From nek5000-users at lists.mcs.anl.gov Sun Nov 3 10:00:17 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 3 Nov 2013 17:00:17 +0100 Subject: [Nek5000-users] prex question Message-ID: Hello everyone, 1, I am trying to create the mesh of the example ext_cyl with genbox, and pretek. After consulting the email archives online, I almost got it works. The question lies on mesh-merging. I used pretex. The commands is listed as follows. I got a mesh ext_cyl.rea identical to the one in the example, when I visualized it with postx. However, when I use xxdiff to examine it, I found several differences. BOUNDARY CONDITIONS: FLUID BOUNDARY CONDITIONS: 11 0.00000 0.00000 ..... For the file in the example, this line is P 11 1337.00 3.00000 ...... So which step did I missed? To set the BC in pretek? Can someone gives a detailed command lines? 2, About creating the mesh, the wiki says that Nek5000 works with Moab Cubit, but this software is not free of charge. Is there any other free software for meshing? In the archive, I found the discussion about converting Gambit (we have Gambit in school) mesh to rea. The guy left an email address cmeador at tamu.edu , which is no more valid. Thank you very much! Best regards Tubois ================================================================== Choose a Name for This session: ext_cyl Beginning Session ext_cyl 1 READ PREVIOUS PARAMETERS 2 TYPE IN NEW PARAMETERS 3 CONJ. HEAT TRANSFER MERGE Choose item: 1 1 Enter name of previous session box.rea 1 BUILD FROM FILE 2 BUILD INTERACTIVELY Choose item: 1 1 Enter name of previous session (Default= box.rea ) I pressed ENTER Will Read Mesh and B.C. data from box.rea Reading Element 29 [ 1C] Reading Element 58 [ 1f] Reading Element 87 [ 1I] Reading Element 116 [ 1l] Reading Element 145 [ 1O] Reading Element 174 [ 1r] Reading Element 203 [ 1U] Reading Element 232 [ 1x] Reading Element 261 [ 1a] Reading Element 290 [ 1D] Reading Element 319 [ 1g] Reading Element 348 [ 1J] Reading Element 377 [ 1m] Reading Element 406 [ 1P] Reading Element 435 [ 1s] Reading Element 464 [ 1V] Reading Element 493 [ 1y] Reading Element 522 [ 1b] Reading Element 551 [ 1E] Reading Element 580 [ 1h] Reading Element 609 [ 1K] Reading Element 638 [ 1n] Reading Element 667 [ 1Q] Reading Element 696 [ 1t] Reading Element 725 [ 1W] Reading Element 754 [ 1z] Reading Element 783 [ 1c] Reading Element 812 [ 1F] Reading Element 841 [ 1i] Reading Element 870 [ 1L] Reading Element 899 [ 1o] Reading Element 928 [ 1R] Reading Element 957 [ 1u] Reading Element 986 [ 1X] Reading Element 1015 [ 1A] Reading Element 1044 [ 1d] Reading Element 1073 [ 1G] Reading Element 1102 [ 1j] Reading Element 1131 [ 1M] Reading Element 1160 [ 1p] Reading Element 1189 [ 1S] Reading Element 1218 [ 1v] Reading Element 1247 [ 1Y] Reading Element 1276 [ 1B] Reading Element 1305 [ 1e] Reading Element 1334 [ 1H] Reading Element 1363 [ 1k] Reading Element 1392 [ 1N] Reading Element 1421 [ 1q] Reading Element 1450 [ 1T] drwobjs: 0 Showing only 90 elements of 1456 *** BUILD MENU *** inside gencen 1456 F 4 done gencen 1456 1 END ELEMENTS 2 MODIFY ELEMENT 3 GLOBAL REFINE 4 CURVE SIDES 5 DELETE ELEMENT 6 ZOOM 7 SET GRID 8 DEFINE OBJECT 9 REDRAW MESH 10 IMPORT MESH 11 IMPORT VTK MESH 12 IMPORT vtx MESH 13 REFLECT MESH Choose item: 10 10 input name of new .rea file import.rea Would you like to displace existing elements in box? y Found 80 curve sides. IFLD: 1 1 T F ***** FLUID BOUNDARY CONDITIONS ***** ***** FLUID BOUNDARY CONDITIONS *****$ This is nel,ncurve old: 1456 0 This is nel,ncurve new: 1536 80 inside gencen 1536 F 4 done gencen 1536 X min/max of new elements: -1.200000 1.200001 Y min/max of new elements: -1.200000 1.200000 NO KEEP: 514 F -1.0500000 -1.0500000 0.0000000 NO KEEP: 515 F -0.75000000 -1.0500000 0.0000000 NO KEEP: 516 F -0.45000002 -1.0500000 0.0000000 NO KEEP: 517 F -0.15000001 -1.0500000 0.0000000 NO KEEP: 518 F 0.15000001 -1.0500000 0.0000000 NO KEEP: 519 F 0.45000002 -1.0500000 0.0000000 NO KEEP: 520 F 0.75000000 -1.0500000 0.0000000 NO KEEP: 521 F 1.0500000 -1.0500000 0.0000000 NO KEEP: 570 F -1.0500000 -0.75000000 0.0000000 NO KEEP: 571 F -0.75000000 -0.75000000 0.0000000 NO KEEP: 572 F -0.45000002 -0.75000000 0.0000000 NO KEEP: 573 F -0.15000001 -0.75000000 0.0000000 NO KEEP: 574 F 0.15000001 -0.75000000 0.0000000 NO KEEP: 575 F 0.45000002 -0.75000000 0.0000000 NO KEEP: 576 F 0.75000000 -0.75000000 0.0000000 NO KEEP: 577 F 1.0500000 -0.75000000 0.0000000 NO KEEP: 626 F -1.0500000 -0.45000002 0.0000000 NO KEEP: 627 F -0.75000000 -0.45000002 0.0000000 NO KEEP: 628 F -0.45000002 -0.45000002 0.0000000 NO KEEP: 629 F -0.15000001 -0.45000002 0.0000000 NO KEEP: 630 F 0.15000001 -0.45000002 0.0000000 NO KEEP: 631 F 0.45000002 -0.45000002 0.0000000 NO KEEP: 632 F 0.75000000 -0.45000002 0.0000000 NO KEEP: 633 F 1.0500000 -0.45000002 0.0000000 NO KEEP: 682 F -1.0500000 -0.15000001 0.0000000 NO KEEP: 683 F -0.75000000 -0.15000001 0.0000000 NO KEEP: 684 F -0.45000002 -0.15000001 0.0000000 NO KEEP: 685 F -0.15000001 -0.15000001 0.0000000 NO KEEP: 686 F 0.15000001 -0.15000001 0.0000000 NO KEEP: 687 F 0.45000002 -0.15000001 0.0000000 NO KEEP: 688 F 0.75000000 -0.15000001 0.0000000 NO KEEP: 689 F 1.0500000 -0.15000001 0.0000000 NO KEEP: 738 F -1.0500000 0.15000001 0.0000000 NO KEEP: 739 F -0.75000000 0.15000001 0.0000000 NO KEEP: 740 F -0.45000002 0.15000001 0.0000000 NO KEEP: 741 F -0.15000001 0.15000001 0.0000000 NO KEEP: 742 F 0.15000001 0.15000001 0.0000000 NO KEEP: 743 F 0.45000002 0.15000001 0.0000000 NO KEEP: 744 F 0.75000000 0.15000001 0.0000000 NO KEEP: 745 F 1.0500000 0.15000001 0.0000000 NO KEEP: 794 F -1.0500000 0.45000002 0.0000000 NO KEEP: 795 F -0.75000000 0.45000002 0.0000000 NO KEEP: 796 F -0.45000002 0.45000002 0.0000000 NO KEEP: 797 F -0.15000001 0.45000002 0.0000000 NO KEEP: 798 F 0.15000001 0.45000002 0.0000000 NO KEEP: 799 F 0.45000002 0.45000002 0.0000000 NO KEEP: 800 F 0.75000000 0.45000002 0.0000000 NO KEEP: 801 F 1.0500000 0.45000002 0.0000000 NO KEEP: 850 F -1.0500000 0.75000000 0.0000000 NO KEEP: 851 F -0.75000000 0.75000000 0.0000000 NO KEEP: 852 F -0.45000002 0.75000000 0.0000000 NO KEEP: 853 F -0.15000001 0.75000000 0.0000000 NO KEEP: 854 F 0.15000001 0.75000000 0.0000000 NO KEEP: 855 F 0.45000002 0.75000000 0.0000000 NO KEEP: 856 F 0.75000000 0.75000000 0.0000000 NO KEEP: 857 F 1.0500000 0.75000000 0.0000000 NO KEEP: 906 F -1.0500000 1.0500000 0.0000000 NO KEEP: 907 F -0.75000000 1.0500000 0.0000000 NO KEEP: 908 F -0.45000002 1.0500000 0.0000000 NO KEEP: 909 F -0.15000001 1.0500000 0.0000000 NO KEEP: 910 F 0.15000001 1.0500000 0.0000000 NO KEEP: 911 F 0.45000002 1.0500000 0.0000000 NO KEEP: 912 F 0.75000000 1.0500000 0.0000000 NO KEEP: 913 F 1.0500000 1.0500000 0.0000000 Deleting element 514 of 1536. Deleting element 515 of 1536. Deleting element 516 of 1536. Deleting element 517 of 1536. Deleting element 518 of 1536. Deleting element 519 of 1536. Deleting element 520 of 1536. Deleting element 521 of 1536. Deleting element 570 of 1536. Deleting element 571 of 1536. Deleting element 572 of 1536. Deleting element 573 of 1536. Deleting element 574 of 1536. Deleting element 575 of 1536. Deleting element 576 of 1536. Deleting element 577 of 1536. Deleting element 626 of 1536. Deleting element 627 of 1536. Deleting element 628 of 1536. Deleting element 629 of 1536. Deleting element 630 of 1536. Deleting element 631 of 1536. Deleting element 632 of 1536. Deleting element 633 of 1536. Deleting element 682 of 1536. Deleting element 683 of 1536. Deleting element 684 of 1536. Deleting element 685 of 1536. Deleting element 686 of 1536. Deleting element 687 of 1536. Deleting element 688 of 1536. Deleting element 689 of 1536. Deleting element 738 of 1536. Deleting element 739 of 1536. Deleting element 740 of 1536. Deleting element 741 of 1536. Deleting element 742 of 1536. Deleting element 743 of 1536. Deleting element 744 of 1536. Deleting element 745 of 1536. Deleting element 794 of 1536. Deleting element 795 of 1536. Deleting element 796 of 1536. Deleting element 797 of 1536. Deleting element 798 of 1536. Deleting element 799 of 1536. Deleting element 800 of 1536. Deleting element 801 of 1536. Deleting element 850 of 1536. Deleting element 851 of 1536. Deleting element 852 of 1536. Deleting element 853 of 1536. Deleting element 854 of 1536. Deleting element 855 of 1536. Deleting element 856 of 1536. Deleting element 857 of 1536. Deleting element 906 of 1536. Deleting element 907 of 1536. Deleting element 908 of 1536. Deleting element 909 of 1536. Deleting element 910 of 1536. Deleting element 911 of 1536. Deleting element 912 of 1536. Deleting element 913 of 1536. drwobjs: 0 Showing only 90 elements of 1472 drwobjs: 0 inside gencen 1472 F 4 done gencen 1472 1 END ELEMENTS 2 MODIFY ELEMENT 3 GLOBAL REFINE 4 CURVE SIDES 5 DELETE ELEMENT 6 ZOOM 7 SET GRID 8 DEFINE OBJECT 9 REDRAW MESH 10 IMPORT MESH 11 IMPORT VTK MESH 12 IMPORT vtx MESH 13 REFLECT MESH Choose item: 1 1 1 ACCEPT MATL,QVOL 2 SELECT ELEMENT 3 SELECT MATL [ 0] 4 SET MATL PROPS,Q 5 SHOW MATL PROPS,Q Choose it 1 1 start locglob_lexico: 4 1472 5888 1.99999996E-02 locglob: 1 1 5888 locglob: 2 81 5888 locglob: 1 1562 5888 locglob: 2 1562 5888 Performing unique_vertex2 self_chk 5888 done locglob_lexico: 1562 1562 5888 5 Performing makecell self_chk 5888 *** MIDWAY BREAK MENU *** ABORT to write build data to file and exit SET B.C'S to continue 1 SET BCs 2 ABORT Choose item: 2 Generating Mesh Points for 1472 Elements 1472 this is nel in prexit Writing Parameters to file Deleting tmp.* files. Exiting session 4.59163468E-41 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Nov 3 10:43:33 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 3 Nov 2013 17:43:33 +0100 Subject: [Nek5000-users] prex question In-Reply-To: References: Message-ID: Hi Tubois, Someone corrects me if I'm wrong, but regarding the gambit/matlab converter, as far as I remember, it can only handle a three-dimensional mesh. For such mesh however, it works pretty nicely. I have been using for almost two years and had almost no problem except when imposing periodic boundary conditions (which can be handle anyway combining the matlab tool with prenek). Regards, 2013/11/3 > Hello everyone, > > 1, I am trying to create the mesh of the example ext_cyl with genbox, and > pretek. After consulting the email archives online, I almost got it works. > The question lies on mesh-merging. I used pretex. The commands is listed as > follows. > > I got a mesh ext_cyl.rea identical to the one in the example, when I > visualized it with postx. However, when I use xxdiff to examine it, I found > several differences. > BOUNDARY CONDITIONS: > FLUID BOUNDARY CONDITIONS: > 11 0.00000 0.00000 ..... > For the file in the example, this line is > P 11 1337.00 3.00000 ...... > > So which step did I missed? To set the BC in pretek? Can someone gives a > detailed command lines? > > 2, About creating the mesh, the wiki says that Nek5000 works with Moab > Cubit, but this software is not free of charge. Is there any other free > software for meshing? In the archive, I found the discussion about > converting Gambit (we have Gambit in school) mesh to rea. The guy left an > email address cmeador at tamu.edu , > which is no more valid. > > Thank you very much! > > Best regards > > Tubois > ================================================================== > > Choose a Name for This session: > ext_cyl > Beginning Session ext_cyl > > 1 READ PREVIOUS PARAMETERS > 2 TYPE IN NEW PARAMETERS > 3 CONJ. HEAT TRANSFER MERGE > Choose item: > 1 > 1 > Enter name of previous session > box.rea > 1 BUILD FROM FILE > 2 BUILD INTERACTIVELY > Choose item: > 1 > 1 > Enter name of previous session > (Default= box.rea ) > I pressed ENTER > > Will Read Mesh and B.C. data from box.rea > Reading Element 29 [ 1C] > Reading Element 58 [ 1f] > Reading Element 87 [ 1I] > Reading Element 116 [ 1l] > Reading Element 145 [ 1O] > Reading Element 174 [ 1r] > Reading Element 203 [ 1U] > Reading Element 232 [ 1x] > Reading Element 261 [ 1a] > Reading Element 290 [ 1D] > Reading Element 319 [ 1g] > Reading Element 348 [ 1J] > Reading Element 377 [ 1m] > Reading Element 406 [ 1P] > Reading Element 435 [ 1s] > Reading Element 464 [ 1V] > Reading Element 493 [ 1y] > Reading Element 522 [ 1b] > Reading Element 551 [ 1E] > Reading Element 580 [ 1h] > Reading Element 609 [ 1K] > Reading Element 638 [ 1n] > Reading Element 667 [ 1Q] > Reading Element 696 [ 1t] > Reading Element 725 [ 1W] > Reading Element 754 [ 1z] > Reading Element 783 [ 1c] > Reading Element 812 [ 1F] > Reading Element 841 [ 1i] > Reading Element 870 [ 1L] > Reading Element 899 [ 1o] > Reading Element 928 [ 1R] > Reading Element 957 [ 1u] > Reading Element 986 [ 1X] > Reading Element 1015 [ 1A] > Reading Element 1044 [ 1d] > Reading Element 1073 [ 1G] > Reading Element 1102 [ 1j] > Reading Element 1131 [ 1M] > Reading Element 1160 [ 1p] > Reading Element 1189 [ 1S] > Reading Element 1218 [ 1v] > Reading Element 1247 [ 1Y] > Reading Element 1276 [ 1B] > Reading Element 1305 [ 1e] > Reading Element 1334 [ 1H] > Reading Element 1363 [ 1k] > Reading Element 1392 [ 1N] > Reading Element 1421 [ 1q] > Reading Element 1450 [ 1T] > drwobjs: 0 > Showing only 90 elements of 1456 > *** BUILD MENU *** > inside gencen 1456 F 4 > done gencen 1456 > 1 END ELEMENTS > 2 MODIFY ELEMENT > 3 GLOBAL REFINE > 4 CURVE SIDES > 5 DELETE ELEMENT > 6 ZOOM > 7 SET GRID > 8 DEFINE OBJECT > 9 REDRAW MESH > 10 IMPORT MESH > 11 IMPORT VTK MESH > 12 IMPORT vtx MESH > 13 REFLECT MESH > Choose item: > 10 > 10 > input name of new .rea file > import.rea > Would you like to displace existing elements in box? > y > Found 80 curve sides. > IFLD: 1 1 T F > ***** FLUID BOUNDARY CONDITIONS ***** > ***** FLUID BOUNDARY CONDITIONS *****$ > > This is nel,ncurve old: 1456 0 > This is nel,ncurve new: 1536 80 > inside gencen 1536 F 4 > done gencen 1536 > X min/max of new elements: -1.200000 1.200001 > Y min/max of new elements: -1.200000 1.200000 > NO KEEP: 514 F -1.0500000 -1.0500000 0.0000000 > NO KEEP: 515 F -0.75000000 -1.0500000 0.0000000 > NO KEEP: 516 F -0.45000002 -1.0500000 0.0000000 > NO KEEP: 517 F -0.15000001 -1.0500000 0.0000000 > NO KEEP: 518 F 0.15000001 -1.0500000 0.0000000 > NO KEEP: 519 F 0.45000002 -1.0500000 0.0000000 > NO KEEP: 520 F 0.75000000 -1.0500000 0.0000000 > NO KEEP: 521 F 1.0500000 -1.0500000 0.0000000 > NO KEEP: 570 F -1.0500000 -0.75000000 0.0000000 > NO KEEP: 571 F -0.75000000 -0.75000000 0.0000000 > NO KEEP: 572 F -0.45000002 -0.75000000 0.0000000 > NO KEEP: 573 F -0.15000001 -0.75000000 0.0000000 > NO KEEP: 574 F 0.15000001 -0.75000000 0.0000000 > NO KEEP: 575 F 0.45000002 -0.75000000 0.0000000 > NO KEEP: 576 F 0.75000000 -0.75000000 0.0000000 > NO KEEP: 577 F 1.0500000 -0.75000000 0.0000000 > NO KEEP: 626 F -1.0500000 -0.45000002 0.0000000 > NO KEEP: 627 F -0.75000000 -0.45000002 0.0000000 > NO KEEP: 628 F -0.45000002 -0.45000002 0.0000000 > NO KEEP: 629 F -0.15000001 -0.45000002 0.0000000 > NO KEEP: 630 F 0.15000001 -0.45000002 0.0000000 > NO KEEP: 631 F 0.45000002 -0.45000002 0.0000000 > NO KEEP: 632 F 0.75000000 -0.45000002 0.0000000 > NO KEEP: 633 F 1.0500000 -0.45000002 0.0000000 > NO KEEP: 682 F -1.0500000 -0.15000001 0.0000000 > NO KEEP: 683 F -0.75000000 -0.15000001 0.0000000 > NO KEEP: 684 F -0.45000002 -0.15000001 0.0000000 > NO KEEP: 685 F -0.15000001 -0.15000001 0.0000000 > NO KEEP: 686 F 0.15000001 -0.15000001 0.0000000 > NO KEEP: 687 F 0.45000002 -0.15000001 0.0000000 > NO KEEP: 688 F 0.75000000 -0.15000001 0.0000000 > NO KEEP: 689 F 1.0500000 -0.15000001 0.0000000 > NO KEEP: 738 F -1.0500000 0.15000001 0.0000000 > NO KEEP: 739 F -0.75000000 0.15000001 0.0000000 > NO KEEP: 740 F -0.45000002 0.15000001 0.0000000 > NO KEEP: 741 F -0.15000001 0.15000001 0.0000000 > NO KEEP: 742 F 0.15000001 0.15000001 0.0000000 > NO KEEP: 743 F 0.45000002 0.15000001 0.0000000 > NO KEEP: 744 F 0.75000000 0.15000001 0.0000000 > NO KEEP: 745 F 1.0500000 0.15000001 0.0000000 > NO KEEP: 794 F -1.0500000 0.45000002 0.0000000 > NO KEEP: 795 F -0.75000000 0.45000002 0.0000000 > NO KEEP: 796 F -0.45000002 0.45000002 0.0000000 > NO KEEP: 797 F -0.15000001 0.45000002 0.0000000 > NO KEEP: 798 F 0.15000001 0.45000002 0.0000000 > NO KEEP: 799 F 0.45000002 0.45000002 0.0000000 > NO KEEP: 800 F 0.75000000 0.45000002 0.0000000 > NO KEEP: 801 F 1.0500000 0.45000002 0.0000000 > NO KEEP: 850 F -1.0500000 0.75000000 0.0000000 > NO KEEP: 851 F -0.75000000 0.75000000 0.0000000 > NO KEEP: 852 F -0.45000002 0.75000000 0.0000000 > NO KEEP: 853 F -0.15000001 0.75000000 0.0000000 > NO KEEP: 854 F 0.15000001 0.75000000 0.0000000 > NO KEEP: 855 F 0.45000002 0.75000000 0.0000000 > NO KEEP: 856 F 0.75000000 0.75000000 0.0000000 > NO KEEP: 857 F 1.0500000 0.75000000 0.0000000 > NO KEEP: 906 F -1.0500000 1.0500000 0.0000000 > NO KEEP: 907 F -0.75000000 1.0500000 0.0000000 > NO KEEP: 908 F -0.45000002 1.0500000 0.0000000 > NO KEEP: 909 F -0.15000001 1.0500000 0.0000000 > NO KEEP: 910 F 0.15000001 1.0500000 0.0000000 > NO KEEP: 911 F 0.45000002 1.0500000 0.0000000 > NO KEEP: 912 F 0.75000000 1.0500000 0.0000000 > NO KEEP: 913 F 1.0500000 1.0500000 0.0000000 > Deleting element 514 of 1536. > Deleting element 515 of 1536. > Deleting element 516 of 1536. > Deleting element 517 of 1536. > Deleting element 518 of 1536. > Deleting element 519 of 1536. > Deleting element 520 of 1536. > Deleting element 521 of 1536. > Deleting element 570 of 1536. > Deleting element 571 of 1536. > Deleting element 572 of 1536. > Deleting element 573 of 1536. > Deleting element 574 of 1536. > Deleting element 575 of 1536. > Deleting element 576 of 1536. > Deleting element 577 of 1536. > Deleting element 626 of 1536. > Deleting element 627 of 1536. > Deleting element 628 of 1536. > Deleting element 629 of 1536. > Deleting element 630 of 1536. > Deleting element 631 of 1536. > Deleting element 632 of 1536. > Deleting element 633 of 1536. > Deleting element 682 of 1536. > Deleting element 683 of 1536. > Deleting element 684 of 1536. > Deleting element 685 of 1536. > Deleting element 686 of 1536. > Deleting element 687 of 1536. > Deleting element 688 of 1536. > Deleting element 689 of 1536. > Deleting element 738 of 1536. > Deleting element 739 of 1536. > Deleting element 740 of 1536. > Deleting element 741 of 1536. > Deleting element 742 of 1536. > Deleting element 743 of 1536. > Deleting element 744 of 1536. > Deleting element 745 of 1536. > Deleting element 794 of 1536. > Deleting element 795 of 1536. > Deleting element 796 of 1536. > Deleting element 797 of 1536. > Deleting element 798 of 1536. > Deleting element 799 of 1536. > Deleting element 800 of 1536. > Deleting element 801 of 1536. > Deleting element 850 of 1536. > Deleting element 851 of 1536. > Deleting element 852 of 1536. > Deleting element 853 of 1536. > Deleting element 854 of 1536. > Deleting element 855 of 1536. > Deleting element 856 of 1536. > Deleting element 857 of 1536. > Deleting element 906 of 1536. > Deleting element 907 of 1536. > Deleting element 908 of 1536. > Deleting element 909 of 1536. > Deleting element 910 of 1536. > Deleting element 911 of 1536. > Deleting element 912 of 1536. > Deleting element 913 of 1536. > drwobjs: 0 > Showing only 90 elements of 1472 > drwobjs: 0 > inside gencen 1472 F 4 > done gencen 1472 > 1 END ELEMENTS > 2 MODIFY ELEMENT > 3 GLOBAL REFINE > 4 CURVE SIDES > 5 DELETE ELEMENT > 6 ZOOM > 7 SET GRID > 8 DEFINE OBJECT > 9 REDRAW MESH > 10 IMPORT MESH > 11 IMPORT VTK MESH > 12 IMPORT vtx MESH > 13 REFLECT MESH > Choose item: > 1 > 1 > 1 ACCEPT MATL,QVOL > 2 SELECT ELEMENT > 3 SELECT MATL [ 0] > 4 SET MATL PROPS,Q > 5 SHOW MATL PROPS,Q > Choose it > 1 > 1 > start locglob_lexico: 4 1472 5888 1.99999996E-02 > locglob: 1 1 5888 > locglob: 2 81 5888 > locglob: 1 1562 5888 > locglob: 2 1562 5888 > Performing unique_vertex2 self_chk 5888 > done locglob_lexico: 1562 1562 5888 5 > Performing makecell self_chk 5888 > > *** MIDWAY BREAK MENU *** > ABORT to write build data to file and exit > SET B.C'S to continue > 1 SET BCs > 2 ABORT > Choose item: > 2 > Generating Mesh Points for 1472 Elements > 1472 this is nel in prexit > Writing Parameters to file > Deleting tmp.* files. > Exiting session 4.59163468E-41 > > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Jean-Christophe Loiseau Homepage -------------- next part 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URL: From nek5000-users at lists.mcs.anl.gov Sun Nov 3 10:46:27 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 3 Nov 2013 10:46:27 -0600 (CST) Subject: [Nek5000-users] prex question In-Reply-To: Message-ID: Hi Tubois, I've just updated this example and have included a script that appears to work. I recommend moving your existing ext_cyl directory to, say, ext_cyl.1, and then svn update ext_cyl. Then, in the new ext_cyl directory you should be able to type: mkmesh The README file is also updated. Have a look at mkmesh and you can see the basic steps. Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Sunday, November 3, 2013 10:00:17 AM Subject: [Nek5000-users] prex question Hello everyone, 1, I am trying to create the mesh of the example ext_cyl with genbox, and pretek. After consulting the email archives online, I almost got it works. The question lies on mesh-merging. I used pretex. The commands is listed as follows. I got a mesh ext_cyl.rea identical to the one in the example, when I visualized it with postx. However, when I use xxdiff to examine it, I found several differences. BOUNDARY CONDITIONS: FLUID BOUNDARY CONDITIONS: 11 0.00000 0.00000 ..... For the file in the example, this line is P 11 1337.00 3.00000 ...... So which step did I missed? To set the BC in pretek? Can someone gives a detailed command lines? 2, About creating the mesh, the wiki says that Nek5000 works with Moab Cubit, but this software is not free of charge. Is there any other free software for meshing? In the archive, I found the discussion about converting Gambit (we have Gambit in school) mesh to rea. The guy left an email address cmeador at tamu.edu , which is no more valid. Thank you very much! Best regards Tubois ================================================================== Choose a Name for This session: ext_cyl Beginning Session ext_cyl 1 READ PREVIOUS PARAMETERS 2 TYPE IN NEW PARAMETERS 3 CONJ. HEAT TRANSFER MERGE Choose item: 1 1 Enter name of previous session box.rea 1 BUILD FROM FILE 2 BUILD INTERACTIVELY Choose item: 1 1 Enter name of previous session (Default= box.rea ) I pressed ENTER Will Read Mesh and B.C. data from box.rea Reading Element 29 [ 1C] Reading Element 58 [ 1f] Reading Element 87 [ 1I] Reading Element 116 [ 1l] Reading Element 145 [ 1O] Reading Element 174 [ 1r] Reading Element 203 [ 1U] Reading Element 232 [ 1x] Reading Element 261 [ 1a] Reading Element 290 [ 1D] Reading Element 319 [ 1g] Reading Element 348 [ 1J] Reading Element 377 [ 1m] Reading Element 406 [ 1P] Reading Element 435 [ 1s] Reading Element 464 [ 1V] Reading Element 493 [ 1y] Reading Element 522 [ 1b] Reading Element 551 [ 1E] Reading Element 580 [ 1h] Reading Element 609 [ 1K] Reading Element 638 [ 1n] Reading Element 667 [ 1Q] Reading Element 696 [ 1t] Reading Element 725 [ 1W] Reading Element 754 [ 1z] Reading Element 783 [ 1c] Reading Element 812 [ 1F] Reading Element 841 [ 1i] Reading Element 870 [ 1L] Reading Element 899 [ 1o] Reading Element 928 [ 1R] Reading Element 957 [ 1u] Reading Element 986 [ 1X] Reading Element 1015 [ 1A] Reading Element 1044 [ 1d] Reading Element 1073 [ 1G] Reading Element 1102 [ 1j] Reading Element 1131 [ 1M] Reading Element 1160 [ 1p] Reading Element 1189 [ 1S] Reading Element 1218 [ 1v] Reading Element 1247 [ 1Y] Reading Element 1276 [ 1B] Reading Element 1305 [ 1e] Reading Element 1334 [ 1H] Reading Element 1363 [ 1k] Reading Element 1392 [ 1N] Reading Element 1421 [ 1q] Reading Element 1450 [ 1T] drwobjs: 0 Showing only 90 elements of 1456 *** BUILD MENU *** inside gencen 1456 F 4 done gencen 1456 1 END ELEMENTS 2 MODIFY ELEMENT 3 GLOBAL REFINE 4 CURVE SIDES 5 DELETE ELEMENT 6 ZOOM 7 SET GRID 8 DEFINE OBJECT 9 REDRAW MESH 10 IMPORT MESH 11 IMPORT VTK MESH 12 IMPORT vtx MESH 13 REFLECT MESH Choose item: 10 10 input name of new .rea file import.rea Would you like to displace existing elements in box? y Found 80 curve sides. IFLD: 1 1 T F ***** FLUID BOUNDARY CONDITIONS ***** ***** FLUID BOUNDARY CONDITIONS *****$ This is nel,ncurve old: 1456 0 This is nel,ncurve new: 1536 80 inside gencen 1536 F 4 done gencen 1536 X min/max of new elements: -1.200000 1.200001 Y min/max of new elements: -1.200000 1.200000 NO KEEP: 514 F -1.0500000 -1.0500000 0.0000000 NO KEEP: 515 F -0.75000000 -1.0500000 0.0000000 NO KEEP: 516 F -0.45000002 -1.0500000 0.0000000 NO KEEP: 517 F -0.15000001 -1.0500000 0.0000000 NO KEEP: 518 F 0.15000001 -1.0500000 0.0000000 NO KEEP: 519 F 0.45000002 -1.0500000 0.0000000 NO KEEP: 520 F 0.75000000 -1.0500000 0.0000000 NO KEEP: 521 F 1.0500000 -1.0500000 0.0000000 NO KEEP: 570 F -1.0500000 -0.75000000 0.0000000 NO KEEP: 571 F -0.75000000 -0.75000000 0.0000000 NO KEEP: 572 F -0.45000002 -0.75000000 0.0000000 NO KEEP: 573 F -0.15000001 -0.75000000 0.0000000 NO KEEP: 574 F 0.15000001 -0.75000000 0.0000000 NO KEEP: 575 F 0.45000002 -0.75000000 0.0000000 NO KEEP: 576 F 0.75000000 -0.75000000 0.0000000 NO KEEP: 577 F 1.0500000 -0.75000000 0.0000000 NO KEEP: 626 F -1.0500000 -0.45000002 0.0000000 NO KEEP: 627 F -0.75000000 -0.45000002 0.0000000 NO KEEP: 628 F -0.45000002 -0.45000002 0.0000000 NO KEEP: 629 F -0.15000001 -0.45000002 0.0000000 NO KEEP: 630 F 0.15000001 -0.45000002 0.0000000 NO KEEP: 631 F 0.45000002 -0.45000002 0.0000000 NO KEEP: 632 F 0.75000000 -0.45000002 0.0000000 NO KEEP: 633 F 1.0500000 -0.45000002 0.0000000 NO KEEP: 682 F -1.0500000 -0.15000001 0.0000000 NO KEEP: 683 F -0.75000000 -0.15000001 0.0000000 NO KEEP: 684 F -0.45000002 -0.15000001 0.0000000 NO KEEP: 685 F -0.15000001 -0.15000001 0.0000000 NO KEEP: 686 F 0.15000001 -0.15000001 0.0000000 NO KEEP: 687 F 0.45000002 -0.15000001 0.0000000 NO KEEP: 688 F 0.75000000 -0.15000001 0.0000000 NO KEEP: 689 F 1.0500000 -0.15000001 0.0000000 NO KEEP: 738 F -1.0500000 0.15000001 0.0000000 NO KEEP: 739 F -0.75000000 0.15000001 0.0000000 NO KEEP: 740 F -0.45000002 0.15000001 0.0000000 NO KEEP: 741 F -0.15000001 0.15000001 0.0000000 NO KEEP: 742 F 0.15000001 0.15000001 0.0000000 NO KEEP: 743 F 0.45000002 0.15000001 0.0000000 NO KEEP: 744 F 0.75000000 0.15000001 0.0000000 NO KEEP: 745 F 1.0500000 0.15000001 0.0000000 NO KEEP: 794 F -1.0500000 0.45000002 0.0000000 NO KEEP: 795 F -0.75000000 0.45000002 0.0000000 NO KEEP: 796 F -0.45000002 0.45000002 0.0000000 NO KEEP: 797 F -0.15000001 0.45000002 0.0000000 NO KEEP: 798 F 0.15000001 0.45000002 0.0000000 NO KEEP: 799 F 0.45000002 0.45000002 0.0000000 NO KEEP: 800 F 0.75000000 0.45000002 0.0000000 NO KEEP: 801 F 1.0500000 0.45000002 0.0000000 NO KEEP: 850 F -1.0500000 0.75000000 0.0000000 NO KEEP: 851 F -0.75000000 0.75000000 0.0000000 NO KEEP: 852 F -0.45000002 0.75000000 0.0000000 NO KEEP: 853 F -0.15000001 0.75000000 0.0000000 NO KEEP: 854 F 0.15000001 0.75000000 0.0000000 NO KEEP: 855 F 0.45000002 0.75000000 0.0000000 NO KEEP: 856 F 0.75000000 0.75000000 0.0000000 NO KEEP: 857 F 1.0500000 0.75000000 0.0000000 NO KEEP: 906 F -1.0500000 1.0500000 0.0000000 NO KEEP: 907 F -0.75000000 1.0500000 0.0000000 NO KEEP: 908 F -0.45000002 1.0500000 0.0000000 NO KEEP: 909 F -0.15000001 1.0500000 0.0000000 NO KEEP: 910 F 0.15000001 1.0500000 0.0000000 NO KEEP: 911 F 0.45000002 1.0500000 0.0000000 NO KEEP: 912 F 0.75000000 1.0500000 0.0000000 NO KEEP: 913 F 1.0500000 1.0500000 0.0000000 Deleting element 514 of 1536. Deleting element 515 of 1536. Deleting element 516 of 1536. Deleting element 517 of 1536. Deleting element 518 of 1536. Deleting element 519 of 1536. Deleting element 520 of 1536. Deleting element 521 of 1536. Deleting element 570 of 1536. Deleting element 571 of 1536. Deleting element 572 of 1536. Deleting element 573 of 1536. Deleting element 574 of 1536. Deleting element 575 of 1536. Deleting element 576 of 1536. Deleting element 577 of 1536. Deleting element 626 of 1536. Deleting element 627 of 1536. Deleting element 628 of 1536. Deleting element 629 of 1536. Deleting element 630 of 1536. Deleting element 631 of 1536. Deleting element 632 of 1536. Deleting element 633 of 1536. Deleting element 682 of 1536. Deleting element 683 of 1536. Deleting element 684 of 1536. Deleting element 685 of 1536. Deleting element 686 of 1536. Deleting element 687 of 1536. Deleting element 688 of 1536. Deleting element 689 of 1536. Deleting element 738 of 1536. Deleting element 739 of 1536. Deleting element 740 of 1536. Deleting element 741 of 1536. Deleting element 742 of 1536. Deleting element 743 of 1536. Deleting element 744 of 1536. Deleting element 745 of 1536. Deleting element 794 of 1536. Deleting element 795 of 1536. Deleting element 796 of 1536. Deleting element 797 of 1536. Deleting element 798 of 1536. Deleting element 799 of 1536. Deleting element 800 of 1536. Deleting element 801 of 1536. Deleting element 850 of 1536. Deleting element 851 of 1536. Deleting element 852 of 1536. Deleting element 853 of 1536. Deleting element 854 of 1536. Deleting element 855 of 1536. Deleting element 856 of 1536. Deleting element 857 of 1536. Deleting element 906 of 1536. Deleting element 907 of 1536. Deleting element 908 of 1536. Deleting element 909 of 1536. Deleting element 910 of 1536. Deleting element 911 of 1536. Deleting element 912 of 1536. Deleting element 913 of 1536. drwobjs: 0 Showing only 90 elements of 1472 drwobjs: 0 inside gencen 1472 F 4 done gencen 1472 1 END ELEMENTS 2 MODIFY ELEMENT 3 GLOBAL REFINE 4 CURVE SIDES 5 DELETE ELEMENT 6 ZOOM 7 SET GRID 8 DEFINE OBJECT 9 REDRAW MESH 10 IMPORT MESH 11 IMPORT VTK MESH 12 IMPORT vtx MESH 13 REFLECT MESH Choose item: 1 1 1 ACCEPT MATL,QVOL 2 SELECT ELEMENT 3 SELECT MATL [ 0] 4 SET MATL PROPS,Q 5 SHOW MATL PROPS,Q Choose it 1 1 start locglob_lexico: 4 1472 5888 1.99999996E-02 locglob: 1 1 5888 locglob: 2 81 5888 locglob: 1 1562 5888 locglob: 2 1562 5888 Performing unique_vertex2 self_chk 5888 done locglob_lexico: 1562 1562 5888 5 Performing makecell self_chk 5888 *** MIDWAY BREAK MENU *** ABORT to write build data to file and exit SET B.C'S to continue 1 SET BCs 2 ABORT Choose item: 2 Generating Mesh Points for 1472 Elements 1472 this is nel in prexit Writing Parameters to file Deleting tmp.* files. Exiting session 4.59163468E-41 _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sun Nov 3 11:35:36 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 3 Nov 2013 18:35:36 +0100 Subject: [Nek5000-users] prex question In-Reply-To: References: Message-ID: Hi Paul, Thank you very much! Just need a confirm about your mesh. 11 SET ENTIRE LEVEL 1 PERIODIC-AUTO means to set the periodic boundary condition for the box except the inlet already set in fpcyl.box? n Is this a lattice for hex-close-packed spheres?: So the boundary condition for the circle will be set to walls automatically? Thank you! Tubois On Sun, Nov 3, 2013 at 5:46 PM, wrote: > > Hi Tubois, > > I've just updated this example and have included a script that appears > to work. > > I recommend moving your existing ext_cyl directory to, say, ext_cyl.1, > and then svn update ext_cyl. > > Then, in the new ext_cyl directory you should be able to type: > > mkmesh > > > The README file is also updated. Have a look at mkmesh and you > can see the basic steps. > > Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Sunday, November 3, 2013 10:00:17 AM > Subject: [Nek5000-users] prex question > > > > Hello everyone, > > > 1, I am trying to create the mesh of the example ext_cyl with genbox, and > pretek. After consulting the email archives online, I almost got it works. > The question lies on mesh-merging. I used pretex. The commands is listed as > follows. > > > I got a mesh ext_cyl.rea identical to the one in the example, when I > visualized it with postx. However, when I use xxdiff to examine it, I found > several differences. > BOUNDARY CONDITIONS: > FLUID BOUNDARY CONDITIONS: > 11 0.00000 0.00000 ..... > For the file in the example, this line is > P 11 1337.00 3.00000 ...... > > > So which step did I missed? To set the BC in pretek? Can someone gives a > detailed command lines? > > > 2, About creating the mesh, the wiki says that Nek5000 works with Moab > Cubit, but this software is not free of charge. Is there any other free > software for meshing? In the archive, I found the discussion about > converting Gambit (we have Gambit in school) mesh to rea. The guy left an > email address cmeador at tamu.edu , which is no more valid. > > > Thank you very much! > > > Best regards > > > Tubois > ================================================================== > > > Choose a Name for This session: > ext_cyl > > Beginning Session ext_cyl > 1 READ PREVIOUS PARAMETERS > 2 TYPE IN NEW PARAMETERS > 3 CONJ. HEAT TRANSFER MERGE > Choose item: > 1 > 1 > Enter name of previous session > box.rea > 1 BUILD FROM FILE > 2 BUILD INTERACTIVELY > Choose item: > 1 > 1 > Enter name of previous session > (Default= box.rea ) > I pressed ENTER > > > > Will Read Mesh and B.C. data from box.rea > Reading Element 29 [ 1C] > Reading Element 58 [ 1f] > Reading Element 87 [ 1I] > Reading Element 116 [ 1l] > Reading Element 145 [ 1O] > Reading Element 174 [ 1r] > Reading Element 203 [ 1U] > Reading Element 232 [ 1x] > Reading Element 261 [ 1a] > Reading Element 290 [ 1D] > Reading Element 319 [ 1g] > Reading Element 348 [ 1J] > Reading Element 377 [ 1m] > Reading Element 406 [ 1P] > Reading Element 435 [ 1s] > Reading Element 464 [ 1V] > Reading Element 493 [ 1y] > Reading Element 522 [ 1b] > Reading Element 551 [ 1E] > Reading Element 580 [ 1h] > Reading Element 609 [ 1K] > Reading Element 638 [ 1n] > Reading Element 667 [ 1Q] > Reading Element 696 [ 1t] > Reading Element 725 [ 1W] > Reading Element 754 [ 1z] > Reading Element 783 [ 1c] > Reading Element 812 [ 1F] > Reading Element 841 [ 1i] > Reading Element 870 [ 1L] > Reading Element 899 [ 1o] > Reading Element 928 [ 1R] > Reading Element 957 [ 1u] > Reading Element 986 [ 1X] > Reading Element 1015 [ 1A] > Reading Element 1044 [ 1d] > Reading Element 1073 [ 1G] > Reading Element 1102 [ 1j] > Reading Element 1131 [ 1M] > Reading Element 1160 [ 1p] > Reading Element 1189 [ 1S] > Reading Element 1218 [ 1v] > Reading Element 1247 [ 1Y] > Reading Element 1276 [ 1B] > Reading Element 1305 [ 1e] > Reading Element 1334 [ 1H] > Reading Element 1363 [ 1k] > Reading Element 1392 [ 1N] > Reading Element 1421 [ 1q] > Reading Element 1450 [ 1T] > drwobjs: 0 > Showing only 90 elements of 1456 > *** BUILD MENU *** > inside gencen 1456 F 4 > done gencen 1456 > 1 END ELEMENTS > 2 MODIFY ELEMENT > 3 GLOBAL REFINE > 4 CURVE SIDES > 5 DELETE ELEMENT > 6 ZOOM > 7 SET GRID > 8 DEFINE OBJECT > 9 REDRAW MESH > 10 IMPORT MESH > 11 IMPORT VTK MESH > 12 IMPORT vtx MESH > 13 REFLECT MESH > Choose item: > 10 > > 10 > input name of new .rea file > import.rea > > Would you like to displace existing elements in box? > y > > Found 80 curve sides. > IFLD: 1 1 T F > ***** FLUID BOUNDARY CONDITIONS ***** > ***** FLUID BOUNDARY CONDITIONS *****$ > This is nel,ncurve old: 1456 0 > This is nel,ncurve new: 1536 80 > inside gencen 1536 F 4 > done gencen 1536 > X min/max of new elements: -1.200000 1.200001 > Y min/max of new elements: -1.200000 1.200000 > NO KEEP: 514 F -1.0500000 -1.0500000 0.0000000 > NO KEEP: 515 F -0.75000000 -1.0500000 0.0000000 > NO KEEP: 516 F -0.45000002 -1.0500000 0.0000000 > NO KEEP: 517 F -0.15000001 -1.0500000 0.0000000 > NO KEEP: 518 F 0.15000001 -1.0500000 0.0000000 > NO KEEP: 519 F 0.45000002 -1.0500000 0.0000000 > NO KEEP: 520 F 0.75000000 -1.0500000 0.0000000 > NO KEEP: 521 F 1.0500000 -1.0500000 0.0000000 > NO KEEP: 570 F -1.0500000 -0.75000000 0.0000000 > NO KEEP: 571 F -0.75000000 -0.75000000 0.0000000 > NO KEEP: 572 F -0.45000002 -0.75000000 0.0000000 > NO KEEP: 573 F -0.15000001 -0.75000000 0.0000000 > NO KEEP: 574 F 0.15000001 -0.75000000 0.0000000 > NO KEEP: 575 F 0.45000002 -0.75000000 0.0000000 > NO KEEP: 576 F 0.75000000 -0.75000000 0.0000000 > NO KEEP: 577 F 1.0500000 -0.75000000 0.0000000 > NO KEEP: 626 F -1.0500000 -0.45000002 0.0000000 > NO KEEP: 627 F -0.75000000 -0.45000002 0.0000000 > NO KEEP: 628 F -0.45000002 -0.45000002 0.0000000 > NO KEEP: 629 F -0.15000001 -0.45000002 0.0000000 > NO KEEP: 630 F 0.15000001 -0.45000002 0.0000000 > NO KEEP: 631 F 0.45000002 -0.45000002 0.0000000 > NO KEEP: 632 F 0.75000000 -0.45000002 0.0000000 > NO KEEP: 633 F 1.0500000 -0.45000002 0.0000000 > NO KEEP: 682 F -1.0500000 -0.15000001 0.0000000 > NO KEEP: 683 F -0.75000000 -0.15000001 0.0000000 > NO KEEP: 684 F -0.45000002 -0.15000001 0.0000000 > NO KEEP: 685 F -0.15000001 -0.15000001 0.0000000 > NO KEEP: 686 F 0.15000001 -0.15000001 0.0000000 > NO KEEP: 687 F 0.45000002 -0.15000001 0.0000000 > NO KEEP: 688 F 0.75000000 -0.15000001 0.0000000 > NO KEEP: 689 F 1.0500000 -0.15000001 0.0000000 > NO KEEP: 738 F -1.0500000 0.15000001 0.0000000 > NO KEEP: 739 F -0.75000000 0.15000001 0.0000000 > NO KEEP: 740 F -0.45000002 0.15000001 0.0000000 > NO KEEP: 741 F -0.15000001 0.15000001 0.0000000 > NO KEEP: 742 F 0.15000001 0.15000001 0.0000000 > NO KEEP: 743 F 0.45000002 0.15000001 0.0000000 > NO KEEP: 744 F 0.75000000 0.15000001 0.0000000 > NO KEEP: 745 F 1.0500000 0.15000001 0.0000000 > NO KEEP: 794 F -1.0500000 0.45000002 0.0000000 > NO KEEP: 795 F -0.75000000 0.45000002 0.0000000 > NO KEEP: 796 F -0.45000002 0.45000002 0.0000000 > NO KEEP: 797 F -0.15000001 0.45000002 0.0000000 > NO KEEP: 798 F 0.15000001 0.45000002 0.0000000 > NO KEEP: 799 F 0.45000002 0.45000002 0.0000000 > NO KEEP: 800 F 0.75000000 0.45000002 0.0000000 > NO KEEP: 801 F 1.0500000 0.45000002 0.0000000 > NO KEEP: 850 F -1.0500000 0.75000000 0.0000000 > NO KEEP: 851 F -0.75000000 0.75000000 0.0000000 > NO KEEP: 852 F -0.45000002 0.75000000 0.0000000 > NO KEEP: 853 F -0.15000001 0.75000000 0.0000000 > NO KEEP: 854 F 0.15000001 0.75000000 0.0000000 > NO KEEP: 855 F 0.45000002 0.75000000 0.0000000 > NO KEEP: 856 F 0.75000000 0.75000000 0.0000000 > NO KEEP: 857 F 1.0500000 0.75000000 0.0000000 > NO KEEP: 906 F -1.0500000 1.0500000 0.0000000 > NO KEEP: 907 F -0.75000000 1.0500000 0.0000000 > NO KEEP: 908 F -0.45000002 1.0500000 0.0000000 > NO KEEP: 909 F -0.15000001 1.0500000 0.0000000 > NO KEEP: 910 F 0.15000001 1.0500000 0.0000000 > NO KEEP: 911 F 0.45000002 1.0500000 0.0000000 > NO KEEP: 912 F 0.75000000 1.0500000 0.0000000 > NO KEEP: 913 F 1.0500000 1.0500000 0.0000000 > Deleting element 514 of 1536. > Deleting element 515 of 1536. > Deleting element 516 of 1536. > Deleting element 517 of 1536. > Deleting element 518 of 1536. > Deleting element 519 of 1536. > Deleting element 520 of 1536. > Deleting element 521 of 1536. > Deleting element 570 of 1536. > Deleting element 571 of 1536. > Deleting element 572 of 1536. > Deleting element 573 of 1536. > Deleting element 574 of 1536. > Deleting element 575 of 1536. > Deleting element 576 of 1536. > Deleting element 577 of 1536. > Deleting element 626 of 1536. > Deleting element 627 of 1536. > Deleting element 628 of 1536. > Deleting element 629 of 1536. > Deleting element 630 of 1536. > Deleting element 631 of 1536. > Deleting element 632 of 1536. > Deleting element 633 of 1536. > Deleting element 682 of 1536. > Deleting element 683 of 1536. > Deleting element 684 of 1536. > Deleting element 685 of 1536. > Deleting element 686 of 1536. > Deleting element 687 of 1536. > Deleting element 688 of 1536. > Deleting element 689 of 1536. > Deleting element 738 of 1536. > Deleting element 739 of 1536. > Deleting element 740 of 1536. > Deleting element 741 of 1536. > Deleting element 742 of 1536. > Deleting element 743 of 1536. > Deleting element 744 of 1536. > Deleting element 745 of 1536. > Deleting element 794 of 1536. > Deleting element 795 of 1536. > Deleting element 796 of 1536. > Deleting element 797 of 1536. > Deleting element 798 of 1536. > Deleting element 799 of 1536. > Deleting element 800 of 1536. > Deleting element 801 of 1536. > Deleting element 850 of 1536. > Deleting element 851 of 1536. > Deleting element 852 of 1536. > Deleting element 853 of 1536. > Deleting element 854 of 1536. > Deleting element 855 of 1536. > Deleting element 856 of 1536. > Deleting element 857 of 1536. > Deleting element 906 of 1536. > Deleting element 907 of 1536. > Deleting element 908 of 1536. > Deleting element 909 of 1536. > Deleting element 910 of 1536. > Deleting element 911 of 1536. > Deleting element 912 of 1536. > Deleting element 913 of 1536. > drwobjs: 0 > Showing only 90 elements of 1472 > drwobjs: 0 > inside gencen 1472 F 4 > done gencen 1472 > 1 END ELEMENTS > 2 MODIFY ELEMENT > 3 GLOBAL REFINE > 4 CURVE SIDES > 5 DELETE ELEMENT > 6 ZOOM > 7 SET GRID > 8 DEFINE OBJECT > 9 REDRAW MESH > 10 IMPORT MESH > 11 IMPORT VTK MESH > 12 IMPORT vtx MESH > 13 REFLECT MESH > Choose item: > 1 > > 1 > 1 ACCEPT MATL,QVOL > 2 SELECT ELEMENT > 3 SELECT MATL [ 0] > 4 SET MATL PROPS,Q > 5 SHOW MATL PROPS,Q > Choose it > > 1 > 1 > start locglob_lexico: 4 1472 5888 1.99999996E-02 > locglob: 1 1 5888 > locglob: 2 81 5888 > locglob: 1 1562 5888 > locglob: 2 1562 5888 > Performing unique_vertex2 self_chk 5888 > done locglob_lexico: 1562 1562 5888 5 > Performing makecell self_chk 5888 > > > *** MIDWAY BREAK MENU *** > ABORT to write build data to file and exit > SET B.C'S to continue > 1 SET BCs > 2 ABORT > Choose item: > > 2 > Generating Mesh Points for 1472 Elements > 1472 this is nel in prexit > Writing Parameters to file > Deleting tmp.* files. > Exiting session 4.59163468E-41 > > > > > > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Nov 3 13:28:43 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 3 Nov 2013 13:28:43 -0600 (CST) Subject: [Nek5000-users] prex question In-Reply-To: Message-ID: Hi Tubois, 11 SET ENTIRE LEVEL applies the next selected boundary condition to any _remaining_ boundaries for which BCs have yet to be defined. In this case, that is just the BCs on the top and bottom of the domain, since the inlet and outlet were prescribed in the box file, while the sides were left blank. The cylinder itself inherits and retains its boundary conditions from the "import.rea" file. Does this clarify? Best, Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Sunday, November 3, 2013 11:35:36 AM Subject: Re: [Nek5000-users] prex question Hi Paul, Thank you very much! Just need a confirm about your mesh. 11 SET ENTIRE LEVEL 1 PERIODIC-AUTO means to set the periodic boundary condition for the box except the inlet already set in fpcyl.box? n Is this a lattice for hex-close-packed spheres?: So the boundary condition for the circle will be set to walls automatically? Thank you! Tubois On Sun, Nov 3, 2013 at 5:46 PM, < nek5000-users at lists.mcs.anl.gov > wrote: Hi Tubois, I've just updated this example and have included a script that appears to work. I recommend moving your existing ext_cyl directory to, say, ext_cyl.1, and then svn update ext_cyl. Then, in the new ext_cyl directory you should be able to type: mkmesh The README file is also updated. Have a look at mkmesh and you can see the basic steps. Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Sunday, November 3, 2013 10:00:17 AM Subject: [Nek5000-users] prex question Hello everyone, 1, I am trying to create the mesh of the example ext_cyl with genbox, and pretek. After consulting the email archives online, I almost got it works. The question lies on mesh-merging. I used pretex. The commands is listed as follows. I got a mesh ext_cyl.rea identical to the one in the example, when I visualized it with postx. However, when I use xxdiff to examine it, I found several differences. BOUNDARY CONDITIONS: FLUID BOUNDARY CONDITIONS: 11 0.00000 0.00000 ..... For the file in the example, this line is P 11 1337.00 3.00000 ...... So which step did I missed? To set the BC in pretek? Can someone gives a detailed command lines? 2, About creating the mesh, the wiki says that Nek5000 works with Moab Cubit, but this software is not free of charge. Is there any other free software for meshing? In the archive, I found the discussion about converting Gambit (we have Gambit in school) mesh to rea. The guy left an email address cmeador at tamu.edu , which is no more valid. Thank you very much! Best regards Tubois ================================================================== Choose a Name for This session: ext_cyl Beginning Session ext_cyl 1 READ PREVIOUS PARAMETERS 2 TYPE IN NEW PARAMETERS 3 CONJ. HEAT TRANSFER MERGE Choose item: 1 1 Enter name of previous session box.rea 1 BUILD FROM FILE 2 BUILD INTERACTIVELY Choose item: 1 1 Enter name of previous session (Default= box.rea ) I pressed ENTER Will Read Mesh and B.C. data from box.rea Reading Element 29 [ 1C] Reading Element 58 [ 1f] Reading Element 87 [ 1I] Reading Element 116 [ 1l] Reading Element 145 [ 1O] Reading Element 174 [ 1r] Reading Element 203 [ 1U] Reading Element 232 [ 1x] Reading Element 261 [ 1a] Reading Element 290 [ 1D] Reading Element 319 [ 1g] Reading Element 348 [ 1J] Reading Element 377 [ 1m] Reading Element 406 [ 1P] Reading Element 435 [ 1s] Reading Element 464 [ 1V] Reading Element 493 [ 1y] Reading Element 522 [ 1b] Reading Element 551 [ 1E] Reading Element 580 [ 1h] Reading Element 609 [ 1K] Reading Element 638 [ 1n] Reading Element 667 [ 1Q] Reading Element 696 [ 1t] Reading Element 725 [ 1W] Reading Element 754 [ 1z] Reading Element 783 [ 1c] Reading Element 812 [ 1F] Reading Element 841 [ 1i] Reading Element 870 [ 1L] Reading Element 899 [ 1o] Reading Element 928 [ 1R] Reading Element 957 [ 1u] Reading Element 986 [ 1X] Reading Element 1015 [ 1A] Reading Element 1044 [ 1d] Reading Element 1073 [ 1G] Reading Element 1102 [ 1j] Reading Element 1131 [ 1M] Reading Element 1160 [ 1p] Reading Element 1189 [ 1S] Reading Element 1218 [ 1v] Reading Element 1247 [ 1Y] Reading Element 1276 [ 1B] Reading Element 1305 [ 1e] Reading Element 1334 [ 1H] Reading Element 1363 [ 1k] Reading Element 1392 [ 1N] Reading Element 1421 [ 1q] Reading Element 1450 [ 1T] drwobjs: 0 Showing only 90 elements of 1456 *** BUILD MENU *** inside gencen 1456 F 4 done gencen 1456 1 END ELEMENTS 2 MODIFY ELEMENT 3 GLOBAL REFINE 4 CURVE SIDES 5 DELETE ELEMENT 6 ZOOM 7 SET GRID 8 DEFINE OBJECT 9 REDRAW MESH 10 IMPORT MESH 11 IMPORT VTK MESH 12 IMPORT vtx MESH 13 REFLECT MESH Choose item: 10 10 input name of new .rea file import.rea Would you like to displace existing elements in box? y Found 80 curve sides. IFLD: 1 1 T F ***** FLUID BOUNDARY CONDITIONS ***** ***** FLUID BOUNDARY CONDITIONS *****$ This is nel,ncurve old: 1456 0 This is nel,ncurve new: 1536 80 inside gencen 1536 F 4 done gencen 1536 X min/max of new elements: -1.200000 1.200001 Y min/max of new elements: -1.200000 1.200000 NO KEEP: 514 F -1.0500000 -1.0500000 0.0000000 NO KEEP: 515 F -0.75000000 -1.0500000 0.0000000 NO KEEP: 516 F -0.45000002 -1.0500000 0.0000000 NO KEEP: 517 F -0.15000001 -1.0500000 0.0000000 NO KEEP: 518 F 0.15000001 -1.0500000 0.0000000 NO KEEP: 519 F 0.45000002 -1.0500000 0.0000000 NO KEEP: 520 F 0.75000000 -1.0500000 0.0000000 NO KEEP: 521 F 1.0500000 -1.0500000 0.0000000 NO KEEP: 570 F -1.0500000 -0.75000000 0.0000000 NO KEEP: 571 F -0.75000000 -0.75000000 0.0000000 NO KEEP: 572 F -0.45000002 -0.75000000 0.0000000 NO KEEP: 573 F -0.15000001 -0.75000000 0.0000000 NO KEEP: 574 F 0.15000001 -0.75000000 0.0000000 NO KEEP: 575 F 0.45000002 -0.75000000 0.0000000 NO KEEP: 576 F 0.75000000 -0.75000000 0.0000000 NO KEEP: 577 F 1.0500000 -0.75000000 0.0000000 NO KEEP: 626 F -1.0500000 -0.45000002 0.0000000 NO KEEP: 627 F -0.75000000 -0.45000002 0.0000000 NO KEEP: 628 F -0.45000002 -0.45000002 0.0000000 NO KEEP: 629 F -0.15000001 -0.45000002 0.0000000 NO KEEP: 630 F 0.15000001 -0.45000002 0.0000000 NO KEEP: 631 F 0.45000002 -0.45000002 0.0000000 NO KEEP: 632 F 0.75000000 -0.45000002 0.0000000 NO KEEP: 633 F 1.0500000 -0.45000002 0.0000000 NO KEEP: 682 F -1.0500000 -0.15000001 0.0000000 NO KEEP: 683 F -0.75000000 -0.15000001 0.0000000 NO KEEP: 684 F -0.45000002 -0.15000001 0.0000000 NO KEEP: 685 F -0.15000001 -0.15000001 0.0000000 NO KEEP: 686 F 0.15000001 -0.15000001 0.0000000 NO KEEP: 687 F 0.45000002 -0.15000001 0.0000000 NO KEEP: 688 F 0.75000000 -0.15000001 0.0000000 NO KEEP: 689 F 1.0500000 -0.15000001 0.0000000 NO KEEP: 738 F -1.0500000 0.15000001 0.0000000 NO KEEP: 739 F -0.75000000 0.15000001 0.0000000 NO KEEP: 740 F -0.45000002 0.15000001 0.0000000 NO KEEP: 741 F -0.15000001 0.15000001 0.0000000 NO KEEP: 742 F 0.15000001 0.15000001 0.0000000 NO KEEP: 743 F 0.45000002 0.15000001 0.0000000 NO KEEP: 744 F 0.75000000 0.15000001 0.0000000 NO KEEP: 745 F 1.0500000 0.15000001 0.0000000 NO KEEP: 794 F -1.0500000 0.45000002 0.0000000 NO KEEP: 795 F -0.75000000 0.45000002 0.0000000 NO KEEP: 796 F -0.45000002 0.45000002 0.0000000 NO KEEP: 797 F -0.15000001 0.45000002 0.0000000 NO KEEP: 798 F 0.15000001 0.45000002 0.0000000 NO KEEP: 799 F 0.45000002 0.45000002 0.0000000 NO KEEP: 800 F 0.75000000 0.45000002 0.0000000 NO KEEP: 801 F 1.0500000 0.45000002 0.0000000 NO KEEP: 850 F -1.0500000 0.75000000 0.0000000 NO KEEP: 851 F -0.75000000 0.75000000 0.0000000 NO KEEP: 852 F -0.45000002 0.75000000 0.0000000 NO KEEP: 853 F -0.15000001 0.75000000 0.0000000 NO KEEP: 854 F 0.15000001 0.75000000 0.0000000 NO KEEP: 855 F 0.45000002 0.75000000 0.0000000 NO KEEP: 856 F 0.75000000 0.75000000 0.0000000 NO KEEP: 857 F 1.0500000 0.75000000 0.0000000 NO KEEP: 906 F -1.0500000 1.0500000 0.0000000 NO KEEP: 907 F -0.75000000 1.0500000 0.0000000 NO KEEP: 908 F -0.45000002 1.0500000 0.0000000 NO KEEP: 909 F -0.15000001 1.0500000 0.0000000 NO KEEP: 910 F 0.15000001 1.0500000 0.0000000 NO KEEP: 911 F 0.45000002 1.0500000 0.0000000 NO KEEP: 912 F 0.75000000 1.0500000 0.0000000 NO KEEP: 913 F 1.0500000 1.0500000 0.0000000 Deleting element 514 of 1536. Deleting element 515 of 1536. Deleting element 516 of 1536. Deleting element 517 of 1536. Deleting element 518 of 1536. Deleting element 519 of 1536. Deleting element 520 of 1536. Deleting element 521 of 1536. Deleting element 570 of 1536. Deleting element 571 of 1536. Deleting element 572 of 1536. Deleting element 573 of 1536. Deleting element 574 of 1536. Deleting element 575 of 1536. Deleting element 576 of 1536. Deleting element 577 of 1536. Deleting element 626 of 1536. Deleting element 627 of 1536. Deleting element 628 of 1536. Deleting element 629 of 1536. Deleting element 630 of 1536. Deleting element 631 of 1536. Deleting element 632 of 1536. Deleting element 633 of 1536. Deleting element 682 of 1536. Deleting element 683 of 1536. Deleting element 684 of 1536. Deleting element 685 of 1536. Deleting element 686 of 1536. Deleting element 687 of 1536. Deleting element 688 of 1536. Deleting element 689 of 1536. Deleting element 738 of 1536. Deleting element 739 of 1536. Deleting element 740 of 1536. Deleting element 741 of 1536. Deleting element 742 of 1536. Deleting element 743 of 1536. Deleting element 744 of 1536. Deleting element 745 of 1536. Deleting element 794 of 1536. Deleting element 795 of 1536. Deleting element 796 of 1536. Deleting element 797 of 1536. Deleting element 798 of 1536. Deleting element 799 of 1536. Deleting element 800 of 1536. Deleting element 801 of 1536. Deleting element 850 of 1536. Deleting element 851 of 1536. Deleting element 852 of 1536. Deleting element 853 of 1536. Deleting element 854 of 1536. Deleting element 855 of 1536. Deleting element 856 of 1536. Deleting element 857 of 1536. Deleting element 906 of 1536. Deleting element 907 of 1536. Deleting element 908 of 1536. Deleting element 909 of 1536. Deleting element 910 of 1536. Deleting element 911 of 1536. Deleting element 912 of 1536. Deleting element 913 of 1536. drwobjs: 0 Showing only 90 elements of 1472 drwobjs: 0 inside gencen 1472 F 4 done gencen 1472 1 END ELEMENTS 2 MODIFY ELEMENT 3 GLOBAL REFINE 4 CURVE SIDES 5 DELETE ELEMENT 6 ZOOM 7 SET GRID 8 DEFINE OBJECT 9 REDRAW MESH 10 IMPORT MESH 11 IMPORT VTK MESH 12 IMPORT vtx MESH 13 REFLECT MESH Choose item: 1 1 1 ACCEPT MATL,QVOL 2 SELECT ELEMENT 3 SELECT MATL [ 0] 4 SET MATL PROPS,Q 5 SHOW MATL PROPS,Q Choose it 1 1 start locglob_lexico: 4 1472 5888 1.99999996E-02 locglob: 1 1 5888 locglob: 2 81 5888 locglob: 1 1562 5888 locglob: 2 1562 5888 Performing unique_vertex2 self_chk 5888 done locglob_lexico: 1562 1562 5888 5 Performing makecell self_chk 5888 *** MIDWAY BREAK MENU *** ABORT to write build data to file and exit SET B.C'S to continue 1 SET BCs 2 ABORT Choose item: 2 Generating Mesh Points for 1472 Elements 1472 this is nel in prexit Writing Parameters to file Deleting tmp.* files. Exiting session 4.59163468E-41 _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sun Nov 3 13:57:59 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 3 Nov 2013 20:57:59 +0100 Subject: [Nek5000-users] prex question In-Reply-To: References: Message-ID: Hi Paul, It is very clear with your explaination. Thank you very much! Best Tubois On Sun, Nov 3, 2013 at 8:28 PM, wrote: > > Hi Tubois, > > 11 SET ENTIRE LEVEL applies the next selected > boundary condition to any _remaining_ boundaries for which > BCs have yet to be defined. > > In this case, that is just the BCs on the top and bottom > of the domain, since the inlet and outlet were prescribed > in the box file, while the sides were left blank. The > cylinder itself inherits and retains its boundary conditions > from the "import.rea" file. > > Does this clarify? > > Best, Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Sunday, November 3, 2013 11:35:36 AM > Subject: Re: [Nek5000-users] prex question > > > > Hi Paul, > > > Thank you very much! Just need a confirm about your mesh. > 11 SET ENTIRE LEVEL > 1 PERIODIC-AUTO > means to set the periodic boundary condition for the box except the inlet > already set in fpcyl.box? > n Is this a lattice for hex-close-packed spheres?: > So the boundary condition for the circle will be set to walls > automatically? > > > Thank you! > > > Tubois > > > > > > On Sun, Nov 3, 2013 at 5:46 PM, < nek5000-users at lists.mcs.anl.gov > wrote: > > > > Hi Tubois, > > I've just updated this example and have included a script that appears > to work. > > I recommend moving your existing ext_cyl directory to, say, ext_cyl.1, > and then svn update ext_cyl. > > Then, in the new ext_cyl directory you should be able to type: > > mkmesh > > > The README file is also updated. Have a look at mkmesh and you > can see the basic steps. > > Paul > > > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: nek5000-users at lists.mcs.anl.gov > Sent: Sunday, November 3, 2013 10:00:17 AM > Subject: [Nek5000-users] prex question > > > > Hello everyone, > > > 1, I am trying to create the mesh of the example ext_cyl with genbox, and > pretek. After consulting the email archives online, I almost got it works. > The question lies on mesh-merging. I used pretex. The commands is listed as > follows. > > > I got a mesh ext_cyl.rea identical to the one in the example, when I > visualized it with postx. However, when I use xxdiff to examine it, I found > several differences. > BOUNDARY CONDITIONS: > FLUID BOUNDARY CONDITIONS: > 11 0.00000 0.00000 ..... > For the file in the example, this line is > P 11 1337.00 3.00000 ...... > > > So which step did I missed? To set the BC in pretek? Can someone gives a > detailed command lines? > > > 2, About creating the mesh, the wiki says that Nek5000 works with Moab > Cubit, but this software is not free of charge. Is there any other free > software for meshing? In the archive, I found the discussion about > converting Gambit (we have Gambit in school) mesh to rea. The guy left an > email address cmeador at tamu.edu , which is no more valid. > > > Thank you very much! > > > Best regards > > > Tubois > ================================================================== > > > Choose a Name for This session: > ext_cyl > > Beginning Session ext_cyl > 1 READ PREVIOUS PARAMETERS > 2 TYPE IN NEW PARAMETERS > 3 CONJ. HEAT TRANSFER MERGE > Choose item: > 1 > 1 > Enter name of previous session > box.rea > 1 BUILD FROM FILE > 2 BUILD INTERACTIVELY > Choose item: > 1 > 1 > Enter name of previous session > (Default= box.rea ) > I pressed ENTER > > > > Will Read Mesh and B.C. data from box.rea > Reading Element 29 [ 1C] > Reading Element 58 [ 1f] > Reading Element 87 [ 1I] > Reading Element 116 [ 1l] > Reading Element 145 [ 1O] > Reading Element 174 [ 1r] > Reading Element 203 [ 1U] > Reading Element 232 [ 1x] > Reading Element 261 [ 1a] > Reading Element 290 [ 1D] > Reading Element 319 [ 1g] > Reading Element 348 [ 1J] > Reading Element 377 [ 1m] > Reading Element 406 [ 1P] > Reading Element 435 [ 1s] > Reading Element 464 [ 1V] > Reading Element 493 [ 1y] > Reading Element 522 [ 1b] > Reading Element 551 [ 1E] > Reading Element 580 [ 1h] > Reading Element 609 [ 1K] > Reading Element 638 [ 1n] > Reading Element 667 [ 1Q] > Reading Element 696 [ 1t] > Reading Element 725 [ 1W] > Reading Element 754 [ 1z] > Reading Element 783 [ 1c] > Reading Element 812 [ 1F] > Reading Element 841 [ 1i] > Reading Element 870 [ 1L] > Reading Element 899 [ 1o] > Reading Element 928 [ 1R] > Reading Element 957 [ 1u] > Reading Element 986 [ 1X] > Reading Element 1015 [ 1A] > Reading Element 1044 [ 1d] > Reading Element 1073 [ 1G] > Reading Element 1102 [ 1j] > Reading Element 1131 [ 1M] > Reading Element 1160 [ 1p] > Reading Element 1189 [ 1S] > Reading Element 1218 [ 1v] > Reading Element 1247 [ 1Y] > Reading Element 1276 [ 1B] > Reading Element 1305 [ 1e] > Reading Element 1334 [ 1H] > Reading Element 1363 [ 1k] > Reading Element 1392 [ 1N] > Reading Element 1421 [ 1q] > Reading Element 1450 [ 1T] > drwobjs: 0 > Showing only 90 elements of 1456 > *** BUILD MENU *** > inside gencen 1456 F 4 > done gencen 1456 > 1 END ELEMENTS > 2 MODIFY ELEMENT > 3 GLOBAL REFINE > 4 CURVE SIDES > 5 DELETE ELEMENT > 6 ZOOM > 7 SET GRID > 8 DEFINE OBJECT > 9 REDRAW MESH > 10 IMPORT MESH > 11 IMPORT VTK MESH > 12 IMPORT vtx MESH > 13 REFLECT MESH > Choose item: > 10 > > 10 > input name of new .rea file > import.rea > > Would you like to displace existing elements in box? > y > > Found 80 curve sides. > IFLD: 1 1 T F > ***** FLUID BOUNDARY CONDITIONS ***** > ***** FLUID BOUNDARY CONDITIONS *****$ > This is nel,ncurve old: 1456 0 > This is nel,ncurve new: 1536 80 > inside gencen 1536 F 4 > done gencen 1536 > X min/max of new elements: -1.200000 1.200001 > Y min/max of new elements: -1.200000 1.200000 > NO KEEP: 514 F -1.0500000 -1.0500000 0.0000000 > NO KEEP: 515 F -0.75000000 -1.0500000 0.0000000 > NO KEEP: 516 F -0.45000002 -1.0500000 0.0000000 > NO KEEP: 517 F -0.15000001 -1.0500000 0.0000000 > NO KEEP: 518 F 0.15000001 -1.0500000 0.0000000 > NO KEEP: 519 F 0.45000002 -1.0500000 0.0000000 > NO KEEP: 520 F 0.75000000 -1.0500000 0.0000000 > NO KEEP: 521 F 1.0500000 -1.0500000 0.0000000 > NO KEEP: 570 F -1.0500000 -0.75000000 0.0000000 > NO KEEP: 571 F -0.75000000 -0.75000000 0.0000000 > NO KEEP: 572 F -0.45000002 -0.75000000 0.0000000 > NO KEEP: 573 F -0.15000001 -0.75000000 0.0000000 > NO KEEP: 574 F 0.15000001 -0.75000000 0.0000000 > NO KEEP: 575 F 0.45000002 -0.75000000 0.0000000 > NO KEEP: 576 F 0.75000000 -0.75000000 0.0000000 > NO KEEP: 577 F 1.0500000 -0.75000000 0.0000000 > NO KEEP: 626 F -1.0500000 -0.45000002 0.0000000 > NO KEEP: 627 F -0.75000000 -0.45000002 0.0000000 > NO KEEP: 628 F -0.45000002 -0.45000002 0.0000000 > NO KEEP: 629 F -0.15000001 -0.45000002 0.0000000 > NO KEEP: 630 F 0.15000001 -0.45000002 0.0000000 > NO KEEP: 631 F 0.45000002 -0.45000002 0.0000000 > NO KEEP: 632 F 0.75000000 -0.45000002 0.0000000 > NO KEEP: 633 F 1.0500000 -0.45000002 0.0000000 > NO KEEP: 682 F -1.0500000 -0.15000001 0.0000000 > NO KEEP: 683 F -0.75000000 -0.15000001 0.0000000 > NO KEEP: 684 F -0.45000002 -0.15000001 0.0000000 > NO KEEP: 685 F -0.15000001 -0.15000001 0.0000000 > NO KEEP: 686 F 0.15000001 -0.15000001 0.0000000 > NO KEEP: 687 F 0.45000002 -0.15000001 0.0000000 > NO KEEP: 688 F 0.75000000 -0.15000001 0.0000000 > NO KEEP: 689 F 1.0500000 -0.15000001 0.0000000 > NO KEEP: 738 F -1.0500000 0.15000001 0.0000000 > NO KEEP: 739 F -0.75000000 0.15000001 0.0000000 > NO KEEP: 740 F -0.45000002 0.15000001 0.0000000 > NO KEEP: 741 F -0.15000001 0.15000001 0.0000000 > NO KEEP: 742 F 0.15000001 0.15000001 0.0000000 > NO KEEP: 743 F 0.45000002 0.15000001 0.0000000 > NO KEEP: 744 F 0.75000000 0.15000001 0.0000000 > NO KEEP: 745 F 1.0500000 0.15000001 0.0000000 > NO KEEP: 794 F -1.0500000 0.45000002 0.0000000 > NO KEEP: 795 F -0.75000000 0.45000002 0.0000000 > NO KEEP: 796 F -0.45000002 0.45000002 0.0000000 > NO KEEP: 797 F -0.15000001 0.45000002 0.0000000 > NO KEEP: 798 F 0.15000001 0.45000002 0.0000000 > NO KEEP: 799 F 0.45000002 0.45000002 0.0000000 > NO KEEP: 800 F 0.75000000 0.45000002 0.0000000 > NO KEEP: 801 F 1.0500000 0.45000002 0.0000000 > NO KEEP: 850 F -1.0500000 0.75000000 0.0000000 > NO KEEP: 851 F -0.75000000 0.75000000 0.0000000 > NO KEEP: 852 F -0.45000002 0.75000000 0.0000000 > NO KEEP: 853 F -0.15000001 0.75000000 0.0000000 > NO KEEP: 854 F 0.15000001 0.75000000 0.0000000 > NO KEEP: 855 F 0.45000002 0.75000000 0.0000000 > NO KEEP: 856 F 0.75000000 0.75000000 0.0000000 > NO KEEP: 857 F 1.0500000 0.75000000 0.0000000 > NO KEEP: 906 F -1.0500000 1.0500000 0.0000000 > NO KEEP: 907 F -0.75000000 1.0500000 0.0000000 > NO KEEP: 908 F -0.45000002 1.0500000 0.0000000 > NO KEEP: 909 F -0.15000001 1.0500000 0.0000000 > NO KEEP: 910 F 0.15000001 1.0500000 0.0000000 > NO KEEP: 911 F 0.45000002 1.0500000 0.0000000 > NO KEEP: 912 F 0.75000000 1.0500000 0.0000000 > NO KEEP: 913 F 1.0500000 1.0500000 0.0000000 > Deleting element 514 of 1536. > Deleting element 515 of 1536. > Deleting element 516 of 1536. > Deleting element 517 of 1536. > Deleting element 518 of 1536. > Deleting element 519 of 1536. > Deleting element 520 of 1536. > Deleting element 521 of 1536. > Deleting element 570 of 1536. > Deleting element 571 of 1536. > Deleting element 572 of 1536. > Deleting element 573 of 1536. > Deleting element 574 of 1536. > Deleting element 575 of 1536. > Deleting element 576 of 1536. > Deleting element 577 of 1536. > Deleting element 626 of 1536. > Deleting element 627 of 1536. > Deleting element 628 of 1536. > Deleting element 629 of 1536. > Deleting element 630 of 1536. > Deleting element 631 of 1536. > Deleting element 632 of 1536. > Deleting element 633 of 1536. > Deleting element 682 of 1536. > Deleting element 683 of 1536. > Deleting element 684 of 1536. > Deleting element 685 of 1536. > Deleting element 686 of 1536. > Deleting element 687 of 1536. > Deleting element 688 of 1536. > Deleting element 689 of 1536. > Deleting element 738 of 1536. > Deleting element 739 of 1536. > Deleting element 740 of 1536. > Deleting element 741 of 1536. > Deleting element 742 of 1536. > Deleting element 743 of 1536. > Deleting element 744 of 1536. > Deleting element 745 of 1536. > Deleting element 794 of 1536. > Deleting element 795 of 1536. > Deleting element 796 of 1536. > Deleting element 797 of 1536. > Deleting element 798 of 1536. > Deleting element 799 of 1536. > Deleting element 800 of 1536. > Deleting element 801 of 1536. > Deleting element 850 of 1536. > Deleting element 851 of 1536. > Deleting element 852 of 1536. > Deleting element 853 of 1536. > Deleting element 854 of 1536. > Deleting element 855 of 1536. > Deleting element 856 of 1536. > Deleting element 857 of 1536. > Deleting element 906 of 1536. > Deleting element 907 of 1536. > Deleting element 908 of 1536. > Deleting element 909 of 1536. > Deleting element 910 of 1536. > Deleting element 911 of 1536. > Deleting element 912 of 1536. > Deleting element 913 of 1536. > drwobjs: 0 > Showing only 90 elements of 1472 > drwobjs: 0 > inside gencen 1472 F 4 > done gencen 1472 > 1 END ELEMENTS > 2 MODIFY ELEMENT > 3 GLOBAL REFINE > 4 CURVE SIDES > 5 DELETE ELEMENT > 6 ZOOM > 7 SET GRID > 8 DEFINE OBJECT > 9 REDRAW MESH > 10 IMPORT MESH > 11 IMPORT VTK MESH > 12 IMPORT vtx MESH > 13 REFLECT MESH > Choose item: > 1 > > 1 > 1 ACCEPT MATL,QVOL > 2 SELECT ELEMENT > 3 SELECT MATL [ 0] > 4 SET MATL PROPS,Q > 5 SHOW MATL PROPS,Q > Choose it > > 1 > 1 > start locglob_lexico: 4 1472 5888 1.99999996E-02 > locglob: 1 1 5888 > locglob: 2 81 5888 > locglob: 1 1562 5888 > locglob: 2 1562 5888 > Performing unique_vertex2 self_chk 5888 > done locglob_lexico: 1562 1562 5888 5 > Performing makecell self_chk 5888 > > > *** MIDWAY BREAK MENU *** > ABORT to write build data to file and exit > SET B.C'S to continue > 1 SET BCs > 2 ABORT > Choose item: > > 2 > Generating Mesh Points for 1472 Elements > 1472 this is nel in prexit > Writing Parameters to file > Deleting tmp.* files. > Exiting session 4.59163468E-41 > > > > > > > > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 4 02:33:30 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 4 Nov 2013 16:33:30 +0800 Subject: [Nek5000-users] hello from a new user (+ a couple of questions) Message-ID: Dear all, Firstly, I am a Nek5000 newbie, so please accept my apologies for any daft questions! - I have been working through the draft user guide, and am trying to view the the eddy_uv case using postx. Unfortunately the GUI seems to be corrupted, with missing text etc. (screengrab here: https://dl.dropboxusercontent.com/u/4391032/Nekton_001.png ) I am using Linux Mint with nvidia proprietary drivers, the problem seems to affect the other NEKTON tools (prex etc.) so I'm guessing it could be an X11 issue? Has anyone encountered this before? How did you fix it? 2) For meshing, I'm interested in fairly idealised, structured geometries, (e.g. impinging jets, boundary layers etc). I have a heap of existing OpenFOAM (hexahedral) blockMeshes already set up for LES. Has anyone managed to convert an OpenFOAM mesh to Nek5000? (Is it even possible to do this with a higher-order spectral code?) I was thinking about trying foamMeshToFluent, and then using the python script written by Mikael Mortensen ( https://bitbucket.org/mikael_mortensen/nek5000-tools ). Is this feasible? Thanks very much! James -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 4 05:26:19 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 4 Nov 2013 12:26:19 +0100 Subject: [Nek5000-users] fld output Message-ID: Hi Katie, Do you mean the looping and output of data occurs in the last part of the 'outfld' subroutine or in the last part of 'prepost.f'? Because I can't seem to figure out where exactly the format of how the data is written to file is set and where it is actually written to file. Thank you, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 4 06:32:04 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 4 Nov 2013 06:32:04 -0600 (CST) Subject: [Nek5000-users] fld output In-Reply-To: References: Message-ID: Hi JP, Just curious regarding your objective -- are you needing to read the files, or trying to write some new data? If I understand this I might be able to point you in the right direction. Best, Paul On Mon, 4 Nov 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi Katie, > > Do you mean the looping and output of data occurs in the last part of the > 'outfld' subroutine or in the last part of 'prepost.f'? Because I can't > seem to figure out where exactly the format of how the data is written to > file is set and where it is actually written to file. > > Thank you, > JP > From nek5000-users at lists.mcs.anl.gov Mon Nov 4 11:15:49 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 4 Nov 2013 11:15:49 -0600 Subject: [Nek5000-users] hello from a new user (+ a couple of questions) In-Reply-To: References: Message-ID: James, I have not done a conversion from openFoam format to Nek format myself, but this should be possible. The only thing Nek needs for elements are the element corners (or, additionally, face curvature information in the case of curved hexahedrals). The location of the internal solution nodes for each element are computed at run-time. All that being said, you might want to use caution when using your existing OpenFOAM meshes in Nek. Directly using a mesh designed for a low order code in a high order code would result in a much larger DOF count than desired, so it may be best to re-design your mesh for use in Nek. - Josh On Mon, Nov 4, 2013 at 2:33 AM, wrote: > Dear all, > > Firstly, I am a Nek5000 newbie, so please accept my apologies for any daft > questions! > > > - I have been working through the draft user guide, and am trying to view > the the eddy_uv case using postx. Unfortunately the GUI seems to be > corrupted, with missing text etc. (screengrab here: > https://dl.dropboxusercontent.com/u/4391032/Nekton_001.png ) > > I am using Linux Mint with nvidia proprietary drivers, the problem seems > to affect the other NEKTON tools (prex etc.) so I'm guessing it could be an > X11 issue? Has anyone encountered this before? How did you fix it? > > > 2) For meshing, I'm interested in fairly idealised, structured geometries, > (e.g. impinging jets, boundary layers etc). I have a heap of existing > OpenFOAM (hexahedral) blockMeshes already set up for LES. Has anyone > managed to convert an OpenFOAM mesh to Nek5000? (Is it even possible to do > this with a higher-order spectral code?) I was thinking about trying > foamMeshToFluent, and then using the python script written by Mikael > Mortensen ( https://bitbucket.org/mikael_mortensen/nek5000-tools ). Is > this feasible? > > > Thanks very much! > > James > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 4 12:28:29 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 4 Nov 2013 12:28:29 -0600 Subject: [Nek5000-users] fld output In-Reply-To: References: Message-ID: Hi JP, The last part of subroutine outfld loops over the elements and outputs the data to the files. (around lines 430-455). Inside this loop, fill_tmp is called. This is where the data is actually loaded into an array (tdump). After the array is loaded with the appropriate data, it is sent to node 0, which calls out_tmp(). out_tmp() is where the data is actually written out into the fld file. As Paul mentioned, we might be able to give you a more specific explanation to achieve your desired results with a better understanding of your objectives. Best, Katie On Mon, Nov 4, 2013 at 6:32 AM, wrote: > > Hi JP, > > Just curious regarding your objective -- are you needing > to read the files, or trying to write some new data? > > If I understand this I might be able to point you in the > right direction. > > Best, Paul > > > > On Mon, 4 Nov 2013, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Katie, >> >> Do you mean the looping and output of data occurs in the last part of the >> 'outfld' subroutine or in the last part of 'prepost.f'? Because I can't >> seem to figure out where exactly the format of how the data is written to >> file is set and where it is actually written to file. >> >> Thank you, >> JP >> >> _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Nov 4 23:22:04 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 5 Nov 2013 10:52:04 +0530 Subject: [Nek5000-users] Variable density flows In-Reply-To: References: Message-ID: These tips are most useful. I am able to run some high Re and high Pe cases but I still need really large meshes to ensure that the scalar stays bounded between [0,1]. Is the characteristic time stepping going to be useful for these cases ? I have read that it allows larger time steps. Since "characteristic" means some upwind effect, I was wondering does it help to maintain better monotonicity of advected scalars ? Thanks praveen On Mon, Oct 14, 2013 at 12:37 AM, wrote: > Hi Praveen, > > Your clipping implementation will as you have it -- I normally would > do it in a single loop: > > n=nx1*ny1*nz1*nelt > do i=1,n > t(i,1,1,1,2)=min(1.,t(i,1,1,1,2)) > t(i,1,1,1,2)=max(0.,t(i,1,1,1,2)) > enddo > > You can turn on filtering by setting param(103) in your .rea file. > Setting p103=.05, say, would reduce the energy in the Nth mode by > 5% each timestep --- this is usually a good choice. Sometimes it > pays to bump this up to, say, .1, but usually a better strategy is > to add another mode to the filter, by setting p101 to 1, or 2. > In this case, the filter amplitude for the N-1 mode is alpha/4 > when p101=1 and when p101=2, we have amplitudes as: > > a(N) = alpha := p103 > a(N-1) = alpha*(2/3)**2 = 4*alpha/9 > a(N-2) = alpha*(1/3)**2 = alpha/9 > > which amounts to fitting a parabola through the filter amplitudes so > that the filter strength decays smoothly to zero. > > p103 = .05 > p101 = 1 > > are my common choices when lx1=8. If lx1 < 8, I typically set p101=0 > as you're otherwise cutting too deeply into low end of the spectrum. > > All this being said, you'll no doubt still need clipping if Sc=100,000. > > Paul > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 5 04:05:25 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 5 Nov 2013 11:05:25 +0100 Subject: [Nek5000-users] fld output Message-ID: Hi Paul, I basically would like to know the exact format of the files to be able to manipulate them. But knowing where the format is set and being able to edit it would allow me to write the files directly in any format. Thank you, JP -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 5 06:32:16 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 5 Nov 2013 06:32:16 -0600 (CST) Subject: [Nek5000-users] Variable density flows In-Reply-To: Message-ID: Hi Praveen, The only way to guarantee monotonicity when under-resolved is to effectively increase viscosity; whether it be uniformly or locally (preferred). ? This is still an active area of research. ? If I were in your place, I would clip until I found a better strategy... (something still foremost in my mind). Note that upwinding, limiters, and the recent (and promising) entropy viscosity method all achieve monotonicity or near-monotonicity via (local) dissipation. ?(With limiters it's not clear that you're diffusing, but in effect that is what happens.) Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: "nek5000" Sent: Monday, November 4, 2013 11:22:04 PM Subject: Re: [Nek5000-users] Variable density flows These tips are most useful. I am able to run some high Re and high Pe cases but I still need really large meshes to ensure that the scalar stays bounded between [0,1]. Is the characteristic time stepping going to be useful for these cases ? I have read that it allows larger time steps. Since "characteristic" means some upwind effect, I was wondering does it help to maintain better monotonicity of advected scalars ? Thanks praveen On Mon, Oct 14, 2013 at 12:37 AM, < nek5000-users at lists.mcs.anl.gov > wrote: Hi Praveen, Your clipping implementation will as you have it -- I normally would do it in a single loop: n=nx1*ny1*nz1*nelt do i=1,n t(i,1,1,1,2)=min(1.,t(i,1,1,1,2)) t(i,1,1,1,2)=max(0.,t(i,1,1,1,2)) enddo You can turn on filtering by setting param(103) in your .rea file. Setting p103=.05, say, would reduce the energy in the Nth mode by 5% each timestep --- this is usually a good choice. Sometimes it pays to bump this up to, say, .1, but usually a better strategy is to add another mode to the filter, by setting p101 to 1, or 2. In this case, the filter amplitude for the N-1 mode is alpha/4 when p101=1 and when p101=2, we have amplitudes as: a(N) = alpha := p103 a(N-1) = alpha*(2/3)**2 = 4*alpha/9 a(N-2) = alpha*(1/3)**2 = alpha/9 which amounts to fitting a parabola through the filter amplitudes so that the filter strength decays smoothly to zero. p103 = .05 p101 = 1 are my common choices when lx1=8. If lx1 < 8, I typically set p101=0 as you're otherwise cutting too deeply into low end of the spectrum. All this being said, you'll no doubt still need clipping if Sc=100,000. Paul _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Tue Nov 5 06:49:33 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 5 Nov 2013 06:49:33 -0600 (CST) Subject: [Nek5000-users] fld output In-Reply-To: References: Message-ID: Hi JP, >From mfo_outv() in prepost .f, I see that the .f0000 file format for a vector field (like velocity or xyz), will be: nxyz values of x nxyz values of y nxyz values of z (if ndim=3) for each element e=1,...,E, where nxyz = lx1*ly1*lz1. They will be in 32-bit reals, unless otherwise specified by the user. Crucial question here is what order the elements are written. That is also specified near the header. Here is the relevant code: #ifdef MPIIO ioff = iHeaderSize + 4 + nelB*isize call byte_set_view (ioff,ifh_mbyte) call byte_write_mpi(lglel,nelt,-1,ifh_mbyte,ierr) #else call byte_write(lglel,nelt,ierr) #endif The array lglel() is the Local-to-Global Element numbering. So, on a given processor, for e=1,...,E_local (aka nelt), spans some ordering in the global element numbering. This ordering is a function of how the domain is partitioned across processors - which impacts the contents of the output file but is not crucial because all of the relevant information (i.e., lglel) is encoded in the header of the f0000 files. The endian (big or little) can be determined when the file is opened for reading by looking at the test word, 6.54321, which is the first real written after the 132 byte header I would recommend looking either at ic.f (where the files are read) or prepost.f (where they are written) to get the precise details. Are you using MPIIO ? If so, the file structure is a bit different -- I didn't write that part so would have to dig to find the precise format in that case. Paul On Tue, 5 Nov 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi Paul, > > I basically would like to know the exact format of the files to be able to > manipulate them. But knowing where the format is set and being able to edit > it would allow me to write the files directly in any format. > > Thank you, > JP > From nek5000-users at lists.mcs.anl.gov Wed Nov 6 22:27:37 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 7 Nov 2013 09:57:37 +0530 Subject: [Nek5000-users] visit visualization question In-Reply-To: References: Message-ID: Hello When I use visit for color plots, I can almost see the mesh as in the attached example. Is this a problem with visit or is my results not correct ? https://www.dropbox.com/s/6gwnwiiide2yn6y/visit0000.png https://www.dropbox.com/s/a49vqx72ft2ajxy/visit0001.png Thanks praveen -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 6 23:39:02 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 6 Nov 2013 21:39:02 -0800 Subject: [Nek5000-users] visit visualization question In-Reply-To: References: Message-ID: Hi Praveen, If it is the issue I think you are referring to, then it has to do with how OpenGL renders. It takes a quadrilateral and splits it into two triangles. If the lower left and bottom right are cyan, and then lower right and upper left are blue, then splitting into two triangles so that lower left and bottom right are connected will make a cyan streak go through the quad ... splitting so that lower right and upper left are connect make a blue streak go through the quad. Best, Hank On Wed, Nov 6, 2013 at 8:27 PM, wrote: > Hello > > When I use visit for color plots, I can almost see the mesh as in the > attached example. Is this a problem with visit or is my results not correct > ? > > https://www.dropbox.com/s/6gwnwiiide2yn6y/visit0000.png > https://www.dropbox.com/s/a49vqx72ft2ajxy/visit0001.png > > Thanks > praveen > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 7 09:12:59 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 7 Nov 2013 16:12:59 +0100 Subject: [Nek5000-users] non-newtonian fluid Message-ID: Hi, I am willing to simulate some non-newtonian fluids by nek5000. I found in the archive some discussions about several models, like *Herschel-Bulkley Bukingham, power law* But none of the models is available online. In the example, there is a var_vis case. I looked into the st2.usr and I do not understand which models is about. Is it to calculate \nu (\nabla^ u)^2 for the diffusion term? Can someone give a detailed discription for this case? I would like to implement a power-law fluid model. There exists an analytical solution in the case of circular pipe so it can be compared with. see http://en.wikipedia.org/wiki/Power-law_fluid If some already implemented this kind of fluids, could you share some sources? Or give a guideline, which subroutine to see. Thank you very much! Tubois -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 7 11:06:21 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 7 Nov 2013 11:06:21 -0600 Subject: [Nek5000-users] non-newtonian fluid In-Reply-To: References: Message-ID: Hi Tubois I can give you some background which may help.. The power law model specifies the visosity as power law in an effective scalar shear rate gamma* so the viscous stress tau is given by tau= eta(gamma*) x gamma where gamma is the tensor dvi/dxj + d vj /dxi and gamma* is sqrt(1/2 gamma::gamma) where :: means two consecutive dot products of the gamma tensor and the function eta for the power law model is eta= m * (gamma*)^n-1 where m and n are material parameters you can start with ket sat n=1/3 or 1/2....etc and the newtonian fluid limit is n=1 for the case of axisymmetric pipe flow vz=f(r) where z is the flow direction and r is the radius ( v_theta=vr=0) it can be shown that the scalar shear rate gamma*= - d vz /d r and that the only stress component is tau_rz and is given by tau_rz=-m*(- d vz /dr ) ^ n-1 * d vz/dr = -m* (-d vz /dr )^n note that gamma tensor has only one non zero component gamma = dvz /d r * [ 0 0 1 ; 0 0 0; 0 0 0] the analytical solution is vz= (n/n+1) * ( (Po-PL)*R / (2*m*L) )^(1/n) *R* [1- (r/R)]^-(n+1)/n Ammar On Thu, Nov 7, 2013 at 9:12 AM, wrote: > Hi, > > I am willing to simulate some non-newtonian fluids by nek5000. I found in > the archive some discussions about several models, like *Herschel-Bulkley > Bukingham, power law* But none of the models is available online. > > In the example, there is a var_vis case. I looked into the st2.usr and I > do not understand which models is about. Is it to calculate \nu (\nabla^ > u)^2 for the diffusion term? Can someone give a detailed discription for > this case? > > I would like to implement a power-law fluid model. There exists an > analytical solution in the case of circular pipe so it can be compared > with. see http://en.wikipedia.org/wiki/Power-law_fluid > > If some already implemented this kind of fluids, could you share some > sources? Or give a guideline, which subroutine to see. > > Thank you very much! > > Tubois > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- http://aelghany.googlepages.com/home -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 7 11:09:12 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 7 Nov 2013 11:09:12 -0600 Subject: [Nek5000-users] non-newtonian fluid In-Reply-To: References: Message-ID: just a small correction gamma = dvz /d r * [ 0 0 1 ; 0 0 0; 1 0 0] and the newtonian limit is n=1 and m= mu Ammar On Thu, Nov 7, 2013 at 11:06 AM, amr7684 . wrote: > Hi Tubois > > I can give you some background which may help.. > > The power law model specifies the visosity as power law in an effective > scalar shear rate gamma* so the viscous stress tau is given by > tau= eta(gamma*) x gamma where gamma is the tensor dvi/dxj + d vj /dxi > > and gamma* is sqrt(1/2 gamma::gamma) where :: means two consecutive dot > products of the gamma tensor > and the function eta for the power law model is eta= m * (gamma*)^n-1 > where m and n are material parameters > you can start with ket sat n=1/3 or 1/2....etc and the newtonian fluid > limit is n=1 > > for the case of axisymmetric pipe flow vz=f(r) where z is the flow > direction and r is the radius ( v_theta=vr=0) > > it can be shown that the scalar shear rate gamma*= - d vz /d r and that > the only stress component is tau_rz and is given by > > tau_rz=-m*(- d vz /dr ) ^ n-1 * d vz/dr = -m* (-d vz /dr )^n > > note that gamma tensor has only one non zero component > gamma = dvz /d r * [ 0 0 1 ; 0 0 0; 0 0 0] > > the analytical solution is > vz= (n/n+1) * ( (Po-PL)*R / (2*m*L) )^(1/n) *R* [1- (r/R)]^-(n+1)/n > > Ammar > > > > > > > > > On Thu, Nov 7, 2013 at 9:12 AM, wrote: > >> Hi, >> >> I am willing to simulate some non-newtonian fluids by nek5000. I found in >> the archive some discussions about several models, like *Herschel-Bulkley >> Bukingham, power law* But none of the models is available online. >> >> In the example, there is a var_vis case. I looked into the st2.usr and I >> do not understand which models is about. Is it to calculate \nu (\nabla^ >> u)^2 for the diffusion term? Can someone give a detailed discription for >> this case? >> >> I would like to implement a power-law fluid model. There exists an >> analytical solution in the case of circular pipe so it can be compared >> with. see http://en.wikipedia.org/wiki/Power-law_fluid >> >> If some already implemented this kind of fluids, could you share some >> sources? Or give a guideline, which subroutine to see. >> >> Thank you very much! >> >> Tubois >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > > -- > http://aelghany.googlepages.com/home > -- http://aelghany.googlepages.com/home -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 7 11:30:58 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 7 Nov 2013 11:30:58 -0600 Subject: [Nek5000-users] visit visualization question In-Reply-To: References: Message-ID: is there any filtering in visit to smooth out features in a given region or below certain length scale? it would be nice for visualization purposes assuming such features do not affect the simulation accuracy. Ammar On Wed, Nov 6, 2013 at 11:39 PM, wrote: > Hi Praveen, > > If it is the issue I think you are referring to, then it has to do with > how OpenGL renders. It takes a quadrilateral and splits it into two > triangles. If the lower left and bottom right are cyan, and then lower > right and upper left are blue, then splitting into two triangles so that > lower left and bottom right are connected will make a cyan streak go > through the quad ... splitting so that lower right and upper left are > connect make a blue streak go through the quad. > > Best, > Hank > > > On Wed, Nov 6, 2013 at 8:27 PM, wrote: > >> Hello >> >> When I use visit for color plots, I can almost see the mesh as in the >> attached example. Is this a problem with visit or is my results not correct >> ? >> >> https://www.dropbox.com/s/6gwnwiiide2yn6y/visit0000.png >> https://www.dropbox.com/s/a49vqx72ft2ajxy/visit0001.png >> >> Thanks >> praveen >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- http://aelghany.googlepages.com/home -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 7 12:07:50 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 7 Nov 2013 10:07:50 -0800 Subject: [Nek5000-users] visit visualization question In-Reply-To: References: Message-ID: Hi Ammar! When you want to make a really pretty picture (for publication), you can apply the Resample operator, which allow you to sample the grid more finely. (The resampling happens on the original mesh ... everything does, except the final rendering stage which is done by graphics hardware.) Best, Hank On Thu, Nov 7, 2013 at 9:30 AM, wrote: > is there any filtering in visit to smooth out features in a given region > or below certain length scale? it would be nice for visualization purposes > assuming such features > do not affect the simulation accuracy. > > Ammar > > > > On Wed, Nov 6, 2013 at 11:39 PM, wrote: > >> Hi Praveen, >> >> If it is the issue I think you are referring to, then it has to do with >> how OpenGL renders. It takes a quadrilateral and splits it into two >> triangles. If the lower left and bottom right are cyan, and then lower >> right and upper left are blue, then splitting into two triangles so that >> lower left and bottom right are connected will make a cyan streak go >> through the quad ... splitting so that lower right and upper left are >> connect make a blue streak go through the quad. >> >> Best, >> Hank >> >> >> On Wed, Nov 6, 2013 at 8:27 PM, wrote: >> >>> Hello >>> >>> When I use visit for color plots, I can almost see the mesh as in the >>> attached example. Is this a problem with visit or is my results not correct >>> ? >>> >>> https://www.dropbox.com/s/6gwnwiiide2yn6y/visit0000.png >>> https://www.dropbox.com/s/a49vqx72ft2ajxy/visit0001.png >>> >>> Thanks >>> praveen >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > > -- > http://aelghany.googlepages.com/home > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 7 12:21:40 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 7 Nov 2013 12:21:40 -0600 Subject: [Nek5000-users] visit visualization question In-Reply-To: References: Message-ID: Thanks a lot Hank! I will try that, Ammar On Thu, Nov 7, 2013 at 12:07 PM, wrote: > Hi Ammar! > > When you want to make a really pretty picture (for publication), you can > apply the Resample operator, which allow you to sample the grid more > finely. (The resampling happens on the original mesh ... everything does, > except the final rendering stage which is done by graphics hardware.) > > Best, > Hank > > > On Thu, Nov 7, 2013 at 9:30 AM, wrote: > >> is there any filtering in visit to smooth out features in a given region >> or below certain length scale? it would be nice for visualization purposes >> assuming such features >> do not affect the simulation accuracy. >> >> Ammar >> >> >> >> On Wed, Nov 6, 2013 at 11:39 PM, wrote: >> >>> Hi Praveen, >>> >>> If it is the issue I think you are referring to, then it has to do with >>> how OpenGL renders. It takes a quadrilateral and splits it into two >>> triangles. If the lower left and bottom right are cyan, and then lower >>> right and upper left are blue, then splitting into two triangles so that >>> lower left and bottom right are connected will make a cyan streak go >>> through the quad ... splitting so that lower right and upper left are >>> connect make a blue streak go through the quad. >>> >>> Best, >>> Hank >>> >>> >>> On Wed, Nov 6, 2013 at 8:27 PM, wrote: >>> >>>> Hello >>>> >>>> When I use visit for color plots, I can almost see the mesh as in the >>>> attached example. Is this a problem with visit or is my results not correct >>>> ? >>>> >>>> https://www.dropbox.com/s/6gwnwiiide2yn6y/visit0000.png >>>> https://www.dropbox.com/s/a49vqx72ft2ajxy/visit0001.png >>>> >>>> Thanks >>>> praveen >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>>> >>>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >> >> >> -- >> http://aelghany.googlepages.com/home >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- http://aelghany.googlepages.com/home -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 7 15:27:16 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 7 Nov 2013 22:27:16 +0100 Subject: [Nek5000-users] Curved sides Message-ID: Hi all, I double and even triple checked with examples, but I keep having to conclusion that the wiki here http://nek5000.mcs.anl.gov/index.php/Curved_Edges_Definition Says exactly the inverse of what is actual concerning positive and negative radius, i.e. I found out that concave/curves inward must have *negative* radius and convex/buldges outward must have *positive* radius Am I alone with this conclusion? (You can test with the example "ext_cyl" for instance for which it is seems quite clear to me) Regards, -- Ismael -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 198 bytes Desc: Digital signature URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 8 01:53:34 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 8 Nov 2013 13:23:34 +0530 Subject: [Nek5000-users] visit visualization question In-Reply-To: References: Message-ID: The latest visit version 2.7 seems to be unable to read my results, I get VisIt could not read from the file "/private/tmp/re10000/channel.nek5000". The generated error message was: There was an error opening /private/tmp/re10000/channel.nek5000. It may be an invalid file. VisIt tried using the following file format readers to open the file: Nek5000, Silo If you know the specific format reader VisIt should use to read this data, you can use Open As... (GUI) or '-o , (CL arg.) and identify that specific reader for VisIt to try. This will possibly give more information on the exact error. Has anybody had success with 2.7 ? My file looks like this filetemplate: channel.fld%02d firsttimestep: 1 numtimesteps: 161 Thanks praveen -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 8 12:29:11 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 8 Nov 2013 12:29:11 -0600 Subject: [Nek5000-users] visit visualization question In-Reply-To: References: Message-ID: Praveen, Another thing you could do is to output your solution onto a uniformly spaced grid within each element(as opposed to the standard GLL points). I have found this to be particularly useful in cases where relatively large, high order elements are used, like I was seeing for my Euler solver. To do this, in usrchk, include the following: (I'm doing this out of memory, so you may want to double check this) subroutine userchk() include 'SIZE' include 'TOTAL' include 'RESTART' ! Not 100% sure about this one integer mynxo mynxo = 10 ifreguo = .true. ! Tells prepost to interpolate to uniformly spaced grid in each element nxo = mynxo ! nxo is the number of points (in each direction) to use within the elements end Theoretically, nxo can be anything from 2 (which would map your solution to linear finite elements) to lxo (which is set in your SIZE file). Although, as I'm writing this, there may be a hard-limit on nxo set somewhere in the source code, so maybe the developers could verify this for me? Using this will output your field files to "_reg" files. Keep in mind that these files will be for output purposes only--restarting from these would incur some potentially heavy interpolation errors. Hope this helps! Josh On Fri, Nov 8, 2013 at 1:53 AM, wrote: > The latest visit version 2.7 seems to be unable to read my results, I get > > VisIt could not read from the file "/private/tmp/re10000/channel.nek5000". > > > The generated error message was: > > > There was an error opening /private/tmp/re10000/channel.nek5000. It may be > an invalid file. > > VisIt tried using the following file format readers to open the file: > Nek5000, Silo > > > If you know the specific format reader VisIt should use to > > read this data, you can use Open As... (GUI) or > > '-o , (CL arg.) and identify that specific reader > > for VisIt to try. This will possibly give more information on > > the exact error. > > > Has anybody had success with 2.7 ? > > > My file looks like this > > > filetemplate: channel.fld%02d > > firsttimestep: 1 > > numtimesteps: 161 > > > Thanks > > praveen > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 8 22:15:05 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 9 Nov 2013 09:45:05 +0530 Subject: [Nek5000-users] visit visualization question In-Reply-To: References: Message-ID: Thank you Josh. This is very useful information. I will try it out on my problem. So this means visit does not make use of the high order definition of the solution but simply does linear interpolation ??? Regards praveen On Fri, Nov 8, 2013 at 11:59 PM, wrote: > Praveen, > > Another thing you could do is to output your solution onto a uniformly > spaced grid within each element(as opposed to the standard GLL points). I > have found this to be particularly useful in cases where relatively large, > high order elements are used, like I was seeing for my Euler solver. > > To do this, in usrchk, include the following: (I'm doing this out of > memory, so you may want to double check this) > > subroutine userchk() > > include 'SIZE' > include 'TOTAL' > include 'RESTART' ! Not 100% sure about this one > > integer mynxo > > mynxo = 10 > ifreguo = .true. ! Tells prepost to interpolate to uniformly spaced > grid in each element > nxo = mynxo ! nxo is the number of points (in each direction) to > use within the elements > > end > > Theoretically, nxo can be anything from 2 (which would map your solution > to linear finite elements) to lxo (which is set in your SIZE file). > Although, as I'm writing this, there may be a hard-limit on nxo set > somewhere in the source code, so maybe the developers could verify this for > me? > > Using this will output your field files to "_reg" files. Keep in mind > that these files will be for output purposes only--restarting from these > would incur some potentially heavy interpolation errors. > > Hope this helps! > > Josh > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Nov 9 10:31:42 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 9 Nov 2013 22:01:42 +0530 Subject: [Nek5000-users] prex question In-Reply-To: References: Message-ID: I have seen that we can read gmsh meshes through moab in 3d. There was a hint that it will be implemented for 2d case also. Is there any chance this will happen ? Thanks praveen On Mon, Nov 4, 2013 at 1:27 AM, wrote: > Hi Paul, > > It is very clear with your explaination. Thank you very much! > > Best > > Tubois > > On Sun, Nov 3, 2013 at 8:28 PM, wrote: > >> >> Hi Tubois, >> >> 11 SET ENTIRE LEVEL applies the next selected >> boundary condition to any _remaining_ boundaries for which >> BCs have yet to be defined. >> >> In this case, that is just the BCs on the top and bottom >> of the domain, since the inlet and outlet were prescribed >> in the box file, while the sides were left blank. The >> cylinder itself inherits and retains its boundary conditions >> from the "import.rea" file. >> >> Does this clarify? >> >> Best, Paul >> >> >> ----- Original Message ----- >> From: nek5000-users at lists.mcs.anl.gov >> To: nek5000-users at lists.mcs.anl.gov >> Sent: Sunday, November 3, 2013 11:35:36 AM >> Subject: Re: [Nek5000-users] prex question >> >> >> >> Hi Paul, >> >> >> Thank you very much! Just need a confirm about your mesh. >> 11 SET ENTIRE LEVEL >> 1 PERIODIC-AUTO >> means to set the periodic boundary condition for the box except the inlet >> already set in fpcyl.box? >> n Is this a lattice for hex-close-packed spheres?: >> So the boundary condition for the circle will be set to walls >> automatically? >> >> >> Thank you! >> >> >> Tubois >> >> >> >> >> >> On Sun, Nov 3, 2013 at 5:46 PM, < nek5000-users at lists.mcs.anl.gov > >> wrote: >> >> >> >> Hi Tubois, >> >> I've just updated this example and have included a script that appears >> to work. >> >> I recommend moving your existing ext_cyl directory to, say, ext_cyl.1, >> and then svn update ext_cyl. >> >> Then, in the new ext_cyl directory you should be able to type: >> >> mkmesh >> >> >> The README file is also updated. Have a look at mkmesh and you >> can see the basic steps. >> >> Paul >> >> >> >> >> ----- Original Message ----- >> From: nek5000-users at lists.mcs.anl.gov >> To: nek5000-users at lists.mcs.anl.gov >> Sent: Sunday, November 3, 2013 10:00:17 AM >> Subject: [Nek5000-users] prex question >> >> >> >> Hello everyone, >> >> >> 1, I am trying to create the mesh of the example ext_cyl with genbox, and >> pretek. After consulting the email archives online, I almost got it works. >> The question lies on mesh-merging. I used pretex. The commands is listed as >> follows. >> >> >> I got a mesh ext_cyl.rea identical to the one in the example, when I >> visualized it with postx. However, when I use xxdiff to examine it, I found >> several differences. >> BOUNDARY CONDITIONS: >> FLUID BOUNDARY CONDITIONS: >> 11 0.00000 0.00000 ..... >> For the file in the example, this line is >> P 11 1337.00 3.00000 ...... >> >> >> So which step did I missed? To set the BC in pretek? Can someone gives a >> detailed command lines? >> >> >> 2, About creating the mesh, the wiki says that Nek5000 works with Moab >> Cubit, but this software is not free of charge. Is there any other free >> software for meshing? In the archive, I found the discussion about >> converting Gambit (we have Gambit in school) mesh to rea. The guy left an >> email address cmeador at tamu.edu , which is no more valid. >> >> >> Thank you very much! >> >> >> Best regards >> >> >> Tubois >> ================================================================== >> >> >> Choose a Name for This session: >> ext_cyl >> >> Beginning Session ext_cyl >> 1 READ PREVIOUS PARAMETERS >> 2 TYPE IN NEW PARAMETERS >> 3 CONJ. HEAT TRANSFER MERGE >> Choose item: >> 1 >> 1 >> Enter name of previous session >> box.rea >> 1 BUILD FROM FILE >> 2 BUILD INTERACTIVELY >> Choose item: >> 1 >> 1 >> Enter name of previous session >> (Default= box.rea ) >> I pressed ENTER >> >> >> >> Will Read Mesh and B.C. data from box.rea >> Reading Element 29 [ 1C] >> Reading Element 58 [ 1f] >> Reading Element 87 [ 1I] >> Reading Element 116 [ 1l] >> Reading Element 145 [ 1O] >> Reading Element 174 [ 1r] >> Reading Element 203 [ 1U] >> Reading Element 232 [ 1x] >> Reading Element 261 [ 1a] >> Reading Element 290 [ 1D] >> Reading Element 319 [ 1g] >> Reading Element 348 [ 1J] >> Reading Element 377 [ 1m] >> Reading Element 406 [ 1P] >> Reading Element 435 [ 1s] >> Reading Element 464 [ 1V] >> Reading Element 493 [ 1y] >> Reading Element 522 [ 1b] >> Reading Element 551 [ 1E] >> Reading Element 580 [ 1h] >> Reading Element 609 [ 1K] >> Reading Element 638 [ 1n] >> Reading Element 667 [ 1Q] >> Reading Element 696 [ 1t] >> Reading Element 725 [ 1W] >> Reading Element 754 [ 1z] >> Reading Element 783 [ 1c] >> Reading Element 812 [ 1F] >> Reading Element 841 [ 1i] >> Reading Element 870 [ 1L] >> Reading Element 899 [ 1o] >> Reading Element 928 [ 1R] >> Reading Element 957 [ 1u] >> Reading Element 986 [ 1X] >> Reading Element 1015 [ 1A] >> Reading Element 1044 [ 1d] >> Reading Element 1073 [ 1G] >> Reading Element 1102 [ 1j] >> Reading Element 1131 [ 1M] >> Reading Element 1160 [ 1p] >> Reading Element 1189 [ 1S] >> Reading Element 1218 [ 1v] >> Reading Element 1247 [ 1Y] >> Reading Element 1276 [ 1B] >> Reading Element 1305 [ 1e] >> Reading Element 1334 [ 1H] >> Reading Element 1363 [ 1k] >> Reading Element 1392 [ 1N] >> Reading Element 1421 [ 1q] >> Reading Element 1450 [ 1T] >> drwobjs: 0 >> Showing only 90 elements of 1456 >> *** BUILD MENU *** >> inside gencen 1456 F 4 >> done gencen 1456 >> 1 END ELEMENTS >> 2 MODIFY ELEMENT >> 3 GLOBAL REFINE >> 4 CURVE SIDES >> 5 DELETE ELEMENT >> 6 ZOOM >> 7 SET GRID >> 8 DEFINE OBJECT >> 9 REDRAW MESH >> 10 IMPORT MESH >> 11 IMPORT VTK MESH >> 12 IMPORT vtx MESH >> 13 REFLECT MESH >> Choose item: >> 10 >> >> 10 >> input name of new .rea file >> import.rea >> >> Would you like to displace existing elements in box? >> y >> >> Found 80 curve sides. >> IFLD: 1 1 T F >> ***** FLUID BOUNDARY CONDITIONS ***** >> ***** FLUID BOUNDARY CONDITIONS *****$ >> This is nel,ncurve old: 1456 0 >> This is nel,ncurve new: 1536 80 >> inside gencen 1536 F 4 >> done gencen 1536 >> X min/max of new elements: -1.200000 1.200001 >> Y min/max of new elements: -1.200000 1.200000 >> NO KEEP: 514 F -1.0500000 -1.0500000 0.0000000 >> NO KEEP: 515 F -0.75000000 -1.0500000 0.0000000 >> NO KEEP: 516 F -0.45000002 -1.0500000 0.0000000 >> NO KEEP: 517 F -0.15000001 -1.0500000 0.0000000 >> NO KEEP: 518 F 0.15000001 -1.0500000 0.0000000 >> NO KEEP: 519 F 0.45000002 -1.0500000 0.0000000 >> NO KEEP: 520 F 0.75000000 -1.0500000 0.0000000 >> NO KEEP: 521 F 1.0500000 -1.0500000 0.0000000 >> NO KEEP: 570 F -1.0500000 -0.75000000 0.0000000 >> NO KEEP: 571 F -0.75000000 -0.75000000 0.0000000 >> NO KEEP: 572 F -0.45000002 -0.75000000 0.0000000 >> NO KEEP: 573 F -0.15000001 -0.75000000 0.0000000 >> NO KEEP: 574 F 0.15000001 -0.75000000 0.0000000 >> NO KEEP: 575 F 0.45000002 -0.75000000 0.0000000 >> NO KEEP: 576 F 0.75000000 -0.75000000 0.0000000 >> NO KEEP: 577 F 1.0500000 -0.75000000 0.0000000 >> NO KEEP: 626 F -1.0500000 -0.45000002 0.0000000 >> NO KEEP: 627 F -0.75000000 -0.45000002 0.0000000 >> NO KEEP: 628 F -0.45000002 -0.45000002 0.0000000 >> NO KEEP: 629 F -0.15000001 -0.45000002 0.0000000 >> NO KEEP: 630 F 0.15000001 -0.45000002 0.0000000 >> NO KEEP: 631 F 0.45000002 -0.45000002 0.0000000 >> NO KEEP: 632 F 0.75000000 -0.45000002 0.0000000 >> NO KEEP: 633 F 1.0500000 -0.45000002 0.0000000 >> NO KEEP: 682 F -1.0500000 -0.15000001 0.0000000 >> NO KEEP: 683 F -0.75000000 -0.15000001 0.0000000 >> NO KEEP: 684 F -0.45000002 -0.15000001 0.0000000 >> NO KEEP: 685 F -0.15000001 -0.15000001 0.0000000 >> NO KEEP: 686 F 0.15000001 -0.15000001 0.0000000 >> NO KEEP: 687 F 0.45000002 -0.15000001 0.0000000 >> NO KEEP: 688 F 0.75000000 -0.15000001 0.0000000 >> NO KEEP: 689 F 1.0500000 -0.15000001 0.0000000 >> NO KEEP: 738 F -1.0500000 0.15000001 0.0000000 >> NO KEEP: 739 F -0.75000000 0.15000001 0.0000000 >> NO KEEP: 740 F -0.45000002 0.15000001 0.0000000 >> NO KEEP: 741 F -0.15000001 0.15000001 0.0000000 >> NO KEEP: 742 F 0.15000001 0.15000001 0.0000000 >> NO KEEP: 743 F 0.45000002 0.15000001 0.0000000 >> NO KEEP: 744 F 0.75000000 0.15000001 0.0000000 >> NO KEEP: 745 F 1.0500000 0.15000001 0.0000000 >> NO KEEP: 794 F -1.0500000 0.45000002 0.0000000 >> NO KEEP: 795 F -0.75000000 0.45000002 0.0000000 >> NO KEEP: 796 F -0.45000002 0.45000002 0.0000000 >> NO KEEP: 797 F -0.15000001 0.45000002 0.0000000 >> NO KEEP: 798 F 0.15000001 0.45000002 0.0000000 >> NO KEEP: 799 F 0.45000002 0.45000002 0.0000000 >> NO KEEP: 800 F 0.75000000 0.45000002 0.0000000 >> NO KEEP: 801 F 1.0500000 0.45000002 0.0000000 >> NO KEEP: 850 F -1.0500000 0.75000000 0.0000000 >> NO KEEP: 851 F -0.75000000 0.75000000 0.0000000 >> NO KEEP: 852 F -0.45000002 0.75000000 0.0000000 >> NO KEEP: 853 F -0.15000001 0.75000000 0.0000000 >> NO KEEP: 854 F 0.15000001 0.75000000 0.0000000 >> NO KEEP: 855 F 0.45000002 0.75000000 0.0000000 >> NO KEEP: 856 F 0.75000000 0.75000000 0.0000000 >> NO KEEP: 857 F 1.0500000 0.75000000 0.0000000 >> NO KEEP: 906 F -1.0500000 1.0500000 0.0000000 >> NO KEEP: 907 F -0.75000000 1.0500000 0.0000000 >> NO KEEP: 908 F -0.45000002 1.0500000 0.0000000 >> NO KEEP: 909 F -0.15000001 1.0500000 0.0000000 >> NO KEEP: 910 F 0.15000001 1.0500000 0.0000000 >> NO KEEP: 911 F 0.45000002 1.0500000 0.0000000 >> NO KEEP: 912 F 0.75000000 1.0500000 0.0000000 >> NO KEEP: 913 F 1.0500000 1.0500000 0.0000000 >> Deleting element 514 of 1536. >> Deleting element 515 of 1536. >> Deleting element 516 of 1536. >> Deleting element 517 of 1536. >> Deleting element 518 of 1536. >> Deleting element 519 of 1536. >> Deleting element 520 of 1536. >> Deleting element 521 of 1536. >> Deleting element 570 of 1536. >> Deleting element 571 of 1536. >> Deleting element 572 of 1536. >> Deleting element 573 of 1536. >> Deleting element 574 of 1536. >> Deleting element 575 of 1536. >> Deleting element 576 of 1536. >> Deleting element 577 of 1536. >> Deleting element 626 of 1536. >> Deleting element 627 of 1536. >> Deleting element 628 of 1536. >> Deleting element 629 of 1536. >> Deleting element 630 of 1536. >> Deleting element 631 of 1536. >> Deleting element 632 of 1536. >> Deleting element 633 of 1536. >> Deleting element 682 of 1536. >> Deleting element 683 of 1536. >> Deleting element 684 of 1536. >> Deleting element 685 of 1536. >> Deleting element 686 of 1536. >> Deleting element 687 of 1536. >> Deleting element 688 of 1536. >> Deleting element 689 of 1536. >> Deleting element 738 of 1536. >> Deleting element 739 of 1536. >> Deleting element 740 of 1536. >> Deleting element 741 of 1536. >> Deleting element 742 of 1536. >> Deleting element 743 of 1536. >> Deleting element 744 of 1536. >> Deleting element 745 of 1536. >> Deleting element 794 of 1536. >> Deleting element 795 of 1536. >> Deleting element 796 of 1536. >> Deleting element 797 of 1536. >> Deleting element 798 of 1536. >> Deleting element 799 of 1536. >> Deleting element 800 of 1536. >> Deleting element 801 of 1536. >> Deleting element 850 of 1536. >> Deleting element 851 of 1536. >> Deleting element 852 of 1536. >> Deleting element 853 of 1536. >> Deleting element 854 of 1536. >> Deleting element 855 of 1536. >> Deleting element 856 of 1536. >> Deleting element 857 of 1536. >> Deleting element 906 of 1536. >> Deleting element 907 of 1536. >> Deleting element 908 of 1536. >> Deleting element 909 of 1536. >> Deleting element 910 of 1536. >> Deleting element 911 of 1536. >> Deleting element 912 of 1536. >> Deleting element 913 of 1536. >> drwobjs: 0 >> Showing only 90 elements of 1472 >> drwobjs: 0 >> inside gencen 1472 F 4 >> done gencen 1472 >> 1 END ELEMENTS >> 2 MODIFY ELEMENT >> 3 GLOBAL REFINE >> 4 CURVE SIDES >> 5 DELETE ELEMENT >> 6 ZOOM >> 7 SET GRID >> 8 DEFINE OBJECT >> 9 REDRAW MESH >> 10 IMPORT MESH >> 11 IMPORT VTK MESH >> 12 IMPORT vtx MESH >> 13 REFLECT MESH >> Choose item: >> 1 >> >> 1 >> 1 ACCEPT MATL,QVOL >> 2 SELECT ELEMENT >> 3 SELECT MATL [ 0] >> 4 SET MATL PROPS,Q >> 5 SHOW MATL PROPS,Q >> Choose it >> >> 1 >> 1 >> start locglob_lexico: 4 1472 5888 1.99999996E-02 >> locglob: 1 1 5888 >> locglob: 2 81 5888 >> locglob: 1 1562 5888 >> locglob: 2 1562 5888 >> Performing unique_vertex2 self_chk 5888 >> done locglob_lexico: 1562 1562 5888 5 >> Performing makecell self_chk 5888 >> >> >> *** MIDWAY BREAK MENU *** >> ABORT to write build data to file and exit >> SET B.C'S to continue >> 1 SET BCs >> 2 ABORT >> Choose item: >> >> 2 >> Generating Mesh Points for 1472 Elements >> 1472 this is nel in prexit >> Writing Parameters to file >> Deleting tmp.* files. >> Exiting session 4.59163468E-41 >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Nov 9 10:42:34 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 9 Nov 2013 10:42:34 -0600 Subject: [Nek5000-users] prex question In-Reply-To: References: Message-ID: MOAB should be able to read the 2d gmsh files too. If you find there are issues, do inform the moab team with sample test cases. Vijay On Nov 9, 2013 10:31 AM, wrote: > I have seen that we can read gmsh meshes through moab in 3d. There was a > hint that it will be implemented for 2d case also. Is there any chance this > will happen ? > > Thanks > praveen > > > On Mon, Nov 4, 2013 at 1:27 AM, wrote: > >> Hi Paul, >> >> It is very clear with your explaination. Thank you very much! >> >> Best >> >> Tubois >> >> On Sun, Nov 3, 2013 at 8:28 PM, wrote: >> >>> >>> Hi Tubois, >>> >>> 11 SET ENTIRE LEVEL applies the next selected >>> boundary condition to any _remaining_ boundaries for which >>> BCs have yet to be defined. >>> >>> In this case, that is just the BCs on the top and bottom >>> of the domain, since the inlet and outlet were prescribed >>> in the box file, while the sides were left blank. The >>> cylinder itself inherits and retains its boundary conditions >>> from the "import.rea" file. >>> >>> Does this clarify? >>> >>> Best, Paul >>> >>> >>> ----- Original Message ----- >>> From: nek5000-users at lists.mcs.anl.gov >>> To: nek5000-users at lists.mcs.anl.gov >>> Sent: Sunday, November 3, 2013 11:35:36 AM >>> Subject: Re: [Nek5000-users] prex question >>> >>> >>> >>> Hi Paul, >>> >>> >>> Thank you very much! Just need a confirm about your mesh. >>> 11 SET ENTIRE LEVEL >>> 1 PERIODIC-AUTO >>> means to set the periodic boundary condition for the box except the >>> inlet already set in fpcyl.box? >>> n Is this a lattice for hex-close-packed spheres?: >>> So the boundary condition for the circle will be set to walls >>> automatically? >>> >>> >>> Thank you! >>> >>> >>> Tubois >>> >>> >>> >>> >>> >>> On Sun, Nov 3, 2013 at 5:46 PM, < nek5000-users at lists.mcs.anl.gov > >>> wrote: >>> >>> >>> >>> Hi Tubois, >>> >>> I've just updated this example and have included a script that appears >>> to work. >>> >>> I recommend moving your existing ext_cyl directory to, say, ext_cyl.1, >>> and then svn update ext_cyl. >>> >>> Then, in the new ext_cyl directory you should be able to type: >>> >>> mkmesh >>> >>> >>> The README file is also updated. Have a look at mkmesh and you >>> can see the basic steps. >>> >>> Paul >>> >>> >>> >>> >>> ----- Original Message ----- >>> From: nek5000-users at lists.mcs.anl.gov >>> To: nek5000-users at lists.mcs.anl.gov >>> Sent: Sunday, November 3, 2013 10:00:17 AM >>> Subject: [Nek5000-users] prex question >>> >>> >>> >>> Hello everyone, >>> >>> >>> 1, I am trying to create the mesh of the example ext_cyl with genbox, >>> and pretek. After consulting the email archives online, I almost got it >>> works. The question lies on mesh-merging. I used pretex. The commands is >>> listed as follows. >>> >>> >>> I got a mesh ext_cyl.rea identical to the one in the example, when I >>> visualized it with postx. However, when I use xxdiff to examine it, I found >>> several differences. >>> BOUNDARY CONDITIONS: >>> FLUID BOUNDARY CONDITIONS: >>> 11 0.00000 0.00000 ..... >>> For the file in the example, this line is >>> P 11 1337.00 3.00000 ...... >>> >>> >>> So which step did I missed? To set the BC in pretek? Can someone gives a >>> detailed command lines? >>> >>> >>> 2, About creating the mesh, the wiki says that Nek5000 works with Moab >>> Cubit, but this software is not free of charge. Is there any other free >>> software for meshing? In the archive, I found the discussion about >>> converting Gambit (we have Gambit in school) mesh to rea. The guy left an >>> email address cmeador at tamu.edu , which is no more valid. >>> >>> >>> Thank you very much! >>> >>> >>> Best regards >>> >>> >>> Tubois >>> ================================================================== >>> >>> >>> Choose a Name for This session: >>> ext_cyl >>> >>> Beginning Session ext_cyl >>> 1 READ PREVIOUS PARAMETERS >>> 2 TYPE IN NEW PARAMETERS >>> 3 CONJ. HEAT TRANSFER MERGE >>> Choose item: >>> 1 >>> 1 >>> Enter name of previous session >>> box.rea >>> 1 BUILD FROM FILE >>> 2 BUILD INTERACTIVELY >>> Choose item: >>> 1 >>> 1 >>> Enter name of previous session >>> (Default= box.rea ) >>> I pressed ENTER >>> >>> >>> >>> Will Read Mesh and B.C. data from box.rea >>> Reading Element 29 [ 1C] >>> Reading Element 58 [ 1f] >>> Reading Element 87 [ 1I] >>> Reading Element 116 [ 1l] >>> Reading Element 145 [ 1O] >>> Reading Element 174 [ 1r] >>> Reading Element 203 [ 1U] >>> Reading Element 232 [ 1x] >>> Reading Element 261 [ 1a] >>> Reading Element 290 [ 1D] >>> Reading Element 319 [ 1g] >>> Reading Element 348 [ 1J] >>> Reading Element 377 [ 1m] >>> Reading Element 406 [ 1P] >>> Reading Element 435 [ 1s] >>> Reading Element 464 [ 1V] >>> Reading Element 493 [ 1y] >>> Reading Element 522 [ 1b] >>> Reading Element 551 [ 1E] >>> Reading Element 580 [ 1h] >>> Reading Element 609 [ 1K] >>> Reading Element 638 [ 1n] >>> Reading Element 667 [ 1Q] >>> Reading Element 696 [ 1t] >>> Reading Element 725 [ 1W] >>> Reading Element 754 [ 1z] >>> Reading Element 783 [ 1c] >>> Reading Element 812 [ 1F] >>> Reading Element 841 [ 1i] >>> Reading Element 870 [ 1L] >>> Reading Element 899 [ 1o] >>> Reading Element 928 [ 1R] >>> Reading Element 957 [ 1u] >>> Reading Element 986 [ 1X] >>> Reading Element 1015 [ 1A] >>> Reading Element 1044 [ 1d] >>> Reading Element 1073 [ 1G] >>> Reading Element 1102 [ 1j] >>> Reading Element 1131 [ 1M] >>> Reading Element 1160 [ 1p] >>> Reading Element 1189 [ 1S] >>> Reading Element 1218 [ 1v] >>> Reading Element 1247 [ 1Y] >>> Reading Element 1276 [ 1B] >>> Reading Element 1305 [ 1e] >>> Reading Element 1334 [ 1H] >>> Reading Element 1363 [ 1k] >>> Reading Element 1392 [ 1N] >>> Reading Element 1421 [ 1q] >>> Reading Element 1450 [ 1T] >>> drwobjs: 0 >>> Showing only 90 elements of 1456 >>> *** BUILD MENU *** >>> inside gencen 1456 F 4 >>> done gencen 1456 >>> 1 END ELEMENTS >>> 2 MODIFY ELEMENT >>> 3 GLOBAL REFINE >>> 4 CURVE SIDES >>> 5 DELETE ELEMENT >>> 6 ZOOM >>> 7 SET GRID >>> 8 DEFINE OBJECT >>> 9 REDRAW MESH >>> 10 IMPORT MESH >>> 11 IMPORT VTK MESH >>> 12 IMPORT vtx MESH >>> 13 REFLECT MESH >>> Choose item: >>> 10 >>> >>> 10 >>> input name of new .rea file >>> import.rea >>> >>> Would you like to displace existing elements in box? >>> y >>> >>> Found 80 curve sides. >>> IFLD: 1 1 T F >>> ***** FLUID BOUNDARY CONDITIONS ***** >>> ***** FLUID BOUNDARY CONDITIONS *****$ >>> This is nel,ncurve old: 1456 0 >>> This is nel,ncurve new: 1536 80 >>> inside gencen 1536 F 4 >>> done gencen 1536 >>> X min/max of new elements: -1.200000 1.200001 >>> Y min/max of new elements: -1.200000 1.200000 >>> NO KEEP: 514 F -1.0500000 -1.0500000 0.0000000 >>> NO KEEP: 515 F -0.75000000 -1.0500000 0.0000000 >>> NO KEEP: 516 F -0.45000002 -1.0500000 0.0000000 >>> NO KEEP: 517 F -0.15000001 -1.0500000 0.0000000 >>> NO KEEP: 518 F 0.15000001 -1.0500000 0.0000000 >>> NO KEEP: 519 F 0.45000002 -1.0500000 0.0000000 >>> NO KEEP: 520 F 0.75000000 -1.0500000 0.0000000 >>> NO KEEP: 521 F 1.0500000 -1.0500000 0.0000000 >>> NO KEEP: 570 F -1.0500000 -0.75000000 0.0000000 >>> NO KEEP: 571 F -0.75000000 -0.75000000 0.0000000 >>> NO KEEP: 572 F -0.45000002 -0.75000000 0.0000000 >>> NO KEEP: 573 F -0.15000001 -0.75000000 0.0000000 >>> NO KEEP: 574 F 0.15000001 -0.75000000 0.0000000 >>> NO KEEP: 575 F 0.45000002 -0.75000000 0.0000000 >>> NO KEEP: 576 F 0.75000000 -0.75000000 0.0000000 >>> NO KEEP: 577 F 1.0500000 -0.75000000 0.0000000 >>> NO KEEP: 626 F -1.0500000 -0.45000002 0.0000000 >>> NO KEEP: 627 F -0.75000000 -0.45000002 0.0000000 >>> NO KEEP: 628 F -0.45000002 -0.45000002 0.0000000 >>> NO KEEP: 629 F -0.15000001 -0.45000002 0.0000000 >>> NO KEEP: 630 F 0.15000001 -0.45000002 0.0000000 >>> NO KEEP: 631 F 0.45000002 -0.45000002 0.0000000 >>> NO KEEP: 632 F 0.75000000 -0.45000002 0.0000000 >>> NO KEEP: 633 F 1.0500000 -0.45000002 0.0000000 >>> NO KEEP: 682 F -1.0500000 -0.15000001 0.0000000 >>> NO KEEP: 683 F -0.75000000 -0.15000001 0.0000000 >>> NO KEEP: 684 F -0.45000002 -0.15000001 0.0000000 >>> NO KEEP: 685 F -0.15000001 -0.15000001 0.0000000 >>> NO KEEP: 686 F 0.15000001 -0.15000001 0.0000000 >>> NO KEEP: 687 F 0.45000002 -0.15000001 0.0000000 >>> NO KEEP: 688 F 0.75000000 -0.15000001 0.0000000 >>> NO KEEP: 689 F 1.0500000 -0.15000001 0.0000000 >>> NO KEEP: 738 F -1.0500000 0.15000001 0.0000000 >>> NO KEEP: 739 F -0.75000000 0.15000001 0.0000000 >>> NO KEEP: 740 F -0.45000002 0.15000001 0.0000000 >>> NO KEEP: 741 F -0.15000001 0.15000001 0.0000000 >>> NO KEEP: 742 F 0.15000001 0.15000001 0.0000000 >>> NO KEEP: 743 F 0.45000002 0.15000001 0.0000000 >>> NO KEEP: 744 F 0.75000000 0.15000001 0.0000000 >>> NO KEEP: 745 F 1.0500000 0.15000001 0.0000000 >>> NO KEEP: 794 F -1.0500000 0.45000002 0.0000000 >>> NO KEEP: 795 F -0.75000000 0.45000002 0.0000000 >>> NO KEEP: 796 F -0.45000002 0.45000002 0.0000000 >>> NO KEEP: 797 F -0.15000001 0.45000002 0.0000000 >>> NO KEEP: 798 F 0.15000001 0.45000002 0.0000000 >>> NO KEEP: 799 F 0.45000002 0.45000002 0.0000000 >>> NO KEEP: 800 F 0.75000000 0.45000002 0.0000000 >>> NO KEEP: 801 F 1.0500000 0.45000002 0.0000000 >>> NO KEEP: 850 F -1.0500000 0.75000000 0.0000000 >>> NO KEEP: 851 F -0.75000000 0.75000000 0.0000000 >>> NO KEEP: 852 F -0.45000002 0.75000000 0.0000000 >>> NO KEEP: 853 F -0.15000001 0.75000000 0.0000000 >>> NO KEEP: 854 F 0.15000001 0.75000000 0.0000000 >>> NO KEEP: 855 F 0.45000002 0.75000000 0.0000000 >>> NO KEEP: 856 F 0.75000000 0.75000000 0.0000000 >>> NO KEEP: 857 F 1.0500000 0.75000000 0.0000000 >>> NO KEEP: 906 F -1.0500000 1.0500000 0.0000000 >>> NO KEEP: 907 F -0.75000000 1.0500000 0.0000000 >>> NO KEEP: 908 F -0.45000002 1.0500000 0.0000000 >>> NO KEEP: 909 F -0.15000001 1.0500000 0.0000000 >>> NO KEEP: 910 F 0.15000001 1.0500000 0.0000000 >>> NO KEEP: 911 F 0.45000002 1.0500000 0.0000000 >>> NO KEEP: 912 F 0.75000000 1.0500000 0.0000000 >>> NO KEEP: 913 F 1.0500000 1.0500000 0.0000000 >>> Deleting element 514 of 1536. >>> Deleting element 515 of 1536. >>> Deleting element 516 of 1536. >>> Deleting element 517 of 1536. >>> Deleting element 518 of 1536. >>> Deleting element 519 of 1536. >>> Deleting element 520 of 1536. >>> Deleting element 521 of 1536. >>> Deleting element 570 of 1536. >>> Deleting element 571 of 1536. >>> Deleting element 572 of 1536. >>> Deleting element 573 of 1536. >>> Deleting element 574 of 1536. >>> Deleting element 575 of 1536. >>> Deleting element 576 of 1536. >>> Deleting element 577 of 1536. >>> Deleting element 626 of 1536. >>> Deleting element 627 of 1536. >>> Deleting element 628 of 1536. >>> Deleting element 629 of 1536. >>> Deleting element 630 of 1536. >>> Deleting element 631 of 1536. >>> Deleting element 632 of 1536. >>> Deleting element 633 of 1536. >>> Deleting element 682 of 1536. >>> Deleting element 683 of 1536. >>> Deleting element 684 of 1536. >>> Deleting element 685 of 1536. >>> Deleting element 686 of 1536. >>> Deleting element 687 of 1536. >>> Deleting element 688 of 1536. >>> Deleting element 689 of 1536. >>> Deleting element 738 of 1536. >>> Deleting element 739 of 1536. >>> Deleting element 740 of 1536. >>> Deleting element 741 of 1536. >>> Deleting element 742 of 1536. >>> Deleting element 743 of 1536. >>> Deleting element 744 of 1536. >>> Deleting element 745 of 1536. >>> Deleting element 794 of 1536. >>> Deleting element 795 of 1536. >>> Deleting element 796 of 1536. >>> Deleting element 797 of 1536. >>> Deleting element 798 of 1536. >>> Deleting element 799 of 1536. >>> Deleting element 800 of 1536. >>> Deleting element 801 of 1536. >>> Deleting element 850 of 1536. >>> Deleting element 851 of 1536. >>> Deleting element 852 of 1536. >>> Deleting element 853 of 1536. >>> Deleting element 854 of 1536. >>> Deleting element 855 of 1536. >>> Deleting element 856 of 1536. >>> Deleting element 857 of 1536. >>> Deleting element 906 of 1536. >>> Deleting element 907 of 1536. >>> Deleting element 908 of 1536. >>> Deleting element 909 of 1536. >>> Deleting element 910 of 1536. >>> Deleting element 911 of 1536. >>> Deleting element 912 of 1536. >>> Deleting element 913 of 1536. >>> drwobjs: 0 >>> Showing only 90 elements of 1472 >>> drwobjs: 0 >>> inside gencen 1472 F 4 >>> done gencen 1472 >>> 1 END ELEMENTS >>> 2 MODIFY ELEMENT >>> 3 GLOBAL REFINE >>> 4 CURVE SIDES >>> 5 DELETE ELEMENT >>> 6 ZOOM >>> 7 SET GRID >>> 8 DEFINE OBJECT >>> 9 REDRAW MESH >>> 10 IMPORT MESH >>> 11 IMPORT VTK MESH >>> 12 IMPORT vtx MESH >>> 13 REFLECT MESH >>> Choose item: >>> 1 >>> >>> 1 >>> 1 ACCEPT MATL,QVOL >>> 2 SELECT ELEMENT >>> 3 SELECT MATL [ 0] >>> 4 SET MATL PROPS,Q >>> 5 SHOW MATL PROPS,Q >>> Choose it >>> >>> 1 >>> 1 >>> start locglob_lexico: 4 1472 5888 1.99999996E-02 >>> locglob: 1 1 5888 >>> locglob: 2 81 5888 >>> locglob: 1 1562 5888 >>> locglob: 2 1562 5888 >>> Performing unique_vertex2 self_chk 5888 >>> done locglob_lexico: 1562 1562 5888 5 >>> Performing makecell self_chk 5888 >>> >>> >>> *** MIDWAY BREAK MENU *** >>> ABORT to write build data to file and exit >>> SET B.C'S to continue >>> 1 SET BCs >>> 2 ABORT >>> Choose item: >>> >>> 2 >>> Generating Mesh Points for 1472 Elements >>> 1472 this is nel in prexit >>> Writing Parameters to file >>> Deleting tmp.* files. >>> Exiting session 4.59163468E-41 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Nov 9 10:47:17 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 9 Nov 2013 22:17:17 +0530 Subject: [Nek5000-users] prex question In-Reply-To: References: Message-ID: I remember this discussion https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2012-November/002002.html which said 2d is not yet supported. Does it work now ? Thanks praveen On Sat, Nov 9, 2013 at 10:12 PM, wrote: > MOAB should be able to read the 2d gmsh files too. If you find there are > issues, do inform the moab team with sample test cases. > > Vijay > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Nov 9 12:21:08 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 9 Nov 2013 12:21:08 -0600 Subject: [Nek5000-users] prex question In-Reply-To: References: Message-ID: Sorry, I misunderstood. I meant native MOAB should not have problems reading the 2-D mesh directly. Misun had few changes that were going to be merged to the NEK code base but I am not sure about the current status of that effort. Aleks might know more. Vijay On Sat, Nov 9, 2013 at 10:47 AM, wrote: > I remember this discussion > > https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2012-November/002002.html > > which said 2d is not yet supported. > > Does it work now ? > > Thanks > praveen > > On Sat, Nov 9, 2013 at 10:12 PM, wrote: >> >> MOAB should be able to read the 2d gmsh files too. If you find there are >> issues, do inform the moab team with sample test cases. >> >> Vijay > > > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Tue Nov 12 22:17:14 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 13 Nov 2013 09:47:14 +0530 Subject: [Nek5000-users] Average solution along lines Message-ID: Hello For a 2d simulation I want to compute averages on y = constant lines ua(y) = (1/L) int_0^L u(x,y) dx My mesh is cartesian so this should be easy to do. I have seen the y_average function which seems to do just this but I need a x_average function I guess. I can modify this for x averages but would like to check first that y_average computes averages along lines in 2d case ??? Thanks praveen -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 13 05:40:21 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 13 Nov 2013 05:40:21 -0600 (CST) Subject: [Nek5000-users] Average solution along lines In-Reply-To: Message-ID: Hi Praveen, Yes, you are correct in assuming that y_average computes ua(x) = 1/L int_0^L u(x,y) dy under the assumptions of: 2D, uniform element length in y, and tensor-product array of elements (e.g., as generated by genbox). I wrote an x_average() routine a few weeks back and have tested it. I've just now added this to navier5.f --- hopefully it will work for you. Be certain you set lelx, lely, and lelz in SIZE, and likewise nelx,nely,nelz in (say) usrdat(), where you must also add: include 'ZPER' Of course, nelz=lelz=1 in your case. I Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: "nek5000" Sent: Tuesday, November 12, 2013 10:17:14 PM Subject: [Nek5000-users] Average solution along lines Hello For a 2d simulation I want to compute averages on y = constant lines ua(y) = (1/L) int_0^L u(x,y) dx My mesh is cartesian so this should be easy to do. I have seen the y_average function which seems to do just this but I need a x_average function I guess. I can modify this for x averages but would like to check first that y_average computes averages along lines in 2d case ??? Thanks praveen _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed Nov 13 06:06:08 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 13 Nov 2013 17:36:08 +0530 Subject: [Nek5000-users] Average solution along lines In-Reply-To: References: Message-ID: Thank you Paul. The routine should work for non-uniform cartesian mesh also right, if the dx2 is calculated. This is done in y_average function but commented out for dy2 ??? Regards praveen On Wed, Nov 13, 2013 at 5:10 PM, wrote: > Hi Praveen, > > Yes, you are correct in assuming that y_average computes > > ua(x) = 1/L int_0^L u(x,y) dy > > under the assumptions of: 2D, uniform element length in y, > and tensor-product array of elements (e.g., as generated > by genbox). > > I wrote an x_average() routine a few weeks back and have > tested it. I've just now added this to navier5.f --- hopefully it > will work for you. > > Be certain you set lelx, lely, and lelz in SIZE, and likewise > nelx,nely,nelz in (say) usrdat(), where you must also add: > > include 'ZPER' > > Of course, nelz=lelz=1 in your case. > > I > > Paul > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 13 06:09:14 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 13 Nov 2013 06:09:14 -0600 (CST) Subject: [Nek5000-users] Average solution along lines In-Reply-To: Message-ID: Yes - that is correct. ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: "nek5000" Sent: Wednesday, November 13, 2013 6:06:08 AM Subject: Re: [Nek5000-users] Average solution along lines Thank you Paul. The routine should work for non-uniform cartesian mesh also right, if the dx2 is calculated. This is done in y_average function but commented out for dy2 ??? Regards praveen On Wed, Nov 13, 2013 at 5:10 PM, < nek5000-users at lists.mcs.anl.gov > wrote: Hi Praveen, Yes, you are correct in assuming that y_average computes ua(x) = 1/L int_0^L u(x,y) dy under the assumptions of: 2D, uniform element length in y, and tensor-product array of elements (e.g., as generated by genbox). I wrote an x_average() routine a few weeks back and have tested it. I've just now added this to navier5.f --- hopefully it will work for you. Be certain you set lelx, lely, and lelz in SIZE, and likewise nelx,nely,nelz in (say) usrdat(), where you must also add: include 'ZPER' Of course, nelz=lelz=1 in your case. I Paul _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Wed Nov 13 12:27:41 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 13 Nov 2013 10:27:41 -0800 Subject: [Nek5000-users] Interpolating data onto an evenly spaced grid Message-ID: I want to interpolate my nek5000 data fields (*.fxxxxx) onto an evenly spaced grid (and globally evenly spaced so g2gi does not help here since my elements are not all of the same size). It seems like hpts is set up for this, where I read in a data file, call hpts (the data in hpts.in is my evenly spaced grid), and output the data to hpts.out. However, I have some pretty big grids, so I need to use the parallelization feature (i.e., set lhis to npts/np, here npts = total number of interpolation points and np = number of processors). However, then the data output to hpts.out is jumbled up. If I instead set lhis to the total number of points, the output data is fine. I suspect there is a bug somewhere in hpts such that it mixes up the data. Any suggestions? Cheers, Janet -- Janet Scheel Assistant Professor of Physics Occidental College 1600 Campus Road, M21 Los Angeles, CA 90041 (323) 259-2777 jscheel at oxy.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 14 07:44:55 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 14 Nov 2013 19:14:55 +0530 Subject: [Nek5000-users] Problem reading file using load_fld Message-ID: Hello I saved some binary *.f??? files and now I try to read them for postprocessing using load_fld function. I get this error done :: set initial conditions call userchk File channel0.f00001 loaded. set initial conditions Checking restart options: channel0.f00001 nekuic (1) for ifld 1 nekuic (1) for ifld 2 nekuic (1) for ifld 3 Reading checkpoint data WARNING: No data read in for file channel0.f00001 Failed on element****, point 0. Last read dump: 0 call exitt 1702a 1 I have set param(66) = param(67) = 6 in usrdat() both for running the simulation and for postprocessing. I used the exact same rea file for simulation and for postprocessing. Do I need to set any other restart options for this to work ? Thanks praveen -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 14 08:05:16 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 14 Nov 2013 19:35:16 +0530 Subject: [Nek5000-users] Problem reading file using load_fld In-Reply-To: References: Message-ID: Sorry. Please ignore my mail. I had not properly set param(66) and param(67) for postprocessing. Thanks praveen On Thu, Nov 14, 2013 at 7:14 PM, Praveen Chandrashekar < nek5000 at praveen.e4ward.com> wrote: > Hello > > I saved some binary *.f??? files and now I try to read them for > postprocessing using load_fld function. I get this error > > done :: set initial conditions > > > > call userchk > > File channel0.f00001 > loaded. > > set initial conditions > > Checking restart options: channel0.f00001 > > > > nekuic (1) for ifld 1 > > nekuic (1) for ifld 2 > > nekuic (1) for ifld 3 > > Reading checkpoint data > > WARNING: No data read in for file channel0.f00001 > > > > Failed on element****, point 0. > > Last read dump: > > > 0 call exitt 1702a 1 > > I have set param(66) = param(67) = 6 in usrdat() both for running the > simulation and for postprocessing. > > I used the exact same rea file for simulation and for postprocessing. > > Do I need to set any other restart options for this to work ? > > Thanks > praveen > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 14 12:18:18 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 14 Nov 2013 13:18:18 -0500 Subject: [Nek5000-users] Postnek problem Message-ID: Hi, Neks When I plot profile points in postnek, some the profile points in the flow field are set to zero where they shouldn't be. Is there a way to overcome this problem? The image below shows some the problem points. My postnek version is 2.6. Mu Xu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 14 13:42:44 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 14 Nov 2013 13:42:44 -0600 (CST) Subject: [Nek5000-users] Postnek problem In-Reply-To: References: Message-ID: Hi Mu, The postnek interpolator is not as robust as the in-nek one. If your interpolation line follows a spectral element edge you can get drop outs... the easiest solution is to just move the interpolation line by (say) .001 away from the edge. Paul On Thu, 14 Nov 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi, Neks > > When I plot profile points in postnek, some the profile points in the flow > field are set to zero where they shouldn't be. Is there a way to overcome > this problem? > The image below shows some the problem points. > My postnek version is 2.6. > > Mu Xu > From nek5000-users at lists.mcs.anl.gov Thu Nov 14 16:56:03 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 14 Nov 2013 17:56:03 -0500 Subject: [Nek5000-users] mapping straight pipe to curved pipe Message-ID: Hello, I am trying to change the usrdat2 in example pipe(helix) to make curved pipe with defined curvature. I changed the .usr file like this: subroutine usrdat2 include 'SIZE' include 'TOTAL' common /ogeom/ ox(lx1,ly1,lz1,lelv) $ , oy(lx1,ly1,lz1,lelv) $ , oz(lx1,ly1,lz1,lelv) diam = 1.0 one = 1. pi = 4.*atan(one) Rcurv = 3 !curvature of the pipe z0 = 0. z1 = pi*Rcurv !equal to area of the curved pipe call rescale_x (zm1,z0,z1) rad = diam/2. radm = -rad call rescale_x (xm1,radm,rad) call rescale_x (ym1,radm,rad) n = nx1*ny1*nz1*nelv call copy(ox,xm1,n) call copy(oy,ym1,n) call copy(oz,zm1,n) do i=1,n ! preset offset twist x = xm1(i,1,1,1) y = ym1(i,1,1,1) z = zm1(i,1,1,1) theta = z/Rcurv zm1 = Rcurv*sin(theta) ym1(i,1,1,1) = y + Rcurv*cos(theta) enddo param(59) = 1. ! All elements deformed ifxyo = .true. return end c----------------------------------------------------------------------- but it comes out with some error associated with vanishing jacobian! I would ask that what is the problem with my modification on mapping straight pipe? Thanks, Ami -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 14 22:03:20 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 15 Nov 2013 09:33:20 +0530 Subject: [Nek5000-users] visit visualization question In-Reply-To: References: Message-ID: Hello I have tried both *.fld## and *.f## formats with visit 2.7.0 and visit refuses to open them. I posted about this on visit forum but I have not received any response yet. I am using visit mac binary from visit website. Thanks praveen On Fri, Nov 8, 2013 at 1:23 PM, Praveen C wrote: > The latest visit version 2.7 seems to be unable to read my results, I get > > VisIt could not read from the file "/private/tmp/re10000/channel.nek5000". > > > The generated error message was: > > > There was an error opening /private/tmp/re10000/channel.nek5000. It may be > an invalid file. > > VisIt tried using the following file format readers to open the file: > Nek5000, Silo > > > If you know the specific format reader VisIt should use to > > read this data, you can use Open As... (GUI) or > > '-o , (CL arg.) and identify that specific reader > > for VisIt to try. This will possibly give more information on > > the exact error. > > > Has anybody had success with 2.7 ? > > > My file looks like this > > > filetemplate: channel.fld%02d > > firsttimestep: 1 > > numtimesteps: 161 > > > Thanks > > praveen > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 14 22:10:38 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 14 Nov 2013 22:10:38 -0600 (CST) Subject: [Nek5000-users] visit visualization question In-Reply-To: Message-ID: Hi Praveen, Are you using the visnek script to generate the requisite meta-date in the *.nek5000 file ? Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: "nek5000" Sent: Thursday, November 14, 2013 10:03:20 PM Subject: Re: [Nek5000-users] visit visualization question Hello I have tried both *.fld## and *.f## formats with visit 2.7.0 and visit refuses to open them. I posted about this on visit forum but I have not received any response yet. I am using visit mac binary from visit website. Thanks praveen On Fri, Nov 8, 2013 at 1:23 PM, Praveen C < cpraveen at gmail.com > wrote: The latest visit version 2.7 seems to be unable to read my results, I get VisIt could not read from the file "/private/tmp/re10000/channel.nek5000". The generated error message was: There was an error opening /private/tmp/re10000/channel.nek5000. It may be an invalid file. VisIt tried using the following file format readers to open the file: Nek5000, Silo If you know the specific format reader VisIt should use to read this data, you can use Open As... (GUI) or '-o , (CL arg.) and identify that specific reader for VisIt to try. This will possibly give more information on the exact error. Has anybody had success with 2.7 ? My file looks like this filetemplate: channel.fld%02d firsttimestep: 1 numtimesteps: 161 Thanks praveen _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Nov 15 07:01:54 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 15 Nov 2013 07:01:54 -0600 (CST) Subject: [Nek5000-users] mapping straight pipe to curved pipe In-Reply-To: Message-ID: Hi Ami, You have a statement: zm1=... this clearly can't be correct in the standard nek usage. You should have something like zm1(i,1,1,1)=... Perhaps this is the issue. Best regards, Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, November 14, 2013 4:56:03 PM Subject: [Nek5000-users] mapping straight pipe to curved pipe Hello, I am trying to change the usrdat2 in example pipe(helix) to make curved pipe with defined curvature. I changed the .usr file like this: subroutine usrdat2 include 'SIZE' include 'TOTAL' common /ogeom/ ox(lx1,ly1,lz1,lelv) $ , oy(lx1,ly1,lz1,lelv) $ , oz(lx1,ly1,lz1,lelv) diam = 1.0 one = 1. pi = 4.*atan(one) Rcurv = 3 !curvature of the pipe z0 = 0. z1 = pi*Rcurv !equal to area of the curved pipe call rescale_x (zm1,z0,z1) rad = diam/2. radm = -rad call rescale_x (xm1,radm,rad) call rescale_x (ym1,radm,rad) n = nx1*ny1*nz1*nelv call copy(ox,xm1,n) call copy(oy,ym1,n) call copy(oz,zm1,n) do i=1,n ! preset offset twist x = xm1(i,1,1,1) y = ym1(i,1,1,1) z = zm1(i,1,1,1) theta = z/Rcurv zm1 = Rcurv*sin(theta) ym1(i,1,1,1) = y + Rcurv*cos(theta) enddo param(59) = 1. ! All elements deformed ifxyo = .true. return end c----------------------------------------------------------------------- but it comes out with some error associated with vanishing jacobian! I would ask that what is the problem with my modification on mapping straight pipe? Thanks, Ami _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Fri Nov 15 10:27:04 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 15 Nov 2013 17:27:04 +0100 Subject: [Nek5000-users] Meshing software for complex geometries Message-ID: Hello, I am looking to use Nek5000 to simulate flow past complex geometries (airfoil, wind turbine, ahmed body, etc.) and I wanted to get some feedback from other users to see what software you use for your meshing. My research group has previous experience with gridgen-c and the nek tools but we are looking for a more sophisticated grid generation tool. We tried out gridgen and liked that but I wanted to see if others had a better experience with another tool. Cubit is another name that has come up. Is there a tool that you recommend for meshing complex geometries that works well with Nek5000? Thanks, Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Nov 19 01:44:49 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 19 Nov 2013 08:44:49 +0100 Subject: [Nek5000-users] help: 3d revolved mesh Message-ID: Dear Neks I have created (and succesfully used) a 2d axisymmetric mesh (see attachment) for two coaxial jets discharging into "free air". What I want to do now is to revolve it around the z (x) axis to create a 3d one and simulate the non-axisymmetric flow . I tried using n2to3 without success with the following input parameters: coaxJets old name coaxJets3 new name 1 For ASCII output only: 0; For .rea/.re2: 1 -10 input number of levels: (1, 2, 3,...; < 0 for circular sweep.): 0 input z min: 360 input z max: 1 input gain (0=custom,1=uniform,other=geometric spacing): no This is for CEM: yes or no: P Enter Z (5) boundary condition (P,v,O): but I get the following error: this is cbz: P P <--- ERROR READING CURVE SIDE DATA ABORTING IN ROUTINE RDCURVE. I have also tried reducing the mesh to the first block only, i.e., the inner tube, but I get the same error. What am I mistaking? ~~~~~~~~~~~~~~ Regards Jacopo Canton -------------- next part -------------- coaxJets.rea 2 spatial dimension 1 number of fields # # # #======================================================== # Box 1 inner tube -60 -15 nel_x, nel_y -5. 0. 1. x0, x1, ratio 0. 0.5 1. y0, y1, ratio v ,E ,A ,W , , (bc's) Box 2 inner segment -100 -15 nel_x, nel_y 0. 100. 1.06 x0, x1, ratio 0. 0.5 1. y0, y1, ratio E ,O ,A ,E , , (bc's) Box 3 wall segment -100 -6 nel_x, nel_y 0. 100. 1.06 x0, x1, ratio 0.5 0.6 1. y0, y1, ratio W ,O ,E ,E , , (bc's) Box 4 outer tube LOWER -60 -8 nel_x, nel_y -5. 0. 1. x0, x1, ratio 0.6 0.8 1. y0, y1, ratio v ,E ,W ,E , , (bc's) Box 5 outer tube UPPER -60 -8 nel_x, nel_y -5. 0. 1. x0, x1, ratio 0.8 1. 1. y0, y1, ratio v ,E ,E ,W , , (bc's) Box 6 outer segment LOWER -100 -8 nel_x, nel_y 0. 100. 1.06 x0, x1, ratio 0.6 0.8 1. y0, y1, ratio E ,O ,E ,E , , (bc's) Box 7 outer segment UPPER -100 -8 nel_x, nel_y 0. 100. 1.06 x0, x1, ratio 0.8 1. 1. y0, y1, ratio E ,O ,E ,E , , (bc's) Box 8 outerOuter segment -100 -20 nel_x, nel_y 0. 100. 1.06 x0, x1, ratio 1. 5. 1.17 y0, y1, ratio W ,O ,E ,ON , , (bc's) From nek5000-users at lists.mcs.anl.gov Tue Nov 19 11:04:25 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 19 Nov 2013 11:04:25 -0600 Subject: [Nek5000-users] help: 3d revolved mesh In-Reply-To: References: Message-ID: Hi, Looking at the error message, it seems there is something wrong with the source file, coaxJets.rea. n2to3 is having trouble reading the curve data, so I would suggest looking there to see that everything looks as expected. After the mesh data, coaxJets.rea should have something like: ***** CURVED SIDE DATA ***** 0 Curved sides follow IEDGE,IEL,CURVE(I),I=1,5, CCURVE ***** BOUNDARY CONDITIONS ***** It is important for the number of curved sides to match the number of lines following it. In this example it is 0, so there are no lines following. If this doesn't solve your problem, please send me the coaxJets.rea file off list to: heisey at mcs.anl.gov and I will take a closer look. Best, Katie On Tue, Nov 19, 2013 at 1:44 AM, wrote: > Dear Neks > > I have created (and succesfully used) a > 2d axisymmetric mesh (see attachment) for > two coaxial jets discharging into "free air". > What I want to do now is to revolve it > around the z (x) axis to create a 3d one > and simulate the non-axisymmetric flow . > > I tried using n2to3 without success with the > following input parameters: > > coaxJets old name > coaxJets3 new name > 1 For ASCII output only: 0; For .rea/.re2: 1 > -10 input number of levels: (1, 2, 3,...; < 0 for > circular sweep.): > 0 input z min: > 360 input z max: > 1 input gain (0=custom,1=uniform,other=geometric > spacing): > no This is for CEM: yes or no: > P Enter Z (5) boundary condition (P,v,O): > > but I get the following error: > this is cbz: P P <--- > ERROR READING CURVE SIDE DATA > ABORTING IN ROUTINE RDCURVE. > > I have also tried reducing the mesh to the first > block only, i.e., the inner tube, but I get the > same error. > > What am I mistaking? > > > ~~~~~~~~~~~~~~ > Regards > Jacopo Canton > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 20 15:50:02 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 20 Nov 2013 16:50:02 -0500 Subject: [Nek5000-users] Extracting data and interpolating Message-ID: Hi Neks, I am currently working on simulation of 3D curved pipe with Nek5000. I would like to export some data in mid-slice surface and specified line along the curvature of pipe. I am using USERCHK, I can export the variables, but how I can interpolate/write data which desired along the lines and sliced surfaces? and If I do this kind of interpolation, interpolation can keep the accuracy of the simulation or not? Thanks, Ami -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Nov 21 11:45:23 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 21 Nov 2013 18:45:23 +0100 Subject: [Nek5000-users] PN field to PN-2 field Message-ID: Hi Nek's, I would like to copy a PN field to a PN-2 field, how can I do that ? let's say "a(lx1,ly1,lz1,nelt)" is given and I want to interpolate "a" onto a field "b(lx2,ly2,lz2,nelt)" and of course I use a PN-PN-2 method, not splitting. Vincent. From nek5000-users at lists.mcs.anl.gov Thu Nov 21 13:27:48 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 21 Nov 2013 13:27:48 -0600 (CST) Subject: [Nek5000-users] PN field to PN-2 field In-Reply-To: References: Message-ID: Hi Vincent, It looks like the routine map12 will do this. It's to be called on an element by element basis --- thus: integer e do e=1,nelt call map12(b(1,1,1,e),a(1,1,1,e)) enddo would yield the desired result. May I inquire as to the application? (There are times when it might be better to use the transpose of the interpolation operator.) Paul On Thu, 21 Nov 2013, nek5000-users at lists.mcs.anl.gov wrote: > Hi Nek's, > > I would like to copy a PN field to a PN-2 field, how can I do that ? > > let's say "a(lx1,ly1,lz1,nelt)" is given and I want to interpolate "a" onto > a field "b(lx2,ly2,lz2,nelt)" and of course I use a PN-PN-2 method, not > splitting. > > Vincent. > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Fri Nov 22 09:48:17 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 22 Nov 2013 10:48:17 -0500 Subject: [Nek5000-users] Fwd: Extracting data and interpolating In-Reply-To: References: Message-ID: Hi Neks, I am currently working on simulation of 3D curved pipe with Nek5000. I would like to export some data in mid-slice surface and specified line along the curvature of pipe. I am using USERCHK, I can export the variables, but how I can interpolate/write data which desired along the lines and sliced surfaces? and If I do this, interpolation can keep the accuracy of the simulation or not? Thanks, Ami -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Fri Nov 22 10:21:55 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Fri, 22 Nov 2013 10:21:55 -0600 (CST) Subject: [Nek5000-users] Fwd: Extracting data and interpolating In-Reply-To: Message-ID: Hi Ami, One way to do this is to use the hpts() utility. Try google nek5000 hpts and you should see the instructions. If you don't want the data at every timestep you can just add something like: if (mod(istep,100).eq.0) call hpts() Best, Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Friday, November 22, 2013 9:48:17 AM Subject: [Nek5000-users] Fwd: Extracting data and interpolating Hi Neks, I am currently working on simulation of 3D curved pipe with Nek5000. I would like to export some data in mid-slice surface and specified line along the curvature of pipe. I am using USERCHK, I can export the variables, but how I can interpolate/write data which desired along the lines and sliced surfaces? and If I do this, interpolation can keep the accuracy of the simulation or not? Thanks, Ami _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sat Nov 23 22:43:51 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 24 Nov 2013 10:13:51 +0530 Subject: [Nek5000-users] hpts.out format problem Message-ID: Hello My hpts.out looks wrong for fourth column # time vx vy [vz] pr T PS1 PS2 ... 0.0000000E+00 0.0000000E+00 2.2770178E-20 0.0000000E+00 1.0000000E+00 0.0000000E+00 0.0000000E+00 1.1128360E-20 0.0000000E+00 1.0000000E+00 0.0000000E+00 0.0000000E+00 1.2207423E-20 0.0000000E+00 1.0000000E+00 1.0000000E-02 1.0322690E+00 4.5900231E-13 1.7812260-214 1.0000000E+00 1.0000000E-02 1.0322690E+00 -3.2178336E-11 -2.8810031-247 1.0000000E+00 1.0000000E-02 1.0322690E+00 5.3625113E-12 8.9518284-279 1.0000000E+00 2.0000000E-02 1.0464112E+00 2.5113139E-12 -2.5577043-172 1.0000000E+00 2.0000000E-02 1.0464112E+00 -1.4864697E-11 -1.0519438-191 1.0000000E+00 2.0000000E-02 1.0464112E+00 6.0078894E-13 6.7786184-210 1.0000000E+00 3.0000000E-02 1.0574510E+00 3.5407894E-12 3.1248404-166 1.0000000E+00 3.0000000E-02 1.0574510E+00 -5.4106217E-12 -4.6568194-186 1.0000000E+00 3.0000000E-02 1.0574510E+00 -2.0092183E-12 2.2559987-203 1.0000000E+00 4'th column is temperature which is nearly zero, but the output is missing the exponent E. Thanks praveen -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Nov 23 22:58:17 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 23 Nov 2013 22:58:17 -0600 (CST) Subject: [Nek5000-users] hpts.out format problem In-Reply-To: Message-ID: Hi Praveen, In my experience, this is what 64-bit output looks like when the exponent goes into 3 digits. Best, Paul ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: "nek5000" Sent: Saturday, November 23, 2013 10:43:51 PM Subject: [Nek5000-users] hpts.out format problem Hello My hpts.out looks wrong for fourth column # time vx vy [vz] pr T PS1 PS2 ... 0.0000000E+00 0.0000000E+00 2.2770178E-20 0.0000000E+00 1.0000000E+00 0.0000000E+00 0.0000000E+00 1.1128360E-20 0.0000000E+00 1.0000000E+00 0.0000000E+00 0.0000000E+00 1.2207423E-20 0.0000000E+00 1.0000000E+00 1.0000000E-02 1.0322690E+00 4.5900231E-13 1.7812260-214 1.0000000E+00 1.0000000E-02 1.0322690E+00 -3.2178336E-11 -2.8810031-247 1.0000000E+00 1.0000000E-02 1.0322690E+00 5.3625113E-12 8.9518284-279 1.0000000E+00 2.0000000E-02 1.0464112E+00 2.5113139E-12 -2.5577043-172 1.0000000E+00 2.0000000E-02 1.0464112E+00 -1.4864697E-11 -1.0519438-191 1.0000000E+00 2.0000000E-02 1.0464112E+00 6.0078894E-13 6.7786184-210 1.0000000E+00 3.0000000E-02 1.0574510E+00 3.5407894E-12 3.1248404-166 1.0000000E+00 3.0000000E-02 1.0574510E+00 -5.4106217E-12 -4.6568194-186 1.0000000E+00 3.0000000E-02 1.0574510E+00 -2.0092183E-12 2.2559987-203 1.0000000E+00 4'th column is temperature which is nearly zero, but the output is missing the exponent E. Thanks praveen _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sat Nov 23 23:04:31 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 24 Nov 2013 10:34:31 +0530 Subject: [Nek5000-users] hpts.out format problem In-Reply-To: References: Message-ID: Yes, it seems that E is suppressed when exponent is 3 digits. Other programs like gnuplot dont seem to understand this if I try to plot hpts.out Thanks praveen On Sun, Nov 24, 2013 at 10:28 AM, wrote: > > Hi Praveen, > > In my experience, this is what 64-bit output looks like > when the exponent goes into 3 digits. > > Best, > > Paul > > > ----- Original Message ----- > From: nek5000-users at lists.mcs.anl.gov > To: "nek5000" > Sent: Saturday, November 23, 2013 10:43:51 PM > Subject: [Nek5000-users] hpts.out format problem > > > > Hello > > > My hpts.out looks wrong for fourth column > > > > > # time vx vy [vz] pr T PS1 PS2 ... > > 0.0000000E+00 0.0000000E+00 2.2770178E-20 0.0000000E+00 1.0000000E+00 > > 0.0000000E+00 0.0000000E+00 1.1128360E-20 0.0000000E+00 1.0000000E+00 > > 0.0000000E+00 0.0000000E+00 1.2207423E-20 0.0000000E+00 1.0000000E+00 > > 1.0000000E-02 1.0322690E+00 4.5900231E-13 1.7812260-214 1.0000000E+00 > > 1.0000000E-02 1.0322690E+00 -3.2178336E-11 -2.8810031-247 1.0000000E+00 > > 1.0000000E-02 1.0322690E+00 5.3625113E-12 8.9518284-279 1.0000000E+00 > > 2.0000000E-02 1.0464112E+00 2.5113139E-12 -2.5577043-172 1.0000000E+00 > > 2.0000000E-02 1.0464112E+00 -1.4864697E-11 -1.0519438-191 1.0000000E+00 > > 2.0000000E-02 1.0464112E+00 6.0078894E-13 6.7786184-210 1.0000000E+00 > > 3.0000000E-02 1.0574510E+00 3.5407894E-12 3.1248404-166 1.0000000E+00 > > 3.0000000E-02 1.0574510E+00 -5.4106217E-12 -4.6568194-186 1.0000000E+00 > > 3.0000000E-02 1.0574510E+00 -2.0092183E-12 2.2559987-203 1.0000000E+00 > > > 4'th column is temperature which is nearly zero, but the output is missing > the exponent E. > > Thanks > praveen > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Nov 24 10:03:05 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 24 Nov 2013 21:33:05 +0530 Subject: [Nek5000-users] Helmholtz iterations seem to converge slowly Message-ID: Hello I am solving a 2d flow with variable viscosity using stress formulation. The viscosity depends on a scalar concentration which is advected/diffused and the viscosity varies by an order of magnitude in the domain. The helmholtz iterations seems to converge slowly as shown here Step 39998, t= 3.9998000E+01, DT= 1.0000000E-03, C= 0.346 7.2489E+03 1.1492E-01 Solving for heat Solving for fluid F T T 39998 Hmholtz TEMP: 7 2.9893E-10 3.3026E+00 1.0000E-09 39998 Hmholtz PS 1: 4 6.7160E-11 2.1011E+00 1.0000E-09 39998 3.9998E+01 6.9721E-03 Heat done 39998 Helmholtz3/fluid: 35 0.9267E-09 0.1000E-08 0.1398E+00 39998 U-PRES gmres: 7 9.4465E-08 1.0000E-07 4.4910E-05 6.1851E-03 1.3509E-02 39998 DNORM, DIVEX 9.44654494640397541E-008 9.44654494679585123E-008 39998 3.9998E+01 4.3178E-02 Fluid done 39998 3 qfilt: 3.6770E-08 7.2251E-10 4.6167E-10 3.8497E-09 Compute statistics ... Is there any way to improve the convergence. My parameters are given below. Thanks praveen ****** PARAMETERS ***** 2.6099999 NEKTON VERSION 2 DIMENSIONAL RUN 118 PARAMETERS FOLLOW 1.00000 p001 DENSITY 1.00000 p002 VISCOS 0.00000 p003 0.00000 p004 0.00000 p005 0.00000 p006 1.00000 p007 RHOCP 0.100000E-01 p008 CONDUCT 0.00000 p009 40.00000 p010 FINTIME 0.00000 p011 NSTEPS 0.10000E-02 p012 DT 0.00000 p013 IOCOMM 0.00000 p014 IOTIME 250.000 p015 IOSTEP 0.00000 p016 PSSOLVER: 0=default 0.00000 p017 0.500000E-01 p018 GRID < 0 --> # cells on screen -1.00000 p019 INTYPE 4.00000 p020 NORDER 0.100000E-06 p021 DIVERGENCE 0.100000E-08 p022 HELMHOLTZ 1 p23 NPSCAL 0.100000E-09 p024 TOLREL 0.100000E-04 p025 TOLABS 1.000000 p026 COURANT/NTAU 3.00000 p027 TORDER 1.00000 p028 TORDER: mesh velocity (0: p28=p27) 0.00000 p029 = magnetic visc if > 0, = -1/Rm if < 0 0.00000 p030 > 0 ==> properties set in uservp() 0.00000 p031 NPERT: #perturbation modes 0.00000 p032 #BCs in re2 file, if > 0 0.00000 p033 0.00000 p034 0.00000 p035 0.00000 p036 0.00000 p037 0.00000 p038 0.00000 p039 0.00000 p040 0.00000 p041 1-->multiplicative SEMG 0.00000 p042 0=gmres/1=pcg 0.00000 p043 0=semg/1=schwarz 0.00000 p044 0=E-based/1=A-based prec. 0.00000 p045 Relaxation factor for DTFS 0.00000 p046 reserved 0.00000 p047 vnu: mesh matieral prop. 0.00000 p048 0.00000 p049 0.00000 p050 0.00000 p051 0.00000 p052 IOHIS 0.00000 p053 0.00000 p054 fixed flow rate dir: |p54|=1,2,3=x,y,z 0.00000 p055 vol.flow rate (p54>0) or Ubar (p54<0) 0.00000 p056 0.00000 p057 0.00000 p058 0.00000 p059 !=0 --> full Jac. eval. for each el. 0.00000 p060 !=0 --> init. velocity to small nonzero 0.00000 p061 0.00000 p062 >0 --> force byte_swap for output 0.00000 p063 =8 --> force 8-byte output 0.00000 p064 =1 --> perturbation restart 0.00000 p065 #iofiles (eg, 0 or 64); <0 --> sep. dirs 6.00000 p066 output : <0=ascii, else binary 6.00000 p067 restart: <0=ascii, else binary 500.00000 p068 iastep: freq for avg_all (0=iostep) 0.00000 p069 0.00000 p070 0.00000 p071 0.00000 p072 0.00000 p073 0.00000 p074 verbose Helmholtz 0.00000 p075 0.00000 p076 0.00000 p077 0.00000 p078 0.00000 p079 0.00000 p080 0.00000 p081 0.00000 p082 0.00000 p083 0.00000 p084 !=0 --> sets initial timestep if p12>0 0.00000 p085 dt ratio if p84 !=0, for timesteps>0 0.00000 p086 reserved 0.00000 p087 0.00000 p088 0.00000 p089 0.00000 p090 0.00000 p091 0.00000 p092 0.0000 p093 Number of previous pressure solns saved 0.00000 p094 start projecting velocity after p94 step 0.00000 p095 start projecting pressure after p95 step 0.00000 p096 0.00000 p097 0.00000 p098 3.00000 p099 dealiasing: <0--> off/3--> old/4--> new 0.00000 p100 0.00000 p101 Number of additional modes to filter 1.00000 p102 Dump out divergence at each time step 0.05000 p103 weight of stabilizing filter (.01) 0.00000 p104 0.00000 p105 0.00000 p106 0.00000 p107 !=0 --> add to h2 array in hlmhotz eqn 0.00000 p108 0.00000 p109 0.00000 p110 0.00000 p111 0.00000 p112 -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Nov 24 11:15:16 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 24 Nov 2013 12:15:16 -0500 Subject: [Nek5000-users] Visit Grid Error Question Message-ID: Hi All, I'm using nek and Visit on a Linux platform, and Visit seems to work fine with my binary output files (param66 and param67 =4). However, if I download all these files to a windows machine, and run visit on them, it gives me the error: "VisIt could not read from the file "C:\temp\wind_base.nek5000". The generated error message was: There was an error opening C:\temp\wind_base.nek5000. It may be an invalid file. VisIt tried using the following file format readers to open the file: Nek5000 The following error(s) may be helpful in identifying the problem: When attempting to use "Nek", the file matched the general format expected by the reader but eventually encountered this error: "The first time step in a Nek file must contain a mesh"." File names are all the same, did binary ftp transfer, transferred all the files (.rea, .usr, etc...; except the obj directory) to make sure I wasn't missing something, and the mesh shows fine on the Linux machine. Any ideas? Thanks, Murph -- *Murphy Leo O'Dea, PE"Murph"* PhD Student, Mechanical Engineering /School Of Engineering And Computer Science/ /Oakland University/ mlodea at oakland.edu http://www.secs.oakland.edu/~mlodea/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Nov 27 06:57:24 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 27 Nov 2013 13:57:24 +0100 Subject: [Nek5000-users] PN field to PN-2 field In-Reply-To: References: Message-ID: Hi Paul, Thanks for your answer and sorry for having been late in answering in return. In fact, I wanted to define a usrdiv based on the temperature field for the perturbation topic that I opened some time ago (see https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2013-October/002334.html) but I now understand that my ideas were wrong. It is not possible to do what I wanted with usrdiv because the problem is fully coupled. I rewrite the set of perturbations equations that I would like to solve below. "k" is the wavelength of the perturbation field (vxp,vyp,tp) in the z direction, and "tp" is used to model the third velocity component "vzp" which is not computed in 2D. Thus the perturbation velocity field has 3 components but (VX,VY) is the baseflow and is 2D. /continuity : d(vpx)/dx + d(vpy)/dy + k * tp=0 / /momentum : d(vpx)/dt + VX dvpx/dx + VY dup/dy = - d(prp)/dx - vpx dVX/dx - vxp dVX/dy + nu (//d^2vxp/dx^2 + d^2vxp/dy^2 - k^2 * vxp ) / / d(vpy)/dt + VX dvpy/dx + VY dvpy/dy = - d(prp)/dy - vpx dVY/dx - vyp dVY/dy + nu (//d^2(vyp)/dx^2 + d^2(vyp)/dy^2 - k^2 * vpy ) / / d(tp)/dt + VX d(tp)/dx + VY d(tp)/dy = -k prp + nu ( d^2(tp)/dx^2 + d^2(tp)/dy^2 - k^2 * tp )/ in which "d" means partial derivative. In my opinion the only solution would be to include the third velocity component in the 2D calculations of the perturbation field in nek which would be useful for any situation in which the baseflow is 2D but the perturbation velocity field is 3D with a harmonic evolution along the normal to the plane direction. Best regards, Vincent. Message: 1 Date: Thu, 21 Nov 2013 13:27:48 -0600 (CST) From:nek5000-users at lists.mcs.anl.gov To:nek5000-users at lists.mcs.anl.gov Subject: Re: [Nek5000-users] PN field to PN-2 field Message-ID: Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Hi Vincent, It looks like the routine map12 will do this. It's to be called on an element by element basis --- thus: integer e do e=1,nelt call map12(b(1,1,1,e),a(1,1,1,e)) enddo would yield the desired result. May I inquire as to the application? (There are times when it might be better to use the transpose of the interpolation operator.) Paul On Thu, 21 Nov 2013,nek5000-users at lists.mcs.anl.gov wrote: > Hi Nek's, > > I would like to copy a PN field to a PN-2 field, how can I do that ? > > let's say "a(lx1,ly1,lz1,nelt)" is given and I want to interpolate "a" onto > a field "b(lx2,ly2,lz2,nelt)" and of course I use a PN-PN-2 method, not > splitting. > > Vincent. > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > ield to PN-2 field -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Nov 30 11:53:01 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 30 Nov 2013 23:23:01 +0530 Subject: [Nek5000-users] nek+moab problem on mac osx 10.9 using macports Message-ID: Hello I have installed moab on osx 10.9 using openmpi from macports. gfortran is also from macports. When I try to compile nek I get this error. openmpicc/c++ uses apple clang but gfortran seems to use gcc48 from macports. Is there any way to fix this. openmpif77 -o nek5000 obj/ray.o obj/drive.o obj/drive1.o obj/drive2.o obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o -L/opt/local/lib -L/Users/praveen/Applications/moab/moab-4.6.2/lib -L/Users/praveen/Applications/moab/moab-4.6.2/lib -liMesh -lMOAB -lnetcdf -lhdf5 -lm -L/opt/local/lib -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -L/opt/local/lib -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ Undefined symbols for architecture x86_64: "std::__1::basic_string, std::__1::allocator >::find_last_of(char const*, unsigned long, unsigned long) const", referenced from: moab::ReaderWriterSet::get_file_extension_reader(std::__1::basic_string, std::__1::allocator > const&) const in libMOAB.a(ReaderWriterSet.o) moab::ReaderWriterSet::extension_from_filename(std::__1::basic_string, std::__1::allocator > const&) in libMOAB.a(ReaderWriterSet.o) moab::ReaderWriterSet::get_file_extension_writer(std::__1::basic_string, std::__1::allocator > const&) const in libMOAB.a(ReaderWriterSet.o) moab::WriteAns::write_file(char const*, bool, moab::FileOptions const&, unsigned long const*, int, std::__1::vector, std::__1::allocator >, std::__1::allocator, std::__1::allocator > > > const&, moab::TagInfo* const*, int, int) in libMOAB.a(WriteAns.o) "std::__1::basic_string, std::__1::allocator >::find_first_of(char const*, unsigned long, unsigned long) const", referenced from: moab::ReadABAQUS::tokenize(std::__1::basic_string, std::__1::allocator > const&, std::__1::vector, std::__1::allocator >, std::__1::allocator, std::__1::allocator > > >&, char const*) in libMOAB.a(ReadABAQUS.o) "std::__1::basic_string, std::__1::allocator >::find_last_not_of(char const*, unsigned long, unsigned long) const", referenced from: _imesh_load_ in libiMesh.a(iMesh_MOAB.o) _imesh_save_ in libiMesh.a(iMesh_MOAB.o) _imesh_createtagwithoptions_ in libiMesh.a(iMesh_MOAB.o) _imesh_gettaghandle_ in libiMesh.a(iMesh_MOAB.o) "std::__1::basic_string, std::__1::allocator >::find_first_not_of(char const*, unsigned long, unsigned long) const", referenced from: moab::ReadABAQUS::tokenize(std::__1::basic_string, std::__1::allocator > const&, std::__1::vector, std::__1::allocator >, std::__1::allocator, std::__1::allocator > > >&, char const*) in libMOAB.a(ReadABAQUS.o) -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Nov 30 20:48:17 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 30 Nov 2013 20:48:17 -0600 Subject: [Nek5000-users] nek+moab problem on mac osx 10.9 using macports In-Reply-To: References: Message-ID: AFAIK, these routines have not been deprecated in clang. Can you print out the version of your compilers so that we can see if some implementation is missing ? clang --version. You should also use LDFLAGS+="-stdlib=libstdc++" on the linker command since OSX Mavericks might have a different behavior by default in choosing the standard C++ runtime libraries. If that doesn't fix the undefined errors, let us know the detailed messages. Vijay On Sat, Nov 30, 2013 at 11:53 AM, wrote: > Hello > > I have installed moab on osx 10.9 using openmpi from macports. gfortran is > also from macports. > > > When I try to compile nek I get this error. openmpicc/c++ uses apple clang > but gfortran seems to use gcc48 from macports. Is there any way to fix this. > > > openmpif77 -o nek5000 obj/ray.o obj/drive.o obj/drive1.o obj/drive2.o > obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o > obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o > obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o > obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o > obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o > obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o > obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o > obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o > obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o > obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o > obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o > obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o > obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o > obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o > obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o > obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o > obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o > obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o > obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o -L/opt/local/lib > -L/Users/praveen/Applications/moab/moab-4.6.2/lib > -L/Users/praveen/Applications/moab/moab-4.6.2/lib -liMesh -lMOAB -lnetcdf > -lhdf5 -lm -L/opt/local/lib > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -L/opt/local/lib > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 > -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi > -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ > > Undefined symbols for architecture x86_64: > > "std::__1::basic_string, > std::__1::allocator >::find_last_of(char const*, unsigned long, > unsigned long) const", referenced from: > > > moab::ReaderWriterSet::get_file_extension_reader(std::__1::basic_string std::__1::char_traits, std::__1::allocator > const&) const in > libMOAB.a(ReaderWriterSet.o) > > > moab::ReaderWriterSet::extension_from_filename(std::__1::basic_string std::__1::char_traits, std::__1::allocator > const&) in > libMOAB.a(ReaderWriterSet.o) > > > moab::ReaderWriterSet::get_file_extension_writer(std::__1::basic_string std::__1::char_traits, std::__1::allocator > const&) const in > libMOAB.a(ReaderWriterSet.o) > > moab::WriteAns::write_file(char const*, bool, moab::FileOptions > const&, unsigned long const*, int, > std::__1::vector, > std::__1::allocator >, > std::__1::allocator std::__1::char_traits, std::__1::allocator > > > const&, > moab::TagInfo* const*, int, int) in libMOAB.a(WriteAns.o) > > "std::__1::basic_string, > std::__1::allocator >::find_first_of(char const*, unsigned long, > unsigned long) const", referenced from: > > moab::ReadABAQUS::tokenize(std::__1::basic_string std::__1::char_traits, std::__1::allocator > const&, > std::__1::vector, > std::__1::allocator >, > std::__1::allocator std::__1::char_traits, std::__1::allocator > > >&, char const*) > in libMOAB.a(ReadABAQUS.o) > > "std::__1::basic_string, > std::__1::allocator >::find_last_not_of(char const*, unsigned long, > unsigned long) const", referenced from: > > _imesh_load_ in libiMesh.a(iMesh_MOAB.o) > > _imesh_save_ in libiMesh.a(iMesh_MOAB.o) > > _imesh_createtagwithoptions_ in libiMesh.a(iMesh_MOAB.o) > > _imesh_gettaghandle_ in libiMesh.a(iMesh_MOAB.o) > > "std::__1::basic_string, > std::__1::allocator >::find_first_not_of(char const*, unsigned long, > unsigned long) const", referenced from: > > moab::ReadABAQUS::tokenize(std::__1::basic_string std::__1::char_traits, std::__1::allocator > const&, > std::__1::vector, > std::__1::allocator >, > std::__1::allocator std::__1::char_traits, std::__1::allocator > > >&, char const*) > in libMOAB.a(ReadABAQUS.o) > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sat Nov 30 23:12:57 2013 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 1 Dec 2013 10:42:57 +0530 Subject: [Nek5000-users] nek+moab problem on mac osx 10.9 using macports In-Reply-To: References: Message-ID: On Sun, Dec 1, 2013 at 8:18 AM, wrote: > AFAIK, these routines have not been deprecated in clang. Can you print > out the version of your compilers so that we can see if some > implementation is missing ? clang --version. > > You should also use LDFLAGS+="-stdlib=libstdc++" on the linker command > since OSX Mavericks might have a different behavior by default in > choosing the standard C++ runtime libraries. If that doesn't fix the > undefined errors, let us know the detailed messages. > > Vijay > Hello Vijay Here is some information on my mpi which is installed from macports clang is from xcode. $ clang -v Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) Target: x86_64-apple-darwin13.0.0 Thread model: posix $ openmpicc -v Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) Target: x86_64-apple-darwin13.0.0 Thread model: posix $ openmpic++ -v Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) Target: x86_64-apple-darwin13.0.0 Thread model: posix $ openmpif77 -v Using built-in specs. COLLECT_GCC=/opt/local/bin/gfortran-mp-4.8 COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin13/4.8.1/lto-wrapper Target: x86_64-apple-darwin13 Configured with: /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc48/gcc48/work/gcc-4.8.1/configure --prefix=/opt/local --build=x86_64-apple-darwin13 --enable-languages=c,c++,objc,obj-c++,lto,fortran,java --libdir=/opt/local/lib/gcc48 --includedir=/opt/local/include/gcc48 --infodir=/opt/local/share/info --mandir=/opt/local/share/man --datarootdir=/opt/local/share/gcc-4.8 --with-local-prefix=/opt/local --with-system-zlib --disable-nls --program-suffix=-mp-4.8 --with-gxx-include-dir=/opt/local/include/gcc48/c++/ --with-gmp=/opt/local --with-mpfr=/opt/local --with-mpc=/opt/local --with-cloog=/opt/local --enable-cloog-backend=isl --disable-cloog-version-check --enable-stage1-checking --disable-multilib --enable-lto --enable-libstdcxx-time --with-as=/opt/local/bin/as --with-ld=/opt/local/bin/ld --with-ar=/opt/local/bin/ar --with-bugurl= https://trac.macports.org/newticket --with-pkgversion='MacPorts gcc48 4.8.1_3' Thread model: posix gcc version 4.8.1 (MacPorts gcc48 4.8.1_3) I configure moab like this ./configure --prefix=`pwd` \ --with-mpi \ --with-hdf5=/opt/local \ --enable-mbzoltan \ --with-zoltan=/opt/trilinos-11.4.1-mpi \ CC=openmpicc CXX=openmpic++ FC=openmpif77 F77=openmpif77 If I add -stdlib=libstdc++ flag it is not recognized makenek - automatic build tool for Nek5000 generating makefile ... openmpif77 -c -O2 -fdefault-real-8 -fdefault-double-8 -x f77-cpp-input -fcray-pointer -DMOAB -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG -I/Users/praveen/rayleigh3 -I/Users/praveen/Applications/nek5_svn/trunk/nek -I./ /Users/praveen/rayleigh3/ray.f -I/Users/praveen/Applications/nek5_svn/trunk/nek/3rd_party -I/Users/praveen/Applications/moab/moab-4.6.2/include -o obj/ray.o openmpif77 -o nek5000 obj/ray.o obj/drive.o obj/drive1.o obj/drive2.o obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o -L/opt/local/lib -L/Users/praveen/Applications/moab/moab-4.6.2/lib -L/Users/praveen/Applications/moab/moab-4.6.2/lib -liMesh -lMOAB -lnetcdf -lhdf5 -lm -L/opt/local/lib -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -L/opt/local/lib -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1 -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm -lmpi_cxx -lstdc++ -stdlib=libstdc++ gfortran-mp-4.8: error: unrecognized command line option '-stdlib=libstdc++' make: *** [nek5000] Error 1 Thanks praveen -------------- next part -------------- An HTML attachment was scrubbed... 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