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

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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Formation of the global linear system
by zhangtengfei＠sjtu.edu.cn 29 Jun '20

29 Jun '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 Nektar users, I am writing a new solver using Nektar++ and it requires solving two different set of global linear systems (GLS1 and GLS2). The two sets of systems are inter-related on the RHS, i.e. therefore iterations between the two gobal linear systems should be performed. The HelmHoltz coefficient matrices for GLS1 is different from GLS2. To solve each linear system, I called the HelmSolve() function respectively for GLS1 and GLS2. Problem is, even though I pass in different spatially variable coefficient maps for GLS1 and GLS2, the formed coefficient matrices for GLS1 and GLS2 seem to be the same. Only the first global linear system is formed correctly, and the second global linear system is recognized to be same as the first one. I found in the HelmSolve() subroutine there is a code snippet GlobalLinSysSharedPtr LinSys = GetGlobalLinSys(key); which scans the m_globalLinSysManager to retrieve the GlobalLinSysSharedPtr that has been formed with key. It seems that the code can only allow the existance of one single holmholtz global linear system, right? If so, does anyone know a way of solving this problem (or is there a solver in the code that I can refer to)? Currently I have to use ClearGlobalLinSysManager() everytime I finish solving a global linear system, which cleans up the space and rebuild the new global linear system. But this is very time-consuming because the global linear systems are constructed again and again during the iteration between GLS1 and GLS2. Best regards, Tengfei Zhang

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Issue Building Nektar++ on Windows
by Victor Hugo Santiago Peron 28 Jun '20

28 Jun '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'm trying to Build Nektar++ on my windows 10, using Visual Studio 2019 according to Jeremy Cohen's instructions from march/2 but I'm facing some trouble in the command *msbuild INSTALL.vcxproj /p:Configuration=Release*., while still in the x64 Native Tools Command Prompt. I've printed the error message and attached it (sorry about it being in Portuguese). Could you please help me? Thanks in advance, Victor

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Quasi 3D for flow around bodies of revolution
by Silvia Ceccacci 27 Jun '20

27 Jun '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 use a Quasi-3D approach for flow around bodies of revolution. From the manual I see parameters can be specified for the harmonic expansion in the z-direction (staring from a 2D mesh) or in the y-direction and z-direction (starting from a 1D mesh). Proving that I have a 2D mesh, is it possible to specify parameters which define the 1D harmonic expansion along the azimuthal direction? Thank you. Kind regards, Silvia

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How do I fix the GPG error “NO_PUBKEY”?
by shan xiangjun 24 Jun '20

24 Jun '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 Nektar: I want to install Nektar++ on Win10-WSL: Ubuntu 18.04 using the pre-compiled packages, but I encountered a problem. After Code: sudo apt-get update I get the following: Get:2 http://security.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB] Hit:3 http://archive.ubuntu.com/ubuntu bionic InRelease Get:4 http://archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB] Get:1 https://www.nektar.info/ubuntu-bionic bionic InRelease [6114 B] Get:5 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB] Err:1 https://www.nektar.info/ubuntu-bionic bionic InRelease The following signatures couldn't be verified because the public key is not available: NO_PUBKEY DB5E71FF7AC99B37 Reading package lists... Done W: GPG error: https://www.nektar.info/ubuntu-bionic bionic InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY DB5E71FF7AC99B37 E: The repository 'http://www.nektar.info/ubuntu-bionic bionic InRelease' is not signed. N: Updating from such a repository can't be done securely, and is therefore disabled by default. N: See apt-secure(8) manpage for repository creation and user configuration details. I have tried the following: Using different servers such as the following: code: curl -sL http://keyserver.ubuntu.com/pks/lookup?op=get&search=0xDB5E71FF7AC99B37 | sudo apt-key add gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv DB5E71FF7AC99B37 curl -sL "https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xDB5E71FF7AC99B37" | sudo apt-key add sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys DB5E71FF7AC99B37 sudo apt-key adv --hkp://keys.gnupg.net--recv-keys DB5E71FF7AC99B37 gpg --keyserver hkp://pgpkeys.mit.edu --recv DB5E71FF7AC99B37 But, no good results.The key could not be found.Examples are listed below: Executing: /tmp/apt-key-gpghome.IoDko6URV5/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys DB5E71FF7AC99B37 gpg: keyserver receive failed: No data gpg: no valid OpenPGP data found. Have tried to see if key exists with command: code: apt-key list but it is not listed there. /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-archive.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 790B C727 7767 219C 42C8 6F93 3B4F E6AC C0B2 1F32 uid [ unknown] Ubuntu Archive Automatic Signing Key (2012) <ftpmaster(a)ubuntu.com> /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) <cdimage(a)ubuntu.com> /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) <ftpmaster(a)ubuntu.com> Regards, Xiangjun x_j_shan(a)outlook.com As you can see, many avenues explored with no good results. Looking for some help, please

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How to set a non-translational body with Coordinate transformations?
by hongfu2233 21 Jun '20

21 Jun '20

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Re: [Nektar-users] Rescaling velocity inlet conditions read from .fld files
by Vishal Saini 17 Jun '20

17 Jun '20

Hi all, I have attached a snippet of a working version. Thank you Spencer and Andrea! Andrea, For rescaling the flow I had to extract the boundary data again outside the flow-rate calculation loop. Anyway, for the record (as you mentioned earlier) I did not see much effect on the number of iterations (and the CPU time) after rescaling (opposed to pimpleFoam). BR, Vishal --- *Vishal SAINI* On Mon, Jun 15, 2020 at 9:45 PM Cassinelli, Andrea < andrea.cassinelli15(a)imperial.ac.uk> wrote: > Hi Vishal, > > I had a look through and cannot spot anything obvious. Just to make sure, > you are expecting to get 1 when you call VerifyFlowRate, is that right? > After you call this method are you supposed to be working in coefficient > space of physical space? > > Alternatively you can try effectively passing bndVelPhys to the > NormaliseFlowRate method to test an alternative approach, without > transforming back and forth. > > Are you using 3D or 2.5D? In the latter case you also need to make sure > you are in the correct space (calling BndExp[bndid]->GetWaveSpace() and > BndExp[bndid]->SetWaveSpace(true) to change it). > > Lastly, have you tried following the execution with a debugger to check > where the values “swap" back? > > Cheers, > > Andrea > > > On 15 Jun 2020, at 17:48, Vishal Saini <vishal.saini.nitj(a)gmail.com> > wrote: > > Hi Andrea, > > Thanks for your reply. I have written a function to calculate the flow > rate through time-dependent BCs. This seems to work fine even with > non-planar inlets. I am however facing problems in re-scaling the > velocities accordingly. I am attaching a snippet for you to have a look. > So, in *NormaliseFlowRate()* when I normalise the *bndVelPhys *in line > 114, it does not reflect in actual velocity values. This is seen from the > output of *VerifyFlowRate()*. Can you spot an obvious mistake? > > As soon as this is fixed, we can flag this as done in the mailing-list. > > BR, > Vishal > > --- > * Vishal SAINI* > > > On Sun, Jun 14, 2020 at 11:52 PM Cassinelli, Andrea < > andrea.cassinelli15(a)imperial.ac.uk> wrote: > >> Hi Spencer, >> >> I had emailed Vishal separately on this matter, which I believe should be >> solved now. @Vishal am I right? >> I not included the mailing list as my answer referred to a branch we had >> been previously discussing so I wasn’t sure it would make sense to include >> everyone. >> >> Cheers, >> >> Andrea >> >> >> On 14 Jun 2020, at 23:09, Sherwin, Spencer J <s.sherwin(a)imperial.ac.uk> >> wrote: >> >> Hi Vishal, >> >> Sorry not to respond sooner. Things have been busy. >> >> Mohammad, has spent some time debugging this feature to add termperature >> field. @Mohammad can you see if you can help Vishal? >> >> Cheers >> Spencer. >> >> Spencer Sherwin FREng, FRAeS >> Head of Aerodynamics Section, >> Director of Research Computing Service, >> Professor of Computational Fluid Mechanics, >> Department of Aeronautics, >> s.sherwin(a)imperial.ac.uk South >> Kensington Campus, >> Phone: +44 (0)20 7594 5052 Imperial College >> London, >> Fax: +44 (0)20 7594 1974 London, SW7 2AZ, >> UK >> http://www.imperial.ac.uk/people/s.sherwin/ >> >> On 1 Jun 2020, at 19:25, Vishal Saini <vishal.saini.nitj(a)gmail.com> >> wrote: >> >> This email from vishal.saini.nitj(a)gmail.com 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 have a little query regarding reading time varying turbulent BC from >> .fld files in IncNSSolver. With Dave 's helping hand I am now able to >> read in the .fld BC files. However, to reduce pressure fluctuations at the >> inlet, I'd like to rescale the inlet flow-rate to a required flow-rate for >> every time-step. This would typically include the following steps: >> >> 1. Find area of the inlet boundary >> 2. Take dot product of area normal and velocity vectors >> 3. Multiply the velocity vector with a correction factor >> (Q_ideal/Q_calculated) >> >> In this regard, the function VelocityCorrectionScheme::MeasureFlowrate >> looks interesting. However, I have little idea where to start with. Could >> someone drop any hints on where can I start with this in the code? >> >> BR, >> Vishal >> >> _______________________________________________ >> Nektar-users mailing list >> Nektar-users(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users >> >> >> _______________________________________________ >> Nektar-users mailing list >> Nektar-users(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users >> >> >> <snippet.cpp> > > >

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Regarding bug in integration of FieldConvert
by Abhishek Kumar 17 Jun '20

17 Jun '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, I want to report a bug in "mean" module of FieldConvert for the 2.5D case. There is an issue in the computation of integral which comes from the error in the computation of "Domain volume". I am taking a test case for channel flow "ChanFlow_3DH1D_FFT.xml." Here Lx = 1, Ly = 1, Lz = 1. So the volume should be 1. But the output depends upon the number of Fourier modes. Below is the output with Nz = 20. ------------------------------------------- Domain volume : 20 Integral (variable u) : 7.14583 Mean (variable u) : 0.357292 Integral (variable v) : 6.25 Mean (variable v) : 0.3125 Integral (variable w) : 5 Mean (variable w) : 0.25 Integral (variable p) : 10 Mean (variable p) : 0.5 ------------------------------------------- and this is one with Nz = 40. ------------------------------------------- Domain volume : 40 Integral (variable u) : 14.2292 Mean (variable u) : 0.355729 Integral (variable v) : 12.5 Mean (variable v) : 0.3125 Integral (variable w) : 10 Mean (variable w) : 0.25 Integral (variable p) : 20 Mean (variable p) : 0.5 --------------------------------------------- Now, by changing the number of Fourier modes the "Domain volume" and "integral" should not change. However, the value of "mean" is correct; thus it seems there is some normalization issue. Similarly, I can see a discrepancy in the "innerproduct" module as well. I have also attached the xml file for the reference. With regards Abhishek --------------------------------------------------------------------------------------- Abhishek Kumar Assistant Professor (Research) Centre for Fluid and Complex Systems Coventry University, Coventry CV15FB The United Kingdom Phone: +44 24 7765 9150 ---------------------------------------------------------------------------------------

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