[Nek5000-users] Periodicity with curvature

nek5000-users at lists.mcs.anl.gov nek5000-users at lists.mcs.anl.gov
Sat Jan 13 18:31:14 CST 2018


Hi Jon,


You raise two separate issues ---


 1. periodic-auto is simply the way that prenek assigns the P-P matching between

 a pair of faces.   It requires the faces to be parallel, aligned, and with unit normals

point in opposite directions.    Generally under these circumstances prenek/pretex will

find the matched pairs and thus generate the correct .rea file.   From there, genmap

and Nek5000 will establish the correct connectivity to execute the code (primarily,

direct stiffness summation).


2. If the faces are not aligned, you need to have a way to assign the P-P association.

    Assuming you can do this then there are two possible cases:


    a)  The unit normals on P-P face pairs are aligned and in opposite direction.

          This case will go through genmap/Nek5000 without any issue.


    b)  The unit normals on P-P faces are not aligned, i.e., you're running the CYCLIC

          case (ifcyc=.true.).   Here, there's going to be an issues in setting up the .map

          file.    genmap likely will not work.     You can recover this inside nek because

          we allow the user to prescribe some connectivity information, but it's clear

          that this will have to be done on a case-by-case basis.


One of things we often do is to have a fake mesh with the same topology but

with a geometry such that the normals are aligned (Case 2.a).   Then generate

the .map file and use it with Case 2.b.


If this isn't possible, I'd suggest you contact me off-list and I can try to give

some guidance.


In the meantime, for your model problem, I'd suggest proceeding with one of

the approaches outlined above, just so you can familiarize yourself with the

overall process for the cyclic bcs.


hth,


Paul



    a)  Unit normals are parallel and in

________________________________
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: Saturday, January 13, 2018 2:34:58 PM
To: nek5000-users at lists.mcs.anl.gov
Subject: Re: [Nek5000-users] Periodicity with curvature

Hi Paul,
In the future, I will need a more complex geometry where cyclic BCs are not in-line. This simple example I presented here is simply a proof of concept for another mesh.
What would be the best method do this, when the geometry isn't simple enough to use auto-periodic?

Thank you,
Jon

On Sat, Jan 13, 2018 at 2:28 PM, <nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>> wrote:


Hi Jon,


It's been awhile since I've run the cyclic BCs that you're trying to use.

(Here:  cyclic = periodic + turning through an angle.)


I can't recall the full workflow at the moment (and am not in a position

to check), but I think you'll have better luck if you build a straight mesh,

run genmap, and then morph the geometry into the desired curved

shape in usrdat2().


The reason for doing so is that you'll then be guaranteed to have

the correct mesh connectivity.


hth,


Paul


________________________________
From: Nek5000-users <nek5000-users-bounces at lists.mcs.anl.gov<mailto:nek5000-users-bounces at lists.mcs.anl.gov>> on behalf of nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov> <nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>>
Sent: Saturday, January 13, 2018 1:00:48 PM
To: nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>
Subject: Re: [Nek5000-users] Periodicity with curvature

My apologies, can you clarify what you mean?
I made global refinements one more time, and re-assigned the periodic BCs within prex. For this 2D case (attached), I have linked the 8 element sides with the right 8 sides. All other sides are walls.

Thank you,
Jon

On Sat, Jan 13, 2018 at 12:49 PM, <nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
can you try again with at least 3 elements in other direction.

On 13 Jan 2018, at 19:42, "nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>" <nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>> wrote:

Thanks for the quick response. I made some global refinements but it seems I'm still getting the same error with genmap.

Attached is the new .rea file with 4 elements in the periodic direction.


On Sat, Jan 13, 2018 at 12:32 PM, <nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>> wrote:
You need to have at least three elements in the periodic direction.

On 13 Jan 2018, at 19:19, "nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>" <nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>> wrote:

Dear Nek Users,

I am trying to get periodicity to work in the lastest version of Nek. I've made an extremely simple mesh within prenek (prex) in polar coordinates and cannot seem to run this case. When I run genmap, I get the error below. Did I do something wrong in setting up this mesh?



>> genmap
 reading a.rea
Input mesh tolerance (default 0.2):
NOTE: smaller is better, but generous is more forgiving for bad meshes.
0.01
 reading mesh data ...
 start locglob_lexico:           4           2           8   1.0000000000000000E-002
 locglob:           1           1           8
 locglob:           2           5           8
 locglob:           1           6           8
 locglob:           2           6           8
 done locglob_lexico:           6           6           8           2
 start periodic vtx:           2           6
     1     4     4  Matrix:    x0
  1   x0    1.0000E+00  1.0000E+00  5.4347-323  4.9407-324
  2   x0   -3.5355E-01  3.5355E-01  6.9423-310  6.9423-310
  3   x0    3.5355E-01 -3.5355E-01  6.9529-310  6.9529-310
  4   x0    6.9423-310  6.9529-310  2.3477-313  3.1632-317
     2     4     4  Matrix:    x1
  1   x1    1.0000E+00  1.0000E+00  6.3240-322  0.0000E+00
  2   x1   -3.5355E-01  3.5355E-01  0.0000E+00  6.9423-310
  3   x1   -3.5355E-01  3.5355E-01  6.9423-310  6.9529-310
  4   x1    6.9423-310  6.9423-310  6.9423-310  6.9529-310
     1     4     4  Matrix:    z0
  1   z0    1.0000E+00  1.0000E+00  5.4347-323  4.9407-324
  2   z0   -2.1213E+00 -1.4142E+00  6.9423-310  6.9423-310
  3   z0    2.1213E+00  1.4142E+00  6.9529-310  6.9529-310
  4   z0    6.9423-310  6.9529-310  2.3477-313  3.1632-317
     2     4     4  Matrix:    z1
  1   z1    1.0000E+00  1.0000E+00  6.3240-322  0.0000E+00
  2   z1    1.4142E+00  2.1213E+00  0.0000E+00  6.9423-310
  3   z1    1.4142E+00  2.1213E+00  6.9423-310  6.9529-310
  4   z1    6.9423-310  6.9423-310  6.9423-310  6.9529-310
           1 3  0  1.00000000E-03  2.12132000E+00 abort: FACE MATCH FAIL
           2 4  3  2.12132000E-03  1.00000031E+00 abort: FACE MATCH FAIL

           0  quit





The mesh within my .rea file is as follows:
   20.0000       20.0000      -8.00000      -4.00000     XFAC,YFAC,XZERO,YZERO
 **MESH DATA** 1st line is X of corner 1,2,3,4. 2nd line is Y.
         2         2         2 NEL,NDIM,NELV
      ELEMENT          1 [    1A]    GROUP     0
  -2.121320      -1.414213     -0.8742276E-07 -0.1311341E-06
   2.121320       1.414213       2.000000       3.000000
      ELEMENT          2 [    1B]    GROUP     0
 -0.1311341E-06 -0.8742276E-07   1.414213       2.121320
   3.000000       2.000000       1.414213       2.121320
  ***** CURVED SIDE DATA *****
         4 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE
  2  1  -2.00000       0.00000       0.00000       0.00000       0.00000     C
  4  1   3.00000       0.00000       0.00000       0.00000       0.00000     C
  2  2  -2.00000       0.00000       0.00000       0.00000       0.00000     C
  4  2   3.00000       0.00000       0.00000       0.00000       0.00000     C
  ***** BOUNDARY CONDITIONS *****
  ***** FLUID   BOUNDARY CONDITIONS *****
 P    1  1   2.00000       3.00000       0.00000       0.00000       0.00000
 W    1  2   0.00000       0.00000       0.00000       0.00000       0.00000
 E    1  3   2.00000       1.00000       0.00000       0.00000       0.00000
 W    1  4   0.00000       0.00000       0.00000       0.00000       0.00000
 E    2  1   1.00000       3.00000       0.00000       0.00000       0.00000
 W    2  2   0.00000       0.00000       0.00000       0.00000       0.00000
 P    2  3   1.00000       1.00000       0.00000       0.00000       0.00000
 W    2  4   0.00000       0.00000       0.00000       0.00000       0.00000
  ***** NO THERMAL BOUNDARY CONDITIONS *****

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