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

Element with max CFL
by Vishal Saini 02 Apr '20

02 Apr '20

Hi all, Quick question: Has anyone tried to check the location of a particular element in the mesh? A log file reports the maximum (?) CFL and the corresponding element as: "CFL: 0.0337915 (in elmt 94488)"? Is there a quick way to locate "elmt 94488"? Cheers, Vishal

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Help - Error in running base condition for a square cylinder
by Manmohan Labh 28 Mar '20

28 Mar '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, My name is Manmohan Labh. I am a Mechanical Engineering Under graduate form Indian Institute of Technology ( Indian School of Mines ) Dhanbad. I am trying to learn Nektar++ for my research on VIV in fluids. I tried running a simulation of flow past a stationary square cylinder, but i am facing difficulty in it. Please help me. I have attached all the generated files in this mail. Error - Fatal level 0 assertion violation NAN found during tìme integration. Regards, Manmohan Labh

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CWIPI-coupling source terms and Base field values
by Nitish Arya 25 Mar '20

25 Mar '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 hope everyone is taking precautions against the COVID-19 threat. This is regarding a problem I am facing in a coupled simulation. I am using Acoustic solver in nektar-5 with CWIPI- coupling. The source terms (fluctuating lamb vector) are sent via Openfoam. I am trying to see acoustics due to flow past a cylinder as a test case for the coupling. The lamb vector at the surface of the cylinder is zero (because the velocity is zero due to no slip boundary condition). However, when i try to visualize the force terms in nektar, it displays an unusually high value at the cylinder wall. Further, the base fields are also received from Openfoam. The mean velocities should vanish at the cylinder wall(they are indeed zero in OpenFoam) . But the values are non zero when they are received in nektar. I guess (and correct me if I am wrong) the source of this error is the interpolation from a finite volume grid to spectral grid and the fact that boundary conditions are not satisfied for base fields and source terms. Is there any way by which I can ensure that the base fields as well as the source terms are zero at the solid boundary? Sincerely, Nitish

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Manipulate 3DH1 chk/fld file in Fourier space
by F Mellibovsky 16 Mar '20

16 Mar '20

Dear all, I have run a 3DH1 simulation and I need to set all Fourier coefficients to zero except those corresponding to a fundamental wavelength and its harmonics (e.g. keep only modes 0, +-5, +-10, etc and set all the rest to zero). I have the intuition that some combination of FieldConvert options can accomplish exactly this, but I am unsure of what is the best (or some) way to proceed. My guess is that the "homplane:wavespace:planeid=?" can be used to extract the individual Fourier modes, but I am unsure as to how the Fourier modes are sorted and which ones must be extracted to recover a chosen fundamental wavelength and its harmonics (both real and imaginary parts, or modulus and argument, or however the Fourier modes are stored). The only one I'm pretty sure of is mode 0 or mean mode. Once I get the individual fld files for each one of the modes, I was intending to use the "addfld:fromfld=mode1.fld:scale=1 mode1.xml mode2.fld newfile.fld" sequentially to build a solution from the chosen modes. The issue here is that the fields extracted with "homplane" seem to be 2D and would therefore need to be recast in 3DH1 form before proceeding to "addfld". How can this be done? Thanks in advance for your help Fer Mellibovksy

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Continuous Integration and Testing
by Chris Cantwell 15 Mar '20

15 Mar '20

Dear all, For those of you who have contributed code back to the Nektar++ project, you may be familiar with our Buildbot continuous integration system we use for testing changes to the code before they are merged into the main codebase. To improve integration with our Gitlab website, we have now transitioned to using Gitlab CI for our testing. When you submit a pull request, you can view the status and all outputs of the testing pipeline directly in the Gitlab interface. Please see the CONTRIBUTING.md in the latest master for details on the new system. We are still refining the process and there are potentially still a few teething issues. If you notice anything not working as you would expect, please contact one of the developer team directly to report it. The Buildbot system has now been decommissioned. Cheers, Chris -- Chris Cantwell Senior Lecturer in Aeronautics Department of Aeronautics Imperial College London South Kensington Campus London SW7 2AZ Tel: +44 (0)20 759 45050 Email: c.cantwell(a)imperial.ac.uk www.imperial.ac.uk/people/c.cantwell

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FInite element formulation and Nektar++
by pavan yadav 13 Mar '20

13 Mar '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 a beginner as a Nektar ++ User, during tutorial part i found one of the thesis named as "Stabilized Space-time Finite Element Formulations for Unsteady Incompressible Flows Involving Fluid-body Interactions: By Sanjay Mittal" Since it is not available at given link( https://books.google.co.in/books?id=MqKHzkq9iC0C) Can any one help me to get this thesis soft copy please. Regards, Pavan

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how to solve using parallelisation
by Srihari Menon 13 Mar '20

13 Mar '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 all! I'm new to Nektar and have been trying to solve for incompressible flow using the MPI parallelisation feature. Problem: I run the command 'mpirun -np 4 $<path to solver>/IncNavierStokesSolver file.xml' and it does not work at all. No error no solver initialization. On running the same command with one modification 'mpirun -np 4 *\*$<path to solver>/IncNavierStokesSolver file.xml' the following error is encountered: -------------------------------------------------------------------------- mpirun was unable to launch the specified application as it could not access or execute an executable: Executable: \<path to solver>/IncNavierStokesSolver Node:XYZ while attempting to start process rank 0. -------------------------------------------------------------------------- 4 total processes failed to start Background: I am certain the server I work on has MPI enabled on it. When configuring the nektar package I switch the NEKTAR_USE_MPI to ON, and leave everything else as is, then install the make. I am also certain the file I'm trying to solve parallely works serially. I am not even being able to parallely execute standard files like Cyl.xml in the Examples of IncNavierStokesSovler. Following is my ccmake configuration list for reference. What am I doing wrong? Kindly advise. Thank you! Regards, Srihari Menon University of Pennsylvania Configuration list: CMAKE_BUILD_TYPE Release CMAKE_INSTALL_PREFIX /home1/s/srimenon/nektar++-4.4.1/build/dist CONVERT /usr/bin/convert NEKTAR_BUILD_DEMOS ON NEKTAR_BUILD_DOC OFF NEKTAR_BUILD_LIBRARY ON NEKTAR_BUILD_SOLVERS ON NEKTAR_BUILD_TESTS ON NEKTAR_BUILD_TIMINGS OFF NEKTAR_BUILD_UNIT_TESTS ON NEKTAR_BUILD_UTILITIES ON NEKTAR_SOLVER_ADR ON NEKTAR_SOLVER_APE ON NEKTAR_SOLVER_CARDIAC_EP ON NEKTAR_SOLVER_COMPRESSIBLE_FLO ON NEKTAR_SOLVER_DIFFUSION ON NEKTAR_SOLVER_ELASTICITY ON NEKTAR_SOLVER_INCNAVIERSTOKES ON NEKTAR_SOLVER_PULSEWAVE ON NEKTAR_SOLVER_SHALLOW_WATER ON NEKTAR_TEST_ALL OFF NEKTAR_TEST_FORCEMPIEXEC OFF NEKTAR_TEST_USE_HOSTFILE OFF NEKTAR_USE_ACML OFF NEKTAR_USE_ARPACK OFF NEKTAR_USE_BLAS_LAPACK ON NEKTAR_USE_CCM OFF NEKTAR_USE_FFTW OFF NEKTAR_USE_HDF5 OFF NEKTAR_USE_MESHGEN OFF NEKTAR_USE_MKL OFF NEKTAR_USE_MPI ON NEKTAR_USE_OPENBLAS ON NEKTAR_USE_PETSC OFF NEKTAR_USE_SCOTCH OFF NEKTAR_USE_SMV OFF NEKTAR_USE_VTK OFF THIRDPARTY_BUILD_BLAS_LAPACK ON THIRDPARTY_BUILD_BOOST ON THIRDPARTY_BUILD_GSMPI ON THIRDPARTY_BUILD_LOKI ON

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Spherical coordinates and time-dependent boundary conditions
by Silvia Ceccacci (HDR) 12 Mar '20

12 Mar '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 trying to simulate a flow induced by a rotating sphere (so I am working with a 3D mesh). I would ramp up the rotation rate from zero to a constant value over a finite time. So, I need to set an angular velocity on the sphere's surface. To do this I would use spherical polar coordinates (r, theta, phi), with corresponding velocity components. Then, I would solve the Navier-Stokes equations subject to my time-dependent boundary conditions. I have seen it is possible to specify time-dependent boundary conditions through the setting USERDEFINEDTYPE="TimeDependent". However, in this case, I also need to change my coordinate system from Cartesian to Spherical. Is this possible? I have seen it is possible to do coordinate transformations by activating the mapping technique so PROPERTY="SolverType" VALUE="VCSMapping". Will this work on a 3D mesh? I have started to write my new coordianates as <FUNCTION NAME="Mapping"> <E VAR="x" VALUE="sqrt(x*x + y*y + z*z)" /> ---> this would be r = radius <E VAR="y" VALUE="atan(sqrt(x*x + y*y) / z )" /> ---> this would be theta = inclination <E VAR="z" VALUE="atan(y / x)" /> ---> this would be phi = azimuth </FUNCTION> using mapping type "General". Now, I am not sure about the MappingVel function (as they will all be 0?) and how this would work in relation to my time-dependent boundary conditions. Could anybody help with this, please? I can also share my code if it can be useful, even though at this stage it is profoundly wrong. Thank you. Kind regards, Silvia

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Nektar++ Workshop 2020
by Chris Cantwell 10 Mar '20

10 Mar '20

Dear all, We are planning to hold the annual Nektar++ Workshop this year at Imperial College London. The purpose of the workshop is to bring together developers and users of all experiences to hear about new and future developments in Nektar++ and some of the exciting science and engineering being undertaken by our users with the code. As usual, registration and refreshments will be free for participants, but we will not be able to cover any travel, accommodation and dinner expenses. The preliminary dates for the workshop are the 11th/12th of June. However, in light of the currently developing situation surrounding the coronavirus outbreak, there is understandably still some uncertainty about whether we will be able to go ahead with the event on these dates. We would therefore encourage you to mark these dates in your calendars, but **please do not commit to any travel or accommodation at this stage**. We will send an update in April to confirm if the workshop will go ahead on these dates, or if it will be postponed to later in the year. We are keen for members of our community to contribute to the programme of talks so, in the meantime, if you are interested in presenting a talk please get in touch with me (c.cantwell(a)imperial.ac.uk) Kind regards, Chris -- Chris Cantwell Senior Lecturer in Aeronautics Department of Aeronautics Imperial College London South Kensington Campus London SW7 2AZ Tel: +44 (0)20 759 45050 Email: c.cantwell(a)imperial.ac.uk www.imperial.ac.uk/people/c.cantwell

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questions on variable coefficients
by zhangtengfei＠sjtu.edu.cn 10 Mar '20

10 Mar '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 trying to implement a new solver using Nektar++ to solve the neutron diffusion equation. This equation has similar form as the Helmholtz equation. One of the differences between my case and all pre-existing solvers is that my solver requires using spatial-dependent constants for each finite element mesh. With the help of Dr. Cantwell I refered to cardiac electrophysiology solver ( in solvers/CardiacEPSolver/EquationSystems/Monodomain.cpp). I copied the code snippet of varying coefficients from CardiacEPSolver into my solver and made changes accordingly. However, something went wrong and it seems that the varying coefficient function does not work properly. I must have some misunderstanding of the variables or omitted some important details. Could anyone please take a look at attached note and see what happens? Thanks, Tengfei Zhang

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