Re: [Nektar-users] FW: FW: Questions regarding APE Solver
Hi Killian, I was hoping to get your take on my setup for the APESolver with forcing from pts files and baseflow from fld files The appropriate sections in my .xml file are as follows * <BOUNDARYCONDITIONS> <FUNCTION NAME="Baseflow"> <!-- Incompressible base flow --> <F VAR="*" TIMEDEPENDENT="1" FILE="nzs1_%4.fld"/> </FUNCTION> <FUNCTION NAME="Source"> <E VAR="p" VALUE="0"/> <F VAR="u" TIMEDEPENDENT="1" FILE="nzs1_vort_ptslamb_%4.pts:L_x"/> <F VAR="v" TIMEDEPENDENT="1" FILE="nzs1_vort_ptslamb_%4.pts:L_y"/> <F VAR="w" TIMEDEPENDENT="1" FILE="nzs1_vort_ptslamb_%4.pts:L_z"/> </FUNCTION> </BOUNDARYCONDITIONS> <FUNCTION NAME="InitialConditions"> <F VAR="*" FILE="nzs1_1500.fld" /></FUNCTION></CONDITIONS><FORCING> <FORCE TYPE="Field"> <FIELDFORCE> Source <FIELDFORCE/> </FORCE> </FORCING>* Where the base flow is taken from files from an incompressible simulation that was run earlier (named as nzs1_1500.fld - nzs1_1503.fld), and the forcing from .pts files which contain the lamb vector fluctuations (named as nzs1_vort_ptslamb_1500.pts-nzs1_vort_ptslamb_1503.pts). The solver fails with a segmentation fault (text shown below), which seems rather strange to me as none of the files involved are particularly large (10 Mb or so). *[nia0412:347383:0:347383] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x10)==== backtrace ==== 0 0x000000000019b649 Nektar::MultiRegions::ExpList::GetBoundaryCondition() ???:0 1 0x000000000016cac5 Nektar::MultiRegions::DisContField2D::GenerateBoundaryConditionExpansion() ???:0 2 0x00000000001730d5 Nektar::MultiRegions::DisContField2D::DisContField2D() ???:0 3 0x000000000013ea91 Nektar::MemoryManager<Nektar::MultiRegions::DisContField2D>::Allocate<boost::shared_ptr<Nektar::LibUtilities::SessionReader>, boost::shared_ptr<Nektar::SpatialDomains::MeshGraph>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >() ???:0 4 0x00000000001360c6 Nektar::SolverUtils::EquationSystem::v_InitObject() ???:0 5 0x000000000017b6c3 Nektar::SolverUtils::UnsteadySystem::v_InitObject() ???:0 6 0x00000000004378ac Nektar::APE::v_InitObject() ???:0 7 0x000000000043ada6 Nektar::APE::create() ???:0 8 0x000000000011608a Nektar::LibUtilities::NekFactory<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, Nektar::SolverUtils::EquationSystem, boost::shared_ptr<Nektar::LibUtilities::SessionReader> const&, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none>::CreateInstance() ???:0 9 0x0000000000115062 Nektar::SolverUtils::Driver::v_InitObject() ???:010 0x000000000012651e Nektar::SolverUtils::DriverStandard::create() ???:011 0x000000000042f926 Nektar::LibUtilities::NekFactory<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, Nektar::SolverUtils::Driver, boost::shared_ptr<Nektar::LibUtilities::SessionReader> const&, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none>::CreateInstance() ???:012 0x0000000000423b99 main() ???:013 0x0000000000021c05 __libc_start_main() ???:014 0x0000000000426dcd _start() ???:0===================Segmentation fault* Any insight would be greatly appreciated. Sincerely, On Fri, Oct 26, 2018 at 7:58 AM Amitvikram Dutta < amitvikram.dutta@uwaterloo.ca> wrote:
*From:* nektar-users-bounces@imperial.ac.ukOn Behalf OfAmitvikram Dutta *Sent:* October 26, 2018 7:57:47 AM (UTC-05:00) Eastern Time (US & Canada) *To:* nektar-users *Subject:* Re: [Nektar-users] FW: Questions regarding APE Solver
Thanks a lot Killian,
Is there a tentative release date for Nektar 5?
On Fri, Oct 26, 2018, 3:58 AM Amitvikram Dutta < amitvikram.dutta@uwaterloo.ca> wrote:
________________________________________ From: nektar-users-bounces@imperial.ac.ukOn Behalf OfKilian Lackhove Sent: October 26, 2018 3:58:07 AM (UTC-05:00) Eastern Time (US & Canada) To: Amitvikram Dutta; nektar-users Subject: Re: [Nektar-users] Questions regarding APE Solver
Hi Amitvikram,
1. Yes, only the lamb vector was used, so the RHS of the pressure equation is zero.
2. It seems the userguide is out of date. In Nektar++ 4.4 the RHS are specified using forcings (see the userguide). See e.g. APE_2DPulseAdv_WeakDG_MODIFIED.xml example how this is set up in the xml file. In short, you would have something like this:
<CONDITIONS> ... <FUNCTION NAME="Source"> <E VAR="p" VALUE="0"/> <E VAR="u" VALUE="define lamb vector here"/> <E VAR="v" VALUE="define lamb vector here"/> <E VAR="w" VALUE="define lamb vector here"/> </FUNCTION> </CONDITIONS> <FORCING> <FORCE TYPE="Field"> <FIELDFORCE> Source <FIELDFORCE/> </FORCE> </FORCING>
3. The next Nektar++ major release will ship a fieldfromstring module, which should be able to compute the source terms without the pts detour. Until then you can just use "FieldConvert foo.xml foo.chk bar.pts" to obtain a pts file with the values at the quadrature points.
In general, Nektar++ 5.0.0 will contain many changes and improvements to the acoustics solver, in particular with regard to hybdrid CAA cosimulations, so you might want to give it a try once its released.
Cheers,
Kilian
Am 26.10.18 um 04:55 schrieb Amitvikram Dutta:
Hi everyone,
I'm trying to use the APE Solver in nektar++ to predict sound generation from a particular industrial flow. The work is similar in scope to that published in this recent paper : http://www.iccfd.org/iccfd10/papers/ICCFD10-248-Paper.pdf. I'm particularly interested in how to define the source term. If I understand the work correctly, in a flow dominated by coherent structures, the Lamb vector becomes the dominant source. This leads to my first question : 1.In the APE-4 formulation there are 2 coupled equations with seperate source terms - one for the pressure fluctuations and one for the velocity fluctuations. In the above paper when the authors state that only the lamb vector was considered as a source, was the source for the RHS of the pressure fluctuations set to zero? 2. If this was the case, how was this specified in the .xml file? The only example I have come across is in the user guide which shows
<FUNCTION NAME="Source"> <E VAR="S" VALUE="0" /> </FUNCTION>
If one wanted to specify the pressure and velocity source terms seperately how would one do it in the .xml file?
3. From older posts in the mailing list I have seen suggestions of a workflow where the .chk/.fld files are written into a .pts file and then post processed to obtain the acoustic source. Is there a relevant filter or an extension the FieldConvert module that allows direct conversion from a .fld/.chk to a .pts format? I know of the interppoints extension that allows export to a .dat format but not the .pts?
Sorry for the lengthy post. Thanks in advance! --
*Amitvikram Dutta*
Graduate Research Assistant
Fluid Mechanics Research Lab
Multi-Physics Interaction Lab
University of Waterloo
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
-- Dr.-Ing. Kilian Lackhove Fachgebiet für Energie- und Kraftwerkstechnik L1|08 114 Technische Universität Darmstadt Otto-Berndt-Straße 3 D-64287 Darmstadt Germany
Tel.: +49 6151 16 - 28915 <+49%206151%201628915> Fax: +49 6151 16 - 6555 <+49%206151%20166555> e-mail: lackhove@ekt.tu-darmstadt.de
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
--
*Amitvikram Dutta*
Graduate Research Assistant
Fluid Mechanics Research Lab
Multi-Physics Interaction Lab
University of Waterloo
-- *Amitvikram Dutta* Graduate Research Assistant Fluid Mechanics Research Lab Multi-Physics Interaction Lab University of Waterloo
Hi Amitvikram, You have defined the "Baseflow" and "Source" functions inside the BOUNDARYCONDITIONS tag, while they should just be in the CONDITIONS tag. Since the the crash seems to happen while setting up the boundary conditions, try moving the functions out of the BOUNDARYCONDITIONS tag. Cheers, Kilian Am 29.10.18 um 19:01 schrieb Amitvikram Dutta:
Hi Killian,
I was hoping to get your take on my setup for the APESolver with forcing from pts files and baseflow from fld files
The appropriate sections in my .xml file are as follows
* <BOUNDARYCONDITIONS> <FUNCTION NAME="Baseflow"> <!-- Incompressible base flow --> <F VAR="*" TIMEDEPENDENT="1" FILE="nzs1_%4.fld"/> </FUNCTION> <FUNCTION NAME="Source"> <E VAR="p" VALUE="0"/> <F VAR="u" TIMEDEPENDENT="1" FILE="nzs1_vort_ptslamb_%4.pts:L_x"/> <F VAR="v" TIMEDEPENDENT="1" FILE="nzs1_vort_ptslamb_%4.pts:L_y"/> <F VAR="w" TIMEDEPENDENT="1" FILE="nzs1_vort_ptslamb_%4.pts:L_z"/> </FUNCTION> </BOUNDARYCONDITIONS> <FUNCTION NAME="InitialConditions"> <F VAR="*" FILE="nzs1_1500.fld" /> </FUNCTION> </CONDITIONS> <FORCING> <FORCE TYPE="Field"> <FIELDFORCE> Source <FIELDFORCE/> </FORCE> </FORCING>*
Where the base flow is taken from files from an incompressible simulation that was run earlier (named as nzs1_1500.fld - nzs1_1503.fld), and the forcing from .pts files which contain the lamb vector fluctuations (named as nzs1_vort_ptslamb_1500.pts-nzs1_vort_ptslamb_1503.pts).
The solver fails with a segmentation fault (text shown below), which seems rather strange to me as none of the files involved are particularly large (10 Mb or so).
*[nia0412:347383:0:347383] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x10) ==== backtrace ==== 0 0x000000000019b649 Nektar::MultiRegions::ExpList::GetBoundaryCondition() ???:0 1 0x000000000016cac5 Nektar::MultiRegions::DisContField2D::GenerateBoundaryConditionExpansion() ???:0 2 0x00000000001730d5 Nektar::MultiRegions::DisContField2D::DisContField2D() ???:0 3 0x000000000013ea91 Nektar::MemoryManager<Nektar::MultiRegions::DisContField2D>::Allocate<boost::shared_ptr<Nektar::LibUtilities::SessionReader>, boost::shared_ptr<Nektar::SpatialDomains::MeshGraph>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >() ???:0 4 0x00000000001360c6 Nektar::SolverUtils::EquationSystem::v_InitObject() ???:0 5 0x000000000017b6c3 Nektar::SolverUtils::UnsteadySystem::v_InitObject() ???:0 6 0x00000000004378ac Nektar::APE::v_InitObject() ???:0 7 0x000000000043ada6 Nektar::APE::create() ???:0 8 0x000000000011608a Nektar::LibUtilities::NekFactory<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, Nektar::SolverUtils::EquationSystem, boost::shared_ptr<Nektar::LibUtilities::SessionReader> const&, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none>::CreateInstance() ???:0 9 0x0000000000115062 Nektar::SolverUtils::Driver::v_InitObject() ???:0 10 0x000000000012651e Nektar::SolverUtils::DriverStandard::create() ???:0 11 0x000000000042f926 Nektar::LibUtilities::NekFactory<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, Nektar::SolverUtils::Driver, boost::shared_ptr<Nektar::LibUtilities::SessionReader> const&, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none, Nektar::LibUtilities::none>::CreateInstance() ???:0 12 0x0000000000423b99 main() ???:0 13 0x0000000000021c05 __libc_start_main() ???:0 14 0x0000000000426dcd _start() ???:0 =================== Segmentation fault*
Any insight would be greatly appreciated.
Sincerely,
On Fri, Oct 26, 2018 at 7:58 AM Amitvikram Dutta <amitvikram.dutta@uwaterloo.ca <mailto:amitvikram.dutta@uwaterloo.ca>> wrote:
*From:* nektar-users-bounces@imperial.ac.ukOn Behalf OfAmitvikram Dutta *Sent:* October 26, 2018 7:57:47 AM (UTC-05:00) Eastern Time (US & Canada) *To:* nektar-users *Subject:* Re: [Nektar-users] FW: Questions regarding APE Solver
Thanks a lot Killian,
Is there a tentative release date for Nektar 5?
On Fri, Oct 26, 2018, 3:58 AM Amitvikram Dutta <amitvikram.dutta@uwaterloo.ca <mailto:amitvikram.dutta@uwaterloo.ca>> wrote:
________________________________________ From: nektar-users-bounces@imperial.ac.ukOn Behalf OfKilian Lackhove Sent: October 26, 2018 3:58:07 AM (UTC-05:00) Eastern Time (US & Canada) To: Amitvikram Dutta; nektar-users Subject: Re: [Nektar-users] Questions regarding APE Solver
Hi Amitvikram,
1. Yes, only the lamb vector was used, so the RHS of the pressure equation is zero.
2. It seems the userguide is out of date. In Nektar++ 4.4 the RHS are specified using forcings (see the userguide). See e.g. APE_2DPulseAdv_WeakDG_MODIFIED.xml example how this is set up in the xml file. In short, you would have something like this:
<CONDITIONS> ... <FUNCTION NAME="Source"> <E VAR="p" VALUE="0"/> <E VAR="u" VALUE="define lamb vector here"/> <E VAR="v" VALUE="define lamb vector here"/> <E VAR="w" VALUE="define lamb vector here"/> </FUNCTION> </CONDITIONS> <FORCING> <FORCE TYPE="Field"> <FIELDFORCE> Source <FIELDFORCE/> </FORCE> </FORCING>
3. The next Nektar++ major release will ship a fieldfromstring module, which should be able to compute the source terms without the pts detour. Until then you can just use "FieldConvert foo.xml foo.chk bar.pts" to obtain a pts file with the values at the quadrature points.
In general, Nektar++ 5.0.0 will contain many changes and improvements to the acoustics solver, in particular with regard to hybdrid CAA cosimulations, so you might want to give it a try once its released.
Cheers,
Kilian
Am 26.10.18 um 04:55 schrieb Amitvikram Dutta: > Hi everyone, > > I'm trying to use the APE Solver in nektar++ to predict sound generation > from a particular industrial flow. The work is similar in scope to that > published in this recent paper : > http://www.iccfd.org/iccfd10/papers/ICCFD10-248-Paper.pdf. > I'm particularly interested in how to define the source term. If I > understand the work correctly, in a flow dominated by coherent > structures, the Lamb vector becomes the dominant source. > This leads to my first question : > 1.In the APE-4 formulation there are 2 coupled equations with seperate > source terms - one for the pressure fluctuations and one for the > velocity fluctuations. In the above paper when the authors state that > only the lamb vector was considered as a source, was the source for the > RHS of the pressure fluctuations set to zero? > 2. If this was the case, how was this specified in the .xml file? The > only example I have come across is in the user guide which shows > > <FUNCTION NAME="Source"> > <E VAR="S" VALUE="0" /> > </FUNCTION> > > If one wanted to specify the pressure and velocity source terms > seperately how would one do it in the .xml file? > > 3. From older posts in the mailing list I have seen suggestions of a > workflow where the .chk/.fld files are written into a .pts file and then > post processed to obtain the acoustic source. Is there a relevant filter > or an extension the FieldConvert module that allows direct conversion > from a .fld/.chk to a .pts format? I know of the interppoints extension > that allows export to a .dat format but not the .pts? > > Sorry for the lengthy post. > Thanks in advance! > -- > > *Amitvikram Dutta* > > Graduate Research Assistant > > Fluid Mechanics Research Lab > > Multi-Physics Interaction Lab > > University of Waterloo > > > _______________________________________________ > Nektar-users mailing list > Nektar-users@imperial.ac.uk <mailto:Nektar-users@imperial.ac.uk> > https://mailman.ic.ac.uk/mailman/listinfo/nektar-users >
-- Dr.-Ing. Kilian Lackhove Fachgebiet für Energie- und Kraftwerkstechnik L1|08 114 Technische Universität Darmstadt Otto-Berndt-Straße 3 D-64287 Darmstadt Germany
Tel.: +49 6151 16 - 28915 <tel:+49%206151%201628915> Fax: +49 6151 16 - 6555 <tel:+49%206151%20166555> e-mail: lackhove@ekt.tu-darmstadt.de <mailto:lackhove@ekt.tu-darmstadt.de>
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk <mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
--
*Amitvikram Dutta*
Graduate Research Assistant
Fluid Mechanics Research Lab
Multi-Physics Interaction Lab
University of Waterloo
--
*Amitvikram Dutta*
Graduate Research Assistant
Fluid Mechanics Research Lab
Multi-Physics Interaction Lab
University of Waterloo
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
-- Dr.-Ing. Kilian Lackhove Fachgebiet für Energie- und Kraftwerkstechnik L1|08 114 Technische Universität Darmstadt Otto-Berndt-Straße 3 D-64287 Darmstadt Germany Tel.: +49 6151 16 - 28915 Fax: +49 6151 16 - 6555 e-mail: lackhove@ekt.tu-darmstadt.de
participants (2)
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Amitvikram Dutta
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Kilian Lackhove