July 2020 - Nektar-users - imperial.ac.uk

time-dependent model reduction
by Martin Wilfried Hess 14 Aug '20

14 Aug '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear all, I would like to implement a time-dependent model reduction. To do that, I want to mirror some of the class structure in the reduced order setting. I would like to start with the UnsteadySystem class, since there the time-stepping takes place. Now I am not so familiar with this factory pattern scheme. What would I need to do to have a, say UnsteadySystem_ReducedOrder class, which (for a start) does the same as the UnsteadySystem class and can be called with a different EQTYPE identifier in the session file? I want to use it for UnsteadyNavierStokes, the incompressible case. Thanks for any help, Martin Hess -- -- Martin Hess, Ph.D., Post-doctoral research fellow SISSA mathLab, International School for Advanced Studies Office A-434 (4th floor), via Bonomea 265, I-34136 Trieste, Italy phone: +39 040 3787 491 email: mhess(a)sissa.it

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Total number of quadrature points in triangular element
by Yong Wang 21 Jul '20

21 Jul '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hello, I am processing the chk file (.fld file) produced by Nektar++ for postprocessing and the mesh I used is a collection of 2D triangular elements with a number of modes of 6 (max. polynomial order = 5). I have a question about the total number of quadrature points in the triangular element: results from the chk file show that each element has totally 30 quadrature points (instead of 31), and coordinates of these points are plotted in the following figure. It seems that these quadrature points don't include the singular point. I wonder why is this the case and could someone kindly recommend references about this issue? It will help me a lot to understand the results generated by Nektar++. Thanks a lot. Best wishes, Yong Wang [image: image.png]

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empty sections in the developers-guide
by Ziad Boutanios 19 Jul '20

19 Jul '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi, Just installed nektar++-5.0.0 from the Contrib repos on Debian stable (10.4). Noticed that some sections in the developers guide are completely empty, like * FieldUtils chapter 11 * SolverUtils chapter 12 * most sections dealing with variables, structures and algorithms Is that currently the case for the developers guide or did I botch my install? Thanks, Ziad

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Failure of instantiation of SessionReader
by Yong Wang 15 Jul '20

15 Jul '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hello, I am trying to implement a post-processing application based on nektar++ library and got stuck in the reading of XML session file into SeesionReader. My main.cpp code is: // main.cpp #include <LibUtilities/BasicUtils/SessionReader.h> #include <iostream> using namespace Nektar; int main(int argc, char* argv[]) { LibUtilities::SessionReaderSharedPtr session = LibUtilities::SessionReader::CreateInstance(argc, argv); std::cout << "Session Name: " << session->GetSessionName() << std::endl; std::cout << "Parameter TimeStep: " << session->GetParameter("TimeStep") << std::endl; return 0; } The main.cpp code can be compiled successfully, but when I run the executive with a session file (eg., ./main ChanFlow_3DH1D_FFT.xml),the method GetParameter produce an error saying the parameter "TimeStep" cannot be found, which actually exists in the session XML file. Could you give me some suggestions about what went wrong here? The required files (main.cpp, CMakeLists.txt, ChanFlow_3DH1D_FFT.xml) are attached in attachments. Thanks, Yong Wang

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robin boundary condition
by zhangtengfei＠sjtu.edu.cn 14 Jul '20

14 Jul '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear all, I am using the robin boundary condition in Nektar+ but have some problems understanding how it works. The b.c. I want to impose is D* gradient {u} + 0.5 * u = 0 in which D is the diffusion constant (same as the D value used in the adjacent element), u is the unknown field. To do this I normalize the b.c. into the form of gradient {u} + 0.5 / D * u = 0, and specify the robin boundary condition as <R VAR="u" PRIMCOEFF="0.5/D" /> This setting does not yield the correct answer, unless the special case that D = 1.0. Could anyone please tell me what is wrong here? Thanks, Tengfei Zhang

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nektar make error
by Professor Ding、 11 Jul '20

11 Jul '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Dear friends: I use cmake-gui to compile nektar, but i met the following error, i cann't figure it out. Could you please give me some suggestions. /home/ztdep/Downloads/nektar++-5.0.0/library/LibUtilities/BasicUtils/FieldIOHdf5.cpp:1028:31: error: implicitly-declared ‘Nektar::LibUtilities::FieldIOHdf5::OffsetHelper& Nektar::LibUtilities::FieldIOHdf5::OffsetHelper::operator=(const Nektar::LibUtilities::FieldIOHdf5::OffsetHelper&)’ is deprecated [-Werror=deprecated-copy] 1028 | decompsToOffsets[i] = running; | ^~~~~~~ | | Professor Ding、 | | ztdepyahoo(a)163.com | 签名由网易邮箱大师定制

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Extraction of boundary points for calculation of moment on body
by Yong Wang 09 Jul '20

09 Jul '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hello, I am new to Nektar++ and now working on vortex-induced vibration. The filter MovingBody can output the drag and lift forces acting on the body, however, I also require the moment data. I am modifying the MovingBody filter and now struck in the extraction of boundary points (used to calculate the moment). I wonder if there exists a method to extract edge points similar to GetEdgeNormal for extraction of edge normals. It will be greatly appreciated if you could give me some suggestions about this issue. Thanks a lot. Y. Wang

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Expansions and IterativeSolverTolerance in Nektar++
by 王昭予 08 Jul '20

08 Jul '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi all, Sorry to disturb you. I have a full 3D simulation with large number of DOF, so I have to do something to reduce the computation cost. Could you please answer my questions on it? 1) The default number of iterative solver tolerance is 1e-10 for velocity components and 1e-9 for pressure components. Under the circumstance where the number of DOF is large, the tolerance is too small and the computation will be costly. So I alternatively use a larger tolerance with 1e-5 for velocity components and 1e-4 for pressure components. Is it accurate enough for simulations? Larger tolerance means less accuracy, but I have to take the computation time into consideration. So Could you please tell me is my set reasonable? 2) When the order expansion for pressure "p" is larger than 1, the CPU time will rise suddenly. I used to set the pressure space order one lower than velocity, but when the order I need is larger than 3 or 4, the cost is still unbearable. So could I set the pressure space order 3 or 4(maybe larger) lower than the velocity? Will it cause some numerical oscillations and incorrect solutions? 3) In user guide, I see that the expansion basis can be specified in detail as a combination of one-dimensional bases. So the heterogeneous polynomial order can be used to increase the resolution in a specified direction like spanwise. Similarly, could I use more quadrature points in a direction without increasing the polynomial order to make the result more accurate? I also encounter a problem when I set the expansions as follow: <EXPANSIONS> <E COMPOSITE="C[6]" BASISTYPE="Modified_A,Modified_A,Modified_A" NUMMODES="5,5,6" POINTSTYPE="GaussLobattoLegendre,GaussLobattoLegendre,GaussLobattoLegendre" NUMPOINTS="6,6,7" FIELDS="u,v,w" /> <E COMPOSITE="C[6]" BASISTYPE="Modified_A,Modified_A,Modified_A" NUMMODES="2,2,2" POINTSTYPE="GaussLobattoLegendre,GaussLobattoLegendre,GaussLobattoLegendre" NUMPOINTS="6,6,7"FIELDS="p" /> </EXPANSIONS> My mesh type is hexahedron and the simulation can't start with a error "NaN found during time integration". I don't konw how to solve it. 4) When I apply variable polynomial order in my field, the use of preconditioner may cause CFL number rise rapidly and the simulation will soon break down. Since the preconditioner is a good choice to reduce the CPU time, could you please tell me how to solve it? I will be very grateful to your reply. Many thanks, Zhaoyu Wang Shanghai Jiao Tong University

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2D moving cylinder-Mapping
by Mahdi Erfanian Nakhchi 08 Jul '20

08 Jul '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi NEKTAR++ users, I wonder if there is anyone could help me to converge my 2D simulations over a moving cylinder with high frequency. I've been stuck with this problem for two months. Actually the case is exactly the same as CylFlow_Mov_mapping.xml case (attached here). I have only increased the vibration frequency (f) to 200 and reduced the amplitude (A) to 0.01. But it is not working at all. I have tried every possible option such as: 1. Using SpectralVanishingViscosity (DGKernel), DEALIASING, SPECTRALHPDEALIASING: Not helpful. I have tried all of the SVV options, but non of them helped me to converge the results. 2. Performing simulations at very low Re numbers and low P orders and then shifting to higher orders : Not helpful. It diverges even at Re=200 and P=4. 3. Using too small time steps (1e-7 or 1e-8): Not helpful. It diverges anyway. 4. Using low frequencies, such as f=2, 3 etc and then shifting gradually to higher frequencies: Not working. It diverges even at f=30 or lower values. 5. Usign HOutflow boundary conditions at the outflow: Not helpful in this study. I would be grateful if someone has experience to resolve the divergence issue of this problem. (The initial conditions are set as default values in the code below.) ****************************** <EXPANSIONS> <E COMPOSITE="C[73]" NUMMODES="5" TYPE="MODIFIED" FIELDS="u,v,p" /> </EXPANSIONS> <CONDITIONS> <SOLVERINFO> </SOLVERINFO> <PARAMETERS> TimeStep = 1e-7 NumSteps = 100000000 IO_CheckSteps = 500 IO_InfoSteps = 100 IO_CFLSteps = 100 Re = 200 Kinvis = 1/Re f = 200 A = 0.01 omega = 2*PI*f </PARAMETERS> <VARIABLES> <V ID="0"> u </V> <V ID="1"> v </V> <V ID="2"> p </V> </VARIABLES> <BOUNDARYREGIONS> C[74]  C[76]  C[77]  C[75]  </BOUNDARYREGIONS> <BOUNDARYCONDITIONS> <REGION REF="0"> <D VAR="u" USERDEFINEDTYPE="MovingBody" VALUE="0" /> <D VAR="v" USERDEFINEDTYPE="MovingBody" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> <REGION REF="1"> <D VAR="u" VALUE="1" /> <D VAR="v" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> <REGION REF="2"> <N VAR="u" VALUE="0" /> <N VAR="v" VALUE="0" /> <D VAR="p" VALUE="0" /> </REGION> <REGION REF="3"> <D VAR="u" VALUE="1" /> <D VAR="v" VALUE="0" /> <N VAR="p" USERDEFINEDTYPE="H" VALUE="0" /> </REGION> </BOUNDARYCONDITIONS> <FUNCTION NAME="Mapping"> <E VAR="x" VALUE="x" /> <E VAR="y" VALUE="y+A*cos(omega*t)" /> </FUNCTION> <FUNCTION NAME="MappingVel"> <E VAR="vx" VALUE="0.0" /> <E VAR="vy" VALUE="-1.0*omega*A*sin(omega*t)" /> </FUNCTION> <FUNCTION NAME="InitialConditions"> <E VAR="u" VALUE="1.0" /> <E VAR="v" VALUE="0.1" /> <E VAR="p" VALUE="0.0"/> </FUNCTION> </CONDITIONS> <MAPPING TYPE="Translation"> <COORDS>Mapping</COORDS> <VEL>MappingVel</VEL> <TIMEDEPENDENT>True</TIMEDEPENDENT> </MAPPING> ************************************ Many thanks Mahdi This message is intended solely for the addressee and may contain confidential and/or legally privileged information. Any use, disclosure or reproduction without the sender’s explicit consent is unauthorised and may be unlawful. If you have received this message in error, please notify Northumbria University immediately and permanently delete it. Any views or opinions expressed in this message are solely those of the author and do not necessarily represent those of the University. Northumbria University email is provided by Microsoft Office365 and is hosted within the EEA, although some information may be replicated globally for backup purposes. The University cannot guarantee that this message or any attachment is virus free or has not been intercepted and/or amended.

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Outflow boundary conditions with an AOA
by 岳泽华 08 Jul '20

08 Jul '20

******************* This email originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list https://spam.ic.ac.uk/SpamConsole/Senders.aspx to disable email stamping for this address. ******************* Hi all, I'm working on a stability and dynamics analysis of a high Re folw past a slender blunt-based axisymmetric body by the IncNavierStokesSolver, then I need to set an angle of attack for the flow.So I set the inflow surface boundary condition by defining its velocity component, and it works well.My question is about the corresponding outflow boundary conditions, if i remain it as the 0-AOA conditions, the streamlines near the outlet surface will become wrong curves. And I tried several definitions of the outflow surface but it always failed.So I'm wondering how to write the outflow boundary conditions with an AOA, I'm really confused。Thanks for your kind attention and help. Many thanks, Zehua Yue Beihang University

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