Timo Heister [Thu, 5 Nov 2015 14:12:33 +0000 (09:12 -0500)]
step-45 requires MPI and Trilinos
Timo Heister [Thu, 5 Nov 2015 14:12:22 +0000 (09:12 -0500)]
remove contract() deprecation warning in step-9
Timo Heister [Thu, 5 Nov 2015 14:02:50 +0000 (09:02 -0500)]
fix tests
- use std_cxx11::bind instead of std::bind
- require Trilinos if we use it
- fe/bdm_*: do not set matrix entries <1e-14 to zero (different on
different machines) and always print 0 entries
- use check_solver_within_range where needed
Wolfgang Bangerth [Thu, 5 Nov 2015 05:18:40 +0000 (14:18 +0900)]
Merge pull request #1834 from gassmoeller/triangulation_weights_callback
Fix test output.
Rene Gassmoeller [Thu, 5 Nov 2015 03:54:27 +0000 (21:54 -0600)]
Fix test output.
Allow calling repartition() even when no_automatic_refinement flag is not set
David Wells [Wed, 4 Nov 2015 22:07:31 +0000 (17:07 -0500)]
Merge pull request #1832 from luca-heltai/fix-matrix-creator
Fixed bug in one version of create_laplace_matrix.
Denis Davydov [Wed, 4 Nov 2015 22:03:55 +0000 (23:03 +0100)]
Merge pull request #1833 from drwells/add-latex-brackets
Add brackets around a LaTeX subscript.
Luca Heltai [Wed, 4 Nov 2015 21:45:25 +0000 (22:45 +0100)]
Fixed bug in matrix creator.
David Wells [Wed, 4 Nov 2015 21:46:57 +0000 (16:46 -0500)]
Add brackets around a LaTeX subscript.
Bruno Turcksin [Tue, 3 Nov 2015 19:29:34 +0000 (13:29 -0600)]
Merge pull request #1823 from bangerth/remove-first_cell-mechanism
Remove first_cell mechanism in FiniteElement
Bruno Turcksin [Tue, 3 Nov 2015 18:56:22 +0000 (12:56 -0600)]
Merge pull request #1777 from drwells/class-names-as-template-arguments
Class names as template arguments
Martin Kronbichler [Tue, 3 Nov 2015 14:32:12 +0000 (15:32 +0100)]
Merge pull request #1769 from jperryhouts/add_erfc
Add erfc function to FunctionParser.
Bruno Turcksin [Tue, 3 Nov 2015 14:27:48 +0000 (08:27 -0600)]
Merge pull request #1828 from tjhei/fix_tests3
fix tests/multigrid/transfer_prebuilt_01
Timo Heister [Tue, 3 Nov 2015 13:51:20 +0000 (08:51 -0500)]
fix tests/multigrid/transfer_prebuilt_01
I forgot to remove the .release.output file (output is now identical
between release and debug mode).
Timo Heister [Tue, 3 Nov 2015 13:11:53 +0000 (08:11 -0500)]
Merge pull request #1827 from bangerth/add-include-guard
Add an include guard to tests/base/functions.h.
Wolfgang Bangerth [Mon, 2 Nov 2015 23:17:21 +0000 (17:17 -0600)]
Add an include guard to tests/base/functions.h.
Not important, but found while playing with collating testcases into
one.
Jonathan Perry-Houts [Mon, 2 Nov 2015 21:14:44 +0000 (13:14 -0800)]
Added muparser erfc test.
Jonathan Perry-Houts [Tue, 20 Oct 2015 22:46:50 +0000 (15:46 -0700)]
Add erfc function to FunctionParser.
Timo Heister [Mon, 2 Nov 2015 17:50:41 +0000 (12:50 -0500)]
Merge pull request #1707 from gassmoeller/triangulation_weights_callback
Triangulation weights callback
David Wells [Mon, 19 Oct 2015 02:48:08 +0000 (22:48 -0400)]
Use VectorType, not InVector, as a template type.
Some functions use a template for the input and output types, but other
functions use InVector. This commit switches the second kind to use VectorType,
which is more consistent with the usage of both VectorType and InVector.
David Wells [Mon, 19 Oct 2015 12:38:06 +0000 (08:38 -0400)]
Use FEValuesType, not FEValues, in templates.
This makes things less ambiguous because 'FEValues' is a valid class
name.
David Wells [Mon, 19 Oct 2015 02:36:43 +0000 (22:36 -0400)]
Prefer QuadratureType to Quadrature in templates.
Writing something like
template<typename Quadrature>
is ambiguous because Quadrature is also a class.
David Wells [Mon, 19 Oct 2015 02:27:59 +0000 (22:27 -0400)]
Use typename BlockMatrixType in templates.
This replaces the use of 'BlockMatrix', which, while it is not a class
name, looks a lot like one.
David Wells [Mon, 19 Oct 2015 01:49:36 +0000 (21:49 -0400)]
Use SP, not SparsityPattern, as a template type.
This commit also exchanges 'SparsityPatternBase' for 'SP' for
consistency.
David Wells [Thu, 22 Oct 2015 23:26:09 +0000 (19:26 -0400)]
Remove unnecessary dealii:: qualifiers.
David Wells [Mon, 19 Oct 2015 01:29:18 +0000 (21:29 -0400)]
Use VectorType, not Vector, as a template type.
Writing something like
template<typename Vector>
is ambiguous because Vector is also a class.
Denis Davydov [Mon, 2 Nov 2015 14:51:04 +0000 (15:51 +0100)]
Merge pull request #1826 from drwells/remove-repeated-typedef
Remove repeated typedef.
David Wells [Mon, 19 Oct 2015 02:48:53 +0000 (22:48 -0400)]
Remove a repeated typedef.
David Wells [Mon, 19 Oct 2015 12:33:12 +0000 (08:33 -0400)]
Use a local typedef to shorten things.
Rene Gassmoeller [Mon, 2 Nov 2015 14:24:15 +0000 (08:24 -0600)]
add entry in changes.h
Rene Gassmoeller [Wed, 30 Sep 2015 14:12:16 +0000 (16:12 +0200)]
Introduce a signal for weighted repartitioning
Matthias Maier [Mon, 2 Nov 2015 14:08:15 +0000 (08:08 -0600)]
Merge pull request #1817 from luca-heltai/fix-mac-pack
Reworded packaging options. We no longer need to export DYLD libraries.
Wolfgang Bangerth [Sun, 1 Nov 2015 15:56:00 +0000 (09:56 -0600)]
Remove the first_cell/is_first_cell/current_update_flags() mechanism from FiniteElement.
What this patch does is address the issue that
`FiniteElement::get_data()` (as was previously the case with Mappings
as well) sets a flag in the returned `InternalData` object that
indicates that we are visiting a cell for the first time. `FEValues`
later sets this flag back once we're done with the first cell.
The way this is used is that the various finite element
implementations query `current_update_flags` in
`FE::fill_fe_*_values()`, which equals `update_each|update_once` if we
are on the first cell, and `update_each` on later cells. That means
that on the first cell we update fields in the output object that we
need to initialize only once, e.g., the values of shape functions on
quadrature points, but we won't do this again on later cells.
I don't particularly like this approach. It is opaque and took even me
a long time to reconstruct when I saw it (see #1305 for a
discussion). My preference is to do things we only need to do once in
`FE::get_data()`, and do things we need to do every time in
`FE::fill_fe_*_values()`. This kind of change was already implemented
for mappings in the patches references from #1305, and the current
pull request goes into the same direction.
The current PR only does one half of the necessary changes in order to
keep the patch reasonably self contained and readable. In particular,
what it really does is simply *always* do everything, by storing
`update_once|update_each` in `FE::InternalDataBase::update_each`. In
other words, it is the equivalent to telling finite element
implementations that we are always on the first cell. This requires
more work than in the previous state, although copying shape values
every time is arguably of small expense compared to transforming
gradients.
I will of course fix this up in upcoming patches. It requires
significant shuffling around. I'll open an issue in a minute
discussing the details. I'd simply like to propose this here already
as an incremental step forward, without making patch review too
onerous. The patch is mostly mechanical once you understand what it
does.
Denis Davydov [Mon, 2 Nov 2015 08:17:36 +0000 (09:17 +0100)]
Merge pull request #1819 from davydden/shared_tria_artificial_bugfix
Shared tria artificial bugfix
Denis Davydov [Fri, 30 Oct 2015 22:48:53 +0000 (23:48 +0100)]
added extra Asserts to shared::Tria tests; do not output partition results
Denis Davydov [Mon, 2 Nov 2015 07:39:44 +0000 (08:39 +0100)]
Merge pull request #1822 from bangerth/doc-update-38
Augment documentation of FE::get_(sub)face_data.
Wolfgang Bangerth [Mon, 2 Nov 2015 07:35:39 +0000 (01:35 -0600)]
Augment documentation of FE::get_(sub)face_data.
Wolfgang Bangerth [Mon, 2 Nov 2015 00:13:58 +0000 (09:13 +0900)]
Merge pull request #1820 from tamiko/fix_includes
CMake: Bugfix: Also use DEAL_II_INCLUDE_DIRS for bundled boost
Matthias Maier [Sun, 1 Nov 2015 23:21:30 +0000 (17:21 -0600)]
Add a news/changes.h entry
Matthias Maier [Sun, 1 Nov 2015 23:17:24 +0000 (17:17 -0600)]
CMake: Bugfix: Also use DEAL_II_INCLUDE_DIRS for bundled boost
This fixes a compilation issue with a zlib library not in a default
location in combination with bundled boost. Many thanks to Lukas Korous for
pointing this out.
Luca Heltai [Sat, 31 Oct 2015 16:44:27 +0000 (17:44 +0100)]
Merge pull request #1808 from bangerth/further-FEValues-cleanups-37
Break dependency of MappingQ from MappingQGeneric.
Denis Davydov [Fri, 30 Oct 2015 22:47:29 +0000 (23:47 +0100)]
fixed a bug in shared::Tria where...
true_subdomain_ids_of_cells was not set up for the case
without artificial cells.
Luca Heltai [Fri, 30 Oct 2015 11:07:57 +0000 (12:07 +0100)]
Fixed wording in dealii.conf.in
Wolfgang Bangerth [Fri, 30 Oct 2015 16:30:12 +0000 (11:30 -0500)]
Merge pull request #1816 from tjhei/fix_expand_inst_ldgold
fix cmake expand_instantiations ldgold workaround
Timo Heister [Fri, 30 Oct 2015 16:12:26 +0000 (12:12 -0400)]
fix cmake expand_instantiations ldgold workaround
Avoid cmake error if DEAL_II_LINKER_FLAGS is empty.
Matthias Maier [Fri, 30 Oct 2015 02:06:26 +0000 (21:06 -0500)]
Merge pull request #1813 from bangerth/fix-1798
Workaround linker bug when compiling expand_instantiations.
Wolfgang Bangerth [Fri, 30 Oct 2015 01:25:29 +0000 (20:25 -0500)]
Workaround linker bug when compiling expand_instantiations.
Do so by removing -fuse-ld=gold from the list of linker flags for this program.
Matthias Maier [Thu, 29 Oct 2015 22:26:32 +0000 (17:26 -0500)]
Merge pull request #1809 from tamiko/tensor_fixes
Fix several Tensor<rank,dim,Number> related bugs:
Matthias Maier [Thu, 29 Oct 2015 22:24:16 +0000 (17:24 -0500)]
reindent
Wolfgang Bangerth [Thu, 29 Oct 2015 15:45:09 +0000 (10:45 -0500)]
Merge pull request #1812 from tjhei/fix_bdm_tests2
add missing changes to fix bdm tests
Timo Heister [Thu, 29 Oct 2015 14:43:40 +0000 (10:43 -0400)]
add missing changes to fix bdm tests
the PR #1778 written to fix tests/fe/bdm_[89], also see #1770, did not
include the necessary changes to the .cc files.
Denis Davydov [Thu, 29 Oct 2015 10:05:40 +0000 (11:05 +0100)]
Merge pull request #1810 from davydden/sharedtria_fix_no_mpi
fix shared::Tria for no-MPI case
Denis Davydov [Thu, 29 Oct 2015 08:49:10 +0000 (09:49 +0100)]
fix shared::Tria for no-MPI case
Matthias Maier [Thu, 29 Oct 2015 03:47:29 +0000 (22:47 -0500)]
Bugfix: Provide missing operator+ and operator- variants
Unfortunately, it is not possible any more to exploit an implicit
conversion from SymmetricTensor to Tensor due to the heavily templated
operator variants for Tensor.
Thus, provide mixed operator types. (And clean up symmetric_tensor.h
later).
Matthias Maier [Thu, 29 Oct 2015 03:31:06 +0000 (22:31 -0500)]
Bugfix: Add additional braces around subobject initializers..
Hopefully this makes icc happy
Wolfgang Bangerth [Wed, 28 Oct 2015 21:54:51 +0000 (16:54 -0500)]
Move a few pieces to a more natural place.
Wolfgang Bangerth [Wed, 28 Oct 2015 21:33:36 +0000 (16:33 -0500)]
Break dependency of MappingQ from MappingQGeneric.
As discussed in #1732, MappingQ doesn't have the is-a property with
regard to MappingQGeneric. Nor does it have it with regard to its previous
base class, MappingQ1, and this was already fixed previously (#1429). Rather, what
it should be is a has-a relationship with regard to both the MappingQGeneric
(used on cells on the boundary) and MappingQ1 (used for interior cells).
This patch implements this. The part of the patch for MappingQ itself is
relatively straightforward: have it store pointers to both Q1 and Qp
mappings, and where it currently dispatches to the base class
MappingQGeneric, just dispatch to the Qp object instead. We can
then break the inheritance from MappingQ
to MappingQGeneric, at the cost of reimplementing a couple of
trivial functions of the Mapping interface that were previously
provided by the MappingQGeneric class.
The bigger problems appear in the MappingQEulerian and
MappingC1 classes which previously overloaded functions
declared in MappingQGeneric and that are now no longer
available to the MappingQGeneric object we now keep a
pointer to, rather than have as base class. This is
worked around by having both MappingQEulerian and
MappingC1 declare their own internal classes derived
from MappingQGeneric that provide the now missing
functions.
Denis Davydov [Wed, 28 Oct 2015 17:06:46 +0000 (18:06 +0100)]
Merge pull request #1806 from QiaoLei-88/fixBraceMismatch
fix one brace mismatch in documentation
Lei Qiao [Wed, 28 Oct 2015 16:48:33 +0000 (11:48 -0500)]
fix one brace mismatch in documentation
David Wells [Tue, 27 Oct 2015 18:46:28 +0000 (14:46 -0400)]
Merge pull request #1802 from tamiko/cmake_cleanup
CMake: Remove obsolete guard in configure_1_lapack.cmake
Matthias Maier [Tue, 27 Oct 2015 18:16:44 +0000 (13:16 -0500)]
CMake: Refactor include to appropriate file
Matthias Maier [Tue, 27 Oct 2015 16:12:39 +0000 (11:12 -0500)]
CMake: Remove obsolete guard in configure_1_lapack.cmake
Matthias Maier [Tue, 27 Oct 2015 16:10:50 +0000 (11:10 -0500)]
Merge pull request #1799 from guidokanschat/cmake_c_compiler
Put the C compiler into the config file and automatic deal.II setup
Denis Davydov [Tue, 27 Oct 2015 15:46:36 +0000 (16:46 +0100)]
Merge pull request #1674 from davydden/shared_tria_artificial
Shared tria artificial
Wolfgang Bangerth [Tue, 27 Oct 2015 15:46:13 +0000 (10:46 -0500)]
Merge pull request #1801 from alistairbntl/BDM_grad_grad
Implemented BDM_grad_grad in 3D
Denis Davydov [Fri, 25 Sep 2015 16:28:44 +0000 (18:28 +0200)]
extend parallel::shared::Triangulation to allow artifical cells
Alistair Bentley [Tue, 27 Oct 2015 15:14:07 +0000 (11:14 -0400)]
Implemented BDM_grad_grad in 3D
* Added second derivative terms to polynomials_bdm class in 3D
* Added tests and output to verify 2nd derivatives are returning
proper values
* I carefully checked the output file to confirm the correct output
is being produced
Guido Kanschat [Tue, 27 Oct 2015 11:54:30 +0000 (12:54 +0100)]
Put the C compiler into the config file and automatic deal.II setup
Wolfgang Bangerth [Tue, 27 Oct 2015 11:19:23 +0000 (06:19 -0500)]
Merge pull request #1796 from kronbichler/master
Simplify code in MGTransferPrebuilt
Martin Kronbichler [Tue, 27 Oct 2015 10:43:38 +0000 (11:43 +0100)]
Silence compile error
Martin Kronbichler [Tue, 27 Oct 2015 10:42:09 +0000 (11:42 +0100)]
Make compile without MPI
Denis Davydov [Tue, 27 Oct 2015 08:29:02 +0000 (09:29 +0100)]
Merge pull request #1797 from asartori86/typo_step_20
fixed typo intro step 20
alberto sartori [Tue, 27 Oct 2015 08:28:38 +0000 (09:28 +0100)]
fixed typo intro step 20
Martin Kronbichler [Tue, 27 Oct 2015 08:04:38 +0000 (09:04 +0100)]
Simplify code in MGTransferPrebuilt
Martin Kronbichler [Tue, 27 Oct 2015 06:53:26 +0000 (07:53 +0100)]
Merge pull request #1768 from tjhei/parmg
[WIP] working parallel geometric multigrid
Martin Kronbichler [Tue, 27 Oct 2015 06:50:34 +0000 (07:50 +0100)]
Merge pull request #1784 from jppelteret/fix_steps_broken_by_1673
Fix steps broken by PR 1673
Wolfgang Bangerth [Tue, 27 Oct 2015 01:35:42 +0000 (20:35 -0500)]
Merge pull request #1795 from tamiko/try_to_make_appvyr_happy
Bugfix: Add a missing space in a build test target
Matthias Maier [Tue, 27 Oct 2015 00:09:43 +0000 (19:09 -0500)]
Bugfix: Add a missing space in a build test target
Wolfgang Bangerth [Tue, 27 Oct 2015 00:05:00 +0000 (19:05 -0500)]
Merge pull request #1794 from tamiko/fix_typo
Documentation: Fix a typo in porting.html
Matthias Maier [Mon, 26 Oct 2015 23:54:50 +0000 (18:54 -0500)]
Documentation: Fix a typo in porting.html
Wolfgang Bangerth [Mon, 26 Oct 2015 23:09:34 +0000 (18:09 -0500)]
Merge pull request #1793 from tamiko/compile_with_flags
Bugfix: Also compile the expand_instantiations macro with our build flags
Matthias Maier [Mon, 26 Oct 2015 22:59:15 +0000 (17:59 -0500)]
Bugfix: Also compile the expand_instantiations macro with our build flags
It turns out that the Windows platform needs this.
Closes #1792
Jean-Paul Pelteret [Mon, 26 Oct 2015 21:11:29 +0000 (22:11 +0100)]
Fixes in relation to #1673.
Changed size_type in PreconditionChebyshev. Added static_asserts that
compare matrix and vector types in precondtioners. Updated
linear_operator_08 test to account for inability to wrap
IterativeInverse in a linear_operator.
Bruno Turcksin [Mon, 26 Oct 2015 19:37:49 +0000 (14:37 -0500)]
Merge pull request #1791 from bangerth/possibly-fix-msvc-problem
Qualify nested types with 'typename'.
Wolfgang Bangerth [Mon, 26 Oct 2015 19:36:21 +0000 (14:36 -0500)]
Qualify nested types with 'typename'.
Matthias Maier [Mon, 26 Oct 2015 15:44:59 +0000 (10:44 -0500)]
Merge pull request #1787 from tamiko/partially_revert_pr_1673
Partially revert pull request 1673
Matthias Maier [Sun, 25 Oct 2015 18:01:57 +0000 (13:01 -0500)]
Partially revert pull request 1673
This reverts all changes to iterative_inverse.h and pointer_matrix.h
introduced by pull request #1673.
Timo Heister [Mon, 26 Oct 2015 13:07:43 +0000 (09:07 -0400)]
Merge remote-tracking branch 'upstream/master' into parmg
Conflicts:
doc/news/changes.h
Timo Heister [Mon, 26 Oct 2015 13:06:05 +0000 (09:06 -0400)]
changelog
Wolfgang Bangerth [Mon, 26 Oct 2015 00:30:22 +0000 (19:30 -0500)]
Merge pull request #1789 from tjhei/remove_typenames
remove typename outside template
Timo Heister [Mon, 26 Oct 2015 00:24:46 +0000 (20:24 -0400)]
Merge pull request #1743 from QiaoLei-88/triaSignalOnCell
Tria signal on cell
Timo Heister [Mon, 26 Oct 2015 00:22:43 +0000 (20:22 -0400)]
remove typename outside template
This fixes building on msvc
Martin Kronbichler [Sun, 25 Oct 2015 18:59:33 +0000 (19:59 +0100)]
Merge pull request #1781 from bangerth/rename_fast_to_skip_initialization
Rename the 'fast' parameter to 'skip_initialization'.
Matthias Maier [Sun, 25 Oct 2015 18:57:51 +0000 (13:57 -0500)]
Merge pull request #1779 from bangerth/hook-in-code-gallery
Hook in code gallery
Wolfgang Bangerth [Fri, 23 Oct 2015 20:23:20 +0000 (15:23 -0500)]
Rename the 'fast' parameter to 'omit_zeroing_entries'.
This is a more accurate representation of what the parameter achieves,
and should be easier to understand. The fact that this mode is also
'fast' is sort of a side effect of the semantics the parameter
really carries.
In the Table class, use omit_default_initialization.
Wolfgang Bangerth [Sun, 25 Oct 2015 16:21:47 +0000 (11:21 -0500)]
Rework the way we pick up the code gallery: instead of checking it out
via git, just find it at a magical location.
Wolfgang Bangerth [Fri, 23 Oct 2015 19:18:19 +0000 (14:18 -0500)]
Adjust the program that builds the tutorial graph to also process the code gallery.
Wolfgang Bangerth [Fri, 23 Oct 2015 19:17:17 +0000 (14:17 -0500)]
Check out and process the code-gallery.
Wolfgang Bangerth [Fri, 23 Oct 2015 02:34:48 +0000 (21:34 -0500)]
Bracket document configuration with empty lines, now that we do some
serious work there.
Wolfgang Bangerth [Thu, 22 Oct 2015 21:41:41 +0000 (16:41 -0500)]
Minor cleanup.
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