October 2017 - Nektar-users

how to use HOBC?
by Kurt Sansom 25 Mar '18

25 Mar '18

Hi, I am trying to use the higher order outlet boundary conditions. I know that is formulated for truncated open domains, but am curious if I can use in the following way, where I want to specify the outlet pressure to some value to create back pressure in the system. I realize that for in-compressible flow it doesn't matter that much, but I am interested in implementing a time varying pressure condition at the outlet. I have tried the following boundary condition for a tube and it doesn't appear to apply the VALUE tag? I want to make sure before I file a bug. <REGION REF="2">  <N VAR="u" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <N VAR="v" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <N VAR="w" USERDEFINEDTYPE="HOutflow" VALUE="0" /> <D VAR="p" USERDEFINEDTYPE="HOutflow" VALUE="10665" /></REGION> Regards, ~Kurt -- Kurt Sansom

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Reynolds Stresses
by wasim sarwar 06 Nov '17

06 Nov '17

Dear All, I am wondering how exactly Reynolds stresses are calculated in Nektar++. I have two questions regarding the calculation of reynolds stresses: 1) Whether these stresses are being calculated at every time step or just at the end of the simulation when we ask it to output the average field. 2) Once it outputs the average field then does it start from zero to compute the next average output field or proceed from the last saved output averaged field. Any feedback would be of great help. cheer

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How are edges used in the mesh
by Kurt Sansom 05 Nov '17

05 Nov '17

The documentation mentions mesh edges being required for 2D and 3D, but how are they used and is there some implicit connection between them and Elements? I would assume the only connection is the vertex Ids should match, but it's unclear to me if I might be missing something there. Regards, ~Kurt -- Kurt Sansom

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vtk convert .vtu to .xml
by Kurt Sansom 26 Oct '17

26 Oct '17

Hi, I am trying to convert a .vtu mesh file to the .xml format. has anyone done this already? NekMesh Doesn't have this feature, I tried implementing it myself, but am having some challenges that I need to work out with how vtk access's each cell. I am also gettting some errors like: Warning: degenerate tetrahedron, 3rd vertex is = 4.74539e-05 from face Any feedback would be of great help. ~Kurt -- Kurt Sansom

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Issue with CompressibleFlowSolver
by Oliviu Sugar 25 Oct '17

25 Oct '17

Dear all, I have run into some problems when trying to run the compressible flow solver. First, some background:- code build was complete without any issues, with all dependencies pre-installed system-wide, and without any problems in linking to these libraries - ran all regression tests, all successful- ran the Incompressible NS Solver, both serial and parallel without issues- ran the ADR Solver without issues The code was compiled and ran on a personal workstation, with Ubuntu 16.04 as the Linux distribution. I am not an advanced Linux user, having started to work in it only recently, and thus identifying the exact issue is not possible for me at this stage. The compressible flow solver always fails, even for the isentropic vortex case provided as example with the distribution. When running in serial, the error is:--------------------------------------------------------------------------------------------------------------------------------------------------------------- [salv08976-ub:03370] *** Process received signal ***[salv08976-ub:03370] Signal: Segmentation fault (11) [salv08976-ub:03370] Signal code: Address not mapped (1) [salv08976-ub:03370] Failing at address: 0x1573bc50 [salv08976-ub:03370] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x354b0)[0x7fb38f0b04b0] [salv08976-ub:03370] [ 1] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities27AnalyticExpressionEvaluator8StorePrm8run_onceEv+0xb)[0x7fb39087b39b] [salv08976-ub:03370] [ 2] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities27AnalyticExpressionEvaluator8EvaluateEi+0x6e)[0x7fb39087514e] [salv08976-ub:03370] [ 3] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libSolverUtils.so.4.4.1(_ZNK6Nektar12LibUtilities8Equation8EvaluateEv+0x38)[0x7fb391cc8508] [salv08976-ub:03370] [ 4] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader14ReadParametersEP12TiXmlElement+0x26d)[0x7fb3907bacbd] [salv08976-ub:03370] [ 5] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader13ParseDocumentEv+0x92)[0x7fb3907c2612] [salv08976-ub:03370] [ 6] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader11InitSessionEv+0x4f)[0x7fb3907c6aff] [salv08976-ub:03370] [ 7] ./CompressibleFlowSolver(_ZN6Nektar12LibUtilities13SessionReader14CreateInstanceEiPPc+0x16d)[0x48ef6d] [salv08976-ub:03370] [ 8] ./CompressibleFlowSolver(main+0x62)[0x454b52] [salv08976-ub:03370] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fb38f09b830] [salv08976-ub:03370] [10] ./CompressibleFlowSolver(_start+0x29)[0x463219] [salv08976-ub:03370] *** End of error message *** Segmentation fault (core dumped)--------------------------------------------------------------------------------------------------------------------------------------------------------------- When running in parallel the error is:The error message is pretty mush the same, only repeated a number of times equal to the number of processing cores, plus the following message at the end:--------------------------------------------------------------------------------------------------------------------------------------------------------------- mpirun noticed that process rank 3 with PID 13368 on node salv08976-ub exited on signal 11 (Segmentation fault).--------------------------------------------------------------------------------------------------------------------------------------------------------------- Any guidance with this issue would be much appreciated. Thank you.Oliviu

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compiling python wrapper
by Rubini R. 25 Oct '17

25 Oct '17

Dear All, I would like to compile the python interface of nektar. I follow the instruction I found on the GitLab repo. I have already compiled both Nektar++ and Boost.python without any problem. However I don't manage to get rid of this error during the compilation: /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_InternFromString' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_FromFormat' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_FromString' /usr/local/lib/libboost_python.so: undefined reference to `PyBytes_Size' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_AsUTF8' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_FromEncodedObject' /usr/local/lib/libboost_python.so: undefined reference to `PyBytes_AsString' /usr/local/lib/libboost_python.so: undefined reference to `_Py_fopen' /usr/local/lib/libboost_python.so: undefined reference to `PyModule_Create2' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_AsWideChar' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_AsUTF8String' /usr/local/lib/libboost_python.so: undefined reference to `PyUnicode_FromStringAndSize' collect2: error: ld returned 1 exit status libs/numpy/example/CMakeFiles/fromdata.dir/build.make:97: recipe for target 'bin/fromdata' failed make[5]: *** [bin/fromdata] Error 1 CMakeFiles/Makefile2:152: recipe for target 'libs/numpy/example/CMakeFiles/fromdata.dir/all' failed make[4]: *** [libs/numpy/example/CMakeFiles/fromdata.dir/all] Error 2 Makefile:138: recipe for target 'all' failed make[3]: *** [all] Error 2 CMakeFiles/boost-numpy.dir/build.make:110: recipe for target 'ThirdParty/stamp/boost-numpy-build' failed make[2]: *** [ThirdParty/stamp/boost-numpy-build] Error 2 CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/boost-numpy.dir/all' failed make[1]: *** [CMakeFiles/boost-numpy.dir/all] Error 2 Makefile:127: recipe for target 'all' failed make: *** [all] Error 2 I'm working on ubuntu 16.04 LST. What am I doing wrong or what am I missing ? Thank you very much for your help. Regards, Riccardo

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Fieldconvert
by Shervin Sammak 23 Oct '17

23 Oct '17

Hi, I have several checkpoints and in each one of them, I have info.xml and couple of fld files, since I run in parallel. I create my vtu files along this line: for j in {0000000..0000003}; do for i in {0..12}; do FieldConvert ../Cyl.xml Cyl_$i.chk/P$j.fld Cyl_$i.chk/P$j.vtu; done done The problem is to create a movie of unsteady results, I need to have all the file in one place. I also tried this: for i in {0..12}; do FieldConvert ../Cyl.xml Cyl_$i.chk/Info.xml Cyl_$i.vtu; done but the output has only the mesh result and not pressure, velocity and etc. Can you please tell what is the easiest way to post-process multiple fld file to make a movie easily? ----------------------------------------------------------- Shervin Sammak Research Assistant Professor Center for Research Computing University of Pittsburgh 4420 Bayard St Pittsburgh, PA 15213 E-mail: shervin.sammak(a)pitt.edu ~ You chase quality and quantity will chase you.

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Nektar++ 4.4.1 Released
by Chris Cantwell 14 Oct '17

14 Oct '17

Dear all, We are pleased to announce the release of Nektar++ v4.4.1. This release includes a number of further bug fixes and minor enhancements to the 4.4 release: **Library** - Remove m_offset_elmt_id and GetOffsetElmtId which fixed problems in 2D when quad elements are listed before tri elements (!758) - Remove the duplicate output of errorutil (!756) - Fix BLAS CMake dependencies (!763) - Fix interpolation issue with Lagrange basis functions (!768) - Fix issue with average fields not working with different polynomial order fields (!776) - Fix rounding of integer parameters (!774) - Fix Hdf5 output in FilterFieldConvert (!781) - Fixed extreme memory consumption of Interpolator when interpolating from pts to fld or between different meshes (!783) - Fix missing entriess in LibUtilities::kPointsTypeStr (!792) - Fix compiler warnings with CommDataType (!793) - Fix deadlock with HDF5 input (!786) - Fix missing entriess in LibUtilities::kPointsTypeStr (!792) - Fix compiler warnings with CommDataType (!793) - Fix ability to set default implementation in Collections and added an option to set eNoCollections in FieldConvert as default (!789) - Fix performance issue in ProcessIsoContour in relation to memory consumption (!821) - Fix performance issue with ExtractPhysToBndElmt (!796) - Fix available classes being listed multiple times (!817) **FieldConvert:** - Fix issue with field ordering in the interppointdatatofld module (!754) - Fix issue with FieldConvert when range flag used (!761) - Fix equispacedoutput for 3DH1D with triangles (!787) **NekMesh**: - Fix memory consumption issue with Gmsh output (!747, !762) - Rework meshing control so that if possible viewable meshes will be dumped when some part of the system fails (!756) - Add manifold meshing option (!756) - Fix issue with older rea input files (!765) - Fix memory leak in variational optimiser, add small optimisations (!785) - Check the dimensionality of the CAD system before running the 2D generator (! 780) - Fix uninitialised memory bug in Nek5000 input module (!801) **IncNavierStokesSolver** - Fix an initialisation issue when using an additional advective field (!779) **Utilities** - Fix vtkToFld missing dependency which prevented compiling with VTK 7.1 (!808) **Packaging** - Added missing package for FieldUtils library (!755) As always, if you encounter any problems please feel free to contact us on the mailing list nektar-users(a)imperial.ac.uk. Cheers, Chris -- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell(a)imperial.ac.uk www.imperial.ac.uk/people/c.cantwell

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Does nektar support the solution of natural convection problem
by ztdepyahoo 09 Oct '17

09 Oct '17

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where to download the "development guid"
by ztdepyahoo 01 Oct '17

01 Oct '17

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