)lists.mcs.anl.gov [nek5000-users-bounces(a)lists.mcs.anl.gov] on behalf of nek5000-users(a)lists.mcs.anl.gov [nek5000-users(a)lists.mcs.anl.gov] > Sent: Friday, September 09, 2016 9:51 AM > To: nek5000-users(a)lists.mcs.anl.gov > Subject: [Nek5000-users] Time of restart > > Dear Nek users, > > I?m using the restart option in *.rea. > How can I force the restart time to 0, instead of the time in restarting file. > The file to restart has format of *.f0000 > > Thank you, > Peng > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mail… > > ------------------------------ > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users(a)lists.mcs.anl.gov > https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mail… > > > End of Nek5000-users Digest, Vol 91, Issue 8 > ********************************************

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Time of restart
by nek5000-users＠lists.mcs.anl.gov 09 Sep '16

09 Sep '16

Dear Nek users, I’m using the restart option in *.rea. How can I force the restart time to 0, instead of the time in restarting file. The file to restart has format of *.f0000 Thank you, Peng

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Tools Compilation Error
by nek5000-users＠lists.mcs.anl.gov 08 Sep '16

08 Sep '16

Hi All, Just thought I'd let everyone know (I assume this has been seen) that in the latest GIT or SVN version, the tools compilation fails when the maketools script gets to postnek, and the reference to the file blas.f cannot be found; need to change the reference in the postnek makefile from "../nek/.." to "../core/.." Thanks, Murph

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constant average velocity at inlet with periodic boundary conditions
by nek5000-users＠lists.mcs.anl.gov 06 Sep '16

06 Sep '16

Dear nek users, I am simulating the flow in a 7 pin bundle mesh with periodic boundary conditions in Nek5000 and set the parameters p054 and p055 to -3 and 1, respectively. With these settings, the average velocity should be 1 in the geometry. This is however not what I am seeing; the maximum velocity is around 0.32. I used the same set up for a 3-D pipe and the numerical solution behaves as expected. Does anybody has details on how the fix mass flow rate/volumetric velocity are enforced in Nek5000? Thanks, Marco

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ERROR: Error reading restart header. Abort. ierr= 2 call exitt: dying ...
by nek5000-users＠lists.mcs.anl.gov 02 Sep '16

02 Sep '16

Hello all, I have been getting this error message for my RESTART calculations, however using the same kind of .rea file in a different calculation (different mesh) seems to work. Any help is appreciated. .rea file is attached. I had to zip it because it exceeds the file upload size limitation. Thanks, Saikat. *Saikat Mukherjee,* *Graduate** Student,* *Engineering Science and Mechanics,* *BEAM,* *Virginia Tech.*

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problem with pressure calculation
by nek5000-users＠lists.mcs.anl.gov 02 Sep '16

02 Sep '16

Hi Neks, I'm having a problem with the computation of my pressure. I am simulating a flow past an airfoil. I'm using user defined velocity bounday condition at the inlet (set as 'v'), and zero gradient at the outlet. I implemented a von Karman isotropic turbulence model at the inlet of my domain, on which I impose in the userbc U+u', v' and w'(flow in x direction). The model gives correct description of the perturbation , spatially and in time. With constant velocity the problem works fine, but when I add the fluctuation, the local pressure becomes randomed and jump from a value to another with no correlation at all. The velocities look just fine in all cases. I tried to use call dsavg(u) to ensure I am C0-continuous, but it didn't work i.e. I guess I am already, and since I use only one random number to generate my von Karman spectra, there is no reason not to be, at least spatially. I have more doubts about my time correlation, where I use a basic asymmetric time filter that seems to induce quite random behavior near low amplitudes fluctuations. Some time ago, I also had the same problem by setting a random noise at the inlet. I also tried to tighten the convergence by decreasing p21(10e-8,10e-9, 10e-10..) in the rea but it have no effect at all. I also checked my model with flow past a flat plate and it gives similar problem. after calling the subroutine in usechk, I just add the fluctuation writing ux=U+utm(ix,iy,iz,e), uy= .... in userbc Any comments will be very much appreciated and thank you in advance. Antoine PS: Below is my parameters in the rea file, and a part of the userbc in case there is something I missed... ****** PARAMETERS ***** 2.6099999 NEKTON VERSION 3 DIMENSIONAL RUN 118 PARAMETERS FOLLOW 1.0000 p001 DENSITY 0.000001 p002 VISCOS 0.00000 p003 0.00000 p004 0.00000 p005 0.00000 p006 1.00000 p007 RHOCP 1.00000 p008 CONDUCT 0.00000 p009 000000.00000 p010 FINTIME 0100.000 p011 NSTEPS 2500.00000 p012 DT 0.00000 p013 IOCOMM 00000.00000 p014 IOTIME 00000025.00 p015 IOSTEP 0.00000 p016 PSSOLVER: 0=default 0.00000 p017 0.500000 p018 GRID < 0 --> # cells on screen -1.00000 p019 INTYPE 10.0000 p020 NORDER 0.100000E-08 p021 DIVERGENCE 0.100000E-07 p022 HELMHOLTZ 0.00000 p023 NPSCAL 0.100000E-01 p024 TOLREL 0.100000E-01 p025 TOLABS 0.600000 p026 COURANT/NTAU 3.00000 p027 TORDER 0.00000 p028 TORDER: mesh velocity (0: p28=p27) 0.00000 p029 = magnetic visc if > 0, = -1/Rm if < 0 0.00000 p030 > 0 ==> properties set in uservp() 0.00000 p031 NPERT: #perturbation modes 0.00000 p032 #BCs in re2 file, if > 0 0.00000 p033 0.00000 p034 0.00000 p035 0.00000 p036 0.00000 p037 0.00000 p038 0.00000 p039 0.00000 p040 0.00000 p041 1-->multiplicative SEMG 0.00000 p042 0=gmres/1=pcg 1.00000 p043 0=semg/1=schwarz 0.00000 p044 0=E-based/1=A-based prec. 0.00000 p045 Relaxation factor for DTFS 0.00000 p046 reserved 0.00000 p047 vnu: mesh matieral prop. 0.00000 p048 0.00000 p049 0.00000 p050 0.00000 p051 0.00000 p052 IOHIS 0.00000 p053 0.00000 p054 fixed flow rate dir: |p54|=1,2,3=x,y,z 0.00000 p055 vol.flow rate (p54>0) or Ubar (p54<0) 0.00000 p056 0.00000 p057 0.00000 p058 0.00000 p059 !=0 --> full Jac. eval. for each el. 0.00000 p060 !=0 --> init. velocity to small nonzero 0.00000 p061 0.00000 p062 >0 --> force byte_swap for output 0.00000 p063 =8 --> force 8-byte output 0.00000 p064 =1 --> perturbation restart 0.00000 p065 #iofiles (eg, 0 or 64); <0 --> sep. dirs 6.00000 p066 output : <0=ascii, else binary 6.00000 p067 restart: <0=ascii, else binary 0.00000 p068 iastep: freq for avg_all (0=iostep) 0.00000 p069 0.00000 p070 0.00000 p071 0.00000 p072 0.00000 p073 0.00000 p074 verbose Helmholtz 0.00000 p075 0.00000 p076 0.00000 p077 0.00000 p078 0.00000 p079 0.00000 p080 0.00000 p081 0.00000 p082 0.00000 p083 0.00000 p084 !=0 --> sets initial timestep if p12>0 0.00000 p085 dt ratio if p84 !=0, for timesteps>0 0.00000 p086 reserved 0.00000 p087 0.00000 p088 0.00000 p089 p89 reserved 0.00000 p090 0.00000 p091 0.00000 p092 20.0000 p093 Number of previous pressure solns saved 5.00000 p094 start projecting velocity after p94 step 5.00000 p095 start projecting pressure after p95 step 1.00000 p096 p96 u0 translational velocity (in 0.300000 p097 p97 v0 translational velocity (i 0.00000 p098 3.00000 p099 dealiasing: <0--> off/3--> old/4--> new 0.00000 p100 0.00000 p101 Number of additional modes to filter 0.00000 p102 Dump out divergence at each time step 0.00000 p103 weight of stabilizing filter (.01) 0.00000 p104 0.00000 p105 0.00000 p106 0.00000 p107 !=0 --> add to h2 array in hlmhotz eqn 0.00000 p108 0.00000 p109 0.00000 p110 0.00000 p111 0.00000 p112 0.00000 p113 0.00000 p114 0.00000 p115 0.00000 p116 !=0: x elements for fast tensor product 0.00000 p117 !=0: y elements for fast tensor product 0.00000 p118 !=0: z elements for fast tensor product 4 Lines of passive scalar data follows2 CONDUCT; 2RHOCP 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000 13 LOGICAL SWITCHES FOLLOW T IFFLOW F IFHEAT T IFTRAN T F F F F F F F F F F IFNAV & IFADVC (convection in P.S. fields) F F T T T T T T T T T T IFTMSH (IF mesh for this field is T mesh) F IFAXIS F IFSTRS F IFSPLIT F IFMGRID F IFMODEL F IFKEPS F IFMVBD F IFCHAR ---------------------------------- subroutine userbc (ix,iy,iz,iside,eg) include 'SIZE' include 'TOTAL' include 'NEKUSE' integer e,eg common /myturb/ utm(lx1,ly1,lz1,lelt),vtm(lx1,ly1,lz1,lelt), ! my fluctuations $ wtm(lx1,ly1,lz1,lelt) e=gllel(eg) ... uy=vtm(ix,iy,iz,e) ux =1.0+utm(ix,iy,iz,e) uz=wtm(ix,iy,iz,e) ...

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Suggestion about choice of Example
by nek5000-users＠lists.mcs.anl.gov 02 Sep '16

02 Sep '16

Hello Neks, I am looking for some suggestions about the choice of example for my model. I want to study the flow around a 3-D bluff body in a wind tunnel set-up to calculate its drag and yawing moment (only velocity field no heat transfer/) so as to compare it with my previous study in which I used RANS SST model in CFX. Being quite new with the NEK code I need some help and useful suggestions. Thanks in advance. Shivang Aggarwal

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Failed in Helmholtz error
by nek5000-users＠lists.mcs.anl.gov 31 Aug '16

31 Aug '16

Hi! nek, I met the 'failed in Helmholtz' error when I was running the example case vortex breakdown in the file 'examples/vortex'. However I still got the .fld results of which the whole velocity field was static. Obviously the results were uncorrect. Do anyone know how to deal with it? Any help is appreciated. -- Xu Bolun, University of Science and Techonology of China, Hefei,Anhui,China

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