Enable usage of residual projection for velocity solvers (#122) #123
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stgeke
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Nov 28, 2020
RonRahaman
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Feb 15, 2021
19906d43f fix interp_free issue if there is only one handle 002ed0280 do not use tarball if source dir exists for parRSB + gslib 221fa8254 Fix minor bug in setting nfldt in re2 bc reading routine (#711) 478fb41d9 allow to specify linker + add support for Fujitsu compiler 8af44d375 add missing SIZE dep a861c3d0f char only convects nelv (#706) 44f5904cd adjust makefile 27c8ee1b8 compile/link only if required a30afa09e fix wrong nfldt for CHT 6eef67ace Update to latest parRSB version 4bac2f447 Add big element count support (#705) 7b732ea4a Update README.md c7f4a5bb4 update to new chan2d short_test 54063dd26 update exo2nek (#687) 8e942ed75 Add char support for CHT (#661) c16acdad1 Nonhomogeneous contribution to outflow bc for linear adjoint (#695) 6f1e7b74e Fix exo2nek build issue (#698) 20a1595fe Revert "makenek resolves compiler aliases and symlinks (#685)" (#690) d7f838b72 Add a gitignore (#689) 849a05d85 makenek resolves compiler aliases and symlinks (#685) 53a9b49bd fix dprocmap caching issues 05abc9b80 Find connectivity at runtime (#686) 3a2398649 print gs statistics of default handle e32c8dcfb fix missing argument (#681) 9b3d9227b Added missing yc setting in geom_reset (#680) b10b1927a print lxd together with lx1/lx2/lx3 ca18c17ef use correct ifield in mesh check 9fbfe1ca4 update to gslib v1.0.7 1d57bd9c7 use correct field in fix_geom (#679) da2d8333a Update tools for conjugate heat transfer (#676) 901ce617e update to latest parRSB e6a49b45f Merge branch 'thilinarmtb-parrcb_api_refactor' 1818d3b36 Fix a typo f4c7caaf4 Revert back to HYBRID (RCB+RSB) bf86e1df8 Fix a typo a85e5b426 Pass the co-ordinates for the entire element 54c31366a use RSB instead of RCB+RSB as default, at least for now c8f2fbd0e Update to latest parRSB version (#674) 6f75df7ac fix undef reference in serial mode 96a2b5e79 update download path for Hypre 7df86a7fd Update add_temp (#660) 47a7ce1d1 fix boundaryID for ifflow=.false. 18de98c24 fix input args for mpi dummy d7b18dd3a replace deprecated MPI_Type_extent 6f5c7eb5d Get MPI_TAG_UB from MPI_COMM_WORLD (#665) d20d88cac add full path to restart file only if required 9365e625e add file from Paul 9205be138 Added filtering for pert field (#659) 6d00ad21c check for io errors in read_con 3f990aa35 fix round off issues #653 0c0540fe2 add loglevel to print stmt f6525b84c Update variable in gencon.f to integer8 (#652) 90f4b5d20 parMETIS build issue 43a7a8142 Fix mesh metric 2D #649 1d1292c3d set correct ifield for lambda2 4f97d476b add option to use algebraic residual norm in cggo 8b5e25afe update to netcdf 4.7.2 5abfb04b0 update relase and license file 58d74209f check if required 3rd-party tools are installed e6c80cd70 update header ddc751450 improve failure handling of maketools 5afb6179d update 3rd party version in nekdist 5ac423b57 fix restart buf size check (#644) 817a0a29c CYCLIC boudary condtion (#642) e51b2ff8b write only on nio == 0 (#641) dfa8a27e4 update to parRSB 0.2 98e969575 print dof correctly e2e94af55 add boundary for t-mesh (#640) 8958b38e2 init cbc_bmap 7c4dc92c2 add cbc_mp ef9a5f8ac add usrdat0 ccd0880a9 update to latest nekExamples 08e8e6672 fix lelr issue f86843067 add pressure:solver to par 633d1d559 add Stokes and steadyHeat eqntype to par 8a46059f7 print correct dofs 4dde21af4 update vtx coord xc,yc,zc in geom_reset 2a810f7c3 avoid arithmetic overflow for large element counts 13553c622 change default coarsening of nekamg_setup 716e35b98 add missing functions to usr f-file 9698043da Remobe dbg stmt c22a7ae71 Update to GSLIB 1.0.5 ee95c8b27 prefix AMG input files (#632) 5c925e8f6 Print required lelr if too small 8fec96ae3 avoid overflow de16385b0 Add smoother iteration check in setup tool 2a2ee520c Workaround for #628 d655ade11 do not abort compiliation if one tool fails a3bdf1eab Change compilation order of tools 47c937d47 fix variable mg_lmax in hsmg.f (#620) ef4b68dad Allow user to set NEK_SOURCE_ROOT (#622) 8a6a42dc1 Do not print some unnecessary infos c9360c04a print header in setup subroutine 635a901b5 add -build-dep option faeaa56d2 compile blas -O0 + cp instead of patch + add cgflex (#617) 98b47b650 Add gmsh2nek + cgns2nek update (#616) 70146147b Fix bug in makeq_aux (#614) ec6abf07b switch to clean:: target 25f58ebd7 forgot to clean one file bf760546d minor change in SIZE.template dac3ca354 minor makefile fix 9d112c919 Fix #611 + PGI issue 5d9e03841 do not overwrite FCFLAGS and CFLAGS f07b633ef do not remove user .f file e8dd6dd29 use cmake for nekamg_setup cfaf7d7b4 Fix nboco issue 30122963c export makenek variables 9db68d463 use boundaryID ac3a313a3 add missing config options ea95653b3 Update RELEASE.md d4b02b821 Import latest updates (#609) c181c745e Import latest changes (#605) c2f51ef3e Update to gslib.h and allow to set a communicator on input (#603) 3a40a062b adding missing logical variable declaration (#602) d71c2bfd5 same ifcomp on all processes in vol_flow (#601) 48284bda5 Fix pressure extrapolation bug in linear solver (#599) f4b2259eb PARRSB change to new API (#597) d4eff1242 Update RELEASE.md d5c351b89 correction of nelt for imported meshes (#592) 1edd7b07b Add non-power-of-two proc support for CHT (#593) 1a04aba8c Fix misspelled boundaryID (#590) f22010931 Print parition statistics 9d83e7d17 Add parMETIS support (#588) a9215e8e3 fix mkSIZE issue if no PROBLEMTYPE section is defined d1a4fd63f flush stdout and rename boundaryIDList to boundaryID b9929d2a1 compile tools with O2 by default + remove some unnecessary calls in gencon to speed it up 9e8d6f638 Latest changes (#587) ca530de88 add FIXITER b9c7cac51 Import latest changes (#586) c779c274c Fix full_restart for rans_komg 2ba43b225 Fix full restart for variable properties and PnPn 4dede5e59 update version info 664af0688 Compile convect2.f without optimizations 33e565d03 Import latest neknek updates (#549) f7d6edac7 Test restart accuracy in io_test(#584) 6616c87a0 Add eddy_mv and chan2d short_test (#582) af1d7fd38 Import latest changes (#581) 1950516d2 Fix restart issues (#580) a7544cd38 Update README.md efdcfb49d Adjusting to a change of variables names in makenek (#577) 2ecfdc8f4 Add basic Travis test for Tools (#579) f3295153a Import LPM code (#573) 396c1fa4d make prenek rea params compatible 88c57229e fix typo 3daf3110a Turn on nek-cmt Travis tests (#575) 45b37fa58 CMT-nek PSAAP II update (#571) 70ceb236b Use explicit filename to untar (#574) 2a45418d8 Split calculation of RANS source terms (#572) b76c2a4a3 Support full stress formulation for PnPn (#421) d004ef88d Set FC for 3rd-party exo2nek install (#564) 32418562c Remove unnecessary print statement 1ea4050a0 use correct pmask #536 6acb99f55 check always for ioinfo #487 c793325a1 add two mesh metrics 9c277f979 hide node numbers in postnek (#523) 220a11ad6 correct changed esolver logic 16bfa9e25 Import latest changes (#557) a2fd3edea Fix wrong index and add threshold as runtime parameter 62bbe7fd1 Merge pull request #520 from stgeke/master a18afcc33 correct gfortran flags for tools and include pr #526 597cdbccd Rename mulisession routines to avoid wrong data type dbacb94db Import latest fem_amg_preco changes 878f7c7ea Resolve #525 #522 a28a5f0b2 do not dssum mesh, see #527 64edf8ae7 import fem_amg changes de2766179 avoid wrong tolerance 1017a37f7 delete box.tmp file f1f07c73c ensure 32bit alignment caefae406 fix incorrect data type + some cosmetic changes 3c6572d8d Fix wrong path 5553a3c00 Remove double free 0cb092b77 Correct stop statement 7a2ad1495 Add missing files 196208710 Add missing file 77bc12f0b Add missing files + download HYPRE if not available in 3rd_party 3dc1de7a7 Import latest fem_amg_hypre changes 3281e553a revert lelg changes and use C exit which is portable 0513d545e Fix #511 b6bf6036a import latest fem_amg_hypre updates 8cc7c7c69 enable CHT for gfldr 93ad5f4bc maketools prints compilation status e943f23d9 remove old MATLAB based amg_setup tool 4960796ed Do not use scratch common block as findpts_setup does not store interpolation mesh internally c902ef522 Add fem_amg_hypre preconditioner (experimental) b71c87762 fixed typo d1a1a9f89 2D fix for interp 619b53466 Update RELEASE.md 8e117a62c Update HEADER d8ddf5d49 Expose get/set_bytesw_write to Fortran #503 a284ef8b5 Correct index for passive scalar lookup by VisIt in-situ #500 b635b29f6 Merge pull request #505 from stgeke/master 41c7df51d disable CMT for now 45f675bbf fix some issues with mixed passive scalar solvers 03fc81032 Add an extra line dee9b1bac Add elapsedTime for writeControl 03bed8224 fix failed Travis tests 9142dc0a6 final polish e1b9b5e88 cleanup some scripts f62df3100 check if nfld match across nek-nek sessions d15f60b99 call setprop before and after userchk at istep=0 2238ae5ca fix deadlock if lelt is too small and add a check if lelt is right sized 0126290d1 refactor object handling 15e799e06 add check for matching data sizes f92a42eec change to MPI 2.2 for one-sided communication 7ed157603 add mesh smoother 57350bb1d add artifical visosity stabilization 9a524ca16 print runtime stats every 100steps fd7efd82e use absolute path for restarts instead of relative to wkdir 9ffcabf1d neknek launch scripts output into separate logfiles 9c6de5969 rename to mkSIZE a1fed2b97 fixed mkSIZE for OIFS 3b08949c5 Enable non-aligned mixed BC for PnPn ff250cb27 Add timer for userchk, makef and makeq 54bde22fd use correct routine to compute cfl in case of varying dt e167b31ad add support for gcc 8.x 11f96dbbc Expose get/set_bytesw_write to Fortran afc20a56b fix large array f at line 1020 9618c9105 fix pound include 37fde2da8 Correct indexing for IFPSCO in the visitgetvariable callback function bba4871d4 Changed VISIT_ERROR for VISIT_INVALID_HANDLE in visit.f (#498) a7324806f Refactoring for NekNek (#492) 61d4e134f use http instead of https to avoid SSL issues 22ff8e187 print time in volflow 081025c3a Support HEX20/QUAD8 elements in exo2nek #485 79badf03c Merge pull request #491 from stgeke/stgeke-master 1bc88380d Support multiple intp instances + correct wrong usage of sizeof f60480eb2 adjust array size 9bc1dbc65 Add field based logical for filtering 00a60b295 maketools prints compiler result edc24ab47 Add mkSIZE script f18570c10 read ma2 in parallel 50c3f5651 Improve performance of inital processor-element mapping and add a test for intp wrapper 696a8198e Add support for legacy SESSION.NAME 359e10229 Ethier tests element-processor mapping 2b09c6a19 Support for HEX20/QUAD8 elements 1938326b6 Update copyright year and release notes b2db2b7e4 Eliminate lelg scaling arrays gllnid/gllel afb3816ed Make NEKNEK runtime parameter + add gtp+multisession gs_op 3429c1d9f Fix #470 Type error for mod bedb9f79b enable stress formulation if cyclic bc are present 0fba52b06 Fix #467 and clean up 7a0e55231 Refactor intp_usr interface and add Ngeom findpts handling 9e485a0b0 use ldimr instead ldim to make ifgtp work f0a6dd029 make postnek compatible with .par + .re2 (#409) 256e82f88 enable import of conjugate-heat-transfer mesh into prenek 375227de0 Add CGS2 full reorthogonalization implementation (#462) 8a1b9f86c Adding return chracter for tool execution. (#465) 469daf94d CMT-nek updates for forces and restarts (#454) c573afe09 (#459) 6b1a61506 #456 6535d8e97 only initialize bx in nekuic if ifmhd=.true. (#455) 9f44c228d aligned basflow and volflow output (#449) 8499b9a5d Import latest changes (#452) bf9f2a6a1 * add start script for MPMD neknek * print div error outside of plan4 6286a2cca add MPI wrapper handling to maketools e48b7240d switch off filtering if users put cutoff=1.0 0bc973849 do not promote real to real8 where not necessary 55efe71c3 increase MAXNEL for tools 6980e4cf9 Import latest changes (#433) fcf826fbd To make InclDef test to run (#418) 62dd30751 make cray compiler happy 97f686807 small corrections to double_shear test (#426) 15679de98 Import latest changes (#429) fa72bcc53 disable ray_9 short test as we reach the logsize limit on Travis aeb028a7a adjust wrong position of lelt 46d3b9e07 clean up short test e9853f86f fix proj for cht a8435e63e fix wget issues f48e705dc make ethier using AMG 79e788733 use default mxm for gslib c2da75643 Adding missing array declaration (#417) fc3256997 do not delete 3rd party tarballs 5e0da2552 Import latest changes (#414) 68686ef40 Prevent compiler from vectorizing givens_rotation (#410) 84e34b61e fix for proj if compiler uses aggressive vectorization 71573b190 disable proj support for scalars ec074d4ff revert to old proj, fix proj for CHT 525984d3a Minimal corrections to make genbox to work with cylinrical meshes (#403) 6f2d45c43 Disable conjHt short test c15827e02 Update RELEASE.md 586e67592 Import latest changes (#404) 38399d8ba add io short test (#378) 88c6a6b8b cleaned up prenek (#400) 70938d938 changed visit.f to run Nek examples with libsim on newer versions of visit (#395) 2853407ae Modify .f file header to add pressure mesh flag (#379) 89be3b600 improve tool build system (#394) c41dfc157 fix missing call to set_fdm_prec_h1A in case of PnPn cdd439819 update to gslib v1.0.0 (#393) a12103a6d Update RELEASE.md d80e6d352 Add HPF (#389) e20580457 fix gen_rea_full and relax tol for eddy_neknek (#390) 6b547ea55 Update README.md 79503dc09 Added missing declaration for incl_def test (#388) 94ede9513 adjust interpolation tolerances to avoid residual stall in minimizer (#386) 7b17522f2 Remove change to right hand side during scalar solve at the end of ngeom = 2 (#387) 38660b55e ortho res in esolve to make sure it is orthogonal to null space (#384) e25202dbd Fix Cvode Travis tests (#385) be07005fe WIP: import latest changes (#383) 57725c1da Neknek pnpn fix (#380) 4f97f6807 gen_rea_full (#377) e76e906c0 WIP: improved timers + genmap fix + defaut pressure settings (#376) 86c345e0a gen_rea_full routine to write top and bottom parts of rea file as well (#371) d58c2b83c Artificial viscosity for shock capturing moved into cmt (#372) c67e6dbd4 call ortho in the exactp subroutine in eddy and eddy_rich short tests (#369) 20fa3ae14 call ortho for the exact pressure in ethier (#370) 94b6d4b11 Boundary condition bugfixes in CMT-nek (#362) 75aa7fcfe Update HEADER bba7e0749 Update RELEASE.md b95f46c59 changes for beta2 f76f0e6fc Use 2*ldim instead of 6 for dimensions of ifqinp and ifeppm (#353) d3b378919 Refactored NekNek (#252) ada1c04d3 cleaned up ophinv_pr and removed ophinvpr() (#355) 3b768cac7 adjusted short_test tolerances d52c9bd36 turn on stress formulation automatically for Pn/Pn with variable properties f1602ce8b add call to CVODE for PnPn 87b663157 Commenting unnecessary write statement in get_vert_map (#351) 745398b8f Clarify param(20) treatment in cggo to avoid tol=0 (#350) ea2aff2d4 update README a04f8d9ef Update README.md e8d054000 restart bug fixed for CMT(#349) f51d75c6c update README 93b9217ab vyp-->vzp bug fix 1781c12e7 resolved which axhmsf to use --- tiny change to subs2.f a7fd46098 Update README.md 06f6ffbb6 Update README.md 7d707a5f3 use velocity tolerance for temperature if p20>0.1 to avoid unexpected bahviour if p20 is NORDER a697b10f1 Residual projection for SS (#330) a14fdd35d updated surf_mean 23282cac1 added undo functionality to prenek (#345) 2d1b8db3f add binary map file (ma2) support (#346) 025cea9e1 Revert "add new binary .ma2 file, add timer for residual projection" 7f2440ce1 add new binary .ma2 file, add timer for residual projection 6fb8dbb8c strip subsequent lines after the first to detect compiler (#334) ab8c40ea3 added autosave feature that stores temporary states to tmp.???.rea (#342) 6ffffed77 Fix interpolation error with Hypre v2.11.2 (#339) 8a579e05a added 'SAVE' option to prenek menu (#333) c102f1bcc Replacing chnnel2D with dfh_cav to add tempersture adjoint (#337) a2649fb54 do not use implicit none by default for zero.usr template 071950d43 test hpts in Ethier short test 572240ccc add missing variable declerations in hpts 2136605f1 Add linear direct/adjoint test (#329) 48596d1a4 add plan5 (#301) 74eca0130 Update README.md a10290a17 use AMG preco for Ethier short test e88cf020c Bug correction raleted to mesh 3 size (#289) 50151978c $HOME is more universal (#294) 3609d2c02 renamed branches. companion to shock-capturing demos in NekExamples PR (#287) 2311548ba call nek5000 in the current directory (#288) 814edc158 Fix "Getting Started" commands (#292) 9f00ab60b Fix typo (#293) e9ad5e3e8 exo2nek_fix (#285) 0d980fa04 Update README.md b3126b90a add 3D NS short test Ethier 91413ddc7 fix wrong lx3 63ad374e7 Add conjugate heat transfer short test dafa387b9 Exact pressure solution (#279) 4542004b2 setics correction (#277) 797ddde5b lfdm moved from SIZE.inc to SIZE (#278) cb4e1f993 remove call to print_stack on exit for portability reasons 47783e581 undo unintended change in plan4 f9d60a362 Remove filtering for igeom=1 when using PNPN fbaac93c9 add missing SIZE dependency 79c1e0b0f Merge branch 'master' of github.com:Nek5000/Nek5000 df8effd59 small corrections to comp_vort3 (#265) 18e53c818 exclude unit tests for gslib f0cc1fa2e enable exit handling for nek in gslib 2d6e17d44 make the switch to gslib fec00f71d fix cvode with characteristics 43ea95419 add install script for CVODE 2cd0a28e1 read/write in .his instead of two file 12ec6affc fix typo d20b46edb WIP: Bring in latest changes (#258) cd12133cb fix name issue with binary fld 716a436d2 Merge branch 'master' of github.com:Nek5000/Nek5000 78a4ede41 add missing cb c1a752ed4 changed "develop" to "master" to not mislead poor users -- because develop doesn't exist (#248) 295697809 Replaced imesh with imsh in the call to setfast in cggo (#247) 9d483c296 Updated neknek script to run in forerground (from fischer1) (#245) 00d95fb5a Import Paul's NEKNEK fix (#244) 6af0d407d Update README.md 8ad0683fb Update RELEASE.md a08f7f8db Rewrite visnek script in bash (#237) d9b9ee5a3 added vortex computation to solid and output vx,vy,vz for e greater than nelv (#239) 562170248 added vortex computation to solid and output vx,vy,vz for e greater than nelv 95b42f08c compile gfldr on default (#235) 3ecf47fd7 * Fix bug for multiple fld files into separate directories * Ensure null-terminated string is passed to C I/O routines * More descriptive subroutine names for re2 handling * Print troughtput instead of time to as a performance measure (#234) 18fe4cd4c corrections for NekExamples (#233) 17609c53e Update documentation and minor fixes (#231) 01fb33637 fix invalid variable name 357315e78 print in the log for the elements which jacobian is negative fa7aa2935 Major viscous update and BC correction (#228) 792b84f0f minor fixes ea5dce919 Add endian handling for generic fld reader Read .re2 in parallel by default Make MPIIO a runtime option instead of a preprocessor symbol a835b9440 add missing argument to avoid SEGFAULT 8c8db4619 Update makefile.template 3d220a6f0 Update README.md 98a61766e overwrite prefix (#226) ed2216ca4 fix to make IBM compiler happy (#225) 5594a993a WIP: various fixes (#223) c05be276c Update RELEASE.md edb6aef1a Update README.md 3e0942afe remove longint check as CVODE is always using long (#221) 3451df947 fix wrong communicator for MPIIO 1056e2985 Merge branch 'develop' of https://github.com/Nek5000/Nek5000 4ae9174de added AMG_DUMP to readme (#220) d5178fa15 Merge branch 'develop' of https://github.com/Nek5000/Nek5000 dc4f7d9b9 import paul's changes (#218) 000a813f7 update genbox to handle .re2 cases without .rea files 29d12858e Update README.md 8d83c8fd6 Update README.md 3ac134cb4 Update README.md dacd60fe8 Fixed regex in NekTests to config makenek correctly (#211) f06ed4abd Update README.md bad513031 Update makenek 207a1b991 Merge branch 'develop' of https://github.com/Nek5000/Nek5000 into develop 18015ea4c Set p0th by default to 1.0 (#210) 07dfd6637 Make it more verbose 687e114f6 Update README.md a7598765c Add parallel .re2 reader (#203) 398b6b5cc Automatically dump AMG files if data files are not found (#208) 5fb22f41f Nicooff issue 205 (#209) 5975ab20f Merge pull request #202 from RonRahaman/issue-153 d09dde4d7 Added short_test for eddy w/ legacy SIZE file 3eb095c88 Update gfldr.f 7c3a58292 Update README.md 0bdab4ff5 Update intp.f 163cb73dc Change license to BSD (#201) 715a37340 Add generic fld reader (#194) 54d82691c Merge pull request #197 from stgeke/cvf 206d53e93 fix for char w/o moving mesh 5072a4154 fix for mixed helm/cvode 2d230db2b Merge pull request #195 from UFCCMT/develop f991ab819 keeping up with the joneses. lpart removed from SIZE.inc a1d6c2411 Merge pull request #30 from Nek5000/develop 73cc3ed4a Merge pull request #191 from RonRahaman/issue-187 24cd22685 Merge pull request #192 from UFCCMT/develop ae4bf7438 Merge pull request #193 from klheisey/re2Fix 2347e6327 Update README.md 3df02e049 update re2torea to be compliant with Nek5k souce code: will read in real*8 and real*8 .re2 files 3bc275b2d Merge pull request #29 from hackljf/develop f5a64e23f Merge pull request #6 from UFCCMT/develop a8b6a06ad Merge pull request #28 from hackljf/develop 06921a7ef new and improved l2norms for inviscid vortex! 92e99a4e2 bad logic for compute_primitive_variables in RHS. Travis, take the wheel! ee5205d9d Merge pull request #26 from hackljf/develop 8d8fbf763 Merge pull request #5 from UFCCMT/develop 56527877d Merge pull request #25 from Nek5000/develop 0f09ce7c0 Added description of NEKNEK to PPLIST help message f5575de38 Update README.md e5ae5078a Update README.md 929dd433b Update README.md b9596917e Update README.md dc6563ff2 Update README.md 261df6362 Update makenek.inc ed9cc44fa Update makenek a6af1782a Update makenek eeac5a09c Update README.md d3fccf847 fixed problem for working with more than about 2.5M elements f6d47feda Merge pull request #184 from ggiannako/ifoutfld f59519c29 ifoutfld 7b25fe4f5 ifoutfld 315690e18 Merge pull request #182 from ggiannako/fix_157 076bf636f Merge pull request #181 from ggiannako/fix_168 6d637bf3b dummy ced4b6885 Set ntdump after userchk d76ff26a4 Update README.md 64978172c Update README.md 6bdb9af71 Don't limit dt for the last timestep d5688f489 Update README.md 7d6cac881 Merge branch 'develop' a363d0884 Update README.md dd3ae2d22 Merge pull request #180 from ggiannako/bgq_mxm_fix 4461332b8 Update README.md 90f5046ac Update README.md 369133601 Update README.md f2f5a1d52 Update README.md f1fc56d6e Merge branch 'develop' of https://github.com/Nek5000/Nek5000 into bgq_mxm_fix dfefda311 Fix for mxm_bgq and add flag for external blas 7fc0bbf74 Merge pull request #179 from stgeke/cv_aos 2b0e93771 make pack/unpack more general and use it for abs tol as well fd29a8f59 Update README.md 7cc1155ce Merge pull request #178 from stgeke/upread 601784a7f add update remote repos f670b3d99 updated readme e361843ba updated readme e497c9264 Merge pull request #176 from stgeke/cv_cat f3232ce95 call dssum for valid gs handles only a5974c6f3 remove unneeded lib dir 9c292286c updated readme 2e6284a13 Merge branch 'develop' of https://github.com/Nek5000/Nek5000 into cv_cat 99e8b93b4 modification for lav surface kinetics 595cec31a Merge pull request #174 from stgeke/cv 9f291b3c3 Updated README 3a6af5a7c add git-hub script f86e1ab50 Merge pull request #172 from stgeke/fixdeals baa83fa34 - avoid zero .rea files in case of .par - correct sign error for ifstr in plan4 - add nekgit scripts fb08cf04b Merge pull request #171 from Nek5000/release/v16.0.0 f530ea833 Merge pull request #139 from Nek5000/release/v16.0.0 561a8717a Merge pull request #170 from stgeke/fixwarn 2987d1797 Merge pull request #99 from mattiasbr/issue-89 215bf999d fixed ifdiff issue 3f983344c bring in my latest changes 4f458d5ed Merge pull request #166 from RonRahaman/parallel-tests-only 4c9009ace Merge pull request #165 from klheisey/release/v16.0.0 271e83836 update prenek/glomod.f to include missing col2 subroutine 20081b829 Reordered matrix entries for better readability bb5f96098 Omitted serial tests when IFMPI=true 2e964530a Merge pull request #164 from RonRahaman/serial-profiling-bugfix 8eac06fea Correct PPLIST when IFPROFILING=true and IFMPI=false 9f3322251 Default for PROFILING is true. d6136c458 Support for 'o' and 'on' boundary conditions added to PN-PN-2. c83c0b7cc Merge pull request #149 from kmittal2/smooth2d d8807ee5b Merge pull request #141 from cliosaglietti/issue-88 4969a50ef Merge pull request #80 from UFCCMT/cmt-merge-2 78b4c7ded Merge pull request #24 from hackljf/cmt-merge-2 e635d06de I stand by my code, but someting happened during the last conflict resolve. I will not have time to deal with it until after the CCMT tri-lab services Team review on December 2. CMT tests skipped for now. commits before 11/23/2016 are trustworthy to CMT-nek. 0cd421441 maybe this will save the day re: travis daedec9ce Merge branch 'release/v16.0.0' of https://github.com/Nek5000/Nek5000 into cmt-merge-2 9388623f9 Merge pull request #3 from UFCCMT/cmt-merge-2 587471288 Merge pull request #23 from hackljf/cmt-merge-2 5fac1bc86 Merge pull request #2 from UFCCMT/cmt-merge-2 36e0c6388 Merge pull request #22 from hackljf/cmt-merge-2 2cd967923 Revert "trying to resolve conflict in ic.f that doesn't involve code I ever use" c219fa1af trying to resolve conflict in ic.f that doesn't involve code I ever use 04439c3de Merge pull request #20 from hackljf/cmt-merge-2 239685ef6 README.md removed 10541dac4 Merge pull request #140 from ananiast/move_char de487d16e Merge pull request #1 from UFCCMT/cmt-merge-2 a9a987864 Merge pull request #19 from RonRahaman/cmt-merge-2 eeebac44d Merge pull request #160 from RonRahaman/release/v16.0.0 52bd53750 Fixed interfaces for CmtInviscidVortex test case 0ae768ace Fixed string-to-bool conversion in NekTests bdfa0fda1 Merge pull request #18 from hackljf/cmt-merge-2 3d4b5f59d see if this works. deleted a filter common block. the first of many a794f4771 Merge remote-tracking branch 'upstream/release/v16.0.0' into cmt-merge-2 f22122e55 Merge pull request #159 from RonRahaman/env-var-refactor e62804ff8 MvCylCvode now fails if CVODE isn't in PPLIST. 1f09eafea Interface uses PPLIST and USR_LFLAGS instead of IFCMT, CVODE_DIR, etc. This is a much more general and future-proofed approach. 2e5a50f48 Merge remote-tracking branch 'upstream/release/v16.0.0' into cmt-merge-2 b996c5453 Merge pull request #158 from RonRahaman/cvode-build d0b2ecb19 Merge pull request #17 from hackljf/cmt-merge-2 e5d7b9be4 some tweaks for v16.0.0.0 aa53f2563 Merge pull request #16 from hackljf/cmt-merge-2 f9291a6f8 Re-inserted IFCMT in .travis.yml. Will PPLIST do what I mean? c25286f78 I'm going to try this: replace IFCMT with PPLIST and see if that gets exported 4faccf486 forgot to update pvort.rea. removed IFFLTR from pvort.rea 9d7557a8a code works with and without -DCMTNEK. fix .travis.yml 0e5516276 Broke makenek pretty hard, but I'm committing anyway because nek5000 still works fine 810c27a11 Merge pull request #14 from hackljf/cmt-merge-2 62b839350 python fix for which line to read from l2norm.dat.ref 4e3ae7964 NOW THIS IS THE CORRECT USR FILE I DO NOT EVER WANT TO SEE VARSIC DECLARED IN L2NORM EVER AGAIN e0bf24ffa Ready to remove IFCMT and transition to compiler directive 92c2e5c7e GRAND EFFORT TO GET CMT OUT OF NON-CMT COMPILATION. COMPARE IC 8fccbb4b9 Omitted MvCylCvode 1e4 timestep from Travis build. 2d4a5abc3 Updated .travis.yml 87b0ed565 Mv_Cyl cvode PnPn tests work locally 801487a96 Changed NekTestCase.build_nek() to support extra makenek options 64ce67723 Corrected setting of SOURCE_ROOT in makenek.tests be9be1ad9 More docs in short_tests/lib 9fc6c3ccc Changed order of args for function signatures 35a67c112 Updated config_makenek and build_nek to match prototype of config_parfile 32aa5f1a6 Updated config_size to match signature of config_parfile 0a20aeb5d New config_parfile method ed20f9557 Merge pull request #155 from stgeke/fix154 327610f52 fixed CFL eval for lx1m=1 409c425e0 Revert "fixed CFL eval for lx1m=1" af918b7a4 fixed CFL eval for lx1m=1 6bd1b51c8 WIP: Updates to file configs 77a4734bb Merge pull request #156 from stgeke/restartCVODE 5c35f64a1 reset time to initial value 278f3ecfa added automatic restart if integrator fails 2c4cbbc61 added handling for old hdr ca5c6ef99 Merge pull request #12 from RonRahaman/cmt-merge-2 25c119f78 Fixed CMT/inviscid_vortex test case 778677efd Fixes to short_tests/lib/nekTestCase.py 5ae625c3b Cleaning up some mistakes from merge 704c4c4eb Merge branch 'release/v16.0.0' of github.com:Nek5000/Nek5000 into cmt-merge-2 cce98d283 Merge pull request #146 from stgeke/lolevels 40a2934e7 fixed typo bfca33fc2 Merge branch 'release/v16.0.0' of https://github.com/Nek5000/Nek5000 into lolevels 94f67a75c Merge pull request #148 from RonRahaman/issue-147 2020eb08e Omitted all serial tests except for eddy 2f528651a Merge pull request #145 from RonRahaman/issue-144 855539e11 added extra include file for preconditioner 960a61a99 Updated SIZE files to fit newest SIZE.template 0e26eb57c Added 'ls' command to checkout CVODE install 831d5cf38 Added cvode build to install steps 58e703eac add missing if-statements 7e647e884 added optlevel and loglevel 34e7d9aa0 2d smoother in prenek e752b7331 convabp, advabp_adjoint changed for passive scalar (T) adjoint advabp_adjoint has an extra term to be considered if ifheat is active convabp has one term less if ifadj is true. ADJOINT common block has extra variables. c5ec96d67 Merge branch 'release/v16.0.0' of https://github.com/Nek5000/Nek5000 into move_char a56a90319 added characteristics for moving mesh 9cf3c8ac3 Merge pull request #137 from RonRahaman/size-fmt-for-tests 948a8528f Merge pull request #138 from stgeke/mv_cyl 4befb75a4 Merge pull request #133 from KTH-ExaFlow/issue-131 5a2680b8f added mv_cyl to short_tests b8cfb73da Omitted tests for total solver time 306c129c5 More updates to README 3c8e563db Added test runner for standalone executable. Updated readme to describe it. 9259d14b8 Set defaults for SOURCE_ROOT, EXAMPLES_ROOT, etc. to match directory structure of this repo 9907f392e Updated SIZE files in short test; now they use SIZE.template 65a372ebb NekTests.py works for short_tests with new SIZE.template 7b0d4e7fe Merge pull request #136 from stgeke/fix_116 8f8dfd9ea Merge pull request #134 from stgeke/p0restart ab98bcdbb set BIGMEM to false and do not build exo2nek by default 6dfff6f38 Now parseSize.py is both a module and and executable e991f1547 First pass at parseSize.py. Regex reads vars correctly 629b5b5f7 added p0th to hdr for restarts 47647a792 Merge pull request #132 from stgeke/xx 31d6c38c3 include uncommited changes c5a4a04e9 Number of saved restart files consistent with time integration order. a6a27f40c WIP: Updated EddyUV to work with new SIZE.template. 44f50c1c7 cleanup and fixes for dp0dt 056871ea6 Added missing variable declerations 3e54ab87e . re-architecting cvode solver . addd additional .par file parameters . don't use libxsmm for very small matrices . updated lowMach_test to use new .par file . check for invalid p0th values e558e47c4 Merge pull request #124 from fischer1/x b6b3f7107 logical conversion byteswap fa9a7cb0f Merge pull request #123 from fischer1/x 60d741c97 clean up ping_loop calls 12ac497b2 Merge pull request #111 from KTH-ExaFlow/issue-#110 30f070e6b Merge pull request #112 from KTH-ExaFlow/issue-#109 8d144f767 Merge pull request #118 from fischer1/release/v16.0.0 43c951d65 fixed indices for DG ops 0a7d92042 Merge pull request #113 from KTH-ExaFlow/issue-23 9bf13ae08 plag initialised for nbd.eq.2 and nbdinp.gt.2 372e3f569 Merge pull request #107 from nicooff/issue-105 1c09962ef Merge pull request #101 from stgeke/feature/SIZE f1aff9c55 negative value of param(27) sets max of nab to nbdinp 63402bb43 corrected dsset initialisation in setup_topo 14daec0cb Fix conflicts with variable names in include files e33359b59 Merge pull request #102 from kmittal2/master cf35f018b Added circular-cartesian 2d mesh capability 4414b00d3 Restored changes of #81 64ad3e9b3 Added new SIZE template 348cc9220 Merge pull request #98 from KTH-ExaFlow/issue_97 436fe650e Merge pull request #79 from nicooff/issue-68 b3a8e68ed replacing NOTIMER in math.f 8c4860c70 Merge pull request #9 from RonRahaman/cmt-merge-2 24129283b Now using line #2 of l2norms.dat.ref as reference values a0927b190 removed gs_counter, gs_new_tstr, xfill-dead code,pf 98817cedc Merge pull request #82 from RonRahaman/serial-travis-tests 6bee1a954 Merge pull request #86 from stgeke/issue_78 3a70d7ed8 Merge pull request #93 from UFCCMT/develop 3f324b31e Merge pull request #8 from hackljf/cmt-merge-2 9137558ce Merge branch 'cmtvisc' into cmt-merge-2 7b4df3b63 MONOLITHIC ARTVISC FINALLY WORKS;EVM OR BUST!!!!! a5af2814e Merge pull request #7 from RonRahaman/cmt-merge-2 3fb3abb61 Removed cmt_cases directory f118aab94 Merge pull request #5 from RonRahaman/cmt-merge-2 6fbf07be5 Renamed file for reference solutions 4b6fcd09f Forgot to add short_tests/CMT/inviscid_vortex directory a56bb8585 Updated NekTests, .travis.yml to include CMT tests 950b738f6 bugfix, more debugging cfa6bd801 Monolithic regularization introduced, but no worky yet 0bcd1ac85 Merge pull request #4 from hackljf/cmt-merge-2 288bc8724 Merge branch 'cmtvisc' into cmt-merge-2 BIG COMMIT AND BIG MERGE WITH THE MOTHERSHIP de82895c5 Viscous term development plodding along 735a0872e name tweaks. nav stokes no worky. off to monolithic regularization for now 0b8d2fde0 now with diffusion number. nav stokes + vortex blows up pretty quick. now the fun really begins 1ebe7adc9 MMerge branch 'cmtvisc' into cmt-merge-2 46688e34f turned most stuff on. integer*8 bug in dg_setup slipped through the cracks 391ae2596 bugfixes in local_grad2_t, navier1.f 3f84807e0 Merge pull request #2 from hackljf/cmt-merge-2 18cdefcf5 SEND IT ALL UPSTREAM THIS IS A HUGE BUGFIX IN EQNSOLVER_CMT Turns out that evaluate_dealiased_conv_h was a huge mess; I had written a needlessly quadratic (but pleasantly compact) flux function for mass AND momentum, but only did about a third of the job. Mass conservation was a mess. Back to setting interpolating U onto H for the mass equation. Whew. 90510a6f0 More bugfixes. Somehow CMTDATA crept back into core/, but it's gone again. 918a48223 JH091416 First working code with Baumann-Oden DGSEM for higher-order terms. Will eventually become compressible Navier-Stokes solver, and host artificial viscosity for shocks. Developer docs will reflect this commit and date. f98b178cc Merge pull request #77 from BlairArchibald/develop a216ceb8d Ignore keys prefixed with '_' in .par file fd21b80b4 Change NOTIMER to TIMER ef1696abf Merge pull request #75 from stgeke/timer 9c6d6a36e Merge pull request #83 from Nek5000/release/v16.0.0 c9439694f Syntax error in .travis.yml 518d8174a Added Travis tests w/o MPI f16881bf0 Merge pull request #81 from RonRahaman/ifmpi-false-fix 19950afed Fixed inclusion of MPI in PPLIST definition when IFCMT==false 2294fbd0d Merge pull request #1 from RonRahaman/cmt-merge-2 66fcbfdd5 Moved CMT README to core/cmt. Restored original README 0d5405396 Added SIZE.template to core 51db6c214 Added variables declaration in include files b322f0856 Ensure NOTIMER disables all operation counting e626b7774 Disbaled timers and fixed issue #72 e81d05de2 When IFCMT=fase, don't append cmt_switch to case_name.f d5c33a641 Patching makenek.inc after previous merge 4e9440b25 Merge branch 'cmt-rebase-1' into cmt-merge-2 bfe3f694e absurdly huge bugfix in compute_transport_props 35a6d8a73 initialization is getting more, not less screwed up; find an answer b4eef0186 JH050316 ic.f fixed to allow restarting (again-ish). 280fecf6b Added particle ability to restart. In order to restart (pending fluid restart issues), set: 1) IFHEAT to T in .rea file 2) PRESOLVE line in .rea file from 0 to 1, also set fld file that you want to restart from on line below (exactly the same as nek5000) 3) see included lines in example part_*/.usr files in usrdat2, but you must set ifrestart-.true. and also set the number of the particle file that you're restarting from (should be 1 less than fld restart file number). a329e015b Merge branch 'cmt-sync' into cmt-merge d94f046d1 Merge pull request #70 from stgeke/mxmcleanup 435a70896 MxM cleanup 77a96f605 Merge pull request #59 from stgeke/par_imprv 1d715892f Merge pull request #67 from maxhutch/script_errors bd391251c Merged with latest release branch 2d57a34ee Merge pull request #62 from nicooff/cray_patch cec856790 Correct subroutine bin_rd1_mesh for cray machines 312076510 Merge pull request #61 from maxhutch/bugfix-47 052c2cc0e Merge branch 'develop' of https://github.com/Nek5000/Nek5000 into par_imprv 657a854b5 Added separate section for CVODE in .par file cfd5f4f02 added uncommited changes 1986adde0 Merge pull request #60 from Nek5000/revert-48-bugfix-47 ffc773a96 Revert "Changing line continuations." 95a9e50f4 Merge pull request #48 from maxhutch/bugfix-47 05d7aafed Merge pull request #58 from stgeke/genmap_fix_par d1829cb36 Forgot to remove suffix e6894b1b3 Merge branch 'develop' of https://github.com/Nek5000/Nek5000 into develop 63ee1437a Updated HEADER for release f0c3a43bf Merge pull request #57 from RonRahaman/nektest-updates 3ace323c0 Synching short_tests with NekExamples. 490028877 Merge pull request #49 from Nek5000/issue-24 30b1b9c47 Merge pull request #53 from RonRahaman/develop a52302ee5 Omitted benard/ray_dd from Travis tests. fe90b2cf5 Synching up short_tests/lib with NekExamples/lib 5874c177e Merge branch 'issue-24' of https://github.com/stgeke/Nek5000 into par_imprv 267edcfcd added support for scalars only 5c9820884 If no .rea file is found, try to read .re2 file. This is needed for the new .par file 659a129fe Merge branch 'develop' of https://github.com/Nek5000/Nek5000 into develop 40b96bd89 Merge branch 'develop' of https://github.com/Nek5000/Nek5000 into issue-24 cdbd84b0e Forgot to remove : 6b83cf8aa Fixed more alignment issues and keywords mismatches in short_tests 524ae255c f77 doesn't like == 1a18c2dc1 nek5000 -> Nek5000 in makenek,pff 4e77b6124 Fixed stdout alignment issues d994e4e5e Forgot about leading whitespaced. Aded blas.o 9ae1d7df0 Changing line continuations. 52fee74b5 Merge branch 'develop' of https://github.com/Nek5000/Nek5000 into develop 9b2e5c9e6 Merge pull request #45 from RonRahaman/maketools-bindir 5083a7075 In maketools, default bindir is Nek5000/bin b75e6d521 Merge pull request #43 from ggiannako/feature-exo2nek c439462cc Merge pull request #41 from RonRahaman/short-tests-rm-obj 04ce61540 Merge pull request #1 from Nek5000/develop 4cc6e8bde Update exo2nek.f dfa7bd4be Update README.md 44260de0a Update README.md 864ecd2fc Merge pull request #40 from RonRahaman/develop f71e44b9f Merge pull request #42 from fischer1/develop 3cba357a1 get rid of element 1 vertex writes,pff 9b8f8b7a8 Merge pull request #39 from Nek5000/revert-31-revert-19-cray_patch a237e9094 Updated README for short_tests 48eb3e313 Forgot to include .re2 file for lowMach_test 983d26503 Added minimal set of files for short_tests fdd021c22 Updated README 3905d21a5 Revert "Revert "Cray patch"" 6a6884bca Merge pull request #38 from ggiannako/feature-exo2nek b9985c558 Merge pull request #35 from nicooff/msh2nek 2f056317b Merge pull request #30 from maxhutch/crayftn_flags ea88f0517 Merge remote-tracking branch 'origin/feature-exo2nek' into feature-exo2nek b3186eed9 Added a new .re2 (v003) version 47e3fe57d Fixed various issues 4be516edf Update README.md 497550374 Update README.md a72324934 Fixed various issues 8fb09038e Merge pull request #10 from maxhutch/xsmm d9472ec22 Merge pull request #37 from RonRahaman/develop 0d09bb40e Updated Travis badge after renaming Nek5000 repo a767d8824 Merge remote-tracking branch 'upstream/develop' into crayftn_flags e96291ab2 Merge remote-tracking branch 'upstream/develop' into script_errors f3f391bf2 Merge remote-tracking branch 'upstream/develop' into xsmm 8862c76b3 Merge pull request #34 from stgeke/develop 17a555722 Update README.md 337da5c3f Added mesh converte from .msh to .rea 578387c4e Update README.md b0e37f4af Update README.md e2c37ed7f Update README.md a531f1df9 Re-enabled BIGMEM support for tools 0cbe8a594 Update maketools 0f130c98f Merge branch 'develop' of github.com:stgeke/Nek5000 into develop 2cc88c8e7 Added USR_LFLAGS to maketools 6028f75c1 Update README.md 08e15d18d Update README.md bfb276da7 Rename README to README.md e5649aac2 Added exo2nek fe7e9a5ae Merge pull request #31 from Nek5000/revert-19-cray_patch e7780a53d Revert "Cray patch" 639a6cee4 Adding flags for cray compiler (PrgEnv-cray module). fbd25f555 Merge pull request #27 from stgeke/develop f9c918dfe Fixed ftn handling 821356d25 Fix compiler detection for ftn c67bc1a76 Redirecting move warnings to /dev/null. Closes #25 757364f0d Merge pull request #21 from maxhutch/readme_singlebranch 0feae50ce Merge pull request #22 from RonRahaman/develop 3ff04ccb3 Updated paths in postnek's makefile 7fd5c905e `--single-branch` doesn't work with git version on MCS machines. e4686f941 Merge branch 'develop' into xsmm dc84b60d4 Merge branch 'develop' of github.com:Nek5000/nek5000 into develop 261b84513 Merge pull request #19 from nicooff/cray_patch 7d37f842d Merge branch 'develop' into xsmm 300494909 Merge branch 'develop' of github.com:Nek5000/nek5000 into develop ee2a34994 Syncing dockerfile. fa0faaee5 Merge branch 'cray_patch' of https://github.com/nicooff/nek5000 into cray_patch 99df412b7 Merge pull request #14 from maxhutch/develop e4acfcc10 Moving license to top-level; adding readme badges. a90653e36 Merge pull request #12 from maxhutch/travis e3cd2305e Wrong image again. ad4cb4244 s/NekBox/nek5000 f140a813c Environment tweaks. 47fd48f5f Added Travis and docker config scripts 3b57e6774 Merge pull request #9 from maxhutch/develop 63a781273 Merge remote-tracking branch 'upstream/develop' into xsmm e33a69930 Changing the default branch. c86e393ab Updating docs to reference `bin` instead of `scripts` 1ba2e76a7 Merge pull request #8 from Nek5000/develop 1610ef2ff Fixed paths in makefile, #includes to match new repo layout 5a0f2455f Merge pull request #4 from maxhutch/bgq_mxm 16e488f80 Merge remote-tracking branch 'upstream/develop' into bgq_mxm e09958e9d Adding readme and contributing guide d7ece7527 Adding lib, tests, 3rd_party place-holders 5783d66c7 Merge NekTools de033fe17 m to c converter 92aabe660 fixed j=1,m to j=2,m bug in projection, pff d258d2f63 no clean-up for ifcmt, pff 51a07947d no clean-up for ifcmt, pff 353c47199 set ifgett to T for ifcmt 8eed10a45 James' improvement of AMG preprocessing matlab scripts f84475220 Added support for variable thermodynamic pressure in low Mach number solver. Fixed some bugs when using CVODE to recover high order splitting error. bca92b40f MS-04/18/16 Sync with nek5000 svn code Rev 1131. Paul has fixed maxjob and restart errors/bugs pointed out by cmt-nek micro sim. 4b144b267 Added param(20) to specify optional tolerance for temp/ps solve. Removed implicit type conversions in .par reader. 94437919c Added check for unknown keys in .par file 1d17e56c1 typo in maxobj, pff 83af91833 Fix hcode declaration in INPUT, pff bbe477cb0 Fix hcode declaration in INPUT, pff ff4e9012e remove deadwood routines..., pff 725bc24d4 Some bug fixes for .par support 9416b5bbe Added support for new .rea file format. Experimental, at least for now. 8a854d54e force userq for conduct, pff 7e9f5b3ce added translate to IMPORT MESH, pff b6b9780cf Sync up with latest nek svn repo. 5f16193d0 Updated the case rarepart2d and the cmtparticles.usrp file found within. 4d7049a28 move lagvel, along with v_extrap, to after IGEOM=2 in plan4, pff 634236766 give early return in cggo if rhs=0, pff 32ea12a63 fix of EXTBAR on BGQ and NEKMOAB b39898051 Updated and fixed some weird behavior with the low storage rk3 time stepping routine for particles. 937b93752 Fix v_extrap() in plan4 and fix common block for ta() in auto_averager, pff b79bbd9fa Updated test cases so that particles are consistent with drive1_cmt.f and CMTDATA files. Also updated these files too so that two way coupling and adding other forces should be straight forward. 945faf2ad Updated particle tracking to include RK3 time step routine so that there were minimal changes in the trunk code. Quasi-steady force corrections have been added according to parmar et al. 2010. Now the setup to add particles is as follows: 3c221110c fixed common array issue for ta() in autoaverager, pff f8a2b646c Adding optional dealiasing in cmt-nek The switch is controlled by setting lxd in SIZE file, if lxd.eq.lx1 then dealiasing is turned off cfaed9b51 updated david_inout2d case for particle testing to fix bug in include file bb329040e Added inout2d example case, but still a work in progress. Used for testing quasi-steady force corrections at different mach/reynolds numbers 6d3c9bef6 Adding sphere cases to CMT examples. These cases have an inflow outflow boundary. Two cases are added, one is meant to get a steady state solution and the other case is used to extract the inviscid unsteady kernel 4807aa9e3 synced folders from previous commit b3356017b Rearranged david_* cases from cmt_cases to examples/CMT/ directory e25b03b7e Fixed bug in mpi io and added quasi-steady force corrections in the .usrp file rarepart2d case. Still in testing. 971a4ad31 cleanup div by zero for x2,pff 0f3fbe9e9 fixed memory problem in getfld.f in postnek, pff 060df97f7 Working on particle forces and organizing cmt_cases folder cf9c68f48 Current developement cases for particles and forces 38118872c Revert "MS022416 Make dealiasing optional." 15ff3e500 Merge branch 'master' of https://bitbucket.org/ccmt/cmt-nek 5f1edd603 Basic giut tutorial 72256d43f my git example e75554be7 removed stop stmt from zipper2.f, pff d64fd7b5d MS022416 Make dealiasing optional. If LXD=LX1 in size file then dealiasing is turned off in cmt-nek. Limited tests performed on inviscid compressible vortes and rarefaction case. 75dbdcba6 Merged in hackljf/cmt-nek (pull request #9) 3bc721d8b Merge branch 'master' of https://bitbucket.org/hackljf/cmt-nek bc1985e09 Fix for restart cmt-nek and modifications to makenek.inc and makefile.template to incorporate cmt_dummy option for compilation eb649a321 MS021816 Update Jason's Fork with cmt_dummy file This is to check if I can use git the way it is ment to be. 2aad5c606 README.md edited online with Bitbucket 12c60773f updated rarefaction.usr; need new grid soon ba60ac914 Merge branch 'master' of https://bitbucket.org/hackljf/cmt-nek ok apparently master wins d6560d5a0 added case sensitivity to 'v ' in InviscidFlux. Added a kludge to inflow_bc until I can get cbu nekasgn'ed correctly. 6323cc706 Cray patch included e7da44a74 Ananias moving meshes 1cf43c0a4 Merged ccmt/cmt-nek into master c964734f5 Merged in hackljf/cmt-nek (pull request #8) 406ded44c cleaned up some comments dfa1ac942 boundary condition repair. thanks, Mrugesh 124c34c37 fix up some curve side stuff, pff 537899d22 Projection calls added (ophinvpr -> ophinv_pr) Nothing done yet for MHD 4d3947151 Fixed the SYM boundary condition 43dd65a3a Hooking in libxsmm. 1a56f7942 Typo in makenek.inc: BGG -> BGQ. Build fixes. 85b21d9fa Merge branch 'master' into bgq_mxm 4f3691886 fixed map_faced for 3D --- there was an error in mxm call, pff 2772a7ff9 minor clean-up, pff 03f72bfb2 Extensive changes for weak-form, dealiased integration. This is almost certainly the right way to do nonlinear DG in nek5000 with Patera elements. Extensive testing must precede an SVN commit, or even a push to bitbucket.org/ccmt/master 6206076d7 Merged ccmt/cmt-nek into master 1b38a3f72 add pa support for neknek and nfld_neknek, pff 83eaf6c56 fixed projection for mvbd case, pff 92ccff722 Avoid divide by zero when tio=0, pff ba3b11468 This fixes MOAB build issues, due to recent CMT updates to Nek e4da01a84 Merged in mrugeshs/cmt-nek (pull request #7) e5ef4530b this repo now resembles the folder hierarchy of nek_svn. CMT examples have been moved inside examples folder. To access cmt examples look in examples/CMT/ All the nek5000 examples are also added to this repo for the convenience of developers and users at CCMT. 0005cc9b7 Merging nek5_svn commit of November 4th 2015. appended few more excursions to the gitignore file b4ac17ce6 Merged ccmt/cmt-nek into master c6c9131a9 keeping up header count, pff 157a655ec move CMTDATA to main source, pff 44a6921e6 Update HEADER to 1085, pff 8d98dbf3b THIS IS THE CMT source addition, pff + JH + MS 692caa5c6 THIS IS THE BIG CMT merge..REV 1, pff + jason H + mrugesh S a0e049d5b Merged in rodbourn/cmt-nek (pull request #6) 3d916ea4d Merge branch 'master' of bitbucket.org:rodbourn/cmt-nek ac3f6e729 Added a quick build script that will copy makenek if needed. 6d987355c fix variable replacement which occurred during review. Added map and rea fd1922e2b Added cmt_cases/charles_particles to contain further particle development work which is initially a copy of the swep_particles example. cmt_cases is meant to be cases in development rather than complete examples. c70aeddb9 Merged ccmt/cmt-nek into master fe4388507 Merged ccmt/cmt-nek into master 1258f2acd Merged ccmt/cmt-nek into master 27632fed4 fixed hmholtz bug (missing CTIMER) found by klh, fix volflow+var.visc option, pff e61891540 Merged in rodbourn/cmt-nek (pull request #5) d44b4d271 Added further ignore patterns. adcdbd088 Added a quick description of how to run an example 7ced32028 Added ignore rules to remove some of the build and run artifacts 90cd38125 Added a cmt_cases directory to contain cases which are under development. 5ca3c5510 Merged in rodbourn/cmt-nek (pull request #4) 546fa14bc Added tools from nek5000 into a tools folder since they are used in the examples (prevent having to fetch code from nek5000 repo) cd10ef34c Merged ccmt/cmt-nek into master 9fd30359c fix rvar allocation in PROJECT routine in navier4.f, pff 056975c80 Merged in mrugeshs/cmt-nek (pull request #3) 3764c38ac Following is the summary of the changes 1) toteq has been moved to SIZE - makenek.inc will search for toteq, if not found, declares toteq=1 when IFCMT=.false. or 5 when IFCMT=.true. NOTE that if the user uses a SIZE from a cmt-nek case to run a nek5000 example then makenek will not modify toteq ! 2) CMTSIZE is removed from examples, all the parameters in CMTSIZE are declared in CMTDATA 3) CMT trunk has been modified. LELT and LELV have been replaced by LELCMT. This modification ensures that when the user is running nek5000 then I can set LELCMT=1 and the memory footprint of cmt-nek will be minimized. LELCMT is set by makenek.inc. The procedure is same as that used to set toteq. 4) cmt directory now resides inside nek 5) Fixed an error in makefile.template, CMT_CORE is always included in the list of object files. 02752468a Merged ccmt/cmt-nek into master 0a1f34085 Added DG option for convection-diffusion; added PROJECT operator, pff a7f756d59 Merged ccmt/cmt-nek into master a522de8d0 Merged in mrugeshs/cmt-nek (pull request #2) 2c9589104 Readme for swept particles 417117c54 Swept_particles example added. 6faac73fa The inviscid vortex case has horizontal boundaries as walls. This modification makes them periodic. This case is meant to have periodic boundary condition in x and y direction. a3997b9b9 Merged ccmt/cmt-nek into master 8e2469756 Merged ccmt/cmt-nek into master 2bcaa2fb7 Merged mrugeshs/cmt-nek into master - Added cat_examples - Modifications to drive1_cmt.f, drive2_cmt.f and diagnostics.f 2bee99bce Modifications drive2_cmt.f - we do not initialize cmt parameters from setup_cmt_param. We initialize them in usrdat or usrdat2 in <casename>.usr. This is done to avoid trampling over param array declared in INPUT in nek5000 codebase. drive1_cmt.f - move compute_primitive_vars is now called after the 3 stages of RK3 step are done. This ensures that we have access to the latest primitive variables are available in userchk. diagnostics.f - out_pvar_nek and out_fld_var are modified. We use scrns common block to copy conserved variables and primitive variables and then passed as arguments to outpost2 6d6e3ad6f Rarefaction example added to cmt_examples. Verified using current version of CMT-nek (mrugeshs fork) fea25b483 Created cmt_examples folder. Added first example, inviscid vortex. This case has been verified with the current version of CMT-nek (mrugeshs fork). 556ab64f0 Test commit option in SourceTree 01f753e38 Revert "Added a sub heading of team to demonstrate a pull request." b643586ff Merged ccmt/cmt-nek into master 765943aa5 Merged in rodbourn/cmt-nek (pull request #1) d7098e28f Added a sub heading of team to demonstrate a pull request. 6b587c1a2 Added title to readme file dcbfc42f5 Initial commit from CMT-Nek CVS repo cac32698f zero out pressure mask in solid domain in bdry.f, pff e6842a218 zero out pm1 in prepost for conj heat transfer cases so p=0 in solid domain, pff 6a9cc2331 fixed bug in usrsetvert call in navier8.f, pff 63018e21d updating prenek, pff 215a69f33 turn off dsavg if ifdg,pff eb2852416 update HEADER to 1072, pff 5632f7480 added ifdg flag, pff 53392973c Added FORTRAN ifc for findpts_eval_local dd1e7e4b5 fixed fs examples and new README for neknek example b9a851996 added moving Neknek dadc77407 added initialization of interface conditions to neknek and removed them from .usr file 09addac5b Adding neknek for pnpn, pff b8ebed297 Fixed AMG setup bug: the case of 1 F-variable was mishandled. 1a13e553e Added o pressure bc option for pnpn2 to navier1.f, pff f5624828a fix zipper2.f array issue acbbd9362 Fix for turbChannel.usr with bg_xlf compiler & less output in add_temp_1() 088b60dd1 clean up last commit of comm_mpi.f, pff cdc00ad3b added more ping-pong tests to comm_mpi, pff 3c7955e8d added comments to turb_outflow in navier5.f, pff a9ecd9338 a bit of meshing cleanup, etc. glomod build and zipper2, pff 72c725194 fixed rax issue in zipper2.f, pff 7199ec015 updated prenek source, pff 81ea64559 Added assmembly version of mxm for BGQ. Changed BG target to BGL. 8e058e310 fixed turb_outflow in navier5.f, pff a68caa2da updated nelb error found by elia, pff 12aefd21e updated HEADER to 1050, pff 543bd2e0d cleaned up a bunch of undefineds, pff d91072399 remove orphaned external links in mxm_std.f, pff deddc9ea5 fixed add_temp to acct for tmult and dssum via setup_top in navier5.f, pff d896c94e9 fix some axisymm+mvmsh stuff, induct navier1 navier4 subs1, pff 86f1beb8e fixed pnpn-2 axisym. solver options in connect2.f, pff, jan 01 2015 f21e70c27 more cleanup to zipper2.f, pff 1bbdd0e9b more fixes to oct/quad split, pff 050814e10 fixed one of the C+m curve incompatibility issues, pff 964b16415 fix fixmska---nface was not initialized, pff 627d1146f fixed scrns conflict in auto_averager---pff 0e5ddf739 fixed tio-divide-by-zero bug, pff 767262c34 added declaration of u() to hsmg_dssum, pff 30af4cca1 Defining the logfile verbosity variable (nio) in MOAB wrappers -- needed due to implicit none declarations 85fac9751 fixed percentage of time for tgop and up HEADER count 18e0e8d09 Added tgop average to runtime stats and changed MPITIMERS to gp2 db127604d bumped HEADER counter, pff 91e0c78f8 fixed kfld output,pff c76daff1f Fixed dual usage of nio in nek b800845d9 Added verbosity control to IO logfile 4deba60ad update BB tests, small fix to velocity projection c65df9ba3 Added new BB tests, turned on projection for Velocity and T/PS fields, clean up multiple projection subroutines, add a check for any open files before exitting the code d150ae01e removed the rm SESSION.NAME stmt, pff 5bb40da27 Updated BB tests, fixed 8-byte genmap error a9b62f7bc Updated BB tests, fixed 8-byte genmap error 1e5b03f7d added missing ierr args to mfi_parse_hdr calls in a couple places in ic.f and postpro.f, pff b3041dd37 fixed cbc bug on line 135 in gfdm_op.f, pff c6d8ab73e fixed gs_op bug in rev 1021 65e0cd5ea 3rd argument of gs_op now 1 for double, 2 for local int (4 bytes), 3 for global int (8 bytes) da583d426 removed some debug junk in subs1.f, pff 78ae20ccd fix ierr=iglsum() error in connect2.f; pff 446bccf7d fix import of bad elements in VTK / VTX import in build.f 3640c2da9 small fix to n2to3 for mhd parameter read, update to BB test aab8029c7 small fix to n2to3 for mhd parameter read, update to BB test cf779621f adjust BB tests 02e8d315e hopefully the last of the p66/p67 changes, fixed a parallel exit for restart files dad791181 fixed restart exit for parallel failure modes 1ebf2310a finished updating examples .rea and .usr to reflect default p66/p67 set to binary output and added EXTBAR flag to makenek.inc for BGQ 51340339f Updated all .rea files and to set p66/p67 to 6 and changed Nek to default p66/p67 to 6 unless using .usr file to edit parameters. ONLY postx/postex will read form from .rea file. N2to3 handle different temp BC, for nel=nelv only. Minor BB update 68120b297 Updated all .rea files and to set p66/p67 to 6 and changed Nek to default p66/p67 to 6 unless using .usr file to edit parameters. ONLY postx/postex will read form from .rea file. N2to3 handle different temp BC, for nel=nelv only. Minor BB update 4fe810f62 Updated the auto_avgerager subroutine c304b8124 fixed divide by zero issue in zoom in screen.f, pff e18ee8760 Updated BB and added re2-8byte read to postnek 21fa0a5be Updated BB and added re2-8byte read to postnek 74b04a79a more fixes to add_temp 265e70b27 fixed turb outflow and add_temp d6a9274a9 updated turb_outflow in navier5.f, pff 13ba3f496 Added checks to genbox for BC and xyz ranges 7da08e70a Added checks to genbox for BC and xyz ranges 59df328df tight locglob tolerance 4cc31be92 fix zmin/zmax check 42150e373 updated re2 8-byte precision support and fixed 8-byte byteswap 9141b01a9 added add_temp to navier5.f pff 757f18dbc Updated genbox to handle when mbox(in SIZE) is equal to the number of boxes in the .box file, including one. ad67efb91 Updated genbox to handle when mbox(in SIZE) is equal to the number of boxes in the .box file, including one. 6189a2dd2 fixed turb_outflow in navier5.f, pff 85e7f272f fix booboo in if_fltv stmt, navier5.f, pff d22c5dc32 added turb_outflow() to navier5.f, pff d1ce9a846 cleaned up surface_int and surface_flux routines in navier5.f, pff ba0338896 no filter of frozen base flow - adam peplinski contribution, pff a5ff0613a fixed minor bug in surface_int, pff 720462cd7 update fix to 8-byte, byte_swapping for .re2 file reading, and changed check for hpts 0dd6843ad fixed istep init and ifsplit-->iftran, pff d946d2096 separated zero and zero_moab.usr files, pff af41d3f66 Added support for non-nek-supplied LAPACK libraries to compile system 22085f5b8 Update hsmg integer passing for compiler update and hpts test in buildbot a7a1420cf fixed long-standing bug in XXT showing up with self-periodic elements 2352be7b2 updated header after navier5.f updates, pff a12c3efad added x avereger and auto_average for files to navier5.f, pff cb75297f7 added x avereger and auto_average for files to navier5.f, pff 0cdc435df commented curve debugging and update HEADER e4b03d79c fixed nelf to nelvv in bound.f 7b200c743 added 8-byte support for re2 input, it will now be the default for genbox,reatore2, and n2to3. Nek is backwards compatible with the 4-byte re2, of course. Also added a gen_re2 subroutine to postpro.f a32f11034 added 8-byte support for re2 input, it will now be the default for genbox,reatore2, and n2to3. Nek is backwards compatible with the 4-byte re2, of course. Also added a gen_re2 subroutine to postpro.f 683132c8a a few fixes in prenek for bcs etc. pff. 00a45bc2a nek multistep in drive1.f and fixed diag prec in hmh, pff. 2e6d2dc02 FIX PERIODIC BC for Conj. HT in genmap.f pff 3b69f66b2 =corrected max particles comment in makenek.inc c5ae72b48 forgot file in nek/jl/CMakeLists.txt 06c707418 individual Lagrange weights routines up to order 24 from 16 bafa42d38 added CMake build system for external library for interpolation 5ad3615d0 fixed external findpts_local.h 81c4c1523 added header for external interface for findpts_local 434b6697a Update BB test to include hpts test b819ceb06 Update BB tests and add note to .usr files for userbc(), fix minor passive scaler .rea read in postnek 81cd5ae86 Update BB tests and add note to .usr files for userbc(), fix minor passive scaler .rea read in postnek 3cdcaee1b added projection for some of the stress functions acac4a02d upgrade bdry mvmesh subs1 subs2 to support more moving mesh cases ec94aa455 removed testdtp testmultd testmom from navier1.f; these perhaps should be added elsewhere as part of test suite 914c13634 I made the following changes to visit.f 594c8e382 Fixed .f000?? file format to include mesh data on first file dump for post-processing purposes bc9b666e3 Changed makenek.inc to optionally compiling cray-pointers with MOAB only, updated error check for hpts, updated 132 support for file names in restart files 035158aa5 Some modifications for MOAB interface. 1) Adding a utility function to get the tag field values based on tag name alone. This allows the problem setup (usr) to not include NEKMOAB directly. 2) Fixing ICC and GCC warnings in the MOAB interface related include blocks. 41538d0a9 Small fix for GFDM for MHD + extend GFDM for Pn-Pn (but not yet in place to actually solve the pressure Poisson problem); updated Buildbot tests; small change to hsmg.f for pn-pn-2s top level poly. order f65e8071d Updated BB tests, fixed genbox real*8 BC error, initialized hmholtz rho to zero(to fix error with Intel compilers) 0dfb1e181 Updated BB tests, fixed genbox real*8 BC error, initialized hmholtz rho to zero(to fix error with Intel compilers) 3bacb7c75 added nek_in_situ to target object list in makefile.template 8ae064e24 Adding VisIt in situ to the Nek5000 code. This is done with the following files: visit.f and nek_in_situ.f. The makefile.template,makenek.inc and makenek were changed to support the VisIt in situ code with the a new flag IFVISIT in the makenek file. af56eee23 Added new scripts to run Nek5000 with VisIt in situ. The nekvisit script is for serial execution and nekvisitmpi is for the mpi execution. They work just like nekmpi. I have updated the README to document them. ecffade2e fixed usage of restrict pointers causing compiler warnings 079c1b29e Fix for passive scalar dump in avg_all() 0766ea7b8 dont trap bc read errors 639d9dd0b EMERGENCY hack in h1mg_solve to ensure continuous pressure! ca7dfe0aa vlngth had an error impacting spherical geometry generation 49e7aefcc updated a few i/o issues - pff 478600d02 slight improvement in hsmg for pn-pn-2 c492bacf1 modify postpro to bcast(npoints,isize) e93d0d81e Fixed cpu_time for mpi_dummy and pgf77 add3f0a08 VTK reader fix cff229b9d Updated C fail routines for amg.c, fixed hpts bug for bcast, closed hpts.out file upon exiting, if opened, updated mpi_dummy wtime to F77 standard. 648389522 set default Poisson parameter for mesh in mvmesh.f d4149b629 Changed makefile to compile genbox in double precision bc1e501e4 Changed makefile to compile genbox in double precision 9396c29fb added generalized z-slice to navier5.f 43697e6d1 Fixed conjugate heat transfer merge for fluid BCs in prenek, updated makefile for prenek and postnek for auto-platform detection, changed typo in n2to3.f e6d6532fb gather-scatter setup reports memory usage 4a49b659e fixed MG bug in pn-pn formulation in hsmg.f a01fb87a3 fixed glvadd in math.f db391e107 Updated BB, nek exit on BG platforms, genbox segfault issue resolved, tools/makefile script default now set to bash, prenek/postnek detect OS for X11 build on Max/Linux a7812d2d3 Updated BB, nek exit on BG platforms, genbox segfault issue resolved, tools/makefile script default now set to bash, prenek/postnek detect OS for X11 build on Max/Linux dcf93a3f4 Freeing memory using iMesh_freeMemory instead of free from fortran, use MOAB version sha df79abd onwards 921efdb16 Fixes for compiler-underscore problem found on BGP. Introducing NEK_GID tag, for restarting a nek simulation, RESTART needs to use the new .h5m (mesh file) dumped from the initial simulation 9fe398297 bug fixes to iolib_no_graph.f bdea27feb Stefans updates for distributed reaction computations dbe7c2a2c fixed (hopefully) bug in tuple_transfer ede015a1a restored previous spherical cap functionality to build2.f 0c3184e43 v.917 in HEADER e3f7478e0 clean up new navier5.f routines, v.917 in HEADER 7a0d9864b added new dist. fct. to navier5.f and fixed cheap_dist() e9e08966e Added cheap_distance function to navier5.f ddb4007d9 updated HEADER counter 5e032d9e2 added cut_off filter and domain_size to navier5.f 2242507b2 major changes to prenek source 3ae85c26d fix bc gswrite error in bound.f 3526f458b restored smaller basics.inc and basicsp.inc 54dda31ef bound, build, etc. not used in postnek 4d21b043d updated HEADER to 906 a41bcf064 induct.f and SOLN updated to store computed CFL for diagnosis e410a823f prenek: Added support for new fcc mesh 76116beec Changed prenek back to single precision c331b3526 Changed prenek back to single precision 9811270be minor fixes to new prenek 6280e0c8b minor fixes to ibc in n2to3.f 6d98be09e Fixed reatore2 reading of BC 7aca29d31 Fixed autoperiodic for 2D; major overhaul of bound.f 37522be07 Cleaned and Added SIZE files for tools, added re2 support for large element cases 0af31a5f1 Cleaned and Added SIZE files for tools, added re2 support for large element cases 2c373e999 Updated tools for double precision, including re2 files 0070d9d77 Updated tools for double precision, including re2 files 78f7fc495 updated prenek to compile on all compilers 6d0fd3054 Delete zipper.f. These routines now in zipper2.f…
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Closes #122