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<div class="moz-cite-prefix">Hi<br>
<br>
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:<br>
parameter (lpelv=lelv,lpelt=lelt,lpert=1) ! perturbation<br>
parameter (lpx1=lx1,lpy1=ly1,lpz1=lz1) ! array sizes<br>
parameter (lpx2=lx2,lpy2=ly2,lpz2=lz2)<br>
<br>
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.<br>
1 PRESOLVE/RESTART OPTIONS *****<br>
baseflow.bsf<br>
7 INITIAL CONDITIONS *****<br>
<br>
Setting p108 = 0 you simply turn off Arnoldi, so only dns is
performed.<br>
Regards<br>
Adam<br>
<br>
<br>
On 2016-03-30 14:25, <a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a> wrote:<br>
</div>
<blockquote
cite="mid:mailman.18472.1459340753.24727.nek5000-users@lists.mcs.anl.gov"
type="cite">
<div dir="ltr">
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<div>
<div>Hi Adam, <br>
<br>
</div>
Thanks for your response. Here is what I
understand the steps I should follow to run the
'ext_cyl' example, from <a
moz-do-not-send="true"
href="https://nek5000.mcs.anl.gov/toolboxes/"
target="_blank"><a class="moz-txt-link-freetext" href="https://nek5000.mcs.anl.gov/toolboxes/">https://nek5000.mcs.anl.gov/toolboxes/</a></a>:<br>
<br>
</div>
Base flow run: Compile with the following
parameter setting:<br>
</div>
<br>
p031 = 0<br>
</div>
p069 = 0<br>
<br>
</div>
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")<br>
<br>
</div>
Hence, I do a base flow run with p031=0, p069=0 and p108 =
0. Am I correct here?<br>
<br>
</div>
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:<br>
<br>
Step 1826, t= 9.1300000E+00, DT= 5.0000000E-03, C= 0.000
3.5844E+02 1.9493E-01<br>
Solving for fluid F T T<br>
1826 100 **ERROR**: Failed in HMHOLTZ: VELX
NaN NaN 1.0000E-10<br>
1826 100 **ERROR**: Failed in HMHOLTZ: VELY
NaN NaN 1.0000E-10<br>
<br>
</div>
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?<br>
<br>
</div>
<div>Regards, <br>
</div>
<div>Ravi<br>
<br>
</div>
<br>
<div>
<div>
<div>
<div>
<div>
<div>
<div><br>
</div>
</div>
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<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Mar 30, 2016 at 6:52 AM, <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank">nek5000-users@lists.mcs.anl.gov</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div>Hi Ravi<br>
<br>
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.<br>
Regards<br>
Adam
<div>
<div class="h5"><br>
<br>
On 2016-03-27 04:45, <a moz-do-not-send="true"
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank">nek5000-users@lists.mcs.anl.gov</a>
wrote:<br>
</div>
</div>
</div>
<div>
<div class="h5">
<blockquote type="cite">
<div dir="ltr">
<div>
<div>
<div>
<div>Hi Adam, <br>
<br>
</div>
I am guessing I am using your code for
stability tools in NEK. I have downloaded
the code from <a moz-do-not-send="true"
href="https://nek5000.mcs.anl.gov/toolboxes/"
target="_blank">https://nek5000.mcs.anl.gov/toolboxes/</a>.<br>
<br>
</div>
I am trying to reproduce the ext_cyl example,
as is, to get some familiarity. <br>
<br>
</div>
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:<br>
<br>
<br>
******************************************************************************************************************<br>
call userchk<br>
ARNOLDI:<br>
Reading checkpoint<br>
0 0 OPEN: ARPext_cyl0.f00005<br>
ARPext_cyl0.f00005<br>
byte_read() :: fopen failure2!<br>
ERROR: mfi_arnp, wrong header; abort.<br>
<br>
call exitt: dying ...<br>
******************************************************************************************************************<br>
</div>
<br>
<div><br>
<div>I have also pasted below the parameters
printed in the log file for your reference. <br>
</div>
<div><br>
******************************************************************************************************************<br>
</div>
122 Parameters from <a moz-do-not-send="true">file:/global/u2/r/rtumkur/eig_Setup/ARNOLDI/ext_cyl.rea</a><br>
1 1.00000 p001 DENSITY<br>
2 -50.0000 p002 VISCOS<br>
7 1.00000 p007 RHOCP<br>
8 1.00000 p008 CONDUCT<br>
11 50003.0 p011 NSTEPS<br>
12 -5.000000E-03 p012 DT<br>
15 2500.00 p015 IOSTEP<br>
17 1.00000 p017<br>
18 0.500000E-01 p018 GRID < 0 --> #
cells on screen<br>
19 -1.00000 p019 INTYPE<br>
20 7.00000 p020 NORDER<br>
21 0.100000E-09 p021 DIVERGENCE<br>
22 0.100000E-09 p022 HELMHOLTZ<br>
24 0.100000E-09 p024 TOLREL<br>
25 0.100000E-04 p025 TOLABS<br>
26 1.00000 p026 COURANT/NTAU<br>
27 3.00000 p027 TORDER<br>
28 0.00000 p028 TORDER: mesh velocity
(0: p28=p27)<br>
31 -1.00000 p031 NPERT: #perturbation
modes<br>
59 0.00000 p059 !=0 --> full Jac.
eval. for each el.<br>
65 1.00000 p065 #iofiles (eg, 0 or
64); <0 --> sep. dirs<br>
66 4.00000 p066 output : <0=ascii,
else binary<br>
67 4.00000 p067 restart: <0=ascii,
else binary<br>
69 1.00000 p069 : PROPER RESTART: 0 -
do not use my_full_restart; 1- use it<br>
71 5.00000 p071 : ARNOLDI: checkpoint
file number for restart (reading)<br>
72 6.00000 p072 : ARNOLDI: checkpoint
file number for saving data<br>
99 3.00000 p099 dealiasing:
<0--> off/3--> old/4--> new<br>
102 1.00000 p102 Dump out divergence
at each time step<br>
108 1.00000 p108 : ARNOLDI: 0 if no
arnoldi<br>
109 40.0000 p109 : ARNOLDI: frequency
of calling arn_solve<br>
110 4.00000 p110 : ARNOLDI: maximal
number of arnoldi cycles<br>
111 90.0000 p111 : ARNOLDI: size of
Krylov space<br>
112 30.0000 p112 : ARNOLDI: number of
eigenvectors<br>
113 1.00000E-06 p113 : ARNOLDI: arpack
tolerance<br>
119 1.00000 p119 : SPONGE STRENGTH<br>
120 25.0000 p120 : SPONGE TOTAL WIDTH<br>
121 3.00000 p121 : SPONGE DROP WIDTH
(INFLOW)<br>
122 5.00000 p122 : SPONGE RISE WIDTH
(OUTFLOW)<br>
******************************************************************************************************************<br>
<br>
</div>
<div>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.<br>
<br>
<br>
</div>
<div>Regards, <br>
</div>
<div>Ravi<br>
<br>
</div>
<div>
<div>
<div><br>
</div>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Mar 15, 2016 at
4:06 AM, <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a></a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">Hi<br>
<br>
To force base flow to be constant you have to
set negative param(31) in your ###.rea file.
Something like<br>
-1.00000 p031 NPERT: #perturbation
modes<br>
Of course you need the base flow as well. It
could be analytical one set in useric, or just
a field read during initialisation.<br>
Regards<br>
Adam
<div>
<div><br>
<br>
<br>
On 2016-03-15 08:49, <a
moz-do-not-send="true"
href="mailto:nek5000-users@lists.mcs.anl.gov"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:nek5000-users@lists.mcs.anl.gov">nek5000-users@lists.mcs.anl.gov</a></a>
wrote:<br>
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex"> Hi Neks,<br>
<br>
I'm trying to use the linear stability
tool of Nek5000.<br>
<br>
To start with, I am trying to run the
ext_cyl example. However, I have found
the following problem:<br>
<br>
ERROR: arnoldi assumes constant base
flow.<br>
<br>
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.<br>
<br>
What should I modify?<br>
<br>
Finally, I have also used a subroutine
defined in the .usr file that reads the
file containing the base flow. However,
the error persist...<br>
<br>
Could you help me, please?<br>
<br>
Cheers<br>
SL<br>
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-- <br>
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<div dir="ltr"><span style="font-family:arial
narrow,sans-serif"><font size="4">Ravi Kumar
R. Tumkur</font>,<b> </b><font size="4">PhD.</font><br>
Phone: <a moz-do-not-send="true"
value="+12177787538">217 778 7538</a></span></div>
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<div dir="ltr"><span style="font-family:arial
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778 7538</a></span></div>
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