[Nek5000-users] Periodic BC & Genmap issue

Tue Jun 22 10:44:59 CDT 2010

Hi, 

Yes, got it now. I don't know why it wasn't working either. I use the same thing to compress files, either way it's good now. Thanks Paul. 

- Michael 

----- Original Message ----- 
From: nek5000-users at lists.mcs.anl.gov 
To: nek5000-users at lists.mcs.anl.gov 
Sent: Tuesday, June 22, 2010 10:40:57 AM GMT -06:00 Guadalajara / Mexico City / Monterrey 
Subject: Re: [Nek5000-users] Periodic BC & Genmap issue 

Hi Michael, 

not sure why gunzip didn't work - it worked here... but I've 
put the unzipped version in: 

www.mcs.anl.gov/~fischer/genmap.f 

Let me know if that works for you. 

Cheers, 

Paul 

On Tue, 22 Jun 2010, nek5000-users at lists.mcs.anl.gov wrote: 

> Paul, 
> 
> Yes I tried gzip and gunzip but it is telling me that it is not in a zipped format: 
> 
> gunzip genmap.f.gz 
> gzip: genmap.f.gz: not in gzip format 
> 
> What do you mean by locale? 
> 
> 
> ----- Original Message ----- 
> From: nek5000-users at lists.mcs.anl.gov 
> To: nek5000-users at lists.mcs.anl.gov 
> Sent: Tuesday, June 22, 2010 10:24:24 AM GMT -06:00 Guadalajara / Mexico City / Monterrey 
> Subject: Re: [Nek5000-users] Periodic BC & Genmap issue 
> 
> 
> did you 
> 
> gunzip genmap.f.gz 
> 
> ? 
> 
> 
> On Tue, 22 Jun 2010, nek5000-users at lists.mcs.anl.gov wrote: 
> 
>> Paul, 
>> 
>> I am having trouble accessing the zipped file, when I try to decompress it tells me that it is not in gzip format. Perhaps try again, or another format? 
>> 
>> - Michael 
>> 
>> ----- Original Message ----- 
>> From: nek5000-users at lists.mcs.anl.gov 
>> To: "Nekton User List" <nek5000-users at lists.mcs.anl.gov> 
>> Sent: Tuesday, June 22, 2010 1:47:35 AM GMT -06:00 Guadalajara / Mexico City / Monterrey 
>> Subject: Re: [Nek5000-users] Periodic BC & Genmap issue 
>> 
>> 
>> Hi Michael, 
>> 
>> It looks like the issue is related to the mesh and to tolerances. 
>> It appears to me that the periodic faces are not congruent - nearly 
>> so, but not 100%. 
>> 
>> I've changed my version of genmap to make the tolerance in the 
>> periodicity check reflect the user-prompted value. I'm not yet 
>> commiting this to the repo because I need to think more about the 
>> consequences. However, the attached code does work when you input 
>> ".1" for the tolerance prompt - and it flags an error when you put 
>> in .01 or smaller. Try diff'g this against your current version 
>> to see the change. 
>> 
>> Paul 
>> 
>> PS - rather than attaching, I'm placing in 
>> www.mcs.anl.gov/~fischer/genmap.f.gz 
>> 
>> 
>> On Mon, 21 Jun 2010, nek5000-users at lists.mcs.anl.gov wrote: 
>> 
>>> Hi, 
>>> 
>>> I am running into an error when trying to use genmap. I believe it has to do with the periodic boundary conditions I have set up. I have checked the elements, and faces and indeed they are given correctly. This leads me to believe that there may be an issue with genmap. I have attached the rea file. This was to test the periodic faces for this geometry. The output is shown below, thanks for any help with this. 
>>> 
>>> - Michael M. 
>>> 
>>> Here is the output: 
>>> 
>>> test 
>>> Input mesh tolerance (default 0.2): 
>>> NOTE: smaller is better, but generous is more forgiving for bad meshes. 
>>> .2 
>>> reading .rea file data ... 
>>> start locglob_lexico: 8 60 480 0.20000000000000001 
>>> locglob: 1 1 480 
>>> locglob: 2 27 480 
>>> locglob: 3 42 480 
>>> locglob: 1 168 480 
>>> locglob: 2 168 480 
>>> locglob: 3 168 480 
>>> locglob: 1 168 480 
>>> locglob: 2 168 480 
>>> locglob: 3 168 480 
>>> done locglob_lexico: 168 168 480 4 
>>> start periodic vtx: 60 168 
>>> 1 3 5 3 3.66325334E-04 1 shift 
>>> 3 4 4 Matrix: x0 
>>> 1 x0 1.7389E-03 2.8363E-03 2.8363E-03 1.7389E-03 
>>> 2 x0 -6.9998E-02 7.0969E-02 6.9026E-02 -6.9998E-02 
>>> 3 x0 2.0879E-02 2.0879E-02 -2.0937E-02 -2.0821E-02 
>>> 4 x0 8.3935E-03 8.0685E-03 -2.4856E-02 8.3935E-03 
>>> 1 4 4 Matrix: x1 
>>> 1 x1 1.7389E-03 1.7389E-03 2.8351E-03 2.8351E-03 
>>> 2 x1 -7.0107E-02 -7.0107E-02 6.8930E-02 7.1286E-02 
>>> 3 x1 2.0876E-02 -2.0824E-02 -2.0927E-02 2.0876E-02 
>>> 4 x1 8.3867E-03 8.3867E-03 -2.4834E-02 8.0608E-03 
>>> 3 4 4 Matrix: z0 
>>> 1 z0 1.7389E-03 2.8363E-03 2.8363E-03 1.7389E-03 
>>> 2 z0 -1.2500E+00 -1.1090E+00 -1.1110E+00 -1.2500E+00 
>>> 3 z0 0.0000E+00 0.0000E+00 -4.1816E-02 -4.1700E-02 
>>> 4 z0 -5.0620E-01 -5.0653E-01 -5.3945E-01 -5.0620E-01 
>>> 1 4 4 Matrix: z1 
>>> 1 z1 1.7389E-03 1.7389E-03 2.8351E-03 2.8351E-03 
>>> 2 z1 -1.2500E+00 -1.2500E+00 -1.1110E+00 -1.1086E+00 
>>> 3 z1 0.0000E+00 -4.1700E-02 -4.1803E-02 0.0000E+00 
>>> 4 z1 4.9380E-01 4.9380E-01 4.6058E-01 4.9347E-01 
>>> 3 4 3 1.00000000E-03 7.09692500E-02 abort: FACE MATCH FAIL 
>>> 1 3 5 7.09692500E-05 3.66325334E-04 abort: FACE MATCH FAIL 
>>> 
>>> 
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