[Nek5000-users] linear stability tool
nek5000-users at lists.mcs.anl.gov
nek5000-users at lists.mcs.anl.gov
Wed Mar 30 09:24:16 CDT 2016
Hi
No, not this way. First of all you have to setup linear simulation. For
this you need to modify SIZE to let all the perturbation variables to be
used. You should have following section setting correct array sizes:
parameter (lpelv=lelv,lpelt=lelt,lpert=1) ! perturbation
parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1) ! array sizes
parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2)
Next you have to set p031 = -1 to have evolution of the single
perturbation with constant base flow. Base flow has to be specified in
and ###.rea file as a restart option; e.g.
1 PRESOLVE/RESTART OPTIONS *****
baseflow.bsf
7 INITIAL CONDITIONS *****
Setting p108 = 0 you simply turn off Arnoldi, so only dns is performed.
Regards
Adam
On 2016-03-30 14:25, nek5000-users at lists.mcs.anl.gov wrote:
> 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
> <mailto: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
> <mailto: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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>
> --
> Ravi Kumar R. Tumkur,**PhD.
> Phone: 217 778 7538
>
>
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