[Nek5000-users] Nek5000-users Digest, Vol 104, Issue 15

nek5000-users at lists.mcs.anl.gov nek5000-users at lists.mcs.anl.gov
Wed Oct 18 09:44:46 CDT 2017


Hi Paul,

Even I used the 2d mesh in example directory with quad multi-split and
n2to3, there still some errors showing element mesh mismatch. I do think
things gonna changed since using genmap where there is always one or some
errors showing some elements were with shift. How can I do that?

......
......
......
 WARNING2 Element mesh mismatch at:
 I,J,K,IE:    8    7    8      175498
 Near Y =  0.42311775      0.79128327       18.648600    , d:
0.48220174E-01   0.0000000       1.2026574
 WARNING2 Element mesh mismatch at:
 I,J,K,IE:    1    8    8      175499
 Near Y =  0.40657800      0.75559000       18.648600    , d:  0.75191377
     0.0000000       1.3234691
 WARNING2 Element mesh mismatch at:
 I,J,K,IE:    2    8    8      175499
 Near Y =  0.41137682      0.75312483       18.648600    , d:   1.0321964
     0.0000000       1.3234691
 WARNING2 Element mesh mismatch at:
 I,J,K,IE:    8    8    8      175500
 Near Y =  0.40657800      0.75559000       18.648600    , d:  0.75191377
   -0.33306691E-15   1.2647709
 Mesh consistency check failed.  EXITING in VRDSMSH.

call exitt: dying ...

backtrace(): obtained 8 stack frames.
./nek5000() [0x6aee70]
./nek5000() [0x877e12]
./nek5000() [0x461c1a]
./nek5000() [0x4082d1]
./nek5000() [0x406e19]
./nek5000() [0x4034be]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7fe817d58c05]
./nek5000() [0x4033c9]


Regards,

ZJ

On 18 October 2017 at 13:42, <nek5000-users-request at lists.mcs.anl.gov>
wrote:

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> Today's Topics:
>
>    1. pipe prenek (nek5000-users at lists.mcs.anl.gov)
>    2. Re: pipe prenek (nek5000-users at lists.mcs.anl.gov)
>    3. Element mesh mismatch in pipe (nek5000-users at lists.mcs.anl.gov)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 18 Oct 2017 10:48:38 +0100
> From: nek5000-users at lists.mcs.anl.gov
> To: nek5000-users at lists.mcs.anl.gov
> Subject: [Nek5000-users] pipe prenek
> Message-ID:
>         <mailman.669.1508320120.19102.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Nek,
>
> Is there anyone knows how to calculate the curvature in .rea file.
> Recently, I want to generate a pipe mesh but it doesn't seem like a pipe in
> which I guess there is something wrong in curvature part in .rea file. I
> have attached the mesh part below.
>
>   **MESH DATA** 1st line is X of corner 1,2,3,4. 2nd line is Y.
>         12         2        12 NEL,NDIM,NELV
>       ELEMENT          1 [    1A]    GROUP     0
>    0.000000      0.350000       0.250000       0.000000
>    0.000000      0.000000       0.250000       0.350000
>       ELEMENT          2 [    1B]    GROUP     0
>    0.500000      0.353554       0.250000       0.350000
>    0.000000      0.353554       0.250000       0.000000
>       ELEMENT          3 [    1C]    GROUP     0
>    0.000000      0.000000       0.250000       0.353554
>    0.500000      0.350000       0.250000       0.353554
>       ELEMENT          4 [    1A]    GROUP     0
>    0.000000      0.000000       0.250000       0.350000
>    0.000000     -0.350000      -0.250000       0.000000
>       ELEMENT          5 [    1B]    GROUP     0
>    0.000000      0.353554       0.250000       0.000000
>   -0.500000     -0.353554      -0.250000      -0.350000
>       ELEMENT          6 [    1C]    GROUP     0
>    0.500000      0.350000       0.250000       0.353554
>    0.000000      0.000000      -0.250000      -0.353554
>       ELEMENT          7 [    1A]    GROUP     0
>    0.000000     -0.350000      -0.250000       0.000000
>    0.000000      0.000000      -0.250000      -0.350000
>       ELEMENT          8 [    1B]    GROUP     0
>   -0.500000     -0.353554      -0.250000      -0.350000
>    0.000000     -0.353554      -0.250000       0.000000
>       ELEMENT          9 [    1C]    GROUP     0
>    0.000000      0.000000      -0.250000      -0.353554
>   -0.500000     -0.350000      -0.250000      -0.353554
>       ELEMENT         10 [    1A]    GROUP     0
>    0.000000      0.000000      -0.250000      -0.350000
>    0.000000      0.350000       0.250000       0.000000
>       ELEMENT         11 [    1B]    GROUP     0
>    0.000000     -0.353554      -0.250000       0.000000
>    0.500000      0.353554       0.250000       0.350000
>       ELEMENT         12 [    1C]    GROUP     0
>   -0.500000     -0.350000      -0.250000      -0.353554
>    0.000000      0.000000       0.250000       0.353554
>   ***** CURVED SIDE DATA *****
>          8 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE
>   1  2  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   4  3  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   1  5  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   4  6  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   1  8  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   4  9  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   1 11  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   4 12  0.50000   0.00000       0.00000       0.00000       0.00000     C
>
>
> Kind regards,
>
> ZJ
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 2
> Date: Wed, 18 Oct 2017 12:18:45 +0000
> From: nek5000-users at lists.mcs.anl.gov
> To: "nek5000-users at lists.mcs.anl.gov"
>         <nek5000-users at lists.mcs.anl.gov>
> Subject: Re: [Nek5000-users] pipe prenek
> Message-ID:
>         <mailman.673.1508329131.19102.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Dear ZJ,
>
>
> In order to parse the characters in the line, nek uses formatted reads for
>
> curve sides and for BC info.
>
>
> The format changes as the number of elements increases in order to
> accommodate the larger integers (i.e., the element number) in the same line,
>
> so you have to check either the reader source or prenek source or a valid
>
> .rea file to see what that formatting looks like.
>
>
> I've fixed your pipe mesh here.  Note that there is a 2D pipe mesh (but
> with a different base template) in NekExamples/pipe/w2dcyl020a.rea
>
>
> Paul
>
>
> ________________________________
> From: Nek5000-users <nek5000-users-bounces at lists.mcs.anl.gov> on behalf
> of nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
> Sent: Wednesday, October 18, 2017 4:48:38 AM
> To: nek5000-users at lists.mcs.anl.gov
> Subject: [Nek5000-users] pipe prenek
>
> Hi Nek,
>
> Is there anyone knows how to calculate the curvature in .rea file.
> Recently, I want to generate a pipe mesh but it doesn't seem like a pipe in
> which I guess there is something wrong in curvature part in .rea file. I
> have attached the mesh part below.
>
>   **MESH DATA** 1st line is X of corner 1,2,3,4. 2nd line is Y.
>         12         2        12 NEL,NDIM,NELV
>       ELEMENT          1 [    1A]    GROUP     0
>    0.000000      0.350000       0.250000       0.000000
>    0.000000      0.000000       0.250000       0.350000
>       ELEMENT          2 [    1B]    GROUP     0
>    0.500000      0.353554       0.250000       0.350000
>    0.000000      0.353554       0.250000       0.000000
>       ELEMENT          3 [    1C]    GROUP     0
>    0.000000      0.000000       0.250000       0.353554
>    0.500000      0.350000       0.250000       0.353554
>       ELEMENT          4 [    1A]    GROUP     0
>    0.000000      0.000000       0.250000       0.350000
>    0.000000     -0.350000      -0.250000       0.000000
>       ELEMENT          5 [    1B]    GROUP     0
>    0.000000      0.353554       0.250000       0.000000
>   -0.500000     -0.353554      -0.250000      -0.350000
>       ELEMENT          6 [    1C]    GROUP     0
>    0.500000      0.350000       0.250000       0.353554
>    0.000000      0.000000      -0.250000      -0.353554
>       ELEMENT          7 [    1A]    GROUP     0
>    0.000000     -0.350000      -0.250000       0.000000
>    0.000000      0.000000      -0.250000      -0.350000
>       ELEMENT          8 [    1B]    GROUP     0
>   -0.500000     -0.353554      -0.250000      -0.350000
>    0.000000     -0.353554      -0.250000       0.000000
>       ELEMENT          9 [    1C]    GROUP     0
>    0.000000      0.000000      -0.250000      -0.353554
>   -0.500000     -0.350000      -0.250000      -0.353554
>       ELEMENT         10 [    1A]    GROUP     0
>    0.000000      0.000000      -0.250000      -0.350000
>    0.000000      0.350000       0.250000       0.000000
>       ELEMENT         11 [    1B]    GROUP     0
>    0.000000     -0.353554      -0.250000       0.000000
>    0.500000      0.353554       0.250000       0.350000
>       ELEMENT         12 [    1C]    GROUP     0
>   -0.500000     -0.350000      -0.250000      -0.353554
>    0.000000      0.000000       0.250000       0.353554
>   ***** CURVED SIDE DATA *****
>          8 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE
>   1  2  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   4  3  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   1  5  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   4  6  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   1  8  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   4  9  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   1 11  0.50000   0.00000       0.00000       0.00000       0.00000     C
>   4 12  0.50000   0.00000       0.00000       0.00000       0.00000     C
>
>
> Kind regards,
>
> ZJ
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>
> ------------------------------
>
> Message: 3
> Date: Wed, 18 Oct 2017 13:42:25 +0100
> From: nek5000-users at lists.mcs.anl.gov
> To: nek5000-users at lists.mcs.anl.gov
> Subject: [Nek5000-users] Element mesh mismatch in pipe
> Message-ID:
>         <mailman.674.1508330579.19102.nek5000-users at lists.mcs.anl.gov>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Nek,
>
> Do you know what can I do for the pipe running. It was good before, but I
> dont know why it doesn't work now it shows the error below when using
> nekmpi. I re-genmap even re-generated the rea file which didn't work.
>
>  I,J,K,IE:    8    7    8      172686
>  Near Y =  0.44264699E-01 -0.45639873       9.3750000    , d:   0.0000000
>    -0.45384730E-01   2.0779221
>  WARNING2 Element mesh mismatch at:
>  I,J,K,IE:    1    8    8      172687
>  Near Y =  0.46328000E-01 -0.47523300       9.3750000    , d:
> 0.55511151E-16 -0.70769971       2.0187379
>  WARNING2 Element mesh mismatch at:
>  I,J,K,IE:    2    8    8      172687
>  Near Y =  0.49283703E-01 -0.47473225       9.3750000    , d:   0.0000000
>    -0.77340445       2.0187379
>  WARNING2 Element mesh mismatch at:
>  I,J,K,IE:    8    8    8      172688
>  Near Y =  0.46328000E-01 -0.47523300       9.3750000    , d:   0.0000000
>    -0.70769971       2.0000000
>  Mesh consistency check failed.  EXITING in VRDSMSH.
>
> call exitt: dying ...
>
> backtrace(): obtained 8 stack frames.
> ./nek5000() [0x6af030]
> ./nek5000() [0x877fa2]
> ./nek5000() [0x461c91]
> ./nek5000() [0x4082b1]
> ./nek5000() [0x406df9]
> ./nek5000() [0x4034be]
> /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f23bb3adc05]
> ./nek5000() [0x4033c9]
>
>
> Kind regards,
>
> ZJ
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>
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>
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>
> End of Nek5000-users Digest, Vol 104, Issue 15
> **********************************************
>
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