[Nek5000-users] Connectivety

Sat Dec 11 12:51:35 CST 2010

Hi Stefan, 

Do you recall the repo at which point this started to be the case? We have a similar code to convert gambit files and a majority of the time is spent getting this connectivity information. If we don't need it then that is welcomed news! 

- Michael M. 

----- Original Message ----- 
From: nek5000-users at lists.mcs.anl.gov 
To: nek5000-users at lists.mcs.anl.gov 
Sent: Friday, December 10, 2010 4:11:26 AM GMT -06:00 US/Canada Central 
Subject: Re: [Nek5000-users] Connectivety 

Antonois: 

I understand your confusion. Let me backup a little bit. 

Genmap will try to establish a unique global numbering for all element vertices. Basically, genmap tries to detect (based on the vertex coordinates) the shared vertices and will assign a global id. We compute what you call the connectivity information on the fly (during the setup phase of Nek) based on the global vertex ids read from the .map file. 

You're right the old ASCII .rea file contains the elemental connectivity but this information is no longer used (we do a formatted dummy read for these lines). The .re2 file does not contain this information anymore. 

hth, 
Stefan 

----- Original Message ----- 
From: nek5000-users at lists.mcs.anl.gov 
To: nek5000-users at lists.mcs.anl.gov 
Sent: Friday, December 10, 2010 10:10:16 AM 
Subject: Re: [Nek5000-users] Connectivety 

Thank you for the responses. 
However maybe my question I was clear before. I try again: Ok, the 
connectivity information comes from the rea file when you run genmap, 
but is it computed based on the spatial coordinates given in the rea 
file, or is it just taken from the connectivity information given later, 
also in the rea file along with the boundary conditions? 

What we experience is that we have a grid which is created in Matlab and 
then we write it in "rea file format" which is later read by genmap and 
reatore2 etc. This rea file, after the spatial coordinates of the 
element corners, contains a list with all the elements and their 
connectivity information. 
Here is what two lines looks like: 

W 4 1 0.000000 0.000000 0.000000 0.000000 0.000000 
E 4 2 5.000000 4.000000 0.000000 0.000000 0.000000 

Here I specify Wall condition for element 4 and face 1 and Element 
condition for face 2 that connects to element 5 with face 4. 
But then when I removed my connectivity info, that is having every where 
zeros in the 4th and 5th column: 

W 4 1 0.000000 0.000000 0.000000 0.000000 0.000000 
E 4 2 0.000000 0.000000 0.000000 0.000000 0.000000 

the case seemed to run fine, and the flow looked correct. 
Does this mean that the connectivity specified there does not matter? 

Best, 
/Antonios 

nek5000-users at lists.mcs.anl.gov wrote: 
> This is correct. 
> -Stefan 
> 
> ----- Original Message ----- 
> From: nek5000-users at lists.mcs.anl.gov 
> To: nek5000-users at lists.mcs.anl.gov 
> Sent: Thursday, December 9, 2010 6:15:02 PM 
> Subject: Re: [Nek5000-users] Connectivety 
> 
> Hi Antonios, 
> 
> I could be wrong but I think that the only connectivity information that 
> Nek5000 need comes from global vertexi element numbering genereated by 
> .map file which is in turn produced by running genmap on .rea file 
> 
> Best, 
> Aleks 
> 
> 
> On Thu, 9 Dec 2010, nek5000-users at lists.mcs.anl.gov wrote: 
> 
>> Hello Paul, 
>> I have a question about the connectivity of the elements. 
>> In the old rea file format (which we convert to the new binary with 
>> reatore2) we have listed the Element geometrical date and after that the 
>> Boundary conditions and connectivity data. 
>> My question is whether the connectivity of the elements stated there is 
>> actually used or it is somehow re-computed while the code runs based on 
>> the node coordinates. I am talking specifically about the connectivity 
>> between the elements, not the boundary conditions with the "outside world". 
>> Best regards, 
>> Antonios 
>> 
>> -- 
>> --------------------------------------------------------------------------------------------- 
>> Antonios Monokrousos 
>> Department of Mechanics email: antonios at mech.kth.se 
>> Royal Institute of Technology (KTH) phone: +46 8 790 68 76 
>> Osquars Backe 18 telefax: +46 8 796 98 50 
>> SE-100 44 Stockholm, SWEDEN 
>> _______________________________________________ 
>> Nek5000-users mailing list 
>> Nek5000-users at lists.mcs.anl.gov 
>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users 
>> 
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-- 
--------------------------------------------------------------------------------------------- 
Antonios Monokrousos 
Department of Mechanics email: antonios at mech.kth.se 
Royal Institute of Technology (KTH) phone: +46 8 790 68 76 
Osquars Backe 18 telefax: +46 8 796 98 50 
SE-100 44 Stockholm, SWEDEN 
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