[deal.II] deal.II Newsletter #103
Hello everyone! This is deal.II newsletter #103. It automatically reports recently merged features and discussions about the deal.II finite element library. ## Below you find a list of recently proposed or merged features: #9125: Feature tensor function parser (proposed by konsim83) https://github.com/dealii/dealii/pull/9125 #9124: New set id method in particle. (proposed by luca-heltai) https://github.com/dealii/dealii/pull/9124 #9122: Silence some unused variable warnings. (proposed by drwells; merged) https://github.com/dealii/dealii/pull/9122 #9121: Fix some to some. (proposed by luca-heltai) https://github.com/dealii/dealii/pull/9121 #9119: Disable warning in python-wrappers only for newer clang (proposed by masterleinad; merged) https://github.com/dealii/dealii/pull/9119 #9118: Remove MF::get_size_info() (proposed by peterrum; merged) https://github.com/dealii/dealii/pull/9118 #9117: Fixed cmake 3.16.0 incompatibility. (proposed by marcfehling) https://github.com/dealii/dealii/pull/9117 #9115: Do not export bundled subdirectory if empty (proposed by tamiko) https://github.com/dealii/dealii/pull/9115 #9113: explicit instanciation is provided for Utilities::MPI::min (proposed by rezarastak; merged) https://github.com/dealii/dealii/pull/9113 #9111: Initial version of step-71 for the biharmonic equation. (proposed by bangerth) https://github.com/dealii/dealii/pull/9111 #9110: Allow using serial triangulations with ParticleHandler (proposed by masterleinad; merged) https://github.com/dealii/dealii/pull/9110 #9109: Add python wrappers for manifolds and extend tria wrappers (proposed by agrayver) https://github.com/dealii/dealii/pull/9109 #9108: Add note on template parameter in doc of GridTools::get_active_neighbors (proposed by simonsticko; merged) https://github.com/dealii/dealii/pull/9108 #9106: Make pft independent of p4est [WIP] (proposed by peterrum) https://github.com/dealii/dealii/pull/9106 #9105: Simplify CUDAWrappers::MatrixFree::free (proposed by masterleinad; merged) https://github.com/dealii/dealii/pull/9105 #9104: Allow using float shape functions (proposed by masterleinad) https://github.com/dealii/dealii/pull/9104 #9103: Relax assumpitions in GridTools::partition_triangulation_zorder (proposed by peterrum; merged) https://github.com/dealii/dealii/pull/9103 #9101: Only allocate some MappingQGeneric internal data if necessary (proposed by kronbichler; merged) https://github.com/dealii/dealii/pull/9101 #9100: Multigrid DataOut (proposed by tjhei) https://github.com/dealii/dealii/pull/9100 #9098: Implement data_out for mg levels (WIP) (proposed by peterrum) https://github.com/dealii/dealii/pull/9098 #9097: Fix MatrixFree::reinit() with FE_Q with face integration facilities (proposed by kronbichler; merged) https://github.com/dealii/dealii/pull/9097 #9096: Support multigrid-level output in DataOut (proposed by tamiko) https://github.com/dealii/dealii/pull/9096 #9095: jenkins: allow testing master (proposed by tjhei; merged) https://github.com/dealii/dealii/pull/9095 #9094: Relax default tolerance for find_all_active_cells_around_point (proposed by kronbichler; merged) https://github.com/dealii/dealii/pull/9094 #9093: add idr(s) solver (proposed by tcclevenger) https://github.com/dealii/dealii/pull/9093 #9092: Fix typo (Genreal -> General) (proposed by drwells; merged) https://github.com/dealii/dealii/pull/9092 #9091: README.md: display build status (proposed by tjhei; merged) https://github.com/dealii/dealii/pull/9091 #9090: make target documentation report location (proposed by tjhei; merged) https://github.com/dealii/dealii/pull/9090 #9089: step-55: doc update, add citation (proposed by tjhei; merged) https://github.com/dealii/dealii/pull/9089 #9088: Suppress warning in python-bindings (proposed by masterleinad; merged) https://github.com/dealii/dealii/pull/9088 #9087: Restrict some MPI tests requiring p4est (proposed by masterleinad; merged) https://github.com/dealii/dealii/pull/9087 #9086: Minor consistency improvements in tensor.h (proposed by masterleinad; merged) https://github.com/dealii/dealii/pull/9086 #9072: Add simple output for particles. (proposed by luca-heltai; merged) https://github.com/dealii/dealii/pull/9072 #9055: Add python wrappers for MappingQGeneric (proposed by agrayver; merged) https://github.com/dealii/dealii/pull/9055 #8999: Step-61 Use FE_DGRT instead of FE_RT (proposed by sophy1029; merged) https://github.com/dealii/dealii/pull/8999 #8963: Update tutorials to use write_vtu_with_pvtu_record (proposed by peterrum; merged) https://github.com/dealii/dealii/pull/8963 #8774: Hdf5 documentation (proposed by jpthiele; merged) https://github.com/dealii/dealii/pull/8774 #8661: FEInterfaceValues: replace step-12 (proposed by tjhei; merged) https://github.com/dealii/dealii/pull/8661 ## And this is a list of recently opened or closed discussions: #9123: LAPACK template wrappers should probably hav
Re: [deal.II] normal vector of boundary faces
Thank you again for your help. I have another question. I want to find the
projection of a point on a face (the point on a face that has the closest
distance to the query point). I think the function:
project_real_point_to_unit_point_on_face should do this task, but I'm not
sure. Can someone help me on this?
On Thursday, November 28, 2019 at 12:57:43 AM UTC-5, navneet roshan wrote:
>
> Hi Shahab,
>
> Please look at the following piece of code, it might be useful to you.
>
>
>unsigned int n_face_q_points = face_quadrature_formula.size();
>FEFaceValues fe_face_values (fe, face_quadrature_formula,
> update_values |
> *update_normal_vectors*
> | update_JxW_values);
>
>typename DoFHandler::active_cell_iterator
> cell = dof_handler.begin_active(),
> endc = dof_handler.end();
>
> // iterate over cells
> for (; cell!=endc; ++cell)
> {
> // iterate over faces
> for (unsigned int face = 0; face < GeometryInfo::faces_per_cell;
> ++face)
> // query if the faces of the cell belong to the boundary id needed
> if (cell->face(face)->*at_boundary()* == true
> && cell->face(face)->*boundary_id()* == 2)
> {
> *fe_face_values.reinit(cell, face)*;
>
> for (unsigned int f_q_point = 0; f_q_point ++f_q_point)
> {
> const Tensor<1, dim> &Nv =
>*fe_face_values.normal_vector*(f_q_point);
> }
> }
> }
>
>
> Best,
> Navneet
>
>
> On Thu, Nov 28, 2019 at 3:26 AM Shahab Golshan > wrote:
>
>> Dear all,
>> I was looking for a function to obtain the normal vectors of boundary
>> faces. Are there any functions in dealII which returns the normal vector of
>> a face?
>> Thank you in advance.
>> Shahab
>>
>> --
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
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>> https://groups.google.com/d/msgid/dealii/1554c651-b524-4c15-b253-a6529dc2887e%40googlegroups.com
>>
>>
>> .
>>
>
--
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Re: [deal.II] normal vector of boundary faces
That was very helpful, thank you Navneet.
Best,
Shahab
On Thursday, November 28, 2019 at 12:57:43 AM UTC-5, navneet roshan wrote:
>
> Hi Shahab,
>
> Please look at the following piece of code, it might be useful to you.
>
>
>unsigned int n_face_q_points = face_quadrature_formula.size();
>FEFaceValues fe_face_values (fe, face_quadrature_formula,
> update_values |
> *update_normal_vectors*
> | update_JxW_values);
>
>typename DoFHandler::active_cell_iterator
> cell = dof_handler.begin_active(),
> endc = dof_handler.end();
>
> // iterate over cells
> for (; cell!=endc; ++cell)
> {
> // iterate over faces
> for (unsigned int face = 0; face < GeometryInfo::faces_per_cell;
> ++face)
> // query if the faces of the cell belong to the boundary id needed
> if (cell->face(face)->*at_boundary()* == true
> && cell->face(face)->*boundary_id()* == 2)
> {
> *fe_face_values.reinit(cell, face)*;
>
> for (unsigned int f_q_point = 0; f_q_point ++f_q_point)
> {
> const Tensor<1, dim> &Nv =
>*fe_face_values.normal_vector*(f_q_point);
> }
> }
> }
>
>
> Best,
> Navneet
>
>
> On Thu, Nov 28, 2019 at 3:26 AM Shahab Golshan > wrote:
>
>> Dear all,
>> I was looking for a function to obtain the normal vectors of boundary
>> faces. Are there any functions in dealII which returns the normal vector of
>> a face?
>> Thank you in advance.
>> Shahab
>>
>> --
>> The deal.II project is located at http://www.dealii.org/
>> For mailing list/forum options, see
>> https://groups.google.com/d/forum/dealii?hl=en
>> ---
>> You received this message because you 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 dea...@googlegroups.com .
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/dealii/1554c651-b524-4c15-b253-a6529dc2887e%40googlegroups.com
>>
>>
>> .
>>
>
--
The deal.II project is located at http://www.dealii.org/
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Re: [deal.II] deal stopped working with latest macOS update (10.15)
Dear community, Luca in particular I have installed the package for Mac OS Catalina that was pointed out. In running the examples I noticed some unexpected errors Illegal instruction: 4 See below. Needless to say, the very same error comes out in running my own code. Any help is appreciated Perhaps you may also address me on this: when running my old deal.ii 8.5.1 version, it does not work anymore. The application just does not open and if I attempt at running via command line, I get this: /Applications/deal.II-8.5.1.app/Contents/Resources/opt/openmpi-1.10.2/bin/mpirun -np 4 ./m4_code ../input/SE_trivial_battery_m dyld: Library not loaded: /Applications/deal.II.app/Contents/Resources/opt/openmpi-1.10.2/lib/libopen-rte.12.dylib Referenced from: /Applications/deal.II-8.5.1.app/Contents/Resources/opt/openmpi-1.10.2/bin/mpirun Reason: image not found Abort trap: 6 tests-MacBook-Pro:Release albertosalvadori$ Any suggestions on how to sort this issue out? Thank you, Alberto --- bash-3.2$ which cmake /Applications/deal.II.app/Contents/Resources/Libraries/bin/cmake bash-3.2$ cmake -G 'Unix Makefiles' . -- The C compiler identification is AppleClang 11.0.0.1133 -- The CXX compiler identification is AppleClang 11.0.0.1133 -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-haswell/clang-11.0.0-apple/openmpi-3.1.4-qcsz2fblznqlgt3j4u7dctfjag4kapar/bin/mpic++ -- Check for working CXX compiler: /Applications/deal.II.app/Contents/Resources/spack/opt/spack/darwin-catalina-haswell/clang-11.0.0-apple/openmpi-3.1.4-qcsz2fblznqlgt3j4u7dctfjag4kapar/bin/mpic++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Autopilot invoked ### # # Project step-20 set up with deal.II-9.1.1 found at # /Applications/deal.II.app/Contents/Resources/Libraries # # CMAKE_BUILD_TYPE: Debug # # You can now run # $ make- to compile and link the program # $ make run- to (compile, link and) run the program # # $ make sign - to sign the executable with the supplied OSX developer key # # $ make debug - to switch the build type to 'Debug' # $ make release- to switch the build type to 'Release' # # $ make edit_cache - to change (cached) configuration variables # and rerun the configure and generate phases of CMake # # $ make strip_comments - to strip the source files in this # directory off their comments; this is irreversible # $ make clean - to remove the generated executable as well as # all intermediate compilation files # $ make runclean - to remove all output generated by the program # $ make distclean - to clean the directory from _all_ generated # files (includes clean, runclean and the removal # of the generated build system) # $ make info - to view this message again # # Have a nice day! # ### -- Configuring done -- Generating done -- Build files have been written to: /Users/albertosalvadori/Codes/dealii-9.1.1/deal.II/examples/step-20 bash-3.2$ make release *Scanning dependencies of target release* [100%] *Switching CMAKE_BUILD_TYPE to Release* -- Autopilot invoked -- Run $ make info to print a detailed help message -- Configuring done -- Generating done -- Build files have been written to: /Users/albertosalvadori/Codes/dealii-9.1.1/deal.II/examples/step-20 *** *** Switched to Release mode. Now recompile with: $ make *** [100%] Built target release bash-3.2$ make *Scanning dependencies of target step-20* [ 50%] Building CXX object CMakeFiles/step-20.dir/step-20.cc.o [100%] *Linking CXX executable step-20* [100%] Built target step-20 bash-3.2$ ./step-20 Illegal instruction: 4 *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3711239 fax 030 3711312 e-mail: alberto.salvad...@unibs.it web-page: http://m4lab.unibs.it/faculty.html On Fri, Oct 25, 2019 at 2:35 PM luca.heltai wrote: > Dear Ester, > > please take a look at the release page: > > https://github.com/dealii/dealii/releases/tag/v9.1.1 > > There is a package for Mac OS Catalina. In Catalina, permis
