Periodicity with curvature
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 ***** [image: Inline image 2]
You need to have at least three elements in the periodic direction. On 13 Jan 2018, at 19:19, "[email protected] <mailto:[email protected]> " <[email protected] <mailto:[email protected]> > 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 ***** <mime-attachment.png> _______________________________________________ Nek5000-users mailing list [email protected] <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
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, <[email protected]> wrote:
You need to have at least three elements in the periodic direction.
On 13 Jan 2018, at 19:19, "[email protected]" < [email protected]> 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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can you try again with at least 3 elements in other direction. On 13 Jan 2018, at 19:42, "[email protected] <mailto:[email protected]> " <[email protected] <mailto:[email protected]> > 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, <[email protected] <mailto:[email protected]> > wrote: You need to have at least three elements in the periodic direction. On 13 Jan 2018, at 19:19, "[email protected] <mailto:[email protected]> " <[email protected] <mailto:[email protected]> > 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 ***** <mime-attachment.png> _______________________________________________ Nek5000-users mailing list [email protected] <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [email protected] <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [email protected] <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <a.rea>
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, <[email protected]> wrote:
can you try again with at least 3 elements in other direction.
On 13 Jan 2018, at 19:42, "[email protected]" < [email protected]> 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, <[email protected]> wrote:
You need to have at least three elements in the periodic direction.
On 13 Jan 2018, at 19:19, "[email protected]" < [email protected]> 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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<a.rea>
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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 <[email protected]> on behalf of [email protected] <[email protected]> Sent: Saturday, January 13, 2018 1:00:48 PM To: [email protected] 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, <[email protected]<mailto:[email protected]>> wrote: can you try again with at least 3 elements in other direction. On 13 Jan 2018, at 19:42, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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, <[email protected]<mailto:[email protected]>> wrote: You need to have at least three elements in the periodic direction. On 13 Jan 2018, at 19:19, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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 ***** <mime-attachment.png> _______________________________________________ Nek5000-users mailing list [email protected]<mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mailman_listinfo_nek5000-2Dusers&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=gP2CkfxBOr64FG89YpFokg&m=ncKzoPY2dwLIbAc1FITAEJsCsTeH2zRgDAqkjXYZe5A&s=nLM4v-0kL5jW9dMNEgiVqdVGDFSs6TFHQxJK53ePw04&e=> _______________________________________________ Nek5000-users mailing list [email protected]<mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mailman_listinfo_nek5000-2Dusers&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=gP2CkfxBOr64FG89YpFokg&m=BAFsct9orEUodBvhKrXssNMVdu-OcqgveZCrA11i8M8&s=DBQt47t5SSmsVmTy3GCoo7VqaiTms-bCOKWC0nrs9xo&e=> _______________________________________________ Nek5000-users mailing list [email protected]<mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mailman_listinfo_nek5000-2Dusers&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=gP2CkfxBOr64FG89YpFokg&m=BAFsct9orEUodBvhKrXssNMVdu-OcqgveZCrA11i8M8&s=DBQt47t5SSmsVmTy3GCoo7VqaiTms-bCOKWC0nrs9xo&e=> <a.rea> _______________________________________________ Nek5000-users mailing list [email protected]<mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
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, <[email protected]> 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 <[email protected]> on behalf of [email protected] <[email protected]> *Sent:* Saturday, January 13, 2018 1:00:48 PM *To:* [email protected] *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, <[email protected]> wrote:
can you try again with at least 3 elements in other direction.
On 13 Jan 2018, at 19:42, "[email protected]" < [email protected]> 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, <[email protected]> wrote:
You need to have at least three elements in the periodic direction.
On 13 Jan 2018, at 19:19, "[email protected]" < [email protected]> 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 *****
<mime-attachment.png>
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<a.rea>
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Yes that’s the way to handle cyclic BCs. In addition you have to set IFCYC=true. Note the surface mesh on the two cyclic patches have to match. What do you mean by „not in-line“? Cheers Stefan On 13 Jan 2018, at 21:35, "[email protected] <mailto:[email protected]> " <[email protected] <mailto:[email protected]> > wrote: 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, <[email protected] <mailto:[email protected]> > 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 <[email protected] <mailto:[email protected]> > on behalf of [email protected] <mailto:[email protected]> <[email protected] <mailto:[email protected]> > Sent: Saturday, January 13, 2018 1:00:48 PM To: [email protected] <mailto:[email protected]> 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, <[email protected] <mailto:[email protected]> > wrote: can you try again with at least 3 elements in other direction. On 13 Jan 2018, at 19:42, "[email protected] <mailto:[email protected]> " <[email protected] <mailto:[email protected]> > 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, <[email protected] <mailto:[email protected]> > wrote: You need to have at least three elements in the periodic direction. On 13 Jan 2018, at 19:19, "[email protected] <mailto:[email protected]> " <[email protected] <mailto:[email protected]> > 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 ***** <mime-attachment.png> _______________________________________________ Nek5000-users mailing list [email protected] <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [email protected] <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [email protected] <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users <a.rea> _______________________________________________ Nek5000-users mailing list [email protected] <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [email protected] <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list [email protected] <mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
Stefan, When I say not in-line, picture an "L" shaped geometry with a cyclic patch on the upper most (north) face and the right most (east) face. Although they point different directions, it should be possible to make them cyclic. I am certain the lengths of my patches are the same size/area. I tried adding "T IFCYC" in the rea logical switch but it doesn't appear to be the problem, as I get the same error when I try to use genmap (see initial post). When I use periodic in a prenek channel mesh, I don't get this error. Only when I use periodic with patches that are not in-line. Thanks, Jon On Sat, Jan 13, 2018 at 3:49 PM, <[email protected]> wrote:
Yes that’s the way to handle cyclic BCs. In addition you have to set IFCYC=true.
Note the surface mesh on the two cyclic patches have to match. What do you mean by „not in-line“?
Cheers Stefan
On 13 Jan 2018, at 21:35, "[email protected]" < [email protected]> wrote:
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, <[email protected]> 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 <[email protected]> on behalf of [email protected] <[email protected] ov> *Sent:* Saturday, January 13, 2018 1:00:48 PM *To:* [email protected] *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, <[email protected]> wrote:
can you try again with at least 3 elements in other direction.
On 13 Jan 2018, at 19:42, "[email protected]" < [email protected]> 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, <[email protected]> wrote:
You need to have at least three elements in the periodic direction.
On 13 Jan 2018, at 19:19, "[email protected]" < [email protected]> 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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<a.rea>
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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 <[email protected]> on behalf of [email protected] <[email protected]> Sent: Saturday, January 13, 2018 2:34:58 PM To: [email protected] 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, <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> on behalf of [email protected]<mailto:[email protected]> <[email protected]<mailto:[email protected]>> Sent: Saturday, January 13, 2018 1:00:48 PM To: [email protected]<mailto:[email protected]> 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, <[email protected]<mailto:[email protected]>> wrote: can you try again with at least 3 elements in other direction. On 13 Jan 2018, at 19:42, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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, <[email protected]<mailto:[email protected]>> wrote: You need to have at least three elements in the periodic direction. On 13 Jan 2018, at 19:19, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> 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 ***** <mime-attachment.png> _______________________________________________ Nek5000-users mailing list [email protected]<mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mailman_listinfo_nek5000-2Dusers&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=gP2CkfxBOr64FG89YpFokg&m=ncKzoPY2dwLIbAc1FITAEJsCsTeH2zRgDAqkjXYZe5A&s=nLM4v-0kL5jW9dMNEgiVqdVGDFSs6TFHQxJK53ePw04&e=> _______________________________________________ Nek5000-users mailing list [email protected]<mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mailman_listinfo_nek5000-2Dusers&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=gP2CkfxBOr64FG89YpFokg&m=BAFsct9orEUodBvhKrXssNMVdu-OcqgveZCrA11i8M8&s=DBQt47t5SSmsVmTy3GCoo7VqaiTms-bCOKWC0nrs9xo&e=> _______________________________________________ Nek5000-users mailing list [email protected]<mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mailman_listinfo_nek5000-2Dusers&d=DwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=gP2CkfxBOr64FG89YpFokg&m=BAFsct9orEUodBvhKrXssNMVdu-OcqgveZCrA11i8M8&s=DBQt47t5SSmsVmTy3GCoo7VqaiTms-bCOKWC0nrs9xo&e=> <a.rea> _______________________________________________ Nek5000-users mailing list [email protected]<mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users<https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.mcs.anl.gov_mailman_listinfo_nek5000-2Dusers&d=DwMFAg&c=ODFT-G5SujMiGrKuoJJjVg&r=gP2CkfxBOr64FG89YpFokg&m=sAFtxxjU2oId9i7igsGJ8tVajh1Q5GHP-CQMMPawlcs&s=NLpzCQaEmDTGEe8B503wySfumBz2BxWtkf6eEvhyGAU&e=> _______________________________________________ Nek5000-users mailing list [email protected]<mailto:[email protected]> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
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