Wolfgang Bangerth [Mon, 18 Aug 2014 10:27:03 +0000 (05:27 -0500)]
Fix a couple more files that accidentally use C++11 auto variables.
Wolfgang Bangerth [Fri, 15 Aug 2014 15:37:16 +0000 (10:37 -0500)]
Merge pull request #87 from agrayver/latest_slepc_support
Add workaround to be able to use SLEPc >= 3.5.0 with deal.II.
Alexander Grayver [Fri, 15 Aug 2014 12:46:51 +0000 (14:46 +0200)]
Add workaround to be able to use SLEPc >= 3.5.0 with deal.II. This requires disabling support for STFOLD spectrum transformation type since it was removed in SLEPc 3.5.0 and newer.
Also log the corresponding entry in changes.h
Matthias Maier [Fri, 15 Aug 2014 06:49:45 +0000 (08:49 +0200)]
Merge pull request #85 from bangerth/fix-invalid-auto
Replace use of 'auto' for variables.
This is only allowed in C++11.
Wolfgang Bangerth [Fri, 15 Aug 2014 04:04:39 +0000 (23:04 -0500)]
Replace use of 'auto' for variables. This is only allowed in C++11.
Guido Kanschat [Thu, 14 Aug 2014 19:08:41 +0000 (21:08 +0200)]
Merge pull request #79 from bangerth/introduce-cxx11-ranges
Provide functions for C++11 range-based for loops. Document C++11 interaction
Wolfgang Bangerth [Thu, 14 Aug 2014 13:28:08 +0000 (08:28 -0500)]
Mention range-based for loops in the tutorials.
Wolfgang Bangerth [Thu, 14 Aug 2014 12:52:59 +0000 (07:52 -0500)]
Add a test that uses range-based fors.
Wolfgang Bangerth [Thu, 7 Aug 2014 15:56:53 +0000 (10:56 -0500)]
Provide functions for C++11 range-based for loops. Document C++11 interaction.
This commit consists of the following individual commits:
Specifically, add Triangulation::cells(), Triangulation::active_cells() and
similar for the ones on a single level.
Fix up code to make it compile.
Fix one compile error.
Also provide similar functions for the two DoFHandler classes.
Augment documentation.
Update the specification of how we implement C++11 range-based for loops.
Link to the new documentation module (still coming up).
Document C++11 features and interaction.
Matthias Maier [Thu, 14 Aug 2014 11:51:35 +0000 (13:51 +0200)]
Merge pull request #83 from bangerth/return-invalid-value
Follow a suggestion by k3daevin:
In TriaAccessor<2,3>::measure(), return a NaN instead of -1e10
to make the error condition clearer.
Wolfgang Bangerth [Thu, 14 Aug 2014 11:09:21 +0000 (06:09 -0500)]
Merge pull request #82 from agrayver/high_order_nedelec
Fix project_boundary_values_curl_conforming for high-order FE_Nedelec
Wolfgang Bangerth [Thu, 14 Aug 2014 11:06:04 +0000 (06:06 -0500)]
Return a NaN instead of just a very large value to make the error condition
clearer.
Alexander Grayver [Thu, 14 Aug 2014 07:46:12 +0000 (09:46 +0200)]
Add test output
Alexander Grayver [Wed, 13 Aug 2014 16:11:31 +0000 (18:11 +0200)]
Fix test for project_boundary_values_curl_conforming
Alexander Grayver [Wed, 13 Aug 2014 16:05:23 +0000 (18:05 +0200)]
Add test for project_boundary_values_curl_conforming
agrayver [Wed, 13 Aug 2014 12:40:48 +0000 (14:40 +0200)]
Fix bug in project_boundary_values_curl_conforming related to the wrong indexing of high-order DoFs in internals::compute_face_projection_curl_conforming.
Wolfgang Bangerth [Wed, 13 Aug 2014 11:28:28 +0000 (06:28 -0500)]
Merge pull request #81 from tamiko/new_testsuite_track
Testsuite: Remove 'Nightly' Track, add 'Continuous'
Matthias Maier [Tue, 12 Aug 2014 21:36:50 +0000 (23:36 +0200)]
Testsuite: Small documentation update
Matthias Maier [Tue, 12 Aug 2014 21:18:17 +0000 (23:18 +0200)]
Testsuite: Remove 'Nightly' Track, add 'Continuous'
This commit removes the obsolete support for a 'Nightly' track and adds a
new 'Continuous' track. The idea is that in future 'tester' uses
exclusively the 'Regression Test' track and simserv04 uses 'Continuous'.
Both testing sites have different strategies: tester goes through all
commits with one configuration (for 32 and 64 bit indices), simserv04 just
checks the latest merge available but for a number of compilers and
configuration. The current mix of test results is just confusing and very
horrible to read :-/
Toby D. Young [Mon, 11 Aug 2014 22:04:02 +0000 (00:04 +0200)]
Merge pull request #80 from bangerth/doc-fixes-6
Minor documentation fixes.
Wolfgang Bangerth [Mon, 11 Aug 2014 21:50:07 +0000 (16:50 -0500)]
Minor documentation fixes.
Guido Kanschat [Sat, 9 Aug 2014 19:47:18 +0000 (21:47 +0200)]
Merge pull request #70 from tjhei/parallel_condense
ConstraintMatrix::condense() working with parallel distributed vectors
Toby D. Young [Fri, 8 Aug 2014 23:35:26 +0000 (01:35 +0200)]
Merge pull request #78 from tamiko/silence_warning
Silence a warning and reindent.
Matthias Maier [Fri, 8 Aug 2014 23:22:38 +0000 (01:22 +0200)]
Silence a warning
A logical construct of the form "EXPR && EXPR || EXPR" in manifold_lib.cc
triggered a bunch of warning. Silence them by explicitly enclosing the
intended precedence: (EXPR && EXPR) || EXPR.
Also run reindent on the file.
Guido Kanschat [Fri, 8 Aug 2014 22:04:37 +0000 (00:04 +0200)]
Merge pull request #75 from luca-heltai/travis_mixed_compilation
Removed release builds from the Travis tests.
Timo Heister [Fri, 8 Aug 2014 21:31:21 +0000 (17:31 -0400)]
Merge pull request #74 from guidokanschat/doxygen_steps_missing
Fix a bug in doxygen causing missing tutorials
The tutorial steps were missing in the online documentation.
This bug fix makes them reappear by creating the string of input directories and files only after the list has been competed.
Luca Heltai [Fri, 8 Aug 2014 21:07:37 +0000 (23:07 +0200)]
Removed release builds.
Guido Kanschat [Fri, 8 Aug 2014 21:03:51 +0000 (23:03 +0200)]
Fix a bug in the generation of the input string for doxygen... now the tutorial should appear again in the online documentation
Matthias Maier [Fri, 8 Aug 2014 20:55:45 +0000 (22:55 +0200)]
Merge pull request #73 from tjhei/pr_documentation
update notify_ready_to_unpack() documentation
Timo Heister [Fri, 8 Aug 2014 20:03:52 +0000 (16:03 -0400)]
update notify_ready_to_unpack documentation
Rombur [Fri, 8 Aug 2014 15:50:17 +0000 (10:50 -0500)]
Merge pull request #72 from masterleinad/fix_Epetra_Import
Adjust TrilinosWrappers::VectorBase::add
Daniel Arndt [Thu, 7 Aug 2014 12:40:15 +0000 (14:40 +0200)]
Adjust TrilinosWrappers::VectorBase::add according to the fix of [Bug 6079] Epetra_Import does not work for anything but Zero flags
Matthias Maier [Thu, 7 Aug 2014 20:38:57 +0000 (22:38 +0200)]
Merge pull request #61 from luca-heltai/travis_ci
Setup Continuous Integration on Travis CI
Let's see what happens...
Timo Heister [Thu, 7 Aug 2014 17:43:44 +0000 (13:43 -0400)]
add test
Timo Heister [Thu, 7 Aug 2014 15:40:13 +0000 (11:40 -0400)]
improve patch slightly
Wolfgang Bangerth [Thu, 7 Aug 2014 15:40:06 +0000 (10:40 -0500)]
Merge pull request #67 from luca-heltai/function_manifold_chart
Function manifold chart
Timo Heister [Thu, 7 Aug 2014 15:39:57 +0000 (11:39 -0400)]
patch by Alexander Grayver for condense()
Wolfgang Bangerth [Thu, 7 Aug 2014 15:37:02 +0000 (10:37 -0500)]
Merge pull request #69 from bangerth/doc-fixes-6
Fix a typo in the documentation of MappingChart.
Wolfgang Bangerth [Thu, 7 Aug 2014 15:36:24 +0000 (10:36 -0500)]
Provide some more documentation.
Luca Heltai [Thu, 7 Aug 2014 15:12:39 +0000 (17:12 +0200)]
Made FlatManifold tolerance relative.
Luca Heltai [Thu, 7 Aug 2014 14:47:48 +0000 (16:47 +0200)]
Refactored ManifoldChart to ChartManifold.
Luca Heltai [Thu, 7 Aug 2014 14:15:26 +0000 (16:15 +0200)]
Refactored FunctionManifold.
Luca Heltai [Thu, 7 Aug 2014 13:50:11 +0000 (15:50 +0200)]
Added relative tolerance, and better comment for owns_pointers.
Timo Heister [Thu, 7 Aug 2014 13:31:54 +0000 (09:31 -0400)]
Merge pull request #65 from bangerth/fix-muparser-if
Change the parsing of functions in muparser.
muparser requires that there be no space between the name of a function and its argument
list. This is incompatible to the behavior we had with fparser that allowed for spaces
in this position. To allow for backward compatible behavior, this patch changes the
parsing in such a way that it eats spaces after the function name for all built-in
and deal.II-defined functions before passing the expression to muparser.
This addresses bug #218 at https://code.google.com/p/dealii/issues/detail?id=218 .
Wolfgang Bangerth [Thu, 7 Aug 2014 13:19:59 +0000 (08:19 -0500)]
Fix a typo.
Then continue to add some more to the documentation in the form of an example.
Luca Heltai [Thu, 7 Aug 2014 13:07:54 +0000 (15:07 +0200)]
Added changelog
Luca Heltai [Thu, 7 Aug 2014 12:53:46 +0000 (14:53 +0200)]
Added two test files for FunctionManifoldChart
Luca Heltai [Wed, 6 Aug 2014 14:01:41 +0000 (16:01 +0200)]
Added FunctionManifoldChart
Luca Heltai [Thu, 7 Aug 2014 13:04:09 +0000 (15:04 +0200)]
Merge pull request #63 from tamiko/fix_manifold_instantiations
This commit reverts the quick fix in commit
982b0683.
The issue why we encountered unresolved references to
dealii::FlatManifold::FlatManifold(dealii::Point, double)
etc. was due to boilerplate instantiations of Triangulation::get_manifold
for cases with spacedim < dim (in order to make TriaAccessor happy).
This commit fixes the issue by using a nullptr-dereference in order to
return an invalid object - the specific code throws an error message before
that and should actually not be reachable at all.
Wolfgang Bangerth [Thu, 7 Aug 2014 12:45:53 +0000 (07:45 -0500)]
Merge pull request #66 from tjhei/fix_doxygen_warnings
fix several doxygen warnings
Wolfgang Bangerth [Thu, 7 Aug 2014 11:50:03 +0000 (06:50 -0500)]
Also update the parsing of all other builtin functions.
Matthias Maier [Thu, 7 Aug 2014 11:07:45 +0000 (13:07 +0200)]
Fix instantiation issue with FlatManifold properly
This commit reverts the quick fix in commit
982b0683.
This commit closes #56
The issue why we encountered unresolved references to
dealii::FlatManifold<3, 2>::FlatManifold(dealii::Point<2, double>, double)
etc. was due to boilerplate instantiations of Triangulation::get_manifold
for cases with spacedim < dim (in order to make TriaAccessor happy).
This commit fixes the issue by using a nullptr-dereference in order to
return an invalid object - the specific code throws an error message before
that and should actually not be reachable at all.
Timo Heister [Thu, 7 Aug 2014 12:36:08 +0000 (08:36 -0400)]
fix several doxygen warnings
Luca Heltai [Thu, 7 Aug 2014 11:32:29 +0000 (13:32 +0200)]
Merge pull request #64 from tamiko/cleanup_whitespace
This commit reindents some manifold and tria related files in order to
remove some bogus whitespace.
Matthias Maier [Thu, 7 Aug 2014 11:15:32 +0000 (13:15 +0200)]
Take the chance to cleanup whitespace and indent
Wolfgang Bangerth [Thu, 7 Aug 2014 10:32:33 +0000 (05:32 -0500)]
Restore backward compatible by converting 'if (' to 'if(' in expressions we pass down to muparser.
Luca Heltai [Thu, 7 Aug 2014 09:52:16 +0000 (11:52 +0200)]
Fixed Matthias suggestions.
Luca Heltai [Thu, 7 Aug 2014 08:59:05 +0000 (10:59 +0200)]
Removed also build tests, added osx
Luca Heltai [Thu, 7 Aug 2014 08:21:18 +0000 (10:21 +0200)]
Merge pull request #60 from bangerth/fix-instantiations
Eric Heien reports that he can't compile deal.II on one Mac machine with missing
symbols. I think we just forgot to instantiate them.
Luca Heltai [Tue, 5 Aug 2014 12:24:11 +0000 (14:24 +0200)]
Added .travis.yml
Wolfgang Bangerth [Thu, 7 Aug 2014 05:40:59 +0000 (00:40 -0500)]
Fix missing instantiations.
Eric Heien reports that he can't compile deal.II on one Mac machine with missing
symbols. I think we just forgot to instantiate them.
Wolfgang Bangerth [Thu, 7 Aug 2014 05:03:54 +0000 (00:03 -0500)]
Reindent some of the documentation and code.
Wolfgang Bangerth [Wed, 6 Aug 2014 22:30:13 +0000 (17:30 -0500)]
Merge pull request #59 from tjhei/fix_latex_formula
fix error in latex formula
Wolfgang Bangerth [Wed, 6 Aug 2014 22:28:59 +0000 (17:28 -0500)]
Merge pull request #58 from tjhei/fix_doxygen_generation
Fix steps no longer in doxygen documentation
Timo Heister [Wed, 6 Aug 2014 22:06:23 +0000 (18:06 -0400)]
fix error in latex formula
eqnarray can not have more than two &s.
Timo Heister [Wed, 6 Aug 2014 21:37:20 +0000 (17:37 -0400)]
add steps back to doxygen
This fixes the bug introduced in
17479c593.
Matthias Maier [Wed, 6 Aug 2014 20:53:42 +0000 (22:53 +0200)]
Merge pull request #57 from luca-heltai/hot_fix_manifold
Fix missing instantiations introduced with merges
6a36497 and
commit
bfe1138.
This closes #56
Luca Heltai [Wed, 6 Aug 2014 19:31:14 +0000 (21:31 +0200)]
Instantiated all possible Manifolds, FlatManifolds and ManifoldCharts
Wolfgang Bangerth [Wed, 6 Aug 2014 14:35:03 +0000 (09:35 -0500)]
Merge pull request #54 from luca-heltai/cylindrical_manifold
CylindricalManifold implementation
Luca Heltai [Wed, 6 Aug 2014 14:32:12 +0000 (16:32 +0200)]
Made CylindricalManifold derived from Manifold instead of FlatManifold.
Martin Kronbichler [Wed, 6 Aug 2014 14:25:27 +0000 (16:25 +0200)]
Merge pull request #55 from bangerth/tutorial-fixes
Write the steps in lowercase.
Wolfgang Bangerth [Wed, 6 Aug 2014 14:22:12 +0000 (09:22 -0500)]
Remove a duplicate section (thanks to Martin Kronbichler for pointing it out).
Wolfgang Bangerth [Wed, 6 Aug 2014 13:44:37 +0000 (08:44 -0500)]
Write the steps in lowercase.
This way, the filter script can replace them automatically with references to
the corresponding pages for each of the tutorial programs. This does not
currently work on http://dealii.org/developer/doxygen/deal.II/Tutorial.html .
Luca Heltai [Wed, 6 Aug 2014 12:56:16 +0000 (14:56 +0200)]
Added cylindrical Manifold and two tests.
Luca Heltai [Wed, 6 Aug 2014 12:33:08 +0000 (14:33 +0200)]
Merge pull request #50 from luca-heltai/manifold_id_step0
This is the first backward compatible version of the manifold id branch. Four methods were added to a class named Manifold, which contains a subset of the Boundary methods. Boundary is now derived from FlatManifold. This fixes issue #27.
Luca Heltai [Mon, 4 Aug 2014 13:26:23 +0000 (15:26 +0200)]
Fixed spelling and indentation.
Replied to most comments by Wolfgang.
Fixed constness of sub_manifold in ManifoldChart, fixed a few comments.
Fixed constness in a few places.
Removed references for simple doubles, and removed empty lines.
Added back references to quad when they are arguments of get_new_point
Made get_default_quadrature query itself the manifold when vertices are not available on subobjects.
Fixed instatiations for invalid Triangulations.
Fixed last reference, and failing test.
Some changes to the documentation.
Luca Heltai [Mon, 4 Aug 2014 08:21:46 +0000 (10:21 +0200)]
Added tolerance to FlatManifold
Added corner case to test flat_manifold_03
Fixed spherical manifold in 3D. This is a bit of a hack, but I don't knonw how else to do this...
Luca Heltai [Fri, 1 Aug 2014 09:08:04 +0000 (11:08 +0200)]
Added buggy spherical manifold.
Fixed compilation bug on Mac.
Modified tests for spherical manifold.
Luca Heltai [Mon, 28 Jul 2014 13:16:36 +0000 (15:16 +0200)]
Fixed documentation, and made default behavior do what we say it does.
Fixed compilation bug in manifold.cc
Added instantiations of ManifoldChart, and fixed a little bug.
Fixed instantiation bug, and tolerance error.
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.
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