August 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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simulation on wall-mounted squared cylinder
by BF MA 10 Sep '17

10 Sep '17

Hi everyone, I am simulating the vortex flow around a squared cylinder mounted a surface using Nektar++ incompressible solver. For this layout (see attached 1), the vortex wakes will become unstable and be shedding as Re >150. However, the current problem is that the computation cannot get the unsteady vortex shedding, it always converges to steady solutions even at Re=500. I even tried giving an incoming disturbance, but the flow fields still cannot converge to vortex shedding. The steady drag coefficients at various Re agree well with the time-averaged results in previous publications, but no vortex shedding occurs. I have simulated the vortex flow past a 2D cylinder, and vortex shedding can be obtained. But for the 3D case, the results are strange. I attached the layout and grid file, and anyone can give some suggestions. Many thanks, Baofeng Baofeng Ma, PH.D Associate Professor Institute of Fluid Mechanics School of Aeronautical Science and Engineering Beihang University Email: bf-ma(a)buaa.edu.cn Tel: 0086 (0)10 82338344

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Nektar++ transition to C++11
by Chris Cantwell 09 Sep '17

09 Sep '17

Dear all, As part of our ongoing efforts to modernise our codebase, we are planning to transition to the C++11 standard in the near future. A consequence of this is that you will in future require a compiler which supports the C++11 standard (either as an option, such as --std=c++11, or by default). Current versions of popular compilers all fully support the standard, but older compilers may only have partial support. We recommend the following compiler versions to minimise the likelihood of problems going forward: - GCC: 4.8 or later - Clang: 3.3 or later - MSVC: 19.0 or later - Intel: 15.0 or later - PGI: 2015 or later We encourage users to test out support for basic C++11 by compiling the branch 'feature/libutils-c++11' from the code repository and updating build scripts and configuration as necessary. Please let us know if you have any problems or concerns. We will be making the transition after the Nektar++ Workshop in mid-June. Cheers, Nektar++ Development Team

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Problems compiling using gcc version 7
by Paulo Jabardo 30 Aug '17

30 Aug '17

I am trying to compile nektar++-4.4.0 on archlinux (actually manjaro but close enough...). This uses a recent version of gcc (gcc-7.1.1) and I am experiencing what, at first sight is a very weird error: cd /home/pjabardo/misc/math/nektar++/nektar++-4.4.0/build-debug/library/LibUtilities && /usr/bin/c++ -DLIB_UTILITIES_EXPORTS -DLibUtilities_EXPORTS -DNEKTAR_MEMORY_POOL_ENABLED -DNEKTAR_USING_BLAS -DNEKTAR_USING_LAPACK -DNEKTAR_VERSION=\"4.4.0\" -DTIXML_USE_STL -isystem /home/pjabardo/misc/math/nektar++/nektar++-4.4.0/build-debug/ThirdParty/dist/include -isystem /usr/lib/../include -I/home/pjabardo/misc/math/nektar++/nektar++-4.4.0 -I/home/pjabardo/misc/math/nektar++/nektar++-4.4.0/library -g -DNEKTAR_DEBUG -Wall -Wno-deprecated -Wno-sign-compare -fpermissive -fPIC -fPIC -o CMakeFiles/LibUtilities.dir/BasicUtils/ArrayEqualityComparison.cpp.o -c /home/pjabardo/misc/math/nektar++/nektar++-4.4.0/library/LibUtilities/BasicUtils/ArrayEqualityComparison.cpp In file included from /usr/include/c++/7.1.1/ext/string_conversions.h:41:0, from /usr/include/c++/7.1.1/bits/basic_string.h:6159, from /usr/include/c++/7.1.1/string:52, from /usr/include/c++/7.1.1/stdexcept:39, from /usr/include/c++/7.1.1/array:39, from /usr/include/c++/7.1.1/tuple:39, from /usr/include/c++/7.1.1/bits/stl_map.h:63, from /usr/include/c++/7.1.1/map:61, from /home/pjabardo/misc/math/nektar++/nektar++-4.4.0/library/LibUtilities/BasicConst/NektarUnivTypeDefs.hpp:39, from /home/pjabardo/misc/math/nektar++/nektar++-4.4.0/library/LibUtilities/BasicUtils/ArrayPolicies.hpp:40, from /home/pjabardo/misc/math/nektar++/nektar++-4.4.0/library/LibUtilities/BasicUtils/SharedArray.hpp:39, from /home/pjabardo/misc/math/nektar++/nektar++-4.4.0/library/LibUtilities/BasicUtils/ArrayEqualityComparison.cpp:35: /usr/include/c++/7.1.1/cstdlib:75:15: fatal error: stdlib.h: No such file or directory #include_next <stdlib.h> ^~~~~~~~~~ I tracked down the error and the problem occurs in newer versions of C++ (6 and newer I think) where including system directories such as /usr/include messes up things. The gcc guys say that this is an issue with the build system and not gcc and they won't do anything about it as you can see in the following link: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=70129 To confirm this, I tried compiling by hand the file where the error was generated above after removing from the compile command the part -isystem /usr/lib/../include and the file compiled just fine. I tried to locate where is this compilation directive coming from but couldn't find it in any of the cmake files. But I don't know cmake very well and I have no idea how to debug it. By the way, if I install gcc version 5 on my system, as expected, nektar compiles. I will try to compile nektar++ with clang++ to see what happens. This error will become more common as new versions of gcc start becoming more common (I think newer versions of ubuntu already use gcc 6.x). The quickest fix is to install gcc version 5. Thanks Paulo Jabardo

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Few questions
by Peltonen Petteri 29 Aug '17

29 Aug '17

For the past weeks I've been testing nektar for incompressible jets and so far I've been able to compile the code on our cluster and to run some simulations with it too. However, I still have a few questions: A) What is the best way to compute the Reynolds stresses in cylindrical coordinates? In jets, it is common to plot the stresses only as function of the radial coordinate and to average azimuthally (like in pipes). Can the stresses be computed in cylindrical coordinates run time or do I have to save snapshots of 3D-fields to disk and do everything in a post processing step? B) How do I restart a simulation? So far I haven't succeeded with the following approach: -Run simulation for some time to produce jet.fld. -FieldConvert base/jet.xml base/jet.fld restart.fld -mv restart.fld base/restart.rst -Set initial conditions to: <FUNCTION NAME="InitialConditions"> <F VAR="u,v,w,p" FILE="restart.rst" /> </FUNCTION> -IncNavierStokesSolver base/mesh.xml base/jet.xml (the mesh is in separate .xml file) -->Unable to open file: restart.rst C) What is the difference between .chk and .fld? I have a hunch that the .chk files could be used to restart the simulation with much less effort... Petteri Peltonen, (M.Sc.) Aalto University, School of Engineering Department of Mechanical Engineering PO Box 14300 FI-00076 Aalto, Finland +358 44 0554984 petteri.peltonen(a)aalto.fi

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Parallel fld file convert
by wkrusz 23 Aug '17

23 Aug '17

Hello, I have a question, how to convert fld files from parallel computation into single Tecplot or Paraview file. I try to find this in doks, but without success. Best regards, Witek

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Proper use of m_comm->AllReduce?
by Kurt Sansom 18 Aug '17

18 Aug '17

Hi community, I have implemented a new boundary condition and I referenced the implementation of the feature/flowrate branch to evaluate the flow rate on a boundary. There were a couple places where m_comm->AllReduce was used and I emulated the form in solvers/IncNavierStokesSolver/EquationSystems/IncNavierStokes.cpp that look like the following: m_RCParams[fldid][bndid]->m_FlowRateArea = BndCondExp->Integral(inArea); m_comm->AllReduce(m_RCParams[fldid][bndid]->m_FlowRateArea, LibUtilities::ReduceMax); and flowrate = BndCondExp->VectorFlux(bndVelocity); m_comm->AllReduce(flowrate, LibUtilities::ReduceSum); but using AllReduce causes the solver to lock/freeze, should I be doing something like if(m_comm.GetRank() == 0)? I can remove the AllReduce, but then I am repeating the calculation on each core correct? is there a best/better way to do this in nektar++? Thanks for all your help and support! -- Kurt Sansom Multiphase & Cardiovascular Flow Lab University of Washington

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ExtractElmtToBndPhys question
by Kurt Sansom 15 Aug '17

15 Aug '17

Hi I am trying to understand the following operation. void <http://doc.nektar.info/doxygen/latest/namespace_nektar.html#a48c0e3cfaa1c2e…> Nektar::MultiRegions::ExpList::ExtractElmtToBndPhys ( int i, Array <http://doc.nektar.info/doxygen/latest/singleton_nektar_1_1_array.html>< OneD <http://doc.nektar.info/doxygen/latest/struct_nektar_1_1_one_d.html>, NekDouble <http://doc.nektar.info/doxygen/latest/namespace_nektar.html#af86b4dd9cf77e9…> > & elmt, Array <http://doc.nektar.info/doxygen/latest/singleton_nektar_1_1_array.html>< OneD <http://doc.nektar.info/doxygen/latest/struct_nektar_1_1_one_d.html>, NekDouble <http://doc.nektar.info/doxygen/latest/namespace_nektar.html#af86b4dd9cf77e9…> > & boundary ) however the documentation doesn't give it a description. I am trying evaluate the flow rate through a boundary and there is something similar in the feature/flowrate branch that uses this operation, but it is unclear to me what it is doing. I believe it is extracting the physical values from a boundary and placing them in the boundary variable but I am not sure what the element array variable is for, can it be an empty array or does it need to be populated with something? I am trying to do something like this. MultiRegions::ExpListSharedPtr BndCondExp; BndCondExp = m_fields[fldid]->GetBndCondExpansions()[bndid]; Array<OneD, Array<OneD, NekDouble> > flux(m_spacedim); //m_fields[0]->GetBndElmtExpansion(n, BndElmtExp, false); // extract the boundary coefficients int i; for(i = 0; i < m_spacedim; i++) { flux[i] = m_fields[i]->GetBndCondExpansions()[boundaryID]->GetCoeffs(); } NekDouble flowrate = 0.0; Array<OneD, Array<OneD, NekDouble> > boundary(m_spacedim); for (i = 0; i < m_spacedim; ++i) { m_fields[i]->ExtractElmtToBndPhys( bndid, flux[i], boundary[i]); } flowrate = BndCondExp->VectorFlux(boundary); m_comm->AllReduce(flowrate, LibUtilities::ReduceSum); flowrate = flowrate / m_RCParams[fldid][bndid]->m_FlowRateArea; -- Kurt Sansom

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Direct stability analysis problem
by wkrusz 11 Aug '17

11 Aug '17

Hello, I have problem with direct stability analysis of flow around NACA airfoil. In my case, I'm using mesh with rectangular elemennts generated in Icem, and than exported as Nastran file to Gmsh. Main proble with my case is connected with "CG iterations made = 5001 using tolerance of 1e-09 (error = 0.0231643, rhs_mag = 1045.02)". I'was trying to identify problem but with no positive results. Which is quite interesting problem occurs only with parallel work using mpi. In serial mode solver starts normaly. Maybe some of you could help me find problem. Best regards, Witold

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Direct stability analysis of flow around Naca airfoil
by wkrusz 09 Aug '17

09 Aug '17

Hello, I have problem with direct stability analysis of flow around NACA airfoil. In my case, I'm using mesh with rectangular elemennts generated in Icem, and than exported as Nastran file to Gmsh. Main proble with my case is connected with "CG iterations made = 5001 using tolerance of 1e-09 (error = 0.0231643, rhs_mag = 1045.02)". I'was trying to identify problem but with no positive results. Maybe some of you could help me find problem.In attachment there are baseflow file and case xml. Best regards, Witold

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