Re: [Nektar-users] Handling Pyramids
Dear Spencer and David, Thanks very much for your prompt replies. 1. Defining the expansions separately still produced the "note" (in Nektar 4.4.1 Release). 2. Compiling the latest master solved the problem. However, I didn't try if defining the expansions collectively i.e. *<E COMPOSITE="C[1,10,11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> *produces any warnings in the latest compilation. BR, Vishal --- *Vishal SAINI* On Mon, Nov 26, 2018 at 4:43 PM Moxey, David <D.Moxey@exeter.ac.uk> wrote:
Hi Vishal,
You might also try a newer version of the code (i.e. latest master), I am not sure that the pyramid collections functions were added in 4.4.1.
Many thanks,
Dave
On 26 Nov 2018, at 14:53, Sherwin, Spencer J <s.sherwin@imperial.ac.uk> wrote:
Dear Vishal,
I do not quite recall but it may be necessary to define the expansions for composites of different shape independently. So please try:
<E COMPOSITE=“C[1]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> <E COMPOSITE=“C[10]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> <E COMPOSITE="C[11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" />
Possibly it is expecting to have a pyramid collection within a tetrahedral expansion and so this is why you see this message.
If this does not work can you send the xml file along.
Thanks, Spencer.
On 26 Nov 2018, at 11:45, Vishal Saini <vishal.saini.nitj@gmail.com> wrote:
Hi all,
I've imported a mesh from gmsh that contains a layer of pyramids for transitioning between hexes and tets using: NekMesh JICF_NektP2_2comp.msh JICF_NektP2_2comp.xml Output: Multiple elements in composite detected; remapped: - Tag 1 => 11 (Tetrahedron), 10 (Pyramid), 1 (Hexahedron) No problem on NekMesh level.
Defining my expansion as: <E COMPOSITE="C[1,10,11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" />
when I run (Nektar++ v 4.4.1) using: mpirun -npernode 28 -np 56 IncNavierStokesSolver -v JICF_NektP2_2comp_xml conditions_JICF_2D.xml (using prepartitioned mesh). I get the following "note": Collection Implemenation for Tetrahedron ( 3 3 3 ) for ngeoms = 24960 Note: Implementation does not exist: Pyramid, BwdTrans, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTDerivBase, SumFac, Modal Note: Implementation does not exist: Pyramid, PhysDeriv, SumFac, Modal Note: Implementation does not exist: Pyramid, BwdTrans, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTDerivBase, SumFac, Modal Note: Implementation does not exist: Pyramid, PhysDeriv, SumFac, Modal
What does it mean? How can I fix it? Do Pyramids need to be treated in a somewhat different way?
BR, Vishal
--- Vishal SAINI _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Spencer Sherwin FREng, FRAeS Head, Aerodynamics, Director of Research Computing Service, Professor of Computational Fluid Mechanics, Department of Aeronautics, s.sherwin@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/
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Hi again, There's another little problem that could be related to the pyramids (Please correct if I am wrong). The simulation runs fine until I introduce History Points in my condition file, where the simulation stops saying: """ ... * Integration Type: IMEXOrder2 Splitting Scheme: Velocity correction (strong press. form) Dealiasing: spectral/hp Smoothing-SpecHP: SVV (spectral/hp Exp Kernel(cut-off = 0.69999999999999996, diff coeff = 0.10000000000000001))=======================================================================Initial Conditions: - Field u: from file Restart_chk12.rst - Field v: from file Restart_chk12.rst - Field w: from file Restart_chk12.rst - Field p: from file Restart_chk12.rstrenaming "JICF_NektP4_Spherigon-all_12.chk" -> "JICF_NektP4_Spherigon-all_12.bak9.chk"Writing: "JICF_NektP4_Spherigon-all_12.chk" (0.78153s, XML)Fatal : Level 0 assertion violationThis function has not been defined for this geometryFatal : Level 0 assertion violationThis function has not been defined for this geometry* """ I introduced point probes as below (in latest master release, Nektar++ version 4.5.0): * <FILTERS> <FILTER TYPE="HistoryPoints"> <PARAM NAME="OutputFile"> PointProbes </PARAM> <PARAM NAME="OutputFrequency"> 10 </PARAM> <PARAM NAME="Points"> 0.050 0.017 -0.0469* * 0.060 0.0 0.0* * </PARAM> </FILTER> </FILTERS>* Has someone seen this problem before? P.S. I'm pretty confident that the points lie inside the domain. BR, Vishal On Tue, Nov 27, 2018 at 11:13 AM Vishal Saini <vishal.saini.nitj@gmail.com> wrote:
Dear Spencer and David,
Thanks very much for your prompt replies.
1. Defining the expansions separately still produced the "note" (in Nektar 4.4.1 Release). 2. Compiling the latest master solved the problem. However, I didn't try if defining the expansions collectively i.e. *<E COMPOSITE="C[1,10,11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> *produces any warnings in the latest compilation.
BR, Vishal
--- *Vishal SAINI*
On Mon, Nov 26, 2018 at 4:43 PM Moxey, David <D.Moxey@exeter.ac.uk> wrote:
Hi Vishal,
You might also try a newer version of the code (i.e. latest master), I am not sure that the pyramid collections functions were added in 4.4.1.
Many thanks,
Dave
On 26 Nov 2018, at 14:53, Sherwin, Spencer J <s.sherwin@imperial.ac.uk> wrote:
Dear Vishal,
I do not quite recall but it may be necessary to define the expansions for composites of different shape independently. So please try:
<E COMPOSITE=“C[1]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> <E COMPOSITE=“C[10]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> <E COMPOSITE="C[11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" />
Possibly it is expecting to have a pyramid collection within a tetrahedral expansion and so this is why you see this message.
If this does not work can you send the xml file along.
Thanks, Spencer.
On 26 Nov 2018, at 11:45, Vishal Saini <vishal.saini.nitj@gmail.com> wrote:
Hi all,
I've imported a mesh from gmsh that contains a layer of pyramids for transitioning between hexes and tets using: NekMesh JICF_NektP2_2comp.msh JICF_NektP2_2comp.xml Output: Multiple elements in composite detected; remapped: - Tag 1 => 11 (Tetrahedron), 10 (Pyramid), 1 (Hexahedron) No problem on NekMesh level.
Defining my expansion as: <E COMPOSITE="C[1,10,11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" />
when I run (Nektar++ v 4.4.1) using: mpirun -npernode 28 -np 56 IncNavierStokesSolver -v JICF_NektP2_2comp_xml conditions_JICF_2D.xml (using prepartitioned mesh). I get the following "note": Collection Implemenation for Tetrahedron ( 3 3 3 ) for ngeoms = 24960 Note: Implementation does not exist: Pyramid, BwdTrans, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTDerivBase, SumFac, Modal Note: Implementation does not exist: Pyramid, PhysDeriv, SumFac, Modal Note: Implementation does not exist: Pyramid, BwdTrans, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTDerivBase, SumFac, Modal Note: Implementation does not exist: Pyramid, PhysDeriv, SumFac, Modal
What does it mean? How can I fix it? Do Pyramids need to be treated in a somewhat different way?
BR, Vishal
--- Vishal SAINI _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Spencer Sherwin FREng, FRAeS Head, Aerodynamics, Director of Research Computing Service, Professor of Computational Fluid Mechanics, Department of Aeronautics, s.sherwin@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/
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Hi Vishal, It is quite possible we have not set up the interpolation operator for the pyramid. Do you need the history point exactly at this location? If not you might shift it for now to get things going which we fix the issue. Could I ask you to report an issue on the nektar++ web page. I have not run the pyramids very extensively so I would be interested to hear how your simulations are coming along. Cheers, Spencer. On 6 Dec 2018, at 22:00, Vishal Saini <vishal.saini.nitj@gmail.com<mailto:vishal.saini.nitj@gmail.com>> wrote: Hi again, There's another little problem that could be related to the pyramids (Please correct if I am wrong). The simulation runs fine until I introduce History Points in my condition file, where the simulation stops saying: """ ... Integration Type: IMEXOrder2 Splitting Scheme: Velocity correction (strong press. form) Dealiasing: spectral/hp Smoothing-SpecHP: SVV (spectral/hp Exp Kernel(cut-off = 0.69999999999999996, diff coeff = 0.10000000000000001)) ======================================================================= Initial Conditions: - Field u: from file Restart_chk12.rst - Field v: from file Restart_chk12.rst - Field w: from file Restart_chk12.rst - Field p: from file Restart_chk12.rst renaming "JICF_NektP4_Spherigon-all_12.chk" -> "JICF_NektP4_Spherigon-all_12.bak9.chk" Writing: "JICF_NektP4_Spherigon-all_12.chk" (0.78153s, XML) Fatal : Level 0 assertion violation This function has not been defined for this geometry Fatal : Level 0 assertion violation This function has not been defined for this geometry """ I introduced point probes as below (in latest master release, Nektar++ version 4.5.0): <FILTERS> <FILTER TYPE="HistoryPoints"> <PARAM NAME="OutputFile"> PointProbes </PARAM> <PARAM NAME="OutputFrequency"> 10 </PARAM> <PARAM NAME="Points"> 0.050 0.017 -0.0469 0.060 0.0 0.0 </PARAM> </FILTER> </FILTERS> Has someone seen this problem before? P.S. I'm pretty confident that the points lie inside the domain. BR, Vishal On Tue, Nov 27, 2018 at 11:13 AM Vishal Saini <vishal.saini.nitj@gmail.com<mailto:vishal.saini.nitj@gmail.com>> wrote: Dear Spencer and David, Thanks very much for your prompt replies. 1. Defining the expansions separately still produced the "note" (in Nektar 4.4.1 Release). 2. Compiling the latest master solved the problem. However, I didn't try if defining the expansions collectively i.e. <E COMPOSITE="C[1,10,11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> produces any warnings in the latest compilation. BR, Vishal --- Vishal SAINI On Mon, Nov 26, 2018 at 4:43 PM Moxey, David <D.Moxey@exeter.ac.uk<mailto:D.Moxey@exeter.ac.uk>> wrote: Hi Vishal, You might also try a newer version of the code (i.e. latest master), I am not sure that the pyramid collections functions were added in 4.4.1. Many thanks, Dave
On 26 Nov 2018, at 14:53, Sherwin, Spencer J <s.sherwin@imperial.ac.uk<mailto:s.sherwin@imperial.ac.uk>> wrote:
Dear Vishal,
I do not quite recall but it may be necessary to define the expansions for composites of different shape independently. So please try:
<E COMPOSITE=“C[1]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> <E COMPOSITE=“C[10]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" /> <E COMPOSITE="C[11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" />
Possibly it is expecting to have a pyramid collection within a tetrahedral expansion and so this is why you see this message.
If this does not work can you send the xml file along.
Thanks, Spencer.
On 26 Nov 2018, at 11:45, Vishal Saini <vishal.saini.nitj@gmail.com<mailto:vishal.saini.nitj@gmail.com>> wrote:
Hi all,
I've imported a mesh from gmsh that contains a layer of pyramids for transitioning between hexes and tets using: NekMesh JICF_NektP2_2comp.msh JICF_NektP2_2comp.xml Output: Multiple elements in composite detected; remapped: - Tag 1 => 11 (Tetrahedron), 10 (Pyramid), 1 (Hexahedron) No problem on NekMesh level.
Defining my expansion as: <E COMPOSITE="C[1,10,11]" NUMMODES="3" FIELDS="u,v,w,p" TYPE="MODIFIED" />
when I run (Nektar++ v 4.4.1) using: mpirun -npernode 28 -np 56 IncNavierStokesSolver -v JICF_NektP2_2comp_xml conditions_JICF_2D.xml (using prepartitioned mesh). I get the following "note": Collection Implemenation for Tetrahedron ( 3 3 3 ) for ngeoms = 24960 Note: Implementation does not exist: Pyramid, BwdTrans, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTDerivBase, SumFac, Modal Note: Implementation does not exist: Pyramid, PhysDeriv, SumFac, Modal Note: Implementation does not exist: Pyramid, BwdTrans, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTBase, SumFac, Modal Note: Implementation does not exist: Pyramid, IProductWRTDerivBase, SumFac, Modal Note: Implementation does not exist: Pyramid, PhysDeriv, SumFac, Modal
What does it mean? How can I fix it? Do Pyramids need to be treated in a somewhat different way?
BR, Vishal
--- Vishal SAINI _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk<mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Spencer Sherwin FREng, FRAeS Head, Aerodynamics, Director of Research Computing Service, Professor of Computational Fluid Mechanics, Department of Aeronautics, s.sherwin@imperial.ac.uk<mailto:s.sherwin@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/
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk<mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk<mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users Spencer Sherwin FREng, FRAeS Head, Aerodynamics, Director of Research Computing Service, Professor of Computational Fluid Mechanics, Department of Aeronautics, s.sherwin@imperial.ac.uk<mailto:s.sherwin@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/
participants (2)
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Sherwin, Spencer J
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Vishal Saini