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ADRSolver epsilon value defaults to 1.0
by ashok jallepalli 07 Sep '17

07 Sep '17

Hi All, I am trying to use ADR solver to run unsteady-advection diffusion reaction with epsilon value set to 0.01. But the simulation always defaults to 1.0. I changed epsilon value to 1.0,0.5 0.01. The end result is always the same (as if epsilon=1.0). Please let me know if anyone has encountered this issue or knows how to fix this bug. I have added the script files to reproduce this issue. Cheers, Ashok.

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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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Nektar
by Kurt Sansom 20 Jul '17

20 Jul '17

Does anyone have the source code for the original nektar code base. I keep finding things that mention it as open source, but it doesn't exist where I have looked. Regards, -Kurt

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AeroForces in Compressible Flow Solver
by Ismael El Houas Ghouddana 17 Jul '17

17 Jul '17

Hello Nektar developers, Is there any way to use the AeroForces filter in a compressible flow simulation? Kind Regards, Ismael

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