[Nek5000-users] linear stability tool
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Wed Mar 30 07:25:26 CDT 2016
Hi Adam,
Thanks for your response. Here is what I understand the steps I should
follow to run the 'ext_cyl' example, from
https://nek5000.mcs.anl.gov/toolboxes/:
Base flow run: Compile with the following parameter setting:
p031 = 0
p069 = 0
and I think I should also set p108 = 0 (without setting p108 = 0, I get an
error saying "ERROR: arnoldi has to be run in perturbation mode")
Hence, I do a base flow run with p031=0, p069=0 and p108 = 0. Am I correct
here?
If I do the base flow run with p031=0, p069=0 and p108 = 0, I see lot of
error in ext_cyl.log file as:
Step 1826, t= 9.1300000E+00, DT= 5.0000000E-03, C= 0.000 3.5844E+02
1.9493E-01
Solving for fluid F T T
1826 100 **ERROR**: Failed in HMHOLTZ: VELX NaN NaN
1.0000E-10
1826 100 **ERROR**: Failed in HMHOLTZ: VELY NaN NaN
1.0000E-10
Nevertheless, I do see a file 'ext_cyl0.f00001' written after some
simulation time, however, I do not see the restart files,
'ARVext_cy0.f00001' and 'ARPext_cy0.f00001', written at the same time. I
will continue to run the base flow simulation for longer duration, in the
meantime, I wanted to confirm if I am on the right path so far?
Regards,
Ravi
On Wed, Mar 30, 2016 at 6:52 AM, <nek5000-users at lists.mcs.anl.gov> wrote:
> 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/>
> 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> 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 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
>>> _______________________________________________
>>> Nek5000-users mailing list
>>> Nek5000-users at lists.mcs.anl.gov
>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>>>
>>
>> _______________________________________________
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>>
>
>
>
> --
> Ravi Kumar R. Tumkur, PhD.
> Phone: 217 778 7538
>
>
> _______________________________________________
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>
>
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>
--
Ravi Kumar R. Tumkur, PhD.
Phone: 217 778 7538
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