[Nek5000-users] linear stability tool
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Wed Mar 30 05:52:28 CDT 2016
Hi Ravi
The first error means you have no restart files, which is obvious for
the first run. Restart files are (ARP### and ARV###) are generated at
the end of the run if the tolerance is not reached. You control it by
parameter 69 in ###.rea. Simply set it to 0 for the first run. In
addition parameters 71 and 72 set the checkpoint number for reading and
writing (to avoid overwriting). Number of files depends on the other
parameters and preprocessing flags used.
Regards
Adam
On 2016-03-27 04:45, nek5000-users at lists.mcs.anl.gov wrote:
> Hi Adam,
>
> I am guessing I am using your code for stability tools in NEK. I have
> downloaded the code from https://nek5000.mcs.anl.gov/toolboxes/.
>
> I am trying to reproduce the ext_cyl example, as is, to get some
> familiarity.
>
> I have been able to compile the code (after some modifications to
> compile on the platform I intent to run my analysis). I have the base
> flow file "ext_cyl0.f00005" in the simulation folder. When I run the
> ext_cyl, I get the following error:
>
>
> ******************************************************************************************************************
> call userchk
> ARNOLDI:
> Reading checkpoint
> 0 0 OPEN: ARPext_cyl0.f00005
> ARPext_cyl0.f00005
> byte_read() :: fopen failure2!
> ERROR: mfi_arnp, wrong header; abort.
>
> call exitt: dying ...
> ******************************************************************************************************************
>
>
> I have also pasted below the parameters printed in the log file for
> your reference.
>
> ******************************************************************************************************************
> 122 Parameters from
> file:/global/u2/r/rtumkur/eig_Setup/ARNOLDI/ext_cyl.rea
> 1 1.00000 p001 DENSITY
> 2 -50.0000 p002 VISCOS
> 7 1.00000 p007 RHOCP
> 8 1.00000 p008 CONDUCT
> 11 50003.0 p011 NSTEPS
> 12 -5.000000E-03 p012 DT
> 15 2500.00 p015 IOSTEP
> 17 1.00000 p017
> 18 0.500000E-01 p018 GRID < 0 --> # cells on screen
> 19 -1.00000 p019 INTYPE
> 20 7.00000 p020 NORDER
> 21 0.100000E-09 p021 DIVERGENCE
> 22 0.100000E-09 p022 HELMHOLTZ
> 24 0.100000E-09 p024 TOLREL
> 25 0.100000E-04 p025 TOLABS
> 26 1.00000 p026 COURANT/NTAU
> 27 3.00000 p027 TORDER
> 28 0.00000 p028 TORDER: mesh velocity (0: p28=p27)
> 31 -1.00000 p031 NPERT: #perturbation modes
> 59 0.00000 p059 !=0 --> full Jac. eval. for each el.
> 65 1.00000 p065 #iofiles (eg, 0 or 64); <0 --> sep. dirs
> 66 4.00000 p066 output : <0=ascii, else binary
> 67 4.00000 p067 restart: <0=ascii, else binary
> 69 1.00000 p069 : PROPER RESTART: 0 - do not use
> my_full_restart; 1- use it
> 71 5.00000 p071 : ARNOLDI: checkpoint file number for
> restart (reading)
> 72 6.00000 p072 : ARNOLDI: checkpoint file number for
> saving data
> 99 3.00000 p099 dealiasing: <0--> off/3--> old/4--> new
> 102 1.00000 p102 Dump out divergence at each time step
> 108 1.00000 p108 : ARNOLDI: 0 if no arnoldi
> 109 40.0000 p109 : ARNOLDI: frequency of calling arn_solve
> 110 4.00000 p110 : ARNOLDI: maximal number of arnoldi cycles
> 111 90.0000 p111 : ARNOLDI: size of Krylov space
> 112 30.0000 p112 : ARNOLDI: number of eigenvectors
> 113 1.00000E-06 p113 : ARNOLDI: arpack tolerance
> 119 1.00000 p119 : SPONGE STRENGTH
> 120 25.0000 p120 : SPONGE TOTAL WIDTH
> 121 3.00000 p121 : SPONGE DROP WIDTH (INFLOW)
> 122 5.00000 p122 : SPONGE RISE WIDTH (OUTFLOW)
> ******************************************************************************************************************
>
> I'd appreciate if you can let me what am I missing in the set up which
> might be leading to this issue? Please let me know if you need any
> other information to understand this issue.
>
>
> Regards,
> Ravi
>
>
>
> On Tue, Mar 15, 2016 at 4:06 AM, <nek5000-users at lists.mcs.anl.gov
> <mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
>
> Hi
>
> To force base flow to be constant you have to set negative
> param(31) in your ###.rea file. Something like
> -1.00000 p031 NPERT: #perturbation modes
> Of course you need the base flow as well. It could be analytical
> one set in useric, or just a field read during initialisation.
> Regards
> Adam
>
>
>
> On 2016-03-15 08:49, nek5000-users at lists.mcs.anl.gov
> <mailto:nek5000-users at lists.mcs.anl.gov> wrote:
>
> Hi Neks,
>
> I'm trying to use the linear stability tool of Nek5000.
>
> To start with, I am trying to run the ext_cyl example.
> However, I have found the following problem:
>
> ERROR: arnoldi assumes constant base flow.
>
> I have found on the README tutorial that the base flow has to
> be specified on the .rea file. I have included a file in the
> PRESOLVE/RESTART option, however I still have the same error.
>
> What should I modify?
>
> Finally, I have also used a subroutine defined in the .usr
> file that reads the file containing the base flow. However,
> the error persist...
>
> Could you help me, please?
>
> Cheers
> SL
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>
>
> --
> Ravi Kumar R. Tumkur,**PhD.
> Phone: 217 778 7538
>
>
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