Luca Heltai [Mon, 28 Jul 2014 12:54:25 +0000 (14:54 +0200)]
Made the default Manifold objects inside Triangulation be Manifold. Now get_boundary and get_manifold do different things.
Luca Heltai [Mon, 28 Jul 2014 10:10:52 +0000 (12:10 +0200)]
Fixed indentation of almost all comments in tria.cc
Luca Heltai [Fri, 25 Jul 2014 21:05:27 +0000 (23:05 +0200)]
Added manifold, copying over the old concept, but retaining dim. Made Boundary<dim,spacedim> derived from Manifold<dim,spacedim>.
Added specific instantiations for invalid accessors. Moved get_default_quadrature into an anonymous namespace.
Made Boundary derived from FlatManifold, and made sure that nothing broke. Added get_new_point_on_cell/hex. Made get_new_point_on_quad not throw an exception in 2d.
Created Manifolds namespace, and made specialization of get_new_point_on_hex only in 3d, instead of multiple specializations for when dim not equal 3.
Added test flat_manifold_01
Fixed 2d problems.
Fixed 3d. Now all tests work, except from machine precision errors.
Added a new test for flat manifold checks on faces.
Completed documentation of manifold and tria_boundary.
Removed commented out functions from Boundary<dim,spacedim>, whose default has been moved to Manifold<dim,spacedim>
Fixed periodicity of FlatManifold, and added a test for it.
Fixed comment on periodicity.
Removed commented instantiations.
Martin Kronbichler [Wed, 6 Aug 2014 06:48:46 +0000 (08:48 +0200)]
Merge pull request #52 from kronbichler/master
New initialize method for Trilinos AMG preconditioner with Epetra_RowMatrix
Martin Kronbichler [Wed, 6 Aug 2014 06:47:11 +0000 (08:47 +0200)]
List change in doc/news/changes.h
Martin Kronbichler [Wed, 6 Aug 2014 06:41:53 +0000 (08:41 +0200)]
Improve documentation
Martin Kronbichler [Wed, 6 Aug 2014 06:30:42 +0000 (08:30 +0200)]
Correct return type of n_global_rows for 32 bit integers.
Martin Kronbichler [Wed, 6 Aug 2014 06:29:00 +0000 (08:29 +0200)]
Merge branch 'master' of https://github.com/dealii/dealii
Timo Heister [Wed, 6 Aug 2014 03:57:54 +0000 (23:57 -0400)]
Merge pull request #45 from guidokanschat/doxygen_cleanup
Some cleanup of doxygen issues:
simplify doxygen input path
reduce warnings from thousands to hundreds as long as major code is undocumented
fix displayed include paths in doxygen output
fix some of the warnings
Timo Heister [Wed, 6 Aug 2014 03:54:03 +0000 (23:54 -0400)]
Merge pull request #53 from bangerth/fix-nedelec-interpolation-matrix
Patch by Alexander Grayver: Fix face interpolation between FE_Nedelec elements.
This patch fixes a bug in the FE_Nedelec::get_face_interpolation_matrix related to the wrong indexing of the DoFs located on element faces. This patch ensures that the code produces an interpolation matrix with full column rank meaning that all DoFs of the FE with lower order are constrained.
Wolfgang Bangerth [Wed, 6 Aug 2014 03:14:06 +0000 (22:14 -0500)]
Patch by Alexander Grayver: Fix face interpolation between FE_Nedelec elements.
This patch fixes a bug in the FE_Nedelec::get_face_interpolation_matrix related to the wrong indexing of the DoFs located on element faces. This patch ensures that the code produces an interpolation matrix with full column rank meaning that all DoFs of the FE with lower order are constrained.
Martin Kronbichler [Tue, 5 Aug 2014 19:42:53 +0000 (21:42 +0200)]
Improve the documentation for the new initialize methods.
Guido Kanschat [Fri, 1 Aug 2014 17:12:29 +0000 (19:12 +0200)]
simplify doxygen input path
reduce warnings from thousands to hundreds as long as major code is undocumented
fix displayed include paths in doxygen output
fix some of the warnings
Martin Kronbichler [Tue, 5 Aug 2014 15:56:55 +0000 (17:56 +0200)]
Implement new initialize method for Trilinos AMG preconditioner: It can be based on an Epetra_RowMatrix object. We can use this code path for the standard initialize method with TrilinosWrappers::SparseMatrix as well.
Matthias Maier [Mon, 4 Aug 2014 20:30:28 +0000 (22:30 +0200)]
Merge pull request #51 from tjhei/fix_data_attach
fix, test, document Triangulation::register_data_attach
* fix a bug in an assertion
* add a test
* document how the CellStatus in the callback function works
Timo Heister [Mon, 4 Aug 2014 19:41:04 +0000 (15:41 -0400)]
add documentation to register_data_attach
Timo Heister [Mon, 4 Aug 2014 19:23:41 +0000 (15:23 -0400)]
add test
Timo Heister [Mon, 4 Aug 2014 19:23:30 +0000 (15:23 -0400)]
fix wrong assert in notify_ready_to_unpack
The offset will always be >=4 because we store the CellStatus in the
data sent to p4est in front of the user data. This means the smallest
offset will 4, no matter how much data is attached.
Martin Kronbichler [Sat, 2 Aug 2014 15:52:22 +0000 (17:52 +0200)]
Merge pull request #49 from bangerth/fix-instantiation
Fix an instantiation.
Wolfgang Bangerth [Sat, 2 Aug 2014 11:34:06 +0000 (06:34 -0500)]
Fix an instantiation.
The existing instantiation works, but is not in line with the actual
declaration of the function. This may or may not be the problem with
the failing tests here http://cdash.kyomu.43-1.org/viewTest.php?onlyfailed&buildid=10664
that result from a missing instantiation.
Matthias Maier [Sat, 2 Aug 2014 08:43:04 +0000 (10:43 +0200)]
Merge pull request #48 from bangerth/doc-fixes-5
Fix an outdated reference to fparser. Add a link.
Wolfgang Bangerth [Sat, 2 Aug 2014 08:41:56 +0000 (03:41 -0500)]
Merge pull request #47 from tamiko/address_testsuite_issues
This pull_request addresses several minor issues with the testsuite:
Wolfgang Bangerth [Sat, 2 Aug 2014 08:40:50 +0000 (03:40 -0500)]
More fixes with references that are now outdated.
Wolfgang Bangerth [Sat, 2 Aug 2014 08:32:00 +0000 (03:32 -0500)]
Fix an outdated reference to fparser. Add a link.
Matthias Maier [Sat, 2 Aug 2014 08:31:43 +0000 (10:31 +0200)]
Testsuite: Also use '<>=,' as numdiff separators
This commit addresses issue #38: We have several tests in which numdiff
fails to recognize a number, because the output contains some unknown
delimiters, such as one of "<>=,".
Matthias Maier [Sat, 2 Aug 2014 08:26:19 +0000 (10:26 +0200)]
Testsuite: Update a comment
Matthias Maier [Sat, 2 Aug 2014 08:23:50 +0000 (10:23 +0200)]
Testsuite: Move forgotten file to correct location
All testsuite stuff is now under ./tests. Consequently,
macro_pickup_tests.cmake should also be moved.
Wolfgang Bangerth [Fri, 1 Aug 2014 23:05:03 +0000 (18:05 -0500)]
Merge pull request #46 from Rombur/time_step_petsc
Add empty virtual destructors for TimeStepping and RungeKutta.
Bruno Turcksin [Fri, 1 Aug 2014 22:56:16 +0000 (17:56 -0500)]
Add empty virtual destructors for TimeStepping and RungeKutta.
Wolfgang Bangerth [Fri, 1 Aug 2014 22:27:07 +0000 (17:27 -0500)]
Merge pull request #43 from guidokanschat/new_multigrid_tests
Fix logical problems in MGConstrainedDoFs and rewrite step 16
Guido Kanschat [Fri, 1 Aug 2014 13:05:03 +0000 (15:05 +0200)]
Fix minor issues in multigrid tests
Guido Kanschat [Thu, 31 Jul 2014 16:46:04 +0000 (18:46 +0200)]
Update documentation of step 16
Guido Kanschat [Fri, 1 Aug 2014 05:29:29 +0000 (07:29 +0200)]
Merge pull request #44 from oneliefleft/master
Correct a minor violation of coding standards in Petsc wrappers
oneliefleft [Fri, 1 Aug 2014 01:43:06 +0000 (01:43 +0000)]
Fix a typo...
oneliefleft [Fri, 1 Aug 2014 01:35:15 +0000 (01:35 +0000)]
Correct a minor violation of coding standards.
Guido Kanschat [Thu, 31 Jul 2014 13:27:03 +0000 (15:27 +0200)]
all existing multigrid tests verified with fixed MGConstrainedDoFs
new test for Neumann data
Guido Kanschat [Thu, 31 Jul 2014 12:35:40 +0000 (14:35 +0200)]
use new logic in multigrid assemblers and switch step 16 to MeshWorker
Timo Heister [Thu, 31 Jul 2014 12:02:12 +0000 (14:02 +0200)]
implement deprecated get_refinement_edge_boundary_indices()
Guido Kanschat [Thu, 31 Jul 2014 11:23:16 +0000 (13:23 +0200)]
Fixing problems with MGConstrainedDoFs
Martin Kronbichler [Thu, 31 Jul 2014 07:17:29 +0000 (09:17 +0200)]
Merge pull request #42 from tamiko/fix_cxx11_setup
CMake: Fix various bugs in check_01_cxx_features
Matthias Maier [Thu, 31 Jul 2014 06:59:12 +0000 (08:59 +0200)]
CMake: Fix various bugs in check_01_cxx_features
This commit fixes a typo of the "-std=c++0x" fallback found by Chad Balen
(mailing list).
Furthermore, the fallback logic was also broken (as reported by Wolfgang).
Timo Heister [Tue, 29 Jul 2014 21:12:37 +0000 (23:12 +0200)]
Merge pull request #40 from bangerth/doc-fixes
Fix numerous doxygen markup problems.
Doxygen got bent all out of shape in various places because formulas were opened
but not closed, and a number of other markup problems as well.
Timo Heister [Tue, 29 Jul 2014 20:46:10 +0000 (22:46 +0200)]
Merge pull request #39 from bangerth/add-patch-generators-2
Rename DoFTools::map_global_to_patch_dof_indices() to get_dofs_on_patch().
Follow Timo's suggestion and revert the mapping from map_global_to_patch_dof_indices(). Consequently, also rename the function to get_dofs_on_patch(). Adjust the test.
Wolfgang Bangerth [Tue, 29 Jul 2014 20:02:15 +0000 (15:02 -0500)]
Fix numerous doxygen markup problems.
Doxygen got bent all out of shape in various places because formulas were opened
but not closed, and a number of other markup problems as well.
Wolfgang Bangerth [Tue, 29 Jul 2014 14:29:12 +0000 (09:29 -0500)]
Rename DoFTools::map_global_to_patch_dof_indices() to get_dofs_on_patch().
Follow Timo's suggestion and revert the mapping from map_global_to_patch_dof_indices().
Consequently, also rename the function to get_dofs_on_patch(). Adjust the test.
Matthias Maier [Mon, 28 Jul 2014 21:12:52 +0000 (23:12 +0200)]
Merge pull request #37 from bangerth/add-patch-generators
Infrastructure functions for local problems on patches
The functions DoFTools::count_dofs_on_patch() and
DoFTools::map_global_dofs_to_patch_indices() help set up
linear systems on patches.
This is joint work with Arezou Ghesmati.
Wolfgang Bangerth [Mon, 28 Jul 2014 02:06:06 +0000 (21:06 -0500)]
Add more functions that deal with the infrastructure for solving local problems on patches around cells.
The functions DoFTools::count_dofs_on_patch() and DoFTools::map_global_dofs_to_patch_indices() help set up linear systems on patches. This is joint work with Arezou Ghesmati.
Matthias Maier [Mon, 28 Jul 2014 06:32:55 +0000 (08:32 +0200)]
Merge pull request #35 from bangerth/doc-fixes-3
Improve the documentation of VectorTools::create_point_source_vector().
Matthias Maier [Mon, 28 Jul 2014 06:31:49 +0000 (08:31 +0200)]
Merge pull request #33 from bangerth/doc-fixes
Improve the wording of an exception.
Matthias Maier [Mon, 28 Jul 2014 06:31:15 +0000 (08:31 +0200)]
Merge pull request #36 from bangerth/doc-fixes-4
Update documentation a bit.
Wolfgang Bangerth [Sun, 27 Jul 2014 21:00:55 +0000 (16:00 -0500)]
Update documentation a bit.
Reading through the documentation of some of the functions in DoFTools, there are a number of functions for which I can't quite figure out what exactly they do. This updates a couple of places, but more work remains. In particular, I have no idea from the description of what DoFTools::make_single_patch() does.
Wolfgang Bangerth [Sun, 27 Jul 2014 19:02:58 +0000 (14:02 -0500)]
Improve the documentation of VectorTools::create_point_source_vector().
The previous version of the documentation was not exactly clear as to what the 'orientation' argument actually referred to.
Guido Kanschat [Sun, 27 Jul 2014 08:35:29 +0000 (10:35 +0200)]
Merge pull request #34 from bangerth/doc-fixes-2
Update the documentation of VectorTools::project_boundary_values() to make it clearer.
Wolfgang Bangerth [Sat, 26 Jul 2014 22:05:04 +0000 (17:05 -0500)]
Update the documentation of VectorTools::project_boundary_values().
This had apparently confused a user on the mailing list earlier today, so structure the
documentation better.
Wolfgang Bangerth [Sat, 26 Jul 2014 12:58:55 +0000 (07:58 -0500)]
Improve the wording of an exception.
I ran into this exception and couldn't figure out what's wrong without looking at the source code.
Luca Heltai [Sat, 26 Jul 2014 11:20:14 +0000 (13:20 +0200)]
Merge pull request #32 from bangerth/doc-fixes
Improve documentation of the mapping cartesian class.
Luca Heltai [Sat, 26 Jul 2014 11:18:40 +0000 (13:18 +0200)]
Merge pull request #31 from bangerth/improve-error-message
Wolfgang.
This is in response to an email on the mailing list that showed an error message that wasn't particularly helpful.
Improve error message.
Wolfgang Bangerth [Sat, 26 Jul 2014 11:11:56 +0000 (06:11 -0500)]
Improve documentation.
Wolfgang Bangerth [Sat, 26 Jul 2014 10:48:05 +0000 (05:48 -0500)]
Improve error message.
This is in response to an email on the mailing list that showed an error message that wasn't particularly helpful.
Luca Heltai [Sat, 26 Jul 2014 08:22:03 +0000 (10:22 +0200)]
Merge pull request #30 from bangerth/move-reports-master
Wolfgang. This file (lost in the conversion from svn to git) was moved to http://www.dealii.org/reports.html since the actual reports are already there. This patch redirects the links there as well.
Fix links to doc/reports/index.html.
Wolfgang Bangerth [Sat, 26 Jul 2014 02:37:58 +0000 (21:37 -0500)]
Fix links to doc/reports/index.html.
This file (lost in the conversion from svn to git) was moved to http://www.dealii.org/reports.html since the actual reports are already there. This patch redirects the links there as well.
Luca Heltai [Fri, 25 Jul 2014 19:33:48 +0000 (21:33 +0200)]
Merge pull request #29 from dealii/fix-testsuite-omission
Wolfgang.
This file was apparently forgotten during the manifold branch merge. Update it to the correct output.
Wolfgang Bangerth [Fri, 25 Jul 2014 18:44:18 +0000 (13:44 -0500)]
Update a test output file.
This file was apparently forgotten during the manifold branch merge. Update it to the correct output.
Wolfgang Bangerth [Fri, 25 Jul 2014 00:35:20 +0000 (19:35 -0500)]
Merge pull request #28 from tamiko/fix_installation
Fix installation.
Matthias Maier [Thu, 24 Jul 2014 23:55:28 +0000 (01:55 +0200)]
Fix installation.
Well, it seems we forgot to update doc/CMakeLists.txt to install the new
README.md file...
Matthias Maier [Thu, 24 Jul 2014 23:00:58 +0000 (01:00 +0200)]
Merge pull request #20 from luca-heltai/pr_switch_to_markdown
Switched README to md format.
Changed the README in such a way that a markdown syntax parser
recognizes code blocks, links and title. Moved it to README.md
Luca Heltai [Wed, 23 Jul 2014 17:31:54 +0000 (19:31 +0200)]
Switched README to md format.
Implemented Matthias' suggestions.
Luca Heltai [Thu, 24 Jul 2014 22:47:08 +0000 (00:47 +0200)]
Merge pull request #26 from tamiko/fix_includes_in_steps
Matthias: This commit fixes up a regression introduced with commit
06a70ba
that removed unnecessary includes of base/multithread_info.h. Both steps
need them for multithread_info.n_threads()
Matthias Maier [Thu, 24 Jul 2014 22:21:52 +0000 (00:21 +0200)]
Add missing includes to step-17 and step-18
This commit fixes up a regression introduced with commit
06a70bad3cbbcbb6abc51e12f29e3b5dfffb928a
that removed unnecessary includes of base/multithread_info.h. Both steps
need them for multithread_info.n_threads()
Matthias Maier [Thu, 24 Jul 2014 22:12:49 +0000 (00:12 +0200)]
Merge pull request #25 from bangerth/doc-fixes-vector
Restructure documentation.
Put all member functions into one of the doxygen sections. Split
sections so that they make more sense.
Matthias Maier [Thu, 24 Jul 2014 22:11:17 +0000 (00:11 +0200)]
Merge pull request #24 from bangerth/doc-fixes
Fix doxygen formatting.
Some of the member functions in smartpointer.h did not have documentation
according to a format that doxygen would pick up.
Matthias Maier [Thu, 24 Jul 2014 22:10:15 +0000 (00:10 +0200)]
Merge pull request #23 from bangerth/fix-changelogs
Remove a file forgotten when converting the changelogs.
This file should have been removed in yesterday's conversion of the
changelogs from html to doxygen format, but I forgot to delete it. This PR
fixes the oversight.
Wolfgang Bangerth [Thu, 24 Jul 2014 20:42:04 +0000 (15:42 -0500)]
Restructure documentation.
Put all member functions into one of the doxygen sections. Split
sections so that they make more sense.
Wolfgang Bangerth [Thu, 24 Jul 2014 19:59:19 +0000 (14:59 -0500)]
Fix doxygen formatting.
Some of the member functions in smartpointer.h did not have documentation according to a format that doxygen would pick up.
Wolfgang Bangerth [Thu, 24 Jul 2014 11:42:54 +0000 (06:42 -0500)]
Remove a file forgotten when converting the changelogs.
Matthias Maier [Thu, 24 Jul 2014 08:29:59 +0000 (10:29 +0200)]
Merge pull request #21 from bangerth/convert-changelogs
Integrate old changelog files into doxygen
Convert old changelog files from straight up .html to .h files that
will be parsed by doxygen. This will make all changelog files behave
the same way.
Wolfgang Bangerth [Thu, 24 Jul 2014 02:44:05 +0000 (21:44 -0500)]
Convert old changelog files from straight up .html to .h files that will be parsed by doxygen.
This will make all changelog files behave the same way.
Luca Heltai [Wed, 23 Jul 2014 17:21:06 +0000 (19:21 +0200)]
Merge pull request #15 from bangerth/doc-fixes-2
Introduce the concept of containers-of-cells and link to it in various places.
Luca Heltai [Wed, 23 Jul 2014 17:12:36 +0000 (19:12 +0200)]
Merge pull request #13 from bangerth/doc-fixes
The previous version of the documentation basically stated why the function exists, not what it does. This is the focus of the new version. I also indented the arguments of this function and the (related) following one.
Wolfgang Bangerth [Wed, 23 Jul 2014 15:54:09 +0000 (10:54 -0500)]
Merge pull request #17 from bangerth/fix_p4est_configuration
Fix p4est configuration
Wolfgang Bangerth [Wed, 23 Jul 2014 15:44:43 +0000 (10:44 -0500)]
Add some description of when the last two IFs can happen in version
number recognition.
Wolfgang Bangerth [Wed, 23 Jul 2014 13:06:24 +0000 (08:06 -0500)]
Introduce the concept of containers-of-cells and link to it in various places.
Matthias Maier [Wed, 23 Jul 2014 10:38:22 +0000 (12:38 +0200)]
CMake: robust version extraction for P4Est
Make the version extraction in P4Est more robust: We should not rely on
the version string to define SUBMINOR and PATCH - this doesn't have to
be the case. So, always set P4EST_VERSION_SUBMINOR and
P4EST_VERSION_PATCH to "0" in FindP4EST.cmake if no valid number could
be extracted.
Wolfgang Bangerth [Wed, 23 Jul 2014 01:59:08 +0000 (20:59 -0500)]
Rewrite the documentation of DoFTools::compute_intergrid_constraints().
The previous version of the documentation basically stated why the function exists, not what it does. This is the focus of the new version. I also indented the arguments of this function and the (related) following one.
Matthias Maier [Tue, 22 Jul 2014 21:43:26 +0000 (23:43 +0200)]
Merge pull request #9 from bangerth/doc-fixes
Update documentation in include/deal.II/dofs/dof_tools.h
- Rename a documentation section to be more descriptive.
- Reshuffle some more functions and group them into appropriate categories. Not all functions are in categories yet, though, see http://www.dealii.org/developer/doxygen/deal.II/namespaceDoFTools.html
Wolfgang Bangerth [Tue, 22 Jul 2014 21:37:07 +0000 (16:37 -0500)]
Merge pull request #10 from tjhei/p4est_update
[minor] compatibility fixes for p4est 1.0
Wolfgang Bangerth [Tue, 22 Jul 2014 21:08:48 +0000 (16:08 -0500)]
Merge pull request #11 from tjhei/p4est_script
[minor] p4est-setup.sh can now also build from source directory
Timo Heister [Tue, 22 Jul 2014 11:03:24 +0000 (13:03 +0200)]
p4est-setup.sh can now also build from source directory
Timo Heister [Tue, 22 Jul 2014 10:48:37 +0000 (12:48 +0200)]
compatibility fixes for p4est 1.0
The deprecated type p4est_connect_type_t got removed in p4est >=1.0. Use
connect_type_t instead.
Wolfgang Bangerth [Mon, 21 Jul 2014 23:33:10 +0000 (18:33 -0500)]
Update documentation of this file.
- Rename a documentation section to be more descriptive.
- Reshuffle some more functions and group them into appropriate categories. Not all functions are in categories yet, though, see http://www.dealii.org/developer/doxygen/deal.II/namespaceDoFTools.html
Matthias Maier [Tue, 22 Jul 2014 13:46:28 +0000 (15:46 +0200)]
Merge pull request #8 from bangerth/add-patch-generators
Add GridTools::get_patch_around_cell().
Implement a function GridTools::get_patch_around_cell() extracts the
set of cells that surround a single cell. This is joint work with
Arezou Ghesmati.
Wolfgang Bangerth [Tue, 22 Jul 2014 12:54:03 +0000 (07:54 -0500)]
Add some documentation.
Wolfgang Bangerth [Mon, 21 Jul 2014 23:26:04 +0000 (18:26 -0500)]
Provide attribution.
Wolfgang Bangerth [Mon, 21 Jul 2014 23:16:23 +0000 (18:16 -0500)]
Joint work with Arezou Ghesmati: Add GridTools::get_patch_around_cell().
Wolfgang Bangerth [Mon, 21 Jul 2014 21:39:37 +0000 (16:39 -0500)]
Fix style issue.
Matthias Maier [Mon, 21 Jul 2014 15:44:16 +0000 (17:44 +0200)]
Merge pull request #6 from bangerth/remove-multithread_info.h-includes
Remove #includes of multithread_info.h in files that don't need it.
Matthias Maier [Mon, 21 Jul 2014 15:43:02 +0000 (17:43 +0200)]
Merge pull request #5 from bangerth/doc-fixes
Augment documentation.
The documentation of MultithreadInfo was unintelligible. It was also
incomplete in some places.
Wolfgang Bangerth [Mon, 21 Jul 2014 15:03:10 +0000 (10:03 -0500)]
Remove #includes of multithread_info.h in files that don't need it.
Wolfgang Bangerth [Mon, 21 Jul 2014 12:58:42 +0000 (07:58 -0500)]
Augment documentation.
The documentation of MultithreadInfo was unintelligible. It was also
incomplete in some places.
Wolfgang Bangerth [Mon, 21 Jul 2014 12:21:00 +0000 (07:21 -0500)]
Merge pull request #4 from tamiko/fix_mesh_converter_tests
Testsuite: Fix path in mesh_converter tests
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