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dealii.git
7 years agoMerge pull request #4828 from drwells/remove-double-underscores
Daniel Arndt [Tue, 15 Aug 2017 06:56:58 +0000 (08:56 +0200)]
Merge pull request #4828 from drwells/remove-double-underscores

Remove double underscores from include guards.

7 years agoMerge pull request #4848 from bangerth/improve-error
Timo Heister [Tue, 15 Aug 2017 00:36:33 +0000 (20:36 -0400)]
Merge pull request #4848 from bangerth/improve-error

Improve a couple of error messages that weren't quite clear.

7 years agoRemove double underscores from include guards. 4828/head
David Wells [Mon, 14 Aug 2017 01:14:39 +0000 (21:14 -0400)]
Remove double underscores from include guards.

Symbols with '__' in them are reserved by the standard.

7 years agoMerge pull request #4847 from luca-heltai/sundials-detection
Luca Heltai [Mon, 14 Aug 2017 23:26:57 +0000 (17:26 -0600)]
Merge pull request #4847 from luca-heltai/sundials-detection

Sundials detection.

7 years agoMerge pull request #4849 from bangerth/doc-update
David Wells [Mon, 14 Aug 2017 23:08:45 +0000 (19:08 -0400)]
Merge pull request #4849 from bangerth/doc-update

Fix a markup problem.

7 years agoCMake: Stylistic fixes 4847/head
Matthias Maier [Mon, 14 Aug 2017 22:51:31 +0000 (17:51 -0500)]
CMake: Stylistic fixes

7 years agoFix a markup problem. 4849/head
Wolfgang Bangerth [Mon, 14 Aug 2017 22:48:20 +0000 (16:48 -0600)]
Fix a markup problem.

HTML doesn't know that  equals opening quotes. Avoid this.

7 years agoImprove a couple of error messages that weren't quite clear. 4848/head
Wolfgang Bangerth [Mon, 14 Aug 2017 22:32:10 +0000 (16:32 -0600)]
Improve a couple of error messages that weren't quite clear.

7 years agoSundials detection mechanism.
Luca Heltai [Mon, 14 Aug 2017 21:13:02 +0000 (15:13 -0600)]
Sundials detection mechanism.

7 years agoMerge pull request #4833 from masterleinad/avoid_warning
Wolfgang Bangerth [Mon, 14 Aug 2017 20:31:56 +0000 (14:31 -0600)]
Merge pull request #4833 from masterleinad/avoid_warning

Avoid warnings related to the deprecation of types_are_equal

7 years agoMerge pull request #4829 from tjhei/mesh_loop_mg
Luca Heltai [Mon, 14 Aug 2017 20:15:36 +0000 (14:15 -0600)]
Merge pull request #4829 from tjhei/mesh_loop_mg

add mesh_loop GMG test

7 years agoMerge pull request #4794 from luca-heltai/new-find-active-cells-around-points
Timo Heister [Mon, 14 Aug 2017 20:15:04 +0000 (16:15 -0400)]
Merge pull request #4794 from luca-heltai/new-find-active-cells-around-points

New find active cells around point.

7 years agoMerge pull request #4844 from luca-heltai/enable-nanoflann-doc
Wolfgang Bangerth [Mon, 14 Aug 2017 20:09:26 +0000 (14:09 -0600)]
Merge pull request #4844 from luca-heltai/enable-nanoflann-doc

Add NANOFLANN to doxygen.

7 years agoMerge pull request #4842 from tjhei/enable_doxygen_for_cuda
Wolfgang Bangerth [Mon, 14 Aug 2017 20:09:01 +0000 (14:09 -0600)]
Merge pull request #4842 from tjhei/enable_doxygen_for_cuda

enable CUDA in doxygen

7 years agoAdded DEAL_II_WITH_NANOFLANN to doxygen. 4844/head
Luca Heltai [Mon, 14 Aug 2017 20:07:26 +0000 (14:07 -0600)]
Added DEAL_II_WITH_NANOFLANN to doxygen.

7 years agoenable CUDA in doxygen 4842/head
Timo Heister [Mon, 14 Aug 2017 20:06:38 +0000 (14:06 -0600)]
enable CUDA in doxygen

7 years agoMerge pull request #4841 from tamiko/kdtree_fixup
Luca Heltai [Mon, 14 Aug 2017 19:20:04 +0000 (13:20 -0600)]
Merge pull request #4841 from tamiko/kdtree_fixup

Bugfix: Make library compile with -DWITH_NANOFLANN=ON

7 years agoBugfix: Make library compile with -DWITH_NANOFLANN=ON 4841/head
Matthias Maier [Mon, 14 Aug 2017 19:17:05 +0000 (14:17 -0500)]
Bugfix: Make library compile with -DWITH_NANOFLANN=ON

We were missing a mandatory include in numerics/kdtree.h

7 years agoNew find active cell around point. 4794/head
Luca Heltai [Sat, 12 Aug 2017 21:53:32 +0000 (15:53 -0600)]
New find active cell around point.

7 years agoVertex to cells center directions.
Luca Heltai [Sat, 12 Aug 2017 21:53:13 +0000 (15:53 -0600)]
Vertex to cells center directions.

7 years agoGet closest vertex to cell.
Luca Heltai [Sat, 12 Aug 2017 21:52:49 +0000 (15:52 -0600)]
Get closest vertex to cell.

7 years agoMerge pull request #4831 from tamiko/remove_obsolete_check
David Wells [Mon, 14 Aug 2017 19:07:37 +0000 (15:07 -0400)]
Merge pull request #4831 from tamiko/remove_obsolete_check

CMake: Bugfix: Remove SuiteSparse_config PIC test

7 years agoMerge pull request #4837 from masterleinad/changelog_4834
Timo Heister [Mon, 14 Aug 2017 17:39:59 +0000 (13:39 -0400)]
Merge pull request #4837 from masterleinad/changelog_4834

Changelog entry for #4834

7 years agoMerge pull request #4821 from bangerth/fix-3
Timo Heister [Mon, 14 Aug 2017 17:38:58 +0000 (13:38 -0400)]
Merge pull request #4821 from bangerth/fix-3

Reverse template arguments to parallel::GridTools::exchange_cell_data_to_ghosts()

7 years agoAvoid warnings related to deprecation of types_are_equal 4833/head
Daniel Arndt [Mon, 14 Aug 2017 05:22:30 +0000 (07:22 +0200)]
Avoid warnings related to deprecation of types_are_equal

7 years agoChangelog entry for #4834 4837/head
Daniel Arndt [Mon, 14 Aug 2017 16:02:40 +0000 (18:02 +0200)]
Changelog entry for #4834

7 years agoadd mesh_loop GMG test 4829/head
Timo Heister [Mon, 14 Aug 2017 01:17:15 +0000 (19:17 -0600)]
add mesh_loop GMG test

7 years agoMerge pull request #4834 from masterleinad/deprecate_constraint_and_return_value
Wolfgang Bangerth [Mon, 14 Aug 2017 14:54:39 +0000 (08:54 -0600)]
Merge pull request #4834 from masterleinad/deprecate_constraint_and_return_value

Deprecate constraint_and_return_value in favor of std::enable_if

7 years agoMerge pull request #4830 from tamiko/guard_nanoflann_tests
Luca Heltai [Mon, 14 Aug 2017 07:36:18 +0000 (01:36 -0600)]
Merge pull request #4830 from tamiko/guard_nanoflann_tests

Bugfix: Only run kdtree tests if nanoflann is configured

7 years agoDeprecate constraint_and_return_value in favor of std::enable_if 4834/head
Daniel Arndt [Mon, 14 Aug 2017 05:21:36 +0000 (07:21 +0200)]
Deprecate constraint_and_return_value in favor of std::enable_if

7 years agoCMake: Bugfix: Remove SuiteSparse_config PIC test 4831/head
Matthias Maier [Mon, 14 Aug 2017 04:46:31 +0000 (23:46 -0500)]
CMake: Bugfix: Remove SuiteSparse_config PIC test

This is a 5 year old workaround for a very old Debian distribution.
Unfortunately, we run into problems with this PIC test - so simply
remove it.

7 years agoOnly run kdtree tests if nanoflann is configured 4830/head
Matthias Maier [Mon, 14 Aug 2017 04:38:02 +0000 (23:38 -0500)]
Only run kdtree tests if nanoflann is configured

7 years agoMerge pull request #4820 from tamiko/clean_up_logstream-3
Wolfgang Bangerth [Mon, 14 Aug 2017 03:47:14 +0000 (21:47 -0600)]
Merge pull request #4820 from tamiko/clean_up_logstream-3

LogStream: Remove timestamp machinery and memory_consumption

7 years agoMerge pull request #4825 from luca-heltai/kdtree
Matthias Maier [Mon, 14 Aug 2017 01:06:38 +0000 (20:06 -0500)]
Merge pull request #4825 from luca-heltai/kdtree

KDTree class.

7 years agoRemoved reference to deal3lkit, fixed KDTree names. 4825/head
Luca Heltai [Mon, 14 Aug 2017 00:40:36 +0000 (18:40 -0600)]
Removed reference to deal3lkit, fixed KDTree names.

7 years agoAddressed comments, renamed classes, externalized implementation
Luca Heltai [Mon, 14 Aug 2017 00:32:10 +0000 (18:32 -0600)]
Addressed comments, renamed classes, externalized implementation

7 years agoMerge pull request #4827 from drwells/skip-arrayview-test-old-boost
Matthias Maier [Mon, 14 Aug 2017 00:01:38 +0000 (19:01 -0500)]
Merge pull request #4827 from drwells/skip-arrayview-test-old-boost

Skip a type checking test on older boost versions.

7 years agoMerge pull request #4826 from masterleinad/fix_trilinos_prec
Matthias Maier [Mon, 14 Aug 2017 00:00:18 +0000 (19:00 -0500)]
Merge pull request #4826 from masterleinad/fix_trilinos_prec

Make trilinos/precondition more robust

7 years agoMake trilinos/precondition more robust 4826/head
Daniel Arndt [Sun, 13 Aug 2017 23:35:49 +0000 (01:35 +0200)]
Make trilinos/precondition more robust

7 years agoMerge pull request #4824 from tjhei/mesh_loop_test
Luca Heltai [Sun, 13 Aug 2017 23:48:51 +0000 (17:48 -0600)]
Merge pull request #4824 from tjhei/mesh_loop_test

Add mesh_loop parallel test and improve MPILogInitAll

7 years agoSkip a type checking test on older boost versions. 4827/head
David Wells [Sun, 13 Aug 2017 23:35:19 +0000 (19:35 -0400)]
Skip a type checking test on older boost versions.

Boost 1.57 does not correctly implement static_vector::const_iterator,
but newer versions of boost fix this problem.

7 years agoFixed indentation.
Luca Heltai [Sun, 13 Aug 2017 23:35:15 +0000 (17:35 -0600)]
Fixed indentation.

7 years agoChanged output arguments and added 3 tests.
Luca Heltai [Sun, 13 Aug 2017 23:30:22 +0000 (17:30 -0600)]
Changed output arguments and added 3 tests.

7 years agoAdd KDTreeDistance implementation
Luca Heltai [Sun, 13 Aug 2017 22:48:56 +0000 (16:48 -0600)]
Add KDTreeDistance implementation

7 years agoMerge pull request #4819 from drwells/deprecate-types-are-equal
David Wells [Sun, 13 Aug 2017 23:23:19 +0000 (19:23 -0400)]
Merge pull request #4819 from drwells/deprecate-types-are-equal

Deprecate types_are_equal.

7 years agoMerge pull request #4812 from davydden/test_fix
Timo Heister [Sun, 13 Aug 2017 23:13:55 +0000 (19:13 -0400)]
Merge pull request #4812 from davydden/test_fix

fix parpack unit test

7 years agoMerge pull request #4816 from masterleinad/revert_4762
Daniel Arndt [Sun, 13 Aug 2017 23:07:31 +0000 (01:07 +0200)]
Merge pull request #4816 from masterleinad/revert_4762

Document the default argument for the coefficient in the create_* functions

7 years agoDocument the default argument for the coefficient 4816/head
Daniel Arndt [Sun, 13 Aug 2017 18:26:41 +0000 (20:26 +0200)]
Document the default argument for the coefficient

7 years agoMerge pull request #4822 from bangerth/fix-4
Timo Heister [Sun, 13 Aug 2017 23:04:32 +0000 (19:04 -0400)]
Merge pull request #4822 from bangerth/fix-4

Better document what the ghost DoF index exchange does.

7 years agoMerge pull request #4823 from tjhei/mesh_loop_test_fix
Wolfgang Bangerth [Sun, 13 Aug 2017 23:00:03 +0000 (17:00 -0600)]
Merge pull request #4823 from tjhei/mesh_loop_test_fix

fix tests/meshworker/mesh_loop_*

7 years agofix tests/meshworker/mesh_loop_ 4823/head
Timo Heister [Sun, 13 Aug 2017 22:49:49 +0000 (18:49 -0400)]
fix tests/meshworker/mesh_loop_

7 years agoadd parallel mesh_loop test 4824/head
Timo Heister [Sun, 13 Aug 2017 22:33:02 +0000 (16:33 -0600)]
add parallel mesh_loop test

7 years agoReverse template arguments to parallel::GridTools::exchange_cell_data_to_ghosts(). 4821/head
Wolfgang Bangerth [Sun, 13 Aug 2017 21:49:31 +0000 (15:49 -0600)]
Reverse template arguments to parallel::GridTools::exchange_cell_data_to_ghosts().

7 years agoUpdate changelog 4820/head
Matthias Maier [Sun, 13 Aug 2017 21:49:54 +0000 (16:49 -0500)]
Update changelog

7 years agotests: Update to latest changes
Matthias Maier [Sun, 13 Aug 2017 21:44:29 +0000 (16:44 -0500)]
tests: Update to latest changes

7 years agoLogStream: Do not default to std::cerr, but std::cout
Matthias Maier [Sun, 13 Aug 2017 22:03:20 +0000 (17:03 -0500)]
LogStream: Do not default to std::cerr, but std::cout

7 years agoallow MPILogInitAll to be used more than once
Timo Heister [Sun, 13 Aug 2017 22:23:52 +0000 (16:23 -0600)]
allow MPILogInitAll to be used more than once

7 years agoMerge pull request #4775 from luca-heltai/meshloop
Wolfgang Bangerth [Sun, 13 Aug 2017 22:20:21 +0000 (16:20 -0600)]
Merge pull request #4775 from luca-heltai/meshloop

Mesh Loop.

7 years agoremove backticks 4775/head
Timo Heister [Sun, 13 Aug 2017 22:16:25 +0000 (16:16 -0600)]
remove backticks

7 years agoreset the CopyData object
Timo Heister [Sun, 13 Aug 2017 22:13:34 +0000 (16:13 -0600)]
reset the CopyData object

7 years agoaddress comments
Timo Heister [Sun, 13 Aug 2017 22:13:02 +0000 (16:13 -0600)]
address comments

7 years agoBetter document what the ghost DoF index exchange does. 4822/head
Wolfgang Bangerth [Sun, 13 Aug 2017 21:50:03 +0000 (15:50 -0600)]
Better document what the ghost DoF index exchange does.

While there, also tighten up the logic of what user flags we set, clear, and
when.

7 years agoLogStream: Remove timestamp machinery and memory_consumption
Matthias Maier [Sun, 13 Aug 2017 21:41:11 +0000 (16:41 -0500)]
LogStream: Remove timestamp machinery and memory_consumption

7 years agoDeprecate types_are_equal. 4819/head
David Wells [Sun, 13 Aug 2017 21:16:41 +0000 (17:16 -0400)]
Deprecate types_are_equal.

C++11 provides std::is_same, which has the same functionality.

7 years agoMerge pull request #4813 from tamiko/clean_up_logstream-2
Matthias Maier [Sun, 13 Aug 2017 19:39:32 +0000 (14:39 -0500)]
Merge pull request #4813 from tamiko/clean_up_logstream-2

LogStream: Remove log_cerr

7 years agoMerge pull request #4817 from bangerth/fix
Matthias Maier [Sun, 13 Aug 2017 19:36:52 +0000 (14:36 -0500)]
Merge pull request #4817 from bangerth/fix

Make DoFAccessor::set_active_fe_index() a 'const' function.

7 years agoMake DoFAccessor::set_active_fe_index() a 'const' function. 4817/head
Wolfgang Bangerth [Sun, 13 Aug 2017 19:21:43 +0000 (13:21 -0600)]
Make DoFAccessor::set_active_fe_index() a 'const' function.

We are not being very consistent in marking which DoFAccessor functions are 'const'
because it's difficult to actually define what 'const' would mean: does it change
the accessor, or does it change the DoFHandler it points to. As a consequence,
the TriaAccessor member functions are *all* const, but the DoFAccessor functions
are more or less random.

Rather than attacking this problem altogether, I'm making the minimal change that
solves the problem I currently have.

7 years agoMerge pull request #4815 from jppelteret/move_sacado_header_tests
Wolfgang Bangerth [Sun, 13 Aug 2017 19:17:07 +0000 (13:17 -0600)]
Merge pull request #4815 from jppelteret/move_sacado_header_tests

Moved Sacado product type header and moved Sacado tests

7 years agoMoved Sacado product type header and moved Sacado tests 4815/head
Jean-Paul Pelteret [Sun, 13 Aug 2017 18:07:07 +0000 (12:07 -0600)]
Moved Sacado product type header and moved Sacado tests

7 years agofix parpack unit test 4812/head
Denis Davydov [Sun, 13 Aug 2017 16:57:41 +0000 (18:57 +0200)]
fix parpack unit test

7 years agoAugment news entry 4813/head
Matthias Maier [Sun, 13 Aug 2017 18:39:47 +0000 (13:39 -0500)]
Augment news entry

7 years agofix a test
Matthias Maier [Sun, 13 Aug 2017 17:04:13 +0000 (12:04 -0500)]
fix a test

7 years agoLogStream: Remove log_cerr
Matthias Maier [Sun, 13 Aug 2017 17:03:07 +0000 (12:03 -0500)]
LogStream: Remove log_cerr

7 years agoupdate documentation
Timo Heister [Sun, 13 Aug 2017 18:31:38 +0000 (12:31 -0600)]
update documentation

7 years agocleanup assemble flags, fix logic, add asserts, adjust tests
Timo Heister [Sun, 13 Aug 2017 18:17:43 +0000 (12:17 -0600)]
cleanup assemble flags, fix logic, add asserts, adjust tests

7 years agoRevert "Allow the create_* functions to be called with nullptr coefficients"
Daniel Arndt [Sun, 13 Aug 2017 18:12:46 +0000 (20:12 +0200)]
Revert "Allow the create_* functions to be called with nullptr coefficients"

This reverts commit 7bd1893bd9084308c2fb9e51aef8cfa2641617e7.

7 years agoMerge pull request #4769 from tamiko/clean_up_logstream
Wolfgang Bangerth [Sun, 13 Aug 2017 18:12:06 +0000 (12:12 -0600)]
Merge pull request #4769 from tamiko/clean_up_logstream

LogStream: Remove testing mode and float manipulation

7 years agotests: Update test output 4769/head
Matthias Maier [Sun, 13 Aug 2017 16:40:17 +0000 (11:40 -0500)]
tests: Update test output

7 years agotests: Update affected tests
Matthias Maier [Sun, 13 Aug 2017 16:39:37 +0000 (11:39 -0500)]
tests: Update affected tests

7 years agoadd a news entry
Matthias Maier [Thu, 10 Aug 2017 17:49:01 +0000 (12:49 -0500)]
add a news entry

7 years agoLogStream: Remove testing mode and float manipulation
Matthias Maier [Thu, 10 Aug 2017 17:45:08 +0000 (12:45 -0500)]
LogStream: Remove testing mode and float manipulation

For reproducible tests we nowadays use numdiff to compare for small
numerical differences. Thus, remove the old functionality in LogStream.

7 years agotests: numdiff: add "[](){}^' as separators
Matthias Maier [Fri, 11 Aug 2017 00:13:01 +0000 (19:13 -0500)]
tests: numdiff: add "[](){}^' as separators

7 years agoMerge pull request #4807 from tjhei/p4est_iterate_cleanup_2
Timo Heister [Sun, 13 Aug 2017 17:57:40 +0000 (13:57 -0400)]
Merge pull request #4807 from tjhei/p4est_iterate_cleanup_2

clean up p4est::iterate

7 years agoMerge pull request #4814 from tamiko/improve_readme_md
Timo Heister [Sun, 13 Aug 2017 17:56:52 +0000 (13:56 -0400)]
Merge pull request #4814 from tamiko/improve_readme_md

README.md: Make a lot of relative paths clickable.

7 years agomake links https 4814/head
Timo Heister [Sun, 13 Aug 2017 17:56:11 +0000 (13:56 -0400)]
make links https

7 years agoREADME.md: Make a lot of relative paths clickable.
Matthias Maier [Sun, 13 Aug 2017 17:23:21 +0000 (12:23 -0500)]
README.md: Make a lot of relative paths clickable.

7 years agoMerge pull request #4783 from jppelteret/cmake_adolc_detection
Timo Heister [Sun, 13 Aug 2017 17:39:26 +0000 (13:39 -0400)]
Merge pull request #4783 from jppelteret/cmake_adolc_detection

CMake Adol-C detection

7 years agoAdd stand-alone tests for Adol-C 4783/head
Jean-Paul Pelteret [Fri, 11 Aug 2017 09:16:01 +0000 (03:16 -0600)]
Add stand-alone tests for Adol-C

7 years agoMerge pull request #4806 from bangerth/active-fe-index-4
Timo Heister [Sun, 13 Aug 2017 17:26:02 +0000 (13:26 -0400)]
Merge pull request #4806 from bangerth/active-fe-index-4

Limit setting active_fe_indices to locally owned cells

7 years agoUpdate documentation. 4806/head
Wolfgang Bangerth [Sun, 13 Aug 2017 00:22:23 +0000 (18:22 -0600)]
Update documentation.

7 years agoUpdate config.h to include Adol-C related settings
Jean-Paul Pelteret [Fri, 11 Aug 2017 09:11:10 +0000 (03:11 -0600)]
Update config.h to include Adol-C related settings

7 years agoCMake: Add a check for ADOL-C compatibility
Matthias Maier [Sat, 12 Aug 2017 21:22:07 +0000 (16:22 -0500)]
CMake: Add a check for ADOL-C compatibility

7 years agoAdd CMake detection for Adol-C
Jean-Paul Pelteret [Fri, 11 Aug 2017 09:10:15 +0000 (03:10 -0600)]
Add CMake detection for Adol-C

7 years agoclean up p4est::iterate 4807/head
Timo Heister [Sun, 13 Aug 2017 00:20:22 +0000 (18:20 -0600)]
clean up p4est::iterate

7 years agoMerge pull request #4810 from tamiko/fix_an_assert
Daniel Arndt [Sun, 13 Aug 2017 14:10:53 +0000 (16:10 +0200)]
Merge pull request #4810 from tamiko/fix_an_assert

Fix an assert: It should read "nullptr", not "null_ptr"

7 years agoFix an assert: It should read "nullptr", not "null_ptr" 4810/head
Matthias Maier [Sun, 13 Aug 2017 08:06:34 +0000 (03:06 -0500)]
Fix an assert: It should read "nullptr", not "null_ptr"

7 years agoMerge pull request #4801 from drwells/remove-have-isfinite
Matthias Maier [Sun, 13 Aug 2017 04:39:38 +0000 (23:39 -0500)]
Merge pull request #4801 from drwells/remove-have-isfinite

Remove DEAL_II_HAVE_ISFINITE.

7 years agoMerge pull request #4805 from bangerth/fix
Matthias Maier [Sun, 13 Aug 2017 04:36:06 +0000 (23:36 -0500)]
Merge pull request #4805 from bangerth/fix

Minor test cleanups.

7 years agoMerge pull request #4808 from tjhei/compile_without_mpi
David Wells [Sun, 13 Aug 2017 03:51:19 +0000 (23:51 -0400)]
Merge pull request #4808 from tjhei/compile_without_mpi

make compile without MPI

7 years agomake compile without MPI 4808/head
Timo Heister [Sun, 13 Aug 2017 00:45:26 +0000 (18:45 -0600)]
make compile without MPI


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