Re: [deal.II] Re: .msh file triangulation failed

2020-09-22 Thread yuesu jin
E") because it was the only > difference with my .geo files. > > Bruno > > Le mar. 22 sept. 2020 à 11:20, yuesu jin a écrit : > > > > Dear Bruno, > > The problem was solved after I removed the > 'SetFactory("OpenCASCADE")'. Here are two mesh files wit

Re: [deal.II] Re: .msh file triangulation failed

2020-09-22 Thread yuesu jin
set the physical groups for the curves and the > points. This means nothing in deal.II. A vertex does not have a > boundary ID. You need all the external surfaces and the volume to have > a physical group. That's it. > > Bruno > > Le mar. 22 sept. 2020 à 10:24, yuesu jin a écrit : > >

Re: [deal.II] Re: .msh file triangulation failed

2020-09-22 Thread yuesu jin
boundary indicator to a line: the line >> with end vertices -1 and 0 does not exist.* >> -------- >> >> I attached the gmsh .geo file in this email. There is no vertex -1 >> actually. Could you tell me what's wrong with my mesh generation

[deal.II] .msh file triangulation failed

2020-09-22 Thread yuesu jin
-1 actually. Could you tell me what's wrong with my mesh generation? Thank you very much! Best regards, -- Yuesu Jin, Ph.D student, University of Houston, College of Natural Sciences and Mathematics, Department of Earth and Atmospheric Sciences, Houston, Texas 77204-5008 346-404-2062 -- T

Re: [deal.II] What is the first and second index of the gradient tensor

2020-09-07 Thread yuesu jin
Dear Dr.Bangerth, I found it just before, it is on the page of FEValuesView ( https://www.dealii.org/current/doxygen/deal.II/classFEValuesViews_1_1Vector.html). Thank you very much! Best regards, Yuesu On Mon, Sep 7, 2020 at 11:00 PM Wolfgang Bangerth wrote: > On 9/7/20 6:21 PM, yuesu

[deal.II] What is the first and second index of the gradient tensor

2020-09-07 Thread yuesu jin
Dear all, I want to contract the gradient tensor with another vector, such as T_ij*n_j, the gradient tensor is d_j u_i (d is the partial differential operator). I am wondering what is the first index of gradient tensor, i or j? Thank you ! Best regards, Yuesu -- Yuesu Jin, Ph.D student

Re: [deal.II] Question about fe_value.divergence

2020-09-03 Thread yuesu jin
Dear Dr. Bangerth, I read the step.20 again. It solves my question. I didn't understand what the non-primitive element talks about, now I know the necessity of that. Thank you! Best regards, Yuesu On Thu, Sep 3, 2020 at 5:38 PM yuesu jin wrote: > Dear Dr. Bangerth, > Thank you very m

Re: [deal.II] Question about fe_value.divergence

2020-09-03 Thread yuesu jin
the gradient of the non-zero component in the vector shape function such that it is a vector? Thank you again! Best regards, On Thu, Sep 3, 2020 at 3:11 PM Wolfgang Bangerth wrote: > On 9/3/20 1:28 PM, yuesu jin wrote: > >I am working on vector value finite element modelin

[deal.II] Question about fe_value.divergence

2020-09-03 Thread yuesu jin
categories. Could you give me the documentation page about these two functions? Best regards, -- Yuesu Jin, Ph.D student, University of Houston, College of Natural Sciences and Mathematics, Department of Earth and Atmospheric Sciences, Houston, Texas 77204-5008 346-404-2062 -- The deal.II project

Re: [deal.II] PETSc iteration does not converge

2020-08-17 Thread yuesu jin
OK, I see. I will do it, thank you! I will let you know if I get any result. On Mon, Aug 17, 2020 at 7:06 PM Wolfgang Bangerth wrote: > On 8/17/20 6:01 PM, yuesu jin wrote: > > I did nothing to verify those properties. because the single thread > CG > > solver conv

Re: [deal.II] PETSc iteration does not converge

2020-08-17 Thread yuesu jin
Dear Dr.Bangerth, I did nothing to verify those properties. because the single thread CG solver converged well. I used different preconditioners in parallel version and single thread version. In the parallel version I used block Jacobi and in the single thread version I used Jacobi. How can I

Re: [deal.II] Question about complex value finite element

2020-08-16 Thread yuesu jin
Sure, I will add my progress following this email. Best regards, On Sun, Aug 16, 2020 at 7:47 PM Wolfgang Bangerth wrote: > On 8/16/20 6:38 PM, yuesu jin wrote: > > Thank you very much! I found step-62 yesterday and I have > compared the > > difference between them. I

Re: [deal.II] PETSc iteration does not converge

2020-08-16 Thread yuesu jin
regards, Yuesu On Sun, Aug 16, 2020 at 7:20 PM Wolfgang Bangerth wrote: > On 8/14/20 9:20 PM, yuesu jin wrote: > > I tried a few levels of the tolerance, 1e-3, 1e-4 ,1e-6 and 1e-8. 1e-3 > > converged because that is in the same level with the solution. Error > occurs > > b

Re: [deal.II] Question about complex value finite element

2020-08-16 Thread yuesu jin
u are subscribed to the Google Groups > "deal.II User Group" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to dealii+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/1

[deal.II] Question about complex value finite element

2020-08-14 Thread yuesu jin
if I directly set up the matrix and rhs vector as complex ? Why does step-29 says "*it is often more convenient to split complex valued functions into their real and imaginary parts and use separate scalar finite element fields for discretizing each one of them*" ? Best wishes, -- Yuesu

Re: [deal.II] PETSc iteration does not converge

2020-08-14 Thread yuesu jin
regards, Yuesu On Fri, Aug 14, 2020 at 10:14 PM Wolfgang Bangerth wrote: > On 8/14/20 5:53 PM, yuesu jin wrote: > > > > I also wrote a single thread CG version, which converges well. The > > preconditioner in the parallel version is blockJacobi but the single > thread &g

[deal.II] PETSc iteration does not converge

2020-08-14 Thread yuesu jin
ll. The preconditioner in the parallel version is blockJacobi but the single thread version I used is SSOR. Does it matter to the convergence? Thank you! Best regards, -- Yuesu Jin, Ph.D student, University of Houston, College of Natural Sciences and Mathematics, Department of Earth and Atmospheric Sciences

[deal.II] A small question about subdomain renumbering

2020-08-05 Thread yuesu jin
the locally_owned_dofs_per_subomain, we can already use this_mpi_process to access the partition vector, which means the subdomain partition has been done according to the n_mpi_processes. Best regards, -- Yuesu Jin, Ph.D student, University of Houston, College of Natural Sciences and Mathematics, Department

Re: [deal.II] Re: Set up boundary id in gmsh

2020-08-05 Thread yuesu jin
ulate a Taylor-Couette flow. > If you wanted to use a 3D mesh, then you would make a Physical Volume(0) > and you would use the Physical Surface for the boundary conditions > > Best > Bruno > > > > On Wednesday, 5 August 2020 20:36:09 UTC-4, yuesu jin wrote: >> >

[deal.II] Set up boundary id in gmsh

2020-08-05 Thread yuesu jin
Dear all, I want to set up one Dirchlet boundary condition and one Neumann boundary condition on a 2d mesh, which is generated by gmsh. How can I set up the mesh file in order to tell dealii with the boundary id when I input the .msh file into dealii? Thanks! Best regards, -- Yuesu Jin, Ph.D

Re: [deal.II] Question about the numbering of DoFs

2020-08-03 Thread yuesu jin
group and stop receiving emails from it, send an > email to dealii+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/feed2cda-81f9-4e22-8089-beaf9b2ae2b0o%40googlegroups.com > . > -- Yuesu Jin, Ph.D student, University o

Re: [deal.II] Question about the numbering of DoFs

2020-08-02 Thread yuesu jin
gle.com/d/msgid/dealii/3c3bd51a-eaf4-49ce-af0f-fd6477100123o%40googlegroups.com > . > -- Yuesu Jin, Ph.D student, University of Houston, College of Natural Sciences and Mathematics, Department of Earth and Atmospheric Sciences, Houston, Texas 77204-5008 346-404-2062 -- The deal.II pr

[deal.II] Question about the numbering of DoFs

2020-08-02 Thread yuesu jin
it gives 2*9+4*1=22 degrees of freedom, it equals the base function with the vector components. [image: image.png] u(0) should have two base element [phi(0),0] and [phi(0) 0], u(1) should have two base elements as well [0 phi(0)] [0 phi(1)], so here should be 4 rather than 2 degrees of freedom. Best r

Re: [deal.II] METIS partition error

2020-07-27 Thread yuesu jin
- >> This message does't appear when I use a single node to run it. Does the >> sparsity tools automatically overload to partition_metis under parallel >> case? >> Thank you! >> Best regards >> -- >> Yuesu Jin, >> Ph.D s

[deal.II] METIS partition error

2020-07-26 Thread yuesu jin
configure deal.II with METIS. This message does't appear when I use a single node to run it. Does the sparsity tools automatically overload to partition_metis under parallel case? Thank you! Best regards -- Yuesu Jin, Ph.D student, University o

Re: [deal.II] Point receivers

2020-07-26 Thread yuesu jin
esponding degree of freedom. > > Best, > Daniel > > Am So., 26. Juli 2020 um 16:58 Uhr schrieb yuesu jin >: > >> Dear all, >> I am working on an elastic wave simulation code which needs to set up >> receivers on the surface boundaries to record the waveform.

[deal.II] Point receivers

2020-07-26 Thread yuesu jin
Dear all, I am working on an elastic wave simulation code which needs to set up receivers on the surface boundaries to record the waveform. In this case, how can I link the point coordinate with the dof handlers and extract values from the solution vector? Thank you! Best regards, -- Yuesu

Re: [deal.II] Cannot find local compiled petsc library

2020-07-24 Thread yuesu jin
Dear all, This problem has been solved. I copied the petscversion.h file to the arch/include folder therefore cmake found all petsc files and finished compilation. Best regards On Fri, Jul 24, 2020 at 3:17 PM yuesu jin wrote: > Dear Daniel, > Thank you for the instruction!

Re: [deal.II] Cannot find local compiled petsc library

2020-07-24 Thread yuesu jin
SC_DIR}/lib64. > See if you can adjust PETSC_DIR accordingly. > > Best, > Daniel > > Am Fr., 24. Juli 2020 um 01:18 Uhr schrieb yuesu jin >: > >> Dear all, >> I am installing deal.ii with petsc on a cluster. After I compiled the >> petsc library (The arch fol

[deal.II] Cannot find local compiled petsc library

2020-07-23 Thread yuesu jin
** Required variable "PETSC_INCLUDE_DIR_ARCH" set to NOTFOUND *** -- Could NOT find PETSC -- DEAL_II_WITH_PETSC has unmet external dependencies. -- Yuesu Jin, Ph.D student, University of Houston, College of Natural Sciences and Mathematics, Department of Earth and Atmospheric Sciences, Houston,

Re: [deal.II] Re: PETSc is not compatible with current MPI

2020-07-23 Thread yuesu jin
Dear Bruno, Thank you very much! I am using mpi/gcc right now. I will change to Intel mpi library. Best regards On Thu, Jul 23, 2020 at 9:08 PM Bruno Turcksin wrote: > Yuesu Jin, > > You don't need to compile your own PETSc but you need to use the same MPI > library than the on

[deal.II] PETSc is not compatible with current MPI

2020-07-23 Thread yuesu jin
ld not find a sufficient PETSC installation: PETSC is compiled against a different MPI library than the one deal.II picked up. -- DEAL_II_WITH_PETSC has unmet external dependencies. -- Yuesu Jin, Ph.D student, University of Houston, College of Natural Sciences and Mathematics, Department of Earth and

Re: [deal.II] Installation stopped

2020-07-23 Thread yuesu jin
Dear all, The problem has been solved. The GCC version was too old to compile the new version of deal.ii. I changed the gcc to a newer version which gave a very good result. Thanks! Best regards On Thu, Jul 23, 2020 at 11:56 AM yuesu jin wrote: > Dear Bruno, > Ok, I will try a n

Re: [deal.II] Installation stopped

2020-07-23 Thread yuesu jin
Dear Bruno, Ok, I will try a new gcc for compilation. Thank you! On Thu, Jul 23, 2020 at 7:57 AM Bruno Turcksin wrote: > Yuesu Lin, > > Do you have access to a newer compiler? gcc 4.8.5 is very old. > > Best, > > Bruno > > On Wednesday, July 22, 2020 at 11:26:0

Re: [deal.II] Installation stopped

2020-07-22 Thread yuesu jin
dealii-9.2.0/source/dofs/dof_tools_sparsity.cc:689:3: note: template void dealii::DoFTools::make_flux_sparsity_pattern(const DoFHandlerType&, SparsityPatternType&) make_flux_sparsity_pattern(const DoFHandlerType , ^ On Wed, Jul 22, 2020 at 9:28 PM Timo Heister wrote: > Yuesu Jin

[deal.II] Installation stopped

2020-07-22 Thread yuesu jin
tor iter = *this; ^ make: *** [all] Error 2 Could you give me some instructions about that? Thank you! -- Yuesu Jin, Ph.D student, University of Houston, College of Natural Sciences and Mathematics, Department of Earth and Atmospheric Sciences, Houston, Texas 77204-5008 346-404-2062 -- The deal.II project is

Re: [deal.II] Re: Little question about constructor

2019-09-04 Thread yuesu jin
Hope that helps. > > Best, > Konrad > > > On Wednesday, September 4, 2019 at 4:44:24 AM UTC+2, yuesu jin wrote: >> >> Hi all, >> >> I have a question about the constructor initialization list. In some >> tutorials, we initialize the dof_handler in

[deal.II] Little question about constructor

2019-09-03 Thread yuesu jin
Hi all, I have a question about the constructor initialization list. In some tutorials, we initialize the dof_handler in the constructor with parameter triangulation, however, the triangulation is initialized in some member function within this class, which means when we initialize the class,

Re: [deal.II] Re: Where can I find member function of cell?

2019-08-27 Thread yuesu jin
t is here: > https://dealii.org/current/doxygen/deal.II/classDoFCellAccessor-members.html > (DofCellAccessor) > > Best, > > Bruno > > On Monday, August 26, 2019 at 10:42:00 PM UTC-4, yuesu jin wrote: >> >> Hi all, >> When we iterate the cell within triangulati

[deal.II] Where can I find member function of cell?

2019-08-26 Thread yuesu jin
Hi all, When we iterate the cell within triangulation/dof_handler, we often use functions such as cell->face(), cell->vertices() etc. Where can I find all the member function in our documentation webpage? Thanks a lot! -- Yuesu Jin, Ph.D student, University of Houston, College of N

Re: [deal.II] Re: Question about constraints

2019-08-22 Thread yuesu jin
up and stop receiving emails from it, send an > email to dealii+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/a9e938ad-06b6-49e1-9e99-91bafd4e8fc4%40googlegroups.com > <https://groups.google.com/d/msgid/dealii/a9e93

[deal.II] Question about constraints

2019-08-21 Thread yuesu jin
on system_matrix and system_rhs. Do those two procedure have the same effect? --- Yuesu Jin, Ph.D student, University of Houston, College of Natural Sciences and Mathematics, Department of Earth and Atmospheric Sciences, Houston, Texas 77204-5008 346-404-2062 -- The deal.II project is located

Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-12 Thread yuesu jin
. It really cost my time! Best regards, Yuesu On Mon, Aug 12, 2019 at 12:12 PM Wolfgang Bangerth wrote: > On 8/12/19 11:01 AM, yuesu jin wrote: > > > > Installation completed, what a stupid mistake I made! Appreciate for > > your support! > > All the p

Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-12 Thread yuesu jin
/libmkl_intel_lp64.so: undefined symbol: mkl_blas_dsyrk* I try to fix it . Best regards, Yuesu On Mon, Aug 12, 2019 at 8:30 AM Wolfgang Bangerth wrote: > On 8/11/19 9:08 PM, yuesu jin wrote: > > AH... I understand,/*cmake -DCMAKE_INSTALL_PREFIX=[Directory you want > to > > insta

Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin
AH... I understand,* cmake -DCMAKE_INSTALL_PREFIX=[Directory you want to install] [Directory you build the program]* I have installed it again in a new folder, the folder now is 3.6GB, which means something has been installed in that. But the message is still there:

Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin
Hi Daniel, Thank you for your reply. I misunderstood build and install. I thought after I setup the build folder and make install, the program should be compiled in that build folder, because I installed the 9.0.1 version just run the command as those in README file. Now, I first input *cmake

Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin
e53%40googlegroups.com > <https://groups.google.com/d/msgid/dealii/fa4a34b5-70c9-4a8a-accb-dfc96cab1e53%40googlegroups.com?utm_medium=email_source=footer> > . > -- Yuesu Jin, Ph.D student, University of Houston, College of Natural Sciences and Mathematics, Department of Earth and Atmospheric Scie

Re: [deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-11 Thread yuesu jin
** [install] Error 1 *** I cannot figure out what is wrong there, can you tell me what is the problem? Thanks a lot! On Sat, Aug 10, 2019 at 9:58 PM yuesu jin wrote: > Hi, all, > I am a novice of deal.II, I begun to learn deal.II since version 9.0.1, > after I updated it

[deal.II] undefined symbol: mkl_blas_dsyrk

2019-08-10 Thread yuesu jin
Hi, all, I am a novice of deal.II, I begun to learn deal.II since version 9.0.1, after I updated it from 9.0.1 to 9.1.1, I found the executable file cannot run, the message is: ./step-5_sec: symbol lookup error: /home/yjin6/anaconda3/lib/libmkl_intel_lp64.so: undefined symbol: