Re: [deal.II] Installation stopped

2020-07-23 Thread Bruno Turcksin
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 11:26:05 PM UTC-4, yuesu jin wrote: > > Dear Timo, > The configuration in summary.log file is: > > deal.II configuration: > #CMAKE_BUILD_TYPE: DebugRelease > #

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

2020-07-23 Thread Bruno Turcksin
Yuesu Jin, You don't need to compile your own PETSc but you need to use the same MPI library than the one that PETSc is using. There are very hard to debug problems that appear when PETSc and deal.II use different MPI libraries. I think that you want to use this MPI library

[deal.II] Location for Boundary Condition Application

2020-07-23 Thread McKenzie Davis
Hello! I'm interested in applying a non-homogeneous Dirichlet boundary condition to a specific edge. However, I'm unsure how to identify or specify a particular edge or face to add the boundary condition to. Could you help clear this up for me? Thank you for your help, McKenzie -- The

[deal.II] Complex-valued distributed matrices in dealii

2020-07-23 Thread Pascal Kraft
Dear Deal.II devs and users, In the latest release a lot of (great) work has been done to make complex numbers more of a first-class citizen in deal, which has made my code a lot more readable. Currently, I am stuck with one problem, though. Are there any distributed datatypes for matrices

Re: [deal.II] Complex-valued distributed matrices in dealii

2020-07-23 Thread Daniel Arndt
Pascal, The wrapped Trilinos matrices are based on Epetra which only supports double AFAICT. That's why you can replace TrilinosScalar easily. On the other hand, you should be able to compile PETSc with complex scalar type and use that with MPI. Best, Daniel Am Do., 23. Juli 2020 um 12:42 Uhr

Re: [deal.II] Location for Boundary Condition Application

2020-07-23 Thread Daniel Arndt
McKenzie, I'm interested in applying a non-homogeneous Dirichlet boundary condition > to a specific edge. However, I'm unsure how to identify or specify a > particular edge or face to add the boundary condition to. Could you help > clear this up for me? What do you know about that particular

Re: [deal.II] Accessing nodal values of a FEM solution

2020-07-23 Thread Xuefeng Li
On Thu, Jul 23, 2020 at 12:43 PM Daniel Arndt wrote: > However, I have two more related questions. BTW, I am a newbie in C++ >> programming. So my questions may seem absurd. >> >>1. Now that we have a vector holding all nodal point coordinates, and >>another vector holding all nodal

[deal.II] KDTree implementation error

2020-07-23 Thread heena patel
Dear all, I had tried to implement KDTree in step_1 tutoria and header file for kdtree is added to the codel. It is as follows: void first_grid() { Triangulation<2> triangulation; GridGenerator::hyper_cube(triangulation); triangulation.refine_global(4); *

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 11:26:05 PM UTC-4, yuesu jin wrote: >>

Re: [deal.II] Accessing nodal values of a FEM solution

2020-07-23 Thread Daniel Arndt
> > However, I have two more related questions. BTW, I am a newbie in C++ > programming. So my questions may seem absurd. > >1. Now that we have a vector holding all nodal point coordinates, and >another vector holding all nodal point values of the solution. How do we >access every

[deal.II] Re: KDTree implementation error

2020-07-23 Thread Bruno Turcksin
Heena, You are missing an include. Try adding #include https://dealii.org/current/doxygen/deal.II/kdtree_8h_source.html>> Best, Bruno On Thursday, July 23, 2020 at 2:55:53 PM UTC-4, heena patel wrote: > > > Dear all, > I had tried to implement KDTree in step_1 >

Re: [deal.II] Accessing nodal values of a FEM solution

2020-07-23 Thread Xuefeng Li
On Sun, Jul 19, 2020 at 7:36 PM Wolfgang Bangerth wrote: > On 7/19/20 6:28 PM, Daniel Arndt wrote: > > > > The tutorial examples show only how to access values of the solution > at > > the quadrature points within each cell. > > > > >

[deal.II] Re: Complex-valued distributed matrices in dealii

2020-07-23 Thread Pascal Kraft
Some additional information: If I try to compile deal with TrilinosScalar = std::complex I get many errors like this: [ 5%] Building CXX object source/numerics/CMakeFiles/obj_numerics_release.dir/data_postprocessor.cc.o [ 5%] Building CXX object

Re: [deal.II] Accessing nodal values of a FEM solution

2020-07-23 Thread Daniel Arndt
> > We need to update function v based on solution u in the following loop. > > for ( x in vector_of_nodal_points ) > v(x) = f(x, u(x)) > > where v(x) and u(x) are the nodal point value for functions v and u, > respectively, and f() is some function depending on function u as well as > the

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

2020-07-23 Thread yuesu jin
Dear all, I installed the Deal.II on a cluster. The first thing I found is that, the /dealii-9.2.0/cmake/configure/configure_1_mpi.cmake automatically set the DEAL_II_WITH_MPI argument as "off", therefore the MPI_FOUND module cannot run. I switched it on and cmake can find the MPI library. The

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 one that PETSc

[deal.II] Cannot find local compiled petsc library

2020-07-23 Thread yuesu jin
Dear all, I am installing deal.ii with petsc on a cluster. After I compiled the petsc library (The arch folder name is arch-linux-c-debug) and gave a cmake argument -DPETSC_DIR=/home/yjin6/petsc cmake cannot find the petsc library .so file(It is in the folder), but it founds the version is 3.13.

Re: [deal.II] Re: KDTree implementation error

2020-07-23 Thread heena patel
Dear Bruno, I had already added kdree.h header file, check the question again. But it seems it does not read KDTree; something is not compatible between class and header file. Regards, Heena On Thu, Jul 23, 2020 at 9:03 PM Bruno Turcksin wrote: > Heena, > > You

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 new gcc for

Re: [deal.II] Complex-valued distributed matrices in dealii

2020-07-23 Thread Pascal Kraft
Hi Daniel, oh, I'm really sorry for asking if that works. I had seen that neither PETSc nor Trilinos Sparse Matrices are templated and assumed that if the more modern version (Trilinos) doesn't work with complex numbers, trying PETSc wouldn't be very promising. But you are right, I will try