Matthias Maier [Wed, 17 Dec 2014 23:11:43 +0000 (00:11 +0100)]
Remove unfinished example steps 47 and 50
Matthias Maier [Wed, 17 Dec 2014 18:01:44 +0000 (19:01 +0100)]
Merge pull request #353 from tamiko/dealii-8.2
Cherry-pick commits to the release branch
Felix Gruber [Wed, 17 Dec 2014 09:33:12 +0000 (10:33 +0100)]
Fix copyright years in doc/users/doxygen.html
The year 2013 is already included in the range 2012 - 2014.
Bruno Turcksin [Wed, 17 Dec 2014 15:52:01 +0000 (09:52 -0600)]
Add instantations for class RungeKutta.
Matthias Maier [Wed, 17 Dec 2014 08:02:22 +0000 (09:02 +0100)]
Merge pull request #349 from tamiko/dealii-8.2
Cherry-pick commits to the release branch
Timo Heister [Wed, 17 Dec 2014 07:49:13 +0000 (02:49 -0500)]
fix doxygen warnings
Matthias Maier [Wed, 17 Dec 2014 00:58:28 +0000 (01:58 +0100)]
try to get the arpack test a bit more stable
Well, it turns out that depending on arpack version and CPU the result for
the first 5 eigenvalues differs. Try to make this a bit more stable by
computing 8 eigenvalues and only print the first 5.
Matthias Maier [Wed, 17 Dec 2014 07:26:33 +0000 (08:26 +0100)]
Update normalize.pl to also substitute 8.2.pre version
Matthias Maier [Tue, 16 Dec 2014 15:28:36 +0000 (16:28 +0100)]
update AUTHORS
Matthias Maier [Tue, 16 Dec 2014 15:08:55 +0000 (16:08 +0100)]
update VERSION
Martin Kronbichler [Tue, 16 Dec 2014 14:59:03 +0000 (15:59 +0100)]
Merge pull request #344 from tamiko/fix_some_tests
Fix a bunch of tests for simserv
Luca Heltai [Tue, 16 Dec 2014 09:45:04 +0000 (10:45 +0100)]
Merge pull request #343 from tamiko/changes_and_doc_update
Release steps 0e 1 1a
Luca Heltai [Tue, 16 Dec 2014 09:44:24 +0000 (10:44 +0100)]
Merge pull request #342 from tamiko/doxygen_fixups_and_reindent
Release steps 0a 0b 0c 0d
Matthias Maier [Tue, 16 Dec 2014 07:55:56 +0000 (08:55 +0100)]
normalize parameter_handler_write_json.output for different boost versions
Matthias Maier [Tue, 16 Dec 2014 01:48:46 +0000 (02:48 +0100)]
Update codim_01.mpirun=3.debug.output
Matthias Maier [Tue, 16 Dec 2014 01:44:37 +0000 (02:44 +0100)]
sort output of arpack/step-36_ar
Matthias Maier [Mon, 15 Dec 2014 23:27:06 +0000 (00:27 +0100)]
update changes.h and tags for release
Matthias Maier [Mon, 15 Dec 2014 23:36:45 +0000 (00:36 +0100)]
Update blurbb for petsc and trilinos
Matthias Maier [Mon, 15 Dec 2014 22:58:31 +0000 (23:58 +0100)]
Bugfix: Fix typo so that our step-graph gets build again...
Matthias Maier [Mon, 15 Dec 2014 22:50:44 +0000 (23:50 +0100)]
manually fix up @ref statements
Matthias Maier [Mon, 15 Dec 2014 22:26:45 +0000 (23:26 +0100)]
Run wrapcomments.py, release step 0c
Matthias Maier [Mon, 15 Dec 2014 21:47:01 +0000 (22:47 +0100)]
reindent dof_handler.h, doxygen fixups
Timo Heister [Sun, 14 Dec 2014 20:33:18 +0000 (15:33 -0500)]
Merge pull request #301 from bangerth/muparser-cleanups
Muparser cleanups
Wolfgang Bangerth [Sat, 13 Dec 2014 04:18:12 +0000 (22:18 -0600)]
Make an error message easier to read.
Enclose strings in <...> so that one can more easily see if there happen
to be spaces in untoward places.
Wolfgang Bangerth [Sat, 13 Dec 2014 03:50:47 +0000 (21:50 -0600)]
Clean up documentation a bit.
Wolfgang Bangerth [Sat, 13 Dec 2014 03:50:36 +0000 (21:50 -0600)]
Reorganize code a bit.
Change the code so that checking whether a function parser object
has already been created now happens at the place where we use
the object, rather than as an early exit in the init_muparser()
function. I find that this makes the code easier to read.
This also allows us to remove the creation of a parser object on the
thread where the object is actually created. In many (most) cases,
we will simply create the parser later on anyway, but not necessarily.
Luca Heltai [Fri, 12 Dec 2014 19:56:45 +0000 (20:56 +0100)]
Merge pull request #299 from bangerth/add-test-2
Add another testcase.
Wolfgang Bangerth [Fri, 12 Dec 2014 19:05:30 +0000 (13:05 -0600)]
Add another testcase.
This is for the same problem as reported by Krishna Garikipati
on the mailing list this week. He verified that this used to fail
and works now, so I would like to add it to the testsuite to make
sure we don't regress in this functionality.
Wolfgang Bangerth [Fri, 12 Dec 2014 18:41:52 +0000 (12:41 -0600)]
Merge pull request #298 from Rombur/workstream
Use parallel_for instead of a pipeline in implementation3 of WorkStream.
Bruno Turcksin [Fri, 12 Dec 2014 18:05:37 +0000 (12:05 -0600)]
Use parallel_for instead of a pipeline in implementation3 of WorkStream.
Wolfgang Bangerth [Fri, 12 Dec 2014 15:14:48 +0000 (09:14 -0600)]
Merge pull request #289 from l-korous/master
Make entire library code compile on MSVC & gcc.
Lukas Korous [Fri, 12 Dec 2014 15:05:07 +0000 (16:05 +0100)]
Squashed changes for build working both on MSVC and other compilers.
Wolfgang Bangerth [Thu, 11 Dec 2014 20:06:21 +0000 (14:06 -0600)]
Merge pull request #297 from tamiko/fix_wno-xxx_detection_for_gcc
CMake: Correctly detect -Wno-... support for gcc
Matthias Maier [Thu, 11 Dec 2014 19:49:34 +0000 (20:49 +0100)]
CMake: Correctly detect -Wno-... support for gcc
gcc does not emit a warning if an unknown -Wno-... flag is specified on the
command line, thus the ENABLE_IF_SUPPORTED macro unconditionally enabled
-Wno-... flags for gcc. Unfortunately, gcc _does_ emit a warning for the
unrecognized compiler option if another warning is emitted in the same
compilation unit. This is now fixed by always querying for the non-negated
version, i.e. -Wfoo instead of -Wno-foo.
Luca Heltai [Thu, 11 Dec 2014 17:33:43 +0000 (18:33 +0100)]
Merge pull request #296 from bangerth/fix-slepc-icc-problem
Elide default initialization.
Wolfgang Bangerth [Thu, 11 Dec 2014 17:12:40 +0000 (11:12 -0600)]
Elide default initialization.
Apparently, the initialization of a std::shared_ptr with NULL is not
allowed with the Intel compiler. It is also not necessary (that's what
the default constructor does anyway), so just remove the line.
Luca Heltai [Thu, 11 Dec 2014 15:25:58 +0000 (16:25 +0100)]
Merge pull request #295 from bangerth/code-reorg
Reorganize code in symmetric_tensor.h.
Wolfgang Bangerth [Thu, 11 Dec 2014 13:09:03 +0000 (07:09 -0600)]
Reorganize code in symmetric_tensor.h.
The current implementation of SymmetricTensor<rank,dim,Number>::unrolled_to_component_indices
and its inverse function was only implemented for rank=2 and looked essentially like this:
Assert (rank == 2, ExcNotImplemented());
Assert (i < n_independent_components, ExcIndexRange(i, 0, n_independent_components));
switch (dim)
{
case 1:
return TableIndices<2>(0,0);
...
Such code cannot be generalized to rank=4 (in fact, it doesn't even compile
for rank=4) because we would have to return objects of different types
in any switch on rank. The only way around this is to use dispatch to
different functions that do the work for a particular rank.
This patch does the first part of this: set up the dispatch. Later patches
may in fact implement this function and its inverse for other ranks than 2.
Luca Heltai [Thu, 11 Dec 2014 07:53:42 +0000 (08:53 +0100)]
Merge pull request #294 from bangerth/add-test
Add a test.
Wolfgang Bangerth [Thu, 11 Dec 2014 02:46:29 +0000 (20:46 -0600)]
Add a test.
Matthias Maier [Wed, 10 Dec 2014 19:24:03 +0000 (20:24 +0100)]
Merge pull request #293 from tamiko/miscellaneous_fixups
Miscellaneous fixups
Matthias Maier [Wed, 10 Dec 2014 14:20:26 +0000 (15:20 +0100)]
also add the 'package' target to $ make info output
Matthias Maier [Wed, 10 Dec 2014 14:13:22 +0000 (15:13 +0100)]
add package component to rewrite rule
Matthias Maier [Wed, 10 Dec 2014 14:10:28 +0000 (15:10 +0100)]
Whitespace and indenting fixups
Matthias Maier [Wed, 10 Dec 2014 13:10:14 +0000 (14:10 +0100)]
Merge pull request #291 from luca-heltai/cpack-support
Added cpack configuration, and Mac Bundle package.
Luca Heltai [Wed, 10 Dec 2014 12:55:35 +0000 (13:55 +0100)]
Fixed licence, restructured setup_cpack
Luca Heltai [Wed, 10 Dec 2014 10:32:14 +0000 (11:32 +0100)]
Merge pull request #292 from bangerth/show-shape-functions
Include pictures of shape functions for FE_Q and FE_Q_Hierarchical.
Wolfgang Bangerth [Wed, 10 Dec 2014 02:15:47 +0000 (20:15 -0600)]
Include pictures of shape functions for FE_Q and FE_Q_Hierarchical.
This patch uses pictures generated by Manuel Quezada de Luna for the shape
functions of FE_Q and FE_Q_Hierarchical.
Luca Heltai [Fri, 14 Nov 2014 09:37:16 +0000 (10:37 +0100)]
Added cpack configuration, and Mac Bundle package.
Wolfgang Bangerth [Tue, 9 Dec 2014 13:12:02 +0000 (07:12 -0600)]
Merge pull request #281 from bangerth/doc-updates-and-test-additions
Doc updates and test additions
Wolfgang Bangerth [Mon, 1 Dec 2014 16:24:37 +0000 (10:24 -0600)]
Rewrite parts of the implementation to make it easier to read.
Wolfgang Bangerth [Mon, 1 Dec 2014 16:10:33 +0000 (10:10 -0600)]
Rewrite documentation for a function.
Luca Heltai [Tue, 9 Dec 2014 13:11:31 +0000 (14:11 +0100)]
Merge pull request #290 from tamiko/miscellaneous_cleanup
Miscellaneous cleanup
Matthias Maier [Tue, 9 Dec 2014 13:01:13 +0000 (14:01 +0100)]
Update CMake documentation
Matthias Maier [Tue, 9 Dec 2014 12:57:35 +0000 (13:57 +0100)]
Cleanup DEAL_II_MSVC testsuite handling
Bruno Turcksin [Mon, 8 Dec 2014 15:31:43 +0000 (09:31 -0600)]
Merge pull request #288 from bangerth/clarify-documentation
Clarify documentation.
Wolfgang Bangerth [Mon, 8 Dec 2014 15:27:12 +0000 (09:27 -0600)]
Clarify documentation.
Wolfgang Bangerth [Mon, 1 Dec 2014 16:09:52 +0000 (10:09 -0600)]
Add tests for a function that currently does not appear to be tested.
Martin Kronbichler [Sat, 6 Dec 2014 15:16:25 +0000 (16:16 +0100)]
Merge pull request #287 from davydden/refinement_optimized
refine_and_coarsen_optmise
Denis Davydov [Sat, 6 Dec 2014 12:59:23 +0000 (13:59 +0100)]
made refine_and_coarsen_optmise easier to read and less error prone
Wolfgang Bangerth [Fri, 5 Dec 2014 17:14:14 +0000 (11:14 -0600)]
Merge pull request #286 from kronbichler/master
Cleanup file of news, added one contribution
Martin Kronbichler [Fri, 5 Dec 2014 16:13:44 +0000 (17:13 +0100)]
Cleanup file of news, added one contribution
Wolfgang Bangerth [Thu, 4 Dec 2014 20:42:25 +0000 (14:42 -0600)]
Merge pull request #285 from tjhei/documentation
clarify documentation of ConstraintMatrix::distribute(VECTOR)
Timo Heister [Thu, 4 Dec 2014 20:37:16 +0000 (15:37 -0500)]
clarify documentation of ConstraintMatrix::distribute(VECTOR)
This came up as a question on the mailing list so we should be more precise.
Martin Kronbichler [Thu, 4 Dec 2014 20:07:07 +0000 (21:07 +0100)]
Merge pull request #284 from bangerth/fix-cuthill-mckee-without-dofs
Fix cuthill mckee without dofs
Michał Wichrowski [Thu, 4 Dec 2014 19:58:03 +0000 (13:58 -0600)]
Add a testcase.
Wolfgang Bangerth [Thu, 4 Dec 2014 19:57:06 +0000 (13:57 -0600)]
DoFRenumbering::Cuthill_McKee failed in parallel when a processor had no dofs.
Wolfgang Bangerth [Thu, 4 Dec 2014 16:47:56 +0000 (10:47 -0600)]
Merge pull request #283 from bangerth/more-ms-vc-fixes
More ms vc fixes
Wolfgang Bangerth [Thu, 4 Dec 2014 16:46:19 +0000 (10:46 -0600)]
Keep the old data types in declarations and only use the workaround for MS Visual Studio.
Lukas Korous [Wed, 3 Dec 2014 23:34:38 +0000 (00:34 +0100)]
Patch by Lukas Korous: Make namespace DerivativeApproximation work with MS Visual Studio.
Wolfgang Bangerth [Wed, 3 Dec 2014 13:19:41 +0000 (07:19 -0600)]
Merge pull request #282 from bangerth/patches-for-ms-vc
Patches for Microsoft Visual Studio
Wolfgang Bangerth [Wed, 3 Dec 2014 13:14:36 +0000 (07:14 -0600)]
Add a news entry.
Wolfgang Bangerth [Wed, 3 Dec 2014 13:13:26 +0000 (07:13 -0600)]
Patch by Lukas Korous: Work around a couple of problems with Microsoft Visual Studio. In the process, fix a couple of oversights and typos.
Wolfgang Bangerth [Wed, 3 Dec 2014 13:11:25 +0000 (07:11 -0600)]
Patch by Lukas Korous: Only include <mm_malloc.h> if not on Microsoft Visual Studio.
Wolfgang Bangerth [Wed, 3 Dec 2014 13:10:52 +0000 (07:10 -0600)]
Patch by Lukas Korous: Only include <mm_malloc.h> if not on Microsoft Visual Studio.
Wolfgang Bangerth [Wed, 3 Dec 2014 13:09:35 +0000 (07:09 -0600)]
Patch by Lukas Korous: Work around a compiler problem in Microsoft Visual Studio by disabling a safety check (for just this compiler) that should never trigger.
Wolfgang Bangerth [Wed, 3 Dec 2014 13:04:42 +0000 (07:04 -0600)]
Patch by Lukas Korous: Remove the explicit instantiation of a function since this creates problems for Microsoft Visual Studio. The instantiation is not strictly needed since the function, internal::MatrixFreeFunctions::ShapeInfo<T>::reinit() is defined in a file that is always included.
Wolfgang Bangerth [Wed, 3 Dec 2014 12:59:07 +0000 (06:59 -0600)]
Patch by Lukas Korous: Apply a workaround for Microsoft Visual Studio.
Wolfgang Bangerth [Wed, 3 Dec 2014 12:54:53 +0000 (06:54 -0600)]
Patch by Lukas Korous: Disable the testsuite for Microsoft Visual Studio because the testsuite uses Unix shell commands.
Toby D. Young [Tue, 2 Dec 2014 08:55:49 +0000 (09:55 +0100)]
Merge pull request #229 from davydden/GHEP
generalised hermitian
Matthias Maier [Mon, 1 Dec 2014 13:00:37 +0000 (14:00 +0100)]
Merge pull request #279 from tamiko/fix_periodic_bc
Fix various bugs in periodic boundary conditions
Matthias Maier [Mon, 1 Dec 2014 11:38:03 +0000 (12:38 +0100)]
code cleanup
Timo Heister [Mon, 1 Dec 2014 02:36:36 +0000 (21:36 -0500)]
Merge pull request #280 from bangerth/doc-update-4
Update documentation in one place.
Wolfgang Bangerth [Mon, 1 Dec 2014 02:27:22 +0000 (20:27 -0600)]
Update documentation in one place.
Matthias Maier [Wed, 26 Nov 2014 22:34:04 +0000 (23:34 +0100)]
make astyle happy
Matthias Maier [Sun, 30 Nov 2014 14:38:23 +0000 (15:38 +0100)]
Avoid unnecessary inversion of a transformation matrix
Matthias Maier [Wed, 26 Nov 2014 23:51:46 +0000 (00:51 +0100)]
Bugfix: adjust rotation for inverted matching
When constraining from face_1 to face_2 we have to use an (orientation,
flip, rotation) bitset that actually gives the relative orientation of
face_2 to face_1 (and not as specified face_1 to face_2).
This worked by accident because the constraining direction face_2 to face_1
is accidentally almost always used in all test cases.
Matthias Maier [Sun, 30 Nov 2014 13:31:46 +0000 (14:31 +0100)]
add another version of the dof_tools_21_b
that also tests for correct behaviour with hanging nodes. This is done by
additionally refining the second cube once. Test that constraining face_1
-> face_2 and the opposite direction face_2 -> face_1 give the exact same
result.
Manually verified that this is indeed the case
Matthias Maier [Sun, 30 Nov 2014 13:37:02 +0000 (14:37 +0100)]
Also check for reverse matching in bits/dof_tools_21_b
Also check for the inverse matching from face_2 to face_1 in the test
bits/dof_tools_21_b. Both directions must produce the same constraint
matrix except for the ordering of the constraints possibly being swapped.
Manually verified that this is the case
Matthias Maier [Wed, 26 Nov 2014 21:53:04 +0000 (22:53 +0100)]
Bugfix: Conditionally use matrix in orthogonal_equality
Only apply the parameter matrix in orthogonal_equality if it is a spacedim
x spacedim matrix and can be interpreted as a rotation.
Further bugfixes and documentation updates.
Matthias Maier [Wed, 26 Nov 2014 22:30:22 +0000 (23:30 +0100)]
Use spacedim in compute_transformation instead of incorrect dim
Matthias Maier [Wed, 26 Nov 2014 22:38:39 +0000 (23:38 +0100)]
Code cleanup and several bugfixes
Refactor the creation of the final (possibly rotated) interpolation matrix
in make_periodicity_constraints into its own function. Add some additional
asserts to catch corner cases.
Return early if nothing to do (fixes dof_tools_21* tests)
Matthias Maier [Wed, 26 Nov 2014 22:38:17 +0000 (23:38 +0100)]
restructure and clean up some code
Martin Kronbichler [Thu, 27 Nov 2014 21:08:57 +0000 (22:08 +0100)]
Merge pull request #278 from bangerth/fix-serialization-of-dof-handlers
Fix serialization of dof handlers
Wolfgang Bangerth [Thu, 27 Nov 2014 05:44:02 +0000 (23:44 -0600)]
Add the corresponding testcase for hp::DoFHandler as well, just to be on the safe side.
Wolfgang Bangerth [Thu, 27 Nov 2014 05:33:44 +0000 (23:33 -0600)]
Fix an issue reported by David Wells.
The problem here is that class DoFHandler only uses pointers to the
DoF faces and levels objects in the .h file, so we thought that we
don't have to #include the respective header files where these classes
are declared. But we also have a serialization function that uses
them and if you call it, the compiler will complain about undeclared
classes being used.
Wolfgang Bangerth [Wed, 26 Nov 2014 18:07:54 +0000 (12:07 -0600)]
Merge pull request #275 from kronbichler/master
Improve error message for out-of-bound access in parallel vector
Martin Kronbichler [Wed, 26 Nov 2014 17:54:27 +0000 (18:54 +0100)]
Improve error message for out-of-bound access in parallel vector
Denis Davydov [Wed, 26 Nov 2014 09:05:57 +0000 (10:05 +0100)]
made target eigenvalue a shared pointer
Denis Davydov [Tue, 25 Nov 2014 09:48:43 +0000 (10:48 +0100)]
added all options with comments
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