[Nek5000-users] simulation termination at istep=0 with NaN
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Wed Jul 26 12:38:17 CDT 2017
I guess something is wrong with your mesh. Can you post a full log file. Please note that mshconvert is a 3rd party tool.
> On 26 Jul 2017, at 19:26, "nek5000-users at lists.mcs.anl.gov" <nek5000-users at lists.mcs.anl.gov> wrote:
>
> Hi NEKs,
>
> I just started working on NEK5000 and am having trouble with my first real simulation (tried both PN/PN and PN/PN-2). I first created a .msh file of simple cylindrical geometry, with velocity-inlet (v), Outlet (O) and surrounding walls (W), in ICEM and used "mshconvert" to get a .rea file. In NEK, the simulation is dying before they actually begin. The error message is as follows:
>
> *************************************************************************
> *************************************************************************
> Matrix: 0 aa 4 4 4
> 0 aa Infinity -4.08542E+02 7.41342E+01 0.00000E+00
> 0 aa -4.08542E+02 4.65569E+02 -1.31161E+02 0.00000E+00
> .
> .
> Matrix: 0 Aeig 4 4 4
> 0 Aeig NaN NaN NaN NaN
> 0 Aeig NaN NaN NaN NaN
> 0 Aeig NaN NaN NaN NaN
> 0 Aeig NaN NaN NaN NaN
> .
> .
> Matrix: 0 Deig 1 4 4
> 0 Deig NaN NaN NaN NaN
> Error in generalev, info= 3 4 1
> Error in generalev, info= 3 4 1
> Error in generalev, info= 3 4 1
> Error in generalev, info= 3 4 1
> Error in generalev, info= 3 4 1
> Error in generalev, info= 3 4 1
> Error in generalev, info= 3 4 1
>
> call exitt: dying ...
> *************************************************************************
> *************************************************************************
>
> I saw an older post regarding a similar problem and that was due to improper boundary conditions. I suspect I may be doing something similar but couldn't find anything until now. The .msh file is fine as I was able to import to "fluent" and run the simulation. Please let me know if you can help in some way. I am posting input files below (please pardon the length of this message):
>
> ************** FROM .rea FILE*********************
> 0 objects found
> 103 Parameters from file:
> 1 1.00000 p1 DENSITY
> 2 -500.000 p2 VISCOS
> 7 1.00000 p7 RHOCP
> 8 1.00000 p8 CONDUCT
> 11 10000 p11 NSTEPS
> 12 0.10000E-05 p12 DT
> 15 5 p15 IOSTEP
> 18 -20.00000 p18 GRID
> 19 -1.00000 p19 INTYPE
> 20 10.0000 p20 NORDER
> 26 1.00000 p26 COURANT/NTAU
> 27 2.00000 p27 TORDER
> 65 1.00000 p65 #iofiles (eg, 0 or 64); <0 --> sep. dirs
> 66 4.00000 p66 output : <0=ascii, else binary
> 67 4.00000 p67 restart: <0=ascii, else binary
> 93 20.0000 p93 Number of previous pressure solns saved
> 94 3.00000 p94 start projecting velocity after p94 step
> 95 5.00000 p95 start projecting pressure after p95 step
> 99 0. p99 dealiasing: <0--> off/3--> old/4--> new
> 102 1.00000 p102 Dump out divergence at each time step
> 103 -1.00000 p103 weight of stabilizing filter (.01)
>
> 13 LOGICAL SWITCHES FOLLOW
> T IFFLOW
> T 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
> .
> .
> **MESH DATA**
> 22620 3 22620 NEL,NDIM,NELV
> ELEMENT 1 [ 1 ] GROUP 0
> 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
> -7.07106729e-01 -6.82106736e-01 -5.66056759e-01 -5.87769989e-01
> 7.07106833e-01 6.82106832e-01 7.76064003e-01 8.08965813e-01
> 1.02564103e+00 1.02564103e+00 1.02564103e+00 1.02564103e+00
> -7.07106715e-01 -6.82106722e-01 -5.65372395e-01 -5.87023410e-01
> 7.07106818e-01 6.82106817e-01 7.75121255e-01 8.07937362e-01
> ELEMENT 2 [ 1 ] GROUP 0
> 1.02564103e+00 1.02564103e+00 1.02564103e+00 1.02564103e+00
> -6.82106722e-01 -5.65372395e-01 -5.43721379e-01 -6.57106729e-01
> 6.82106817e-01 7.75121255e-01 7.42305149e-01 6.57106816e-01
> 0.00000000e+00 0.00000000e+00 0.00000000e+00 0.00000000e+00
> -6.82106736e-01 -5.66056759e-01 -5.44343529e-01 -6.57106742e-01
> 6.82106832e-01 7.76064003e-01 7.43162193e-01 6.57106831e-01
> .
> .
> ***** FLUID BOUNDARY CONDITIONS *****
> E 1 1 1.4149000e+04 1.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00
> E 1 2 2.0000000e+00 1.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00
> E 1 3 1.3000000e+01 1.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00
> W 1 4 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00
> v 1 5 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00
> .
> O 22620 6 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00
> **************************************************************
>
> ************** .usr FILE**************
> c All my user functions are empty except userbc to deal with the "v" condition
>
> subroutine userbc (ix,iy,iz,iside,ieg)
> include 'SIZE'
> include 'TSTEP'
> include 'INPUT'
> include 'NEKUSE'
>
> ux=0.005
> uy=0.0
> uz=0.0
>
> return
> end
> ****************************************
>
> ***********************FIRST FEW LINES OF .map FILE***********
> 22620 24040 14 16384 180960 24040 0
> 3597 14 4574 4561 4560 4562 4575 5164 5162
> 3596 4575 5162 4581 5160 4574 4560 4580 4579
> 3601 4581 5160 4572 5158 4580 4579 4571 4566
> 3603 4572 5158 4570 5182 4571 4566 4569 5181
> 3607 4570 5182 4693 5178 4569 5181 4692 5177
> 3681 4693 5178 4645 5176 4692 5177 4644 5175
> 3683 4645 5176 4649 5174 4644 5175 4648 5173
> 3691 4649 5174 5277 5276 4648 5173 5275 5274
> 3107 5277 5276 4035 4020 5275 5274 4034 4019
> 3106 4035 4020 4033 4026 4034 4019 4032 4024
> 3119 4033 4026 4025 4277 4032 4024 4023 4276
> 3119 4025 4277 4055 4273 4023 4276 4022 4272
> 3599 5164 4561 5172 5171 5162 4560 5170 5169
> ******************************************************************************
>
> Thanks,
> Ajay
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